Starting phenix.real_space_refine on Fri Mar 6 15:20:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u8n_20688/03_2026/6u8n_20688.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u8n_20688/03_2026/6u8n_20688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6u8n_20688/03_2026/6u8n_20688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u8n_20688/03_2026/6u8n_20688.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6u8n_20688/03_2026/6u8n_20688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u8n_20688/03_2026/6u8n_20688.map" } resolution = 3.29 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= 0.073 sd= 2.647 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: 5 Type Number sf(0) Gaussians P 72 5.49 5 S 176 5.16 5 C 19656 2.51 5 N 5400 2.21 5 O 6224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 136 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31528 Number of models: 1 Model: "" Number of chains: 24 Chain: "I" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "A" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "J" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "B" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "K" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "C" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "L" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "D" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "M" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "E" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "N" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "F" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "O" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "G" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "P" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "H" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "G" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 6.40, per 1000 atoms: 0.20 Number of scatterers: 31528 At special positions: 0 Unit cell: (156.45, 156.45, 141.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 176 16.00 P 72 15.00 O 6224 8.00 N 5400 7.00 C 19656 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=24, symmetry=0 Number of additional bonds: simple=24, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.3 seconds 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7280 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 48 sheets defined 37.1% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'I' and resid 1 through 6 Processing helix chain 'A' and resid 19 through 25 removed outlier: 3.775A pdb=" N ASN A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 75 through 85 removed outlier: 3.907A pdb=" N ALA A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 110 removed outlier: 3.538A pdb=" N GLN A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 137 removed outlier: 4.411A pdb=" N VAL A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 removed outlier: 4.069A pdb=" N GLU A 177 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE A 178 " --> pdb=" O LEU A 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 178' Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 225 through 228 Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.721A pdb=" N ARG A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.517A pdb=" N ILE A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 356 removed outlier: 3.562A pdb=" N SER A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.998A pdb=" N ILE A 373 " --> pdb=" O ASN A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 420 Processing helix chain 'A' and resid 456 through 472 Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'J' and resid 2 through 6 Processing helix chain 'B' and resid 19 through 25 removed outlier: 3.776A pdb=" N ASN B 25 " --> pdb=" O GLN B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 75 through 85 removed outlier: 3.907A pdb=" N ALA B 81 " --> pdb=" O GLY B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 110 removed outlier: 3.538A pdb=" N GLN B 100 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 137 removed outlier: 4.411A pdb=" N VAL B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 removed outlier: 4.069A pdb=" N GLU B 177 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE B 178 " --> pdb=" O LEU B 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 174 through 178' Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 225 through 228 Processing helix chain 'B' and resid 255 through 267 removed outlier: 3.722A pdb=" N ARG B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 262 " --> pdb=" O TYR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.517A pdb=" N ILE B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 342 through 356 removed outlier: 3.560A pdb=" N SER B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 removed outlier: 3.998A pdb=" N ILE B 373 " --> pdb=" O ASN B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 420 Processing helix chain 'B' and resid 456 through 472 Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 501 Processing helix chain 'K' and resid 2 through 6 Processing helix chain 'C' and resid 19 through 25 removed outlier: 3.776A pdb=" N ASN C 25 " --> pdb=" O GLN C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 75 through 85 removed outlier: 3.906A pdb=" N ALA C 81 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 110 removed outlier: 3.538A pdb=" N GLN C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR C 110 " --> pdb=" O LYS C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 137 removed outlier: 4.411A pdb=" N VAL C 130 " --> pdb=" O ARG C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 removed outlier: 4.067A pdb=" N GLU C 177 " --> pdb=" O PHE C 174 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE C 178 " --> pdb=" O LEU C 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 174 through 178' Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 225 through 228 Processing helix chain 'C' and resid 255 through 267 removed outlier: 3.721A pdb=" N ARG C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 262 " --> pdb=" O TYR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 removed outlier: 3.518A pdb=" N ILE C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 342 through 356 removed outlier: 3.561A pdb=" N SER C 351 " --> pdb=" O VAL C 347 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 removed outlier: 3.999A pdb=" N ILE C 373 " --> pdb=" O ASN C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 420 Processing helix chain 'C' and resid 456 through 472 Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 494 through 501 Processing helix chain 'L' and resid 2 through 6 Processing helix chain 'D' and resid 19 through 25 removed outlier: 3.776A pdb=" N ASN D 25 " --> pdb=" O GLN D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 75 through 85 removed outlier: 3.907A pdb=" N ALA D 81 " --> pdb=" O GLY D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 110 removed outlier: 3.538A pdb=" N GLN D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 137 removed outlier: 4.411A pdb=" N VAL D 130 " --> pdb=" O ARG D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 178 removed outlier: 4.068A pdb=" N GLU D 177 " --> pdb=" O PHE D 174 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE D 178 " --> pdb=" O LEU D 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 174 through 178' Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 225 through 228 Processing helix chain 'D' and resid 255 through 267 removed outlier: 3.722A pdb=" N ARG D 259 " --> pdb=" O ASP D 255 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 262 " --> pdb=" O TYR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.518A pdb=" N ILE D 284 " --> pdb=" O SER D 280 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 315 Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 342 through 356 removed outlier: 3.561A pdb=" N SER D 351 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 removed outlier: 3.998A pdb=" N ILE D 373 " --> pdb=" O ASN D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 420 Processing helix chain 'D' and resid 456 through 472 Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 501 Processing helix chain 'M' and resid 2 through 6 Processing helix chain 'E' and resid 19 through 25 removed outlier: 3.776A pdb=" N ASN E 25 " --> pdb=" O GLN E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 75 through 85 removed outlier: 3.907A pdb=" N ALA E 81 " --> pdb=" O GLY E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 110 removed outlier: 3.538A pdb=" N GLN E 100 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR E 110 " --> pdb=" O LYS E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 137 removed outlier: 4.411A pdb=" N VAL E 130 " --> pdb=" O ARG E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 178 removed outlier: 4.068A pdb=" N GLU E 177 " --> pdb=" O PHE E 174 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE E 178 " --> pdb=" O LEU E 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 174 through 178' Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 225 through 228 Processing helix chain 'E' and resid 255 through 267 removed outlier: 3.722A pdb=" N ARG E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU E 262 " --> pdb=" O TYR E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 removed outlier: 3.518A pdb=" N ILE E 284 " --> pdb=" O SER E 280 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS E 293 " --> pdb=" O TYR E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 315 Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 342 through 356 removed outlier: 3.561A pdb=" N SER E 351 " --> pdb=" O VAL E 347 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 removed outlier: 3.999A pdb=" N ILE E 373 " --> pdb=" O ASN E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 420 Processing helix chain 'E' and resid 456 through 472 Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 494 through 501 Processing helix chain 'N' and resid 2 through 6 Processing helix chain 'F' and resid 19 through 25 removed outlier: 3.775A pdb=" N ASN F 25 " --> pdb=" O GLN F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 75 through 85 removed outlier: 3.907A pdb=" N ALA F 81 " --> pdb=" O GLY F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 110 removed outlier: 3.538A pdb=" N GLN F 100 " --> pdb=" O THR F 96 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS F 109 " --> pdb=" O ARG F 105 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 137 removed outlier: 4.412A pdb=" N VAL F 130 " --> pdb=" O ARG F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 178 removed outlier: 4.069A pdb=" N GLU F 177 " --> pdb=" O PHE F 174 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE F 178 " --> pdb=" O LEU F 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 174 through 178' Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 225 through 228 Processing helix chain 'F' and resid 255 through 267 removed outlier: 3.722A pdb=" N ARG F 259 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU F 262 " --> pdb=" O TYR F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 removed outlier: 3.517A pdb=" N ILE F 284 " --> pdb=" O SER F 280 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS F 293 " --> pdb=" O TYR F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 315 Processing helix chain 'F' and resid 332 through 337 Processing helix chain 'F' and resid 342 through 356 removed outlier: 3.561A pdb=" N SER F 351 " --> pdb=" O VAL F 347 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 379 removed outlier: 3.998A pdb=" N ILE F 373 " --> pdb=" O ASN F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 420 Processing helix chain 'F' and resid 456 through 472 Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 494 through 501 Processing helix chain 'O' and resid 2 through 6 Processing helix chain 'G' and resid 19 through 25 removed outlier: 3.776A pdb=" N ASN G 25 " --> pdb=" O GLN G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 75 through 85 removed outlier: 3.907A pdb=" N ALA G 81 " --> pdb=" O GLY G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 110 removed outlier: 3.538A pdb=" N GLN G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS G 109 " --> pdb=" O ARG G 105 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR G 110 " --> pdb=" O LYS G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 137 removed outlier: 4.411A pdb=" N VAL G 130 " --> pdb=" O ARG G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 178 removed outlier: 4.068A pdb=" N GLU G 177 " --> pdb=" O PHE G 174 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE G 178 " --> pdb=" O LEU G 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 174 through 178' Processing helix chain 'G' and resid 193 through 205 Processing helix chain 'G' and resid 225 through 228 Processing helix chain 'G' and resid 255 through 267 removed outlier: 3.721A pdb=" N ARG G 259 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU G 262 " --> pdb=" O TYR G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 removed outlier: 3.517A pdb=" N ILE G 284 " --> pdb=" O SER G 280 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS G 293 " --> pdb=" O TYR G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 315 Processing helix chain 'G' and resid 332 through 337 Processing helix chain 'G' and resid 342 through 356 removed outlier: 3.561A pdb=" N SER G 351 " --> pdb=" O VAL G 347 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 379 removed outlier: 3.998A pdb=" N ILE G 373 " --> pdb=" O ASN G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 420 Processing helix chain 'G' and resid 456 through 472 Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'G' and resid 494 through 501 Processing helix chain 'P' and resid 2 through 6 Processing helix chain 'H' and resid 19 through 25 removed outlier: 3.775A pdb=" N ASN H 25 " --> pdb=" O GLN H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 75 through 85 removed outlier: 3.907A pdb=" N ALA H 81 " --> pdb=" O GLY H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 110 removed outlier: 3.538A pdb=" N GLN H 100 " --> pdb=" O THR H 96 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS H 109 " --> pdb=" O ARG H 105 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR H 110 " --> pdb=" O LYS H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 137 removed outlier: 4.411A pdb=" N VAL H 130 " --> pdb=" O ARG H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 178 removed outlier: 4.069A pdb=" N GLU H 177 " --> pdb=" O PHE H 174 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE H 178 " --> pdb=" O LEU H 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 174 through 178' Processing helix chain 'H' and resid 193 through 205 Processing helix chain 'H' and resid 225 through 228 Processing helix chain 'H' and resid 255 through 267 removed outlier: 3.721A pdb=" N ARG H 259 " --> pdb=" O ASP H 255 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU H 262 " --> pdb=" O TYR H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 removed outlier: 3.518A pdb=" N ILE H 284 " --> pdb=" O SER H 280 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS H 293 " --> pdb=" O TYR H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 315 Processing helix chain 'H' and resid 332 through 337 Processing helix chain 'H' and resid 342 through 356 removed outlier: 3.561A pdb=" N SER H 351 " --> pdb=" O VAL H 347 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 removed outlier: 3.998A pdb=" N ILE H 373 " --> pdb=" O ASN H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 420 Processing helix chain 'H' and resid 456 through 472 Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 494 through 501 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 66 removed outlier: 6.483A pdb=" N VAL A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N MET A 385 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL A 271 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLY A 302 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 145 Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 189 removed outlier: 6.930A pdb=" N ALA A 188 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 403 removed outlier: 4.165A pdb=" N SER A 444 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 508 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.690A pdb=" N SER A 508 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER D 444 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'B' and resid 65 through 66 removed outlier: 6.484A pdb=" N VAL B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N MET B 385 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 271 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY B 302 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA B 248 " --> pdb=" O VAL B 272 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 142 through 145 Processing sheet with id=AB3, first strand: chain 'B' and resid 188 through 189 removed outlier: 6.929A pdb=" N ALA B 188 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 401 through 403 removed outlier: 4.171A pdb=" N SER B 444 " --> pdb=" O GLU C 510 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER C 508 " --> pdb=" O ALA B 446 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'C' and resid 65 through 66 removed outlier: 6.483A pdb=" N VAL C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N MET C 385 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASN C 303 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL C 271 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY C 302 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 142 through 145 Processing sheet with id=AB9, first strand: chain 'C' and resid 188 through 189 removed outlier: 6.929A pdb=" N ALA C 188 " --> pdb=" O VAL C 212 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 401 through 403 removed outlier: 4.174A pdb=" N SER C 444 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER D 508 " --> pdb=" O ALA C 446 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AC3, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC4, first strand: chain 'D' and resid 65 through 66 removed outlier: 6.484A pdb=" N VAL D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N MET D 385 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL D 271 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY D 302 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA D 248 " --> pdb=" O VAL D 272 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 142 through 145 Processing sheet with id=AC6, first strand: chain 'D' and resid 188 through 189 removed outlier: 6.928A pdb=" N ALA D 188 " --> pdb=" O VAL D 212 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 65 through 66 removed outlier: 6.483A pdb=" N VAL E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N MET E 385 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL E 271 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY E 302 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 142 through 145 Processing sheet with id=AD2, first strand: chain 'E' and resid 188 through 189 removed outlier: 6.929A pdb=" N ALA E 188 " --> pdb=" O VAL E 212 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 401 through 403 removed outlier: 4.173A pdb=" N SER E 444 " --> pdb=" O GLU F 510 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER F 508 " --> pdb=" O ALA E 446 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 508 through 510 removed outlier: 3.685A pdb=" N SER E 508 " --> pdb=" O ALA H 446 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER H 444 " --> pdb=" O GLU E 510 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AD6, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD7, first strand: chain 'F' and resid 65 through 66 removed outlier: 6.484A pdb=" N VAL F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N MET F 385 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL F 271 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLY F 302 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA F 248 " --> pdb=" O VAL F 272 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 142 through 145 Processing sheet with id=AD9, first strand: chain 'F' and resid 188 through 189 removed outlier: 6.929A pdb=" N ALA F 188 " --> pdb=" O VAL F 212 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 401 through 403 removed outlier: 4.169A pdb=" N SER F 444 " --> pdb=" O GLU G 510 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER G 508 " --> pdb=" O ALA F 446 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AE3, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE4, first strand: chain 'G' and resid 65 through 66 removed outlier: 6.483A pdb=" N VAL G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N MET G 385 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL G 271 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY G 302 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA G 248 " --> pdb=" O VAL G 272 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 142 through 145 Processing sheet with id=AE6, first strand: chain 'G' and resid 188 through 189 removed outlier: 6.930A pdb=" N ALA G 188 " --> pdb=" O VAL G 212 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 401 through 403 removed outlier: 4.167A pdb=" N SER G 444 " --> pdb=" O GLU H 510 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER H 508 " --> pdb=" O ALA G 446 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AE9, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AF1, first strand: chain 'H' and resid 65 through 66 removed outlier: 6.483A pdb=" N VAL H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N MET H 385 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASN H 303 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL H 271 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY H 302 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 142 through 145 Processing sheet with id=AF3, first strand: chain 'H' and resid 188 through 189 removed outlier: 6.929A pdb=" N ALA H 188 " --> pdb=" O VAL H 212 " (cutoff:3.500A) 1009 hydrogen bonds defined for protein. 2835 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: 6.01 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5285 1.30 - 1.42: 7683 1.42 - 1.55: 18572 1.55 - 1.68: 228 1.68 - 1.80: 304 Bond restraints: 32072 Sorted by residual: bond pdb=" C2' ATP E 601 " pdb=" C3' ATP E 601 " ideal model delta sigma weight residual 1.531 1.241 0.290 1.20e-02 6.94e+03 5.83e+02 bond pdb=" C2' ATP B 601 " pdb=" C3' ATP B 601 " ideal model delta sigma weight residual 1.531 1.241 0.290 1.20e-02 6.94e+03 5.83e+02 bond pdb=" C2' ATP G 601 " pdb=" C3' ATP G 601 " ideal model delta sigma weight residual 1.531 1.241 0.290 1.20e-02 6.94e+03 5.83e+02 bond pdb=" C2' ATP D 601 " pdb=" C3' ATP D 601 " ideal model delta sigma weight residual 1.531 1.242 0.289 1.20e-02 6.94e+03 5.82e+02 bond pdb=" C2' ATP F 601 " pdb=" C3' ATP F 601 " ideal model delta sigma weight residual 1.531 1.242 0.289 1.20e-02 6.94e+03 5.81e+02 ... (remaining 32067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.27: 42019 4.27 - 8.55: 1168 8.55 - 12.82: 189 12.82 - 17.10: 53 17.10 - 21.37: 59 Bond angle restraints: 43488 Sorted by residual: angle pdb=" PB ATP F 602 " pdb=" O3B ATP F 602 " pdb=" PG ATP F 602 " ideal model delta sigma weight residual 139.87 118.50 21.37 1.00e+00 1.00e+00 4.57e+02 angle pdb=" PB ATP E 602 " pdb=" O3B ATP E 602 " pdb=" PG ATP E 602 " ideal model delta sigma weight residual 139.87 118.53 21.34 1.00e+00 1.00e+00 4.55e+02 angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 118.53 21.34 1.00e+00 1.00e+00 4.55e+02 angle pdb=" PB ATP D 602 " pdb=" O3B ATP D 602 " pdb=" PG ATP D 602 " ideal model delta sigma weight residual 139.87 118.54 21.33 1.00e+00 1.00e+00 4.55e+02 angle pdb=" PB ATP A 602 " pdb=" O3B ATP A 602 " pdb=" PG ATP A 602 " ideal model delta sigma weight residual 139.87 118.54 21.33 1.00e+00 1.00e+00 4.55e+02 ... (remaining 43483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.34: 17016 16.34 - 32.69: 1712 32.69 - 49.03: 664 49.03 - 65.37: 432 65.37 - 81.72: 32 Dihedral angle restraints: 19856 sinusoidal: 8448 harmonic: 11408 Sorted by residual: dihedral pdb=" CA ILE F 437 " pdb=" C ILE F 437 " pdb=" N LYS F 438 " pdb=" CA LYS F 438 " ideal model delta harmonic sigma weight residual -180.00 -142.81 -37.19 0 5.00e+00 4.00e-02 5.53e+01 dihedral pdb=" CA ILE A 437 " pdb=" C ILE A 437 " pdb=" N LYS A 438 " pdb=" CA LYS A 438 " ideal model delta harmonic sigma weight residual -180.00 -142.81 -37.19 0 5.00e+00 4.00e-02 5.53e+01 dihedral pdb=" CA ILE E 437 " pdb=" C ILE E 437 " pdb=" N LYS E 438 " pdb=" CA LYS E 438 " ideal model delta harmonic sigma weight residual 180.00 -142.82 -37.18 0 5.00e+00 4.00e-02 5.53e+01 ... (remaining 19853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3032 0.064 - 0.127: 1404 0.127 - 0.191: 349 0.191 - 0.254: 142 0.254 - 0.318: 41 Chirality restraints: 4968 Sorted by residual: chirality pdb=" CB VAL O 13 " pdb=" CA VAL O 13 " pdb=" CG1 VAL O 13 " pdb=" CG2 VAL O 13 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CB VAL M 13 " pdb=" CA VAL M 13 " pdb=" CG1 VAL M 13 " pdb=" CG2 VAL M 13 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CB VAL I 13 " pdb=" CA VAL I 13 " pdb=" CG1 VAL I 13 " pdb=" CG2 VAL I 13 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 4965 not shown) Planarity restraints: 5448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS H 108 " -0.021 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C LYS H 108 " 0.070 2.00e-02 2.50e+03 pdb=" O LYS H 108 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS H 109 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 108 " 0.021 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C LYS F 108 " -0.070 2.00e-02 2.50e+03 pdb=" O LYS F 108 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS F 109 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 108 " -0.021 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C LYS E 108 " 0.069 2.00e-02 2.50e+03 pdb=" O LYS E 108 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS E 109 " -0.024 2.00e-02 2.50e+03 ... (remaining 5445 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 8896 2.79 - 3.32: 30144 3.32 - 3.84: 54335 3.84 - 4.37: 63420 4.37 - 4.90: 102989 Nonbonded interactions: 259784 Sorted by model distance: nonbonded pdb=" O ALA B 83 " pdb=" OG SER B 237 " model vdw 2.260 3.040 nonbonded pdb=" O ALA G 83 " pdb=" OG SER G 237 " model vdw 2.260 3.040 nonbonded pdb=" O ALA A 83 " pdb=" OG SER A 237 " model vdw 2.260 3.040 nonbonded pdb=" O ALA E 83 " pdb=" OG SER E 237 " model vdw 2.260 3.040 nonbonded pdb=" O ALA H 83 " pdb=" OG SER H 237 " model vdw 2.260 3.040 ... (remaining 259779 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.010 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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 : 0.020 0.377 32096 Z= 1.241 Angle : 1.891 21.373 43488 Z= 1.163 Chirality : 0.083 0.318 4968 Planarity : 0.007 0.044 5448 Dihedral : 17.956 81.715 12576 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.27 % Favored : 91.33 % Rotamer: Outliers : 9.05 % Allowed : 8.68 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -4.35 (0.11), residues: 3968 helix: -3.54 (0.09), residues: 1272 sheet: -2.60 (0.17), residues: 632 loop : -2.50 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.003 ARG B 128 TYR 0.033 0.004 TYR H 484 PHE 0.022 0.005 PHE A 131 HIS 0.005 0.002 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.01871 (32072) covalent geometry : angle 1.89120 (43488) hydrogen bonds : bond 0.18170 ( 1009) hydrogen bonds : angle 8.17454 ( 2835) Misc. bond : bond 0.21720 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1361 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 296 poor density : 1065 time to evaluate : 1.152 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: A 16 ASP cc_start: 0.8308 (t0) cc_final: 0.8050 (t0) REVERT: A 75 GLU cc_start: 0.6903 (pm20) cc_final: 0.6458 (pm20) REVERT: A 105 ARG cc_start: 0.8259 (mtm110) cc_final: 0.8023 (ttp80) REVERT: A 132 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8658 (pt0) REVERT: A 137 HIS cc_start: 0.8230 (m90) cc_final: 0.7973 (m-70) REVERT: A 157 ILE cc_start: 0.9101 (mm) cc_final: 0.8759 (mm) REVERT: A 179 MET cc_start: 0.7808 (pp-130) cc_final: 0.6938 (ppp) REVERT: A 198 ASN cc_start: 0.9205 (m-40) cc_final: 0.8666 (m-40) REVERT: A 203 ARG cc_start: 0.8640 (tpp-160) cc_final: 0.8262 (ttp-110) REVERT: A 209 LEU cc_start: 0.7847 (tt) cc_final: 0.7636 (tt) REVERT: A 214 GLU cc_start: 0.8592 (mm-30) cc_final: 0.7963 (tm-30) REVERT: A 256 ASP cc_start: 0.8332 (p0) cc_final: 0.7620 (p0) REVERT: A 272 VAL cc_start: 0.8882 (t) cc_final: 0.8526 (m) REVERT: A 277 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8516 (tm-30) REVERT: A 319 ASP cc_start: 0.8203 (m-30) cc_final: 0.7771 (m-30) REVERT: A 327 SER cc_start: 0.8666 (p) cc_final: 0.8390 (p) REVERT: A 352 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8328 (tm-30) REVERT: A 412 ARG cc_start: 0.8430 (ttp80) cc_final: 0.7944 (ptt90) REVERT: A 496 SER cc_start: 0.9130 (p) cc_final: 0.8924 (p) REVERT: A 507 HIS cc_start: 0.8540 (t-90) cc_final: 0.7900 (t-90) REVERT: B 16 ASP cc_start: 0.8347 (t0) cc_final: 0.8142 (t0) REVERT: B 28 ASP cc_start: 0.8239 (m-30) cc_final: 0.8020 (m-30) REVERT: B 75 GLU cc_start: 0.6891 (pm20) cc_final: 0.6496 (pm20) REVERT: B 105 ARG cc_start: 0.8275 (mtm110) cc_final: 0.8050 (ttp80) REVERT: B 132 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8641 (pt0) REVERT: B 137 HIS cc_start: 0.8215 (m90) cc_final: 0.7961 (m-70) REVERT: B 157 ILE cc_start: 0.9145 (mm) cc_final: 0.8807 (mm) REVERT: B 179 MET cc_start: 0.7965 (pp-130) cc_final: 0.7109 (ppp) REVERT: B 198 ASN cc_start: 0.9110 (m-40) cc_final: 0.8563 (m-40) REVERT: B 199 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7812 (tp30) REVERT: B 203 ARG cc_start: 0.8656 (tpp-160) cc_final: 0.8172 (ttp-110) REVERT: B 206 LYS cc_start: 0.8503 (mtpp) cc_final: 0.8283 (mtmm) REVERT: B 214 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8032 (tm-30) REVERT: B 256 ASP cc_start: 0.8383 (p0) cc_final: 0.7737 (p0) REVERT: B 277 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8355 (tm-30) REVERT: B 319 ASP cc_start: 0.8226 (m-30) cc_final: 0.7976 (m-30) REVERT: B 327 SER cc_start: 0.8622 (p) cc_final: 0.8371 (p) REVERT: B 352 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8345 (tm-30) REVERT: B 412 ARG cc_start: 0.8425 (ttp80) cc_final: 0.8005 (ptt90) REVERT: B 470 ASP cc_start: 0.8947 (m-30) cc_final: 0.8720 (m-30) REVERT: B 496 SER cc_start: 0.9106 (p) cc_final: 0.8858 (p) REVERT: B 507 HIS cc_start: 0.8517 (t-90) cc_final: 0.7873 (t-90) REVERT: C 16 ASP cc_start: 0.8297 (t0) cc_final: 0.8051 (t0) REVERT: C 75 GLU cc_start: 0.6894 (pm20) cc_final: 0.6467 (pm20) REVERT: C 105 ARG cc_start: 0.8307 (mtm110) cc_final: 0.8070 (ttp80) REVERT: C 132 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8679 (pt0) REVERT: C 157 ILE cc_start: 0.9093 (mm) cc_final: 0.8784 (mm) REVERT: C 179 MET cc_start: 0.7783 (pp-130) cc_final: 0.7016 (ppp) REVERT: C 198 ASN cc_start: 0.9136 (m-40) cc_final: 0.8581 (m-40) REVERT: C 203 ARG cc_start: 0.8698 (tpp-160) cc_final: 0.8207 (ttp-110) REVERT: C 209 LEU cc_start: 0.7805 (tt) cc_final: 0.7596 (tt) REVERT: C 214 GLU cc_start: 0.8548 (mm-30) cc_final: 0.7955 (tm-30) REVERT: C 256 ASP cc_start: 0.8384 (p0) cc_final: 0.7744 (p0) REVERT: C 277 GLN cc_start: 0.8835 (tm-30) cc_final: 0.8467 (tm-30) REVERT: C 300 ILE cc_start: 0.8455 (mm) cc_final: 0.8238 (mm) REVERT: C 319 ASP cc_start: 0.8296 (m-30) cc_final: 0.7852 (m-30) REVERT: C 327 SER cc_start: 0.8612 (p) cc_final: 0.8334 (p) REVERT: C 352 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8377 (tm-30) REVERT: C 412 ARG cc_start: 0.8426 (ttp80) cc_final: 0.7985 (ptt90) REVERT: C 496 SER cc_start: 0.9078 (p) cc_final: 0.8843 (p) REVERT: C 507 HIS cc_start: 0.8539 (t-90) cc_final: 0.7883 (t-90) REVERT: D 16 ASP cc_start: 0.8277 (t0) cc_final: 0.8013 (t0) REVERT: D 34 ASP cc_start: 0.9071 (t0) cc_final: 0.8822 (t0) REVERT: D 75 GLU cc_start: 0.7034 (pm20) cc_final: 0.6644 (pm20) REVERT: D 105 ARG cc_start: 0.8312 (mtm110) cc_final: 0.8055 (ttp80) REVERT: D 121 LEU cc_start: 0.8348 (mm) cc_final: 0.8147 (mp) REVERT: D 132 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8660 (pt0) REVERT: D 137 HIS cc_start: 0.8221 (m90) cc_final: 0.7973 (m-70) REVERT: D 157 ILE cc_start: 0.9145 (mm) cc_final: 0.8805 (mm) REVERT: D 179 MET cc_start: 0.7989 (pp-130) cc_final: 0.7109 (ppp) REVERT: D 198 ASN cc_start: 0.9186 (m-40) cc_final: 0.8624 (m-40) REVERT: D 203 ARG cc_start: 0.8656 (tpp-160) cc_final: 0.8096 (mtp-110) REVERT: D 214 GLU cc_start: 0.8572 (mm-30) cc_final: 0.7980 (tm-30) REVERT: D 277 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8443 (tm-30) REVERT: D 286 MET cc_start: 0.8991 (tmt) cc_final: 0.8502 (tmt) REVERT: D 319 ASP cc_start: 0.8204 (m-30) cc_final: 0.7958 (m-30) REVERT: D 327 SER cc_start: 0.8646 (p) cc_final: 0.8403 (p) REVERT: D 352 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8373 (tm-30) REVERT: D 412 ARG cc_start: 0.8434 (ttp80) cc_final: 0.8006 (ptt90) REVERT: D 470 ASP cc_start: 0.8881 (m-30) cc_final: 0.8678 (m-30) REVERT: D 507 HIS cc_start: 0.8567 (t-90) cc_final: 0.7914 (t-90) REVERT: E 26 CYS cc_start: 0.8516 (m) cc_final: 0.8315 (t) REVERT: E 34 ASP cc_start: 0.9042 (t0) cc_final: 0.8836 (t0) REVERT: E 75 GLU cc_start: 0.6940 (pm20) cc_final: 0.6515 (pm20) REVERT: E 105 ARG cc_start: 0.8244 (mtm110) cc_final: 0.8030 (ttp80) REVERT: E 132 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8658 (pt0) REVERT: E 137 HIS cc_start: 0.8304 (m90) cc_final: 0.8078 (m-70) REVERT: E 157 ILE cc_start: 0.9089 (mm) cc_final: 0.8803 (mm) REVERT: E 173 CYS cc_start: 0.7451 (p) cc_final: 0.6880 (p) REVERT: E 179 MET cc_start: 0.7828 (pp-130) cc_final: 0.7096 (ppp) REVERT: E 198 ASN cc_start: 0.9123 (m-40) cc_final: 0.8624 (m-40) REVERT: E 203 ARG cc_start: 0.8647 (tpp-160) cc_final: 0.8205 (ttp-110) REVERT: E 214 GLU cc_start: 0.8566 (mm-30) cc_final: 0.7999 (tm-30) REVERT: E 256 ASP cc_start: 0.8280 (p0) cc_final: 0.7572 (p0) REVERT: E 272 VAL cc_start: 0.8852 (t) cc_final: 0.8572 (m) REVERT: E 277 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8463 (tm-30) REVERT: E 300 ILE cc_start: 0.8448 (mm) cc_final: 0.8235 (mm) REVERT: E 319 ASP cc_start: 0.8241 (m-30) cc_final: 0.7808 (m-30) REVERT: E 327 SER cc_start: 0.8587 (p) cc_final: 0.8319 (p) REVERT: E 352 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8351 (tm-30) REVERT: E 412 ARG cc_start: 0.8429 (ttp80) cc_final: 0.8014 (ptt90) REVERT: E 496 SER cc_start: 0.9038 (p) cc_final: 0.8782 (p) REVERT: E 507 HIS cc_start: 0.8549 (t-90) cc_final: 0.7919 (t-90) REVERT: F 16 ASP cc_start: 0.8245 (t0) cc_final: 0.8023 (t0) REVERT: F 28 ASP cc_start: 0.8305 (m-30) cc_final: 0.8079 (m-30) REVERT: F 75 GLU cc_start: 0.7022 (pm20) cc_final: 0.6650 (pm20) REVERT: F 105 ARG cc_start: 0.8311 (mtm110) cc_final: 0.8019 (ttp80) REVERT: F 121 LEU cc_start: 0.8335 (mm) cc_final: 0.8131 (mp) REVERT: F 132 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8661 (pt0) REVERT: F 137 HIS cc_start: 0.8261 (m90) cc_final: 0.7997 (m-70) REVERT: F 157 ILE cc_start: 0.9143 (mm) cc_final: 0.8805 (mm) REVERT: F 179 MET cc_start: 0.7934 (pp-130) cc_final: 0.7053 (ppp) REVERT: F 198 ASN cc_start: 0.9145 (m-40) cc_final: 0.8696 (m-40) REVERT: F 199 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7769 (tp30) REVERT: F 203 ARG cc_start: 0.8590 (tpp-160) cc_final: 0.8064 (ttp-110) REVERT: F 209 LEU cc_start: 0.7876 (tt) cc_final: 0.7671 (tt) REVERT: F 214 GLU cc_start: 0.8520 (mm-30) cc_final: 0.7909 (tm-30) REVERT: F 277 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8412 (tm-30) REVERT: F 286 MET cc_start: 0.8992 (tmt) cc_final: 0.8527 (tmt) REVERT: F 319 ASP cc_start: 0.8222 (m-30) cc_final: 0.7836 (m-30) REVERT: F 327 SER cc_start: 0.8665 (p) cc_final: 0.8428 (p) REVERT: F 352 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8397 (tm-30) REVERT: F 412 ARG cc_start: 0.8422 (ttp80) cc_final: 0.8008 (ptt90) REVERT: F 470 ASP cc_start: 0.8901 (m-30) cc_final: 0.8701 (m-30) REVERT: F 496 SER cc_start: 0.9005 (p) cc_final: 0.8788 (p) REVERT: F 507 HIS cc_start: 0.8560 (t-90) cc_final: 0.7933 (t-90) REVERT: G 16 ASP cc_start: 0.8301 (t0) cc_final: 0.8086 (t0) REVERT: G 34 ASP cc_start: 0.9063 (t0) cc_final: 0.8851 (t0) REVERT: G 75 GLU cc_start: 0.6973 (pm20) cc_final: 0.6562 (pm20) REVERT: G 105 ARG cc_start: 0.8287 (mtm110) cc_final: 0.8008 (ttp80) REVERT: G 137 HIS cc_start: 0.8198 (m90) cc_final: 0.7920 (m-70) REVERT: G 157 ILE cc_start: 0.9107 (mm) cc_final: 0.8787 (mm) REVERT: G 179 MET cc_start: 0.7840 (pp-130) cc_final: 0.7099 (ppp) REVERT: G 198 ASN cc_start: 0.9137 (m-40) cc_final: 0.8691 (m-40) REVERT: G 209 LEU cc_start: 0.7774 (tt) cc_final: 0.7566 (tt) REVERT: G 214 GLU cc_start: 0.8543 (mm-30) cc_final: 0.7897 (tm-30) REVERT: G 272 VAL cc_start: 0.8926 (t) cc_final: 0.8541 (m) REVERT: G 277 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8577 (tm-30) REVERT: G 286 MET cc_start: 0.8942 (tmt) cc_final: 0.8330 (tmt) REVERT: G 319 ASP cc_start: 0.8222 (m-30) cc_final: 0.7781 (m-30) REVERT: G 327 SER cc_start: 0.8613 (p) cc_final: 0.8323 (p) REVERT: G 352 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8394 (tm-30) REVERT: G 412 ARG cc_start: 0.8451 (ttp80) cc_final: 0.8015 (ptt90) REVERT: G 496 SER cc_start: 0.9134 (p) cc_final: 0.8909 (p) REVERT: G 507 HIS cc_start: 0.8564 (t-90) cc_final: 0.7915 (t-90) REVERT: H 16 ASP cc_start: 0.8374 (t0) cc_final: 0.8112 (t0) REVERT: H 28 ASP cc_start: 0.8245 (m-30) cc_final: 0.8017 (m-30) REVERT: H 75 GLU cc_start: 0.6947 (pm20) cc_final: 0.6552 (pm20) REVERT: H 105 ARG cc_start: 0.8280 (mtm110) cc_final: 0.8047 (ttp80) REVERT: H 137 HIS cc_start: 0.8215 (m90) cc_final: 0.7964 (m-70) REVERT: H 157 ILE cc_start: 0.9148 (mm) cc_final: 0.8826 (mm) REVERT: H 179 MET cc_start: 0.8062 (pp-130) cc_final: 0.7235 (ppp) REVERT: H 198 ASN cc_start: 0.9087 (m-40) cc_final: 0.8624 (m-40) REVERT: H 203 ARG cc_start: 0.8630 (tpp-160) cc_final: 0.8173 (ttp-110) REVERT: H 214 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8001 (tm-30) REVERT: H 272 VAL cc_start: 0.8927 (t) cc_final: 0.8604 (m) REVERT: H 277 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8364 (tm-30) REVERT: H 286 MET cc_start: 0.8977 (tmt) cc_final: 0.8481 (tmt) REVERT: H 319 ASP cc_start: 0.8184 (m-30) cc_final: 0.7938 (m-30) REVERT: H 327 SER cc_start: 0.8619 (p) cc_final: 0.8286 (p) REVERT: H 352 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8292 (tm-30) REVERT: H 412 ARG cc_start: 0.8447 (ttp80) cc_final: 0.7993 (ptt90) REVERT: H 470 ASP cc_start: 0.8938 (m-30) cc_final: 0.8727 (m-30) REVERT: H 496 SER cc_start: 0.9094 (p) cc_final: 0.8802 (p) REVERT: H 507 HIS cc_start: 0.8540 (t-90) cc_final: 0.7894 (t-90) outliers start: 296 outliers final: 107 residues processed: 1203 average time/residue: 0.2089 time to fit residues: 394.8294 Evaluate side-chains 857 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 742 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 126 ARG Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 126 ARG Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 126 ARG Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 362 ILE Chi-restraints excluded: chain G residue 389 LEU Chi-restraints excluded: chain G residue 399 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 126 ARG Chi-restraints excluded: chain H residue 199 GLU Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 399 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS A 112 GLN A 198 ASN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN A 478 GLN B 93 HIS B 198 ASN ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN B 454 HIS B 478 GLN C 112 GLN C 198 ASN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN C 454 HIS C 478 GLN D 198 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 343 GLN D 454 HIS D 478 GLN E 21 GLN E 25 ASN E 93 HIS E 112 GLN E 198 ASN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN E 454 HIS E 478 GLN F 198 ASN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN F 454 HIS F 478 GLN G 112 GLN G 198 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 GLN G 478 GLN H 93 HIS H 198 ASN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 GLN H 454 HIS H 478 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.135860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102685 restraints weight = 54610.164| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.70 r_work: 0.3071 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32096 Z= 0.154 Angle : 0.783 8.369 43488 Z= 0.400 Chirality : 0.048 0.196 4968 Planarity : 0.004 0.035 5448 Dihedral : 15.931 79.157 5586 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.06 % Favored : 92.54 % Rotamer: Outliers : 5.96 % Allowed : 15.74 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.08 (0.12), residues: 3968 helix: -2.03 (0.11), residues: 1280 sheet: -1.85 (0.21), residues: 560 loop : -2.09 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 126 TYR 0.011 0.001 TYR C 348 PHE 0.015 0.001 PHE E 401 HIS 0.003 0.001 HIS E 253 Details of bonding type rmsd covalent geometry : bond 0.00348 (32072) covalent geometry : angle 0.78321 (43488) hydrogen bonds : bond 0.03730 ( 1009) hydrogen bonds : angle 5.73577 ( 2835) Misc. bond : bond 0.00100 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1179 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 984 time to evaluate : 1.141 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: A 25 ASN cc_start: 0.8933 (m-40) cc_final: 0.8606 (p0) REVERT: A 36 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8349 (pp) REVERT: A 75 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6476 (mp0) REVERT: A 137 HIS cc_start: 0.8100 (m90) cc_final: 0.7684 (m-70) REVERT: A 179 MET cc_start: 0.7760 (pp-130) cc_final: 0.6506 (ppp) REVERT: A 198 ASN cc_start: 0.9227 (m110) cc_final: 0.8669 (m-40) REVERT: A 199 GLU cc_start: 0.8114 (pt0) cc_final: 0.7854 (tp30) REVERT: A 202 GLN cc_start: 0.8324 (pp30) cc_final: 0.7813 (pp30) REVERT: A 214 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8057 (tm-30) REVERT: A 245 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8235 (mm) REVERT: A 256 ASP cc_start: 0.8565 (p0) cc_final: 0.8172 (p0) REVERT: A 319 ASP cc_start: 0.8513 (m-30) cc_final: 0.8212 (m-30) REVERT: A 327 SER cc_start: 0.8769 (p) cc_final: 0.8255 (p) REVERT: A 352 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8536 (tm-30) REVERT: A 353 TYR cc_start: 0.8945 (t80) cc_final: 0.8672 (t80) REVERT: A 412 ARG cc_start: 0.8044 (ttp80) cc_final: 0.7187 (tmm-80) REVERT: A 420 MET cc_start: 0.6812 (mtm) cc_final: 0.6593 (mtm) REVERT: A 455 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8549 (mmmm) REVERT: A 474 LYS cc_start: 0.8819 (mtpt) cc_final: 0.8569 (mtpt) REVERT: A 483 MET cc_start: 0.9305 (tmm) cc_final: 0.8715 (tmm) REVERT: A 496 SER cc_start: 0.9085 (p) cc_final: 0.8794 (p) REVERT: A 507 HIS cc_start: 0.8828 (t-90) cc_final: 0.8385 (t-90) REVERT: B 16 ASP cc_start: 0.8508 (t0) cc_final: 0.8273 (t0) REVERT: B 25 ASN cc_start: 0.8802 (m-40) cc_final: 0.8555 (p0) REVERT: B 36 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8356 (pp) REVERT: B 75 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6602 (pm20) REVERT: B 94 ASN cc_start: 0.9280 (t0) cc_final: 0.8970 (t0) REVERT: B 179 MET cc_start: 0.7892 (pp-130) cc_final: 0.6678 (ppp) REVERT: B 198 ASN cc_start: 0.9207 (m110) cc_final: 0.8635 (m-40) REVERT: B 199 GLU cc_start: 0.8150 (pt0) cc_final: 0.7859 (tp30) REVERT: B 205 LYS cc_start: 0.9109 (mtpp) cc_final: 0.8432 (ttmm) REVERT: B 206 LYS cc_start: 0.8354 (mtpp) cc_final: 0.7990 (mtmm) REVERT: B 214 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8269 (tm-30) REVERT: B 245 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8228 (mm) REVERT: B 319 ASP cc_start: 0.8643 (m-30) cc_final: 0.8322 (m-30) REVERT: B 327 SER cc_start: 0.8705 (p) cc_final: 0.8186 (p) REVERT: B 352 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8616 (tm-30) REVERT: B 353 TYR cc_start: 0.9047 (t80) cc_final: 0.8785 (t80) REVERT: B 412 ARG cc_start: 0.8025 (ttp80) cc_final: 0.7448 (ptt90) REVERT: B 420 MET cc_start: 0.6812 (mtm) cc_final: 0.6606 (mtm) REVERT: B 448 GLN cc_start: 0.8243 (pt0) cc_final: 0.8042 (pt0) REVERT: B 461 ILE cc_start: 0.8915 (pp) cc_final: 0.8588 (mt) REVERT: B 507 HIS cc_start: 0.8781 (t-90) cc_final: 0.8348 (t-90) REVERT: C 16 ASP cc_start: 0.8534 (t0) cc_final: 0.8327 (t0) REVERT: C 75 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6571 (mp0) REVERT: C 174 PHE cc_start: 0.8342 (m-80) cc_final: 0.8051 (t80) REVERT: C 179 MET cc_start: 0.7654 (pp-130) cc_final: 0.6428 (ppp) REVERT: C 198 ASN cc_start: 0.9213 (m110) cc_final: 0.8652 (m-40) REVERT: C 199 GLU cc_start: 0.8112 (pt0) cc_final: 0.7739 (tp30) REVERT: C 203 ARG cc_start: 0.8727 (tpp-160) cc_final: 0.8045 (mtp-110) REVERT: C 205 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8451 (ttmm) REVERT: C 209 LEU cc_start: 0.8166 (tt) cc_final: 0.7939 (tt) REVERT: C 214 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8136 (tm-30) REVERT: C 245 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8123 (mm) REVERT: C 319 ASP cc_start: 0.8605 (m-30) cc_final: 0.8289 (m-30) REVERT: C 327 SER cc_start: 0.8734 (p) cc_final: 0.8453 (p) REVERT: C 352 GLU cc_start: 0.9146 (tm-30) cc_final: 0.8607 (tm-30) REVERT: C 353 TYR cc_start: 0.9024 (t80) cc_final: 0.8772 (t80) REVERT: C 412 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7460 (ptt90) REVERT: C 420 MET cc_start: 0.6833 (mtm) cc_final: 0.6609 (mtm) REVERT: C 455 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8607 (mmmm) REVERT: C 474 LYS cc_start: 0.8784 (mtpt) cc_final: 0.8511 (mtpt) REVERT: C 507 HIS cc_start: 0.8842 (t-90) cc_final: 0.8398 (t-90) REVERT: D 16 ASP cc_start: 0.8572 (t0) cc_final: 0.8351 (t0) REVERT: D 36 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8436 (pp) REVERT: D 75 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6763 (pm20) REVERT: D 105 ARG cc_start: 0.8363 (mtm110) cc_final: 0.8105 (ttp80) REVERT: D 137 HIS cc_start: 0.8125 (m90) cc_final: 0.7725 (m-70) REVERT: D 174 PHE cc_start: 0.8187 (m-80) cc_final: 0.7522 (t80) REVERT: D 179 MET cc_start: 0.8027 (pp-130) cc_final: 0.6887 (ppp) REVERT: D 198 ASN cc_start: 0.9270 (m110) cc_final: 0.8770 (m-40) REVERT: D 199 GLU cc_start: 0.8154 (pt0) cc_final: 0.7868 (tp30) REVERT: D 202 GLN cc_start: 0.8440 (pp30) cc_final: 0.7960 (pp30) REVERT: D 205 LYS cc_start: 0.9098 (mtpp) cc_final: 0.8484 (ttmm) REVERT: D 214 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8091 (tm-30) REVERT: D 245 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8282 (mm) REVERT: D 286 MET cc_start: 0.9305 (OUTLIER) cc_final: 0.8755 (tmt) REVERT: D 319 ASP cc_start: 0.8559 (m-30) cc_final: 0.8257 (m-30) REVERT: D 327 SER cc_start: 0.8805 (p) cc_final: 0.8516 (p) REVERT: D 352 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8572 (tm-30) REVERT: D 353 TYR cc_start: 0.9023 (t80) cc_final: 0.8763 (t80) REVERT: D 412 ARG cc_start: 0.8002 (ttp80) cc_final: 0.7216 (tmm-80) REVERT: D 420 MET cc_start: 0.6781 (mtm) cc_final: 0.6540 (mtm) REVERT: D 455 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8617 (mmmm) REVERT: D 474 LYS cc_start: 0.8744 (mtpt) cc_final: 0.8494 (mtpt) REVERT: D 507 HIS cc_start: 0.8831 (t-90) cc_final: 0.8385 (t-90) REVERT: E 25 ASN cc_start: 0.8867 (m110) cc_final: 0.8581 (p0) REVERT: E 26 CYS cc_start: 0.8909 (m) cc_final: 0.8624 (t) REVERT: E 75 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6699 (pm20) REVERT: E 179 MET cc_start: 0.7732 (pp-130) cc_final: 0.6606 (ppp) REVERT: E 198 ASN cc_start: 0.9177 (m110) cc_final: 0.8621 (m-40) REVERT: E 199 GLU cc_start: 0.8123 (pt0) cc_final: 0.7709 (tp30) REVERT: E 202 GLN cc_start: 0.8334 (pp30) cc_final: 0.7892 (pp30) REVERT: E 203 ARG cc_start: 0.8671 (tpp-160) cc_final: 0.8051 (mtp-110) REVERT: E 209 LEU cc_start: 0.8077 (tt) cc_final: 0.7850 (tt) REVERT: E 214 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8136 (tm-30) REVERT: E 245 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8204 (mm) REVERT: E 256 ASP cc_start: 0.8325 (p0) cc_final: 0.7952 (p0) REVERT: E 327 SER cc_start: 0.8686 (p) cc_final: 0.8462 (p) REVERT: E 352 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8572 (tm-30) REVERT: E 412 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7461 (ptt90) REVERT: E 420 MET cc_start: 0.6806 (mtm) cc_final: 0.6586 (mtm) REVERT: E 455 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8583 (mmmm) REVERT: E 483 MET cc_start: 0.9326 (tmm) cc_final: 0.8725 (tmm) REVERT: E 496 SER cc_start: 0.9142 (p) cc_final: 0.8852 (p) REVERT: E 507 HIS cc_start: 0.8820 (t-90) cc_final: 0.8408 (t-90) REVERT: F 16 ASP cc_start: 0.8545 (t0) cc_final: 0.8302 (t0) REVERT: F 34 ASP cc_start: 0.9227 (t0) cc_final: 0.9009 (t0) REVERT: F 75 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6849 (pm20) REVERT: F 174 PHE cc_start: 0.8005 (m-80) cc_final: 0.7299 (t80) REVERT: F 179 MET cc_start: 0.7893 (pp-130) cc_final: 0.6794 (ppp) REVERT: F 198 ASN cc_start: 0.9220 (m110) cc_final: 0.8685 (m-40) REVERT: F 199 GLU cc_start: 0.8086 (pt0) cc_final: 0.7630 (tp30) REVERT: F 202 GLN cc_start: 0.8331 (pp30) cc_final: 0.7888 (pp30) REVERT: F 203 ARG cc_start: 0.8629 (tpp-160) cc_final: 0.8025 (mtp-110) REVERT: F 214 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8056 (tm-30) REVERT: F 245 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8140 (mm) REVERT: F 256 ASP cc_start: 0.8431 (p0) cc_final: 0.8212 (p0) REVERT: F 286 MET cc_start: 0.9312 (OUTLIER) cc_final: 0.8803 (tmt) REVERT: F 319 ASP cc_start: 0.8565 (m-30) cc_final: 0.8261 (m-30) REVERT: F 327 SER cc_start: 0.8754 (p) cc_final: 0.8515 (p) REVERT: F 352 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8576 (tm-30) REVERT: F 353 TYR cc_start: 0.9046 (t80) cc_final: 0.8799 (t80) REVERT: F 409 LYS cc_start: 0.8277 (ttmm) cc_final: 0.8024 (tppt) REVERT: F 412 ARG cc_start: 0.8017 (ttp80) cc_final: 0.7242 (tmm-80) REVERT: F 420 MET cc_start: 0.6737 (mtm) cc_final: 0.6488 (mtm) REVERT: F 455 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8656 (mmmm) REVERT: F 474 LYS cc_start: 0.8744 (mtpt) cc_final: 0.8507 (mtpt) REVERT: F 483 MET cc_start: 0.9276 (tmm) cc_final: 0.8658 (tmm) REVERT: F 507 HIS cc_start: 0.8847 (t-90) cc_final: 0.8408 (t-90) REVERT: G 75 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6601 (mp0) REVERT: G 105 ARG cc_start: 0.8391 (mtm110) cc_final: 0.8147 (ttp-110) REVERT: G 174 PHE cc_start: 0.8005 (m-80) cc_final: 0.7728 (t80) REVERT: G 179 MET cc_start: 0.7752 (pp-130) cc_final: 0.6513 (ppp) REVERT: G 198 ASN cc_start: 0.9200 (m110) cc_final: 0.8702 (m-40) REVERT: G 199 GLU cc_start: 0.8113 (pt0) cc_final: 0.7749 (tp30) REVERT: G 202 GLN cc_start: 0.8440 (pp30) cc_final: 0.8082 (pp30) REVERT: G 203 ARG cc_start: 0.8754 (tpp-160) cc_final: 0.8010 (mtp-110) REVERT: G 214 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8043 (tm-30) REVERT: G 245 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8145 (mm) REVERT: G 259 ARG cc_start: 0.8436 (mtp85) cc_final: 0.8190 (mtp180) REVERT: G 286 MET cc_start: 0.9221 (OUTLIER) cc_final: 0.8692 (tmt) REVERT: G 319 ASP cc_start: 0.8520 (m-30) cc_final: 0.8187 (m-30) REVERT: G 327 SER cc_start: 0.8786 (p) cc_final: 0.8506 (p) REVERT: G 352 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8546 (tm-30) REVERT: G 353 TYR cc_start: 0.8955 (t80) cc_final: 0.8722 (t80) REVERT: G 412 ARG cc_start: 0.8133 (ttp80) cc_final: 0.7269 (tmm-80) REVERT: G 455 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8648 (mmmm) REVERT: G 474 LYS cc_start: 0.8830 (mtpt) cc_final: 0.8583 (mtpt) REVERT: G 487 GLU cc_start: 0.8995 (tt0) cc_final: 0.8573 (tt0) REVERT: G 507 HIS cc_start: 0.8846 (t-90) cc_final: 0.8401 (t-90) REVERT: H 36 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8342 (pp) REVERT: H 75 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6624 (pm20) REVERT: H 105 ARG cc_start: 0.8348 (mtm110) cc_final: 0.8142 (ttp80) REVERT: H 179 MET cc_start: 0.8061 (pp-130) cc_final: 0.6932 (ppp) REVERT: H 198 ASN cc_start: 0.9205 (m110) cc_final: 0.8649 (m-40) REVERT: H 199 GLU cc_start: 0.8103 (pt0) cc_final: 0.7783 (tp30) REVERT: H 202 GLN cc_start: 0.8413 (pp30) cc_final: 0.7928 (pp30) REVERT: H 205 LYS cc_start: 0.8854 (mmmm) cc_final: 0.8605 (mmmm) REVERT: H 214 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8127 (tm-30) REVERT: H 245 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8195 (mm) REVERT: H 256 ASP cc_start: 0.8426 (p0) cc_final: 0.8209 (p0) REVERT: H 286 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8761 (tmt) REVERT: H 319 ASP cc_start: 0.8609 (m-30) cc_final: 0.8280 (m-30) REVERT: H 327 SER cc_start: 0.8614 (p) cc_final: 0.8399 (p) REVERT: H 352 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8512 (tm-30) REVERT: H 353 TYR cc_start: 0.9020 (t80) cc_final: 0.8761 (t80) REVERT: H 412 ARG cc_start: 0.8053 (ttp80) cc_final: 0.7451 (ptt90) REVERT: H 483 MET cc_start: 0.9284 (tmm) cc_final: 0.8689 (tmm) REVERT: H 507 HIS cc_start: 0.8797 (t-90) cc_final: 0.8367 (t-90) outliers start: 195 outliers final: 100 residues processed: 1110 average time/residue: 0.2012 time to fit residues: 356.9016 Evaluate side-chains 925 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 795 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain J residue 11 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain K residue 11 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain M residue 11 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain O residue 11 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 389 LEU Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 389 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 281 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 391 optimal weight: 6.9990 chunk 91 optimal weight: 0.0170 chunk 98 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 251 optimal weight: 0.9980 chunk 369 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 387 optimal weight: 0.8980 overall best weight: 1.0220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN C 198 ASN ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 HIS D 92 HIS ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 HIS E 21 GLN E 25 ASN E 102 ASN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 HIS F 92 HIS ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 HIS ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 HIS ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 454 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.135595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.102338 restraints weight = 54928.182| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.68 r_work: 0.3070 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32096 Z= 0.163 Angle : 0.732 8.037 43488 Z= 0.376 Chirality : 0.049 0.178 4968 Planarity : 0.004 0.048 5448 Dihedral : 14.844 73.625 5452 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 5.13 % Allowed : 20.26 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.26 (0.13), residues: 3968 helix: -0.96 (0.13), residues: 1288 sheet: -1.60 (0.20), residues: 600 loop : -1.80 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 493 TYR 0.011 0.001 TYR E 348 PHE 0.013 0.001 PHE E 24 HIS 0.003 0.001 HIS F 454 Details of bonding type rmsd covalent geometry : bond 0.00382 (32072) covalent geometry : angle 0.73248 (43488) hydrogen bonds : bond 0.03486 ( 1009) hydrogen bonds : angle 5.25410 ( 2835) Misc. bond : bond 0.00113 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 908 time to evaluate : 1.191 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: A 25 ASN cc_start: 0.8895 (m-40) cc_final: 0.8616 (p0) REVERT: A 75 GLU cc_start: 0.7184 (pm20) cc_final: 0.6633 (mp0) REVERT: A 100 GLN cc_start: 0.9315 (OUTLIER) cc_final: 0.9079 (pt0) REVERT: A 108 LYS cc_start: 0.8685 (tptp) cc_final: 0.8306 (tppt) REVERT: A 179 MET cc_start: 0.7821 (pp-130) cc_final: 0.6527 (ppp) REVERT: A 198 ASN cc_start: 0.9232 (m110) cc_final: 0.8735 (m-40) REVERT: A 199 GLU cc_start: 0.8227 (pt0) cc_final: 0.7849 (tp30) REVERT: A 202 GLN cc_start: 0.8500 (pp30) cc_final: 0.8034 (pp30) REVERT: A 203 ARG cc_start: 0.8743 (tpp-160) cc_final: 0.8205 (mtp-110) REVERT: A 214 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8178 (tm-30) REVERT: A 245 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8136 (mm) REVERT: A 279 ASN cc_start: 0.8553 (t0) cc_final: 0.8013 (t0) REVERT: A 319 ASP cc_start: 0.8558 (m-30) cc_final: 0.8291 (m-30) REVERT: A 325 MET cc_start: 0.8082 (ptm) cc_final: 0.7824 (ptm) REVERT: A 327 SER cc_start: 0.8743 (p) cc_final: 0.8447 (p) REVERT: A 352 GLU cc_start: 0.9088 (tm-30) cc_final: 0.8496 (tm-30) REVERT: A 353 TYR cc_start: 0.8933 (t80) cc_final: 0.8660 (t80) REVERT: A 412 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7448 (ptt90) REVERT: A 420 MET cc_start: 0.6778 (mtm) cc_final: 0.6533 (mtm) REVERT: A 455 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8587 (mmmm) REVERT: A 474 LYS cc_start: 0.8893 (mtpt) cc_final: 0.8646 (mtpt) REVERT: A 507 HIS cc_start: 0.8825 (t-90) cc_final: 0.8408 (t-90) REVERT: B 16 ASP cc_start: 0.8468 (t0) cc_final: 0.8209 (t0) REVERT: B 25 ASN cc_start: 0.8788 (m-40) cc_final: 0.8565 (p0) REVERT: B 75 GLU cc_start: 0.7088 (pm20) cc_final: 0.6614 (mp0) REVERT: B 94 ASN cc_start: 0.9187 (t0) cc_final: 0.8936 (t0) REVERT: B 100 GLN cc_start: 0.9282 (OUTLIER) cc_final: 0.9079 (pt0) REVERT: B 150 MET cc_start: 0.7979 (ttt) cc_final: 0.7456 (tpp) REVERT: B 174 PHE cc_start: 0.7973 (m-80) cc_final: 0.7761 (m-80) REVERT: B 179 MET cc_start: 0.7931 (pp-130) cc_final: 0.6752 (ppp) REVERT: B 194 LEU cc_start: 0.8724 (mm) cc_final: 0.8284 (mm) REVERT: B 198 ASN cc_start: 0.9220 (m110) cc_final: 0.8646 (m-40) REVERT: B 199 GLU cc_start: 0.8149 (pt0) cc_final: 0.7819 (tp30) REVERT: B 202 GLN cc_start: 0.8449 (pp30) cc_final: 0.7960 (pp30) REVERT: B 205 LYS cc_start: 0.9112 (mtpp) cc_final: 0.8485 (ttmm) REVERT: B 214 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8140 (tm-30) REVERT: B 245 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8101 (mm) REVERT: B 319 ASP cc_start: 0.8524 (m-30) cc_final: 0.8289 (m-30) REVERT: B 325 MET cc_start: 0.8110 (ptm) cc_final: 0.7899 (ptm) REVERT: B 352 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8590 (tm-30) REVERT: B 353 TYR cc_start: 0.9003 (t80) cc_final: 0.8750 (t80) REVERT: B 412 ARG cc_start: 0.8034 (ttp80) cc_final: 0.7450 (ptt90) REVERT: B 420 MET cc_start: 0.6768 (mtm) cc_final: 0.6538 (mtm) REVERT: B 448 GLN cc_start: 0.8226 (pt0) cc_final: 0.7986 (pt0) REVERT: B 461 ILE cc_start: 0.8967 (pp) cc_final: 0.8684 (mt) REVERT: B 507 HIS cc_start: 0.8787 (t-90) cc_final: 0.8371 (t-90) REVERT: C 75 GLU cc_start: 0.7199 (pm20) cc_final: 0.6777 (mp0) REVERT: C 92 HIS cc_start: 0.9265 (p-80) cc_final: 0.9062 (p-80) REVERT: C 94 ASN cc_start: 0.9223 (t0) cc_final: 0.8833 (t0) REVERT: C 108 LYS cc_start: 0.8627 (tptp) cc_final: 0.8206 (tppt) REVERT: C 150 MET cc_start: 0.8045 (ttt) cc_final: 0.7459 (tpp) REVERT: C 174 PHE cc_start: 0.8412 (m-80) cc_final: 0.8145 (t80) REVERT: C 175 LEU cc_start: 0.8308 (mt) cc_final: 0.7858 (mt) REVERT: C 179 MET cc_start: 0.7662 (pp-130) cc_final: 0.6382 (ppp) REVERT: C 198 ASN cc_start: 0.9160 (m-40) cc_final: 0.8585 (m-40) REVERT: C 199 GLU cc_start: 0.8164 (pt0) cc_final: 0.7789 (tp30) REVERT: C 202 GLN cc_start: 0.8431 (pp30) cc_final: 0.8002 (pp30) REVERT: C 203 ARG cc_start: 0.8826 (tpp-160) cc_final: 0.8167 (mtp-110) REVERT: C 205 LYS cc_start: 0.9105 (mtpp) cc_final: 0.8502 (ttmm) REVERT: C 209 LEU cc_start: 0.8183 (tt) cc_final: 0.7971 (tt) REVERT: C 214 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8061 (tm-30) REVERT: C 245 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8122 (mm) REVERT: C 261 ASP cc_start: 0.9091 (m-30) cc_final: 0.8798 (m-30) REVERT: C 319 ASP cc_start: 0.8634 (m-30) cc_final: 0.8370 (m-30) REVERT: C 327 SER cc_start: 0.8581 (p) cc_final: 0.8055 (p) REVERT: C 352 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8595 (tm-30) REVERT: C 353 TYR cc_start: 0.8945 (t80) cc_final: 0.8685 (t80) REVERT: C 412 ARG cc_start: 0.8008 (ttp80) cc_final: 0.7496 (ptt90) REVERT: C 420 MET cc_start: 0.6771 (mtm) cc_final: 0.6546 (mtm) REVERT: C 455 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8599 (mmmm) REVERT: C 474 LYS cc_start: 0.8815 (mtpt) cc_final: 0.8561 (mtpt) REVERT: C 507 HIS cc_start: 0.8829 (t-90) cc_final: 0.8404 (t-90) REVERT: D 16 ASP cc_start: 0.8479 (t0) cc_final: 0.8239 (t0) REVERT: D 34 ASP cc_start: 0.9263 (t0) cc_final: 0.9037 (t0) REVERT: D 75 GLU cc_start: 0.7157 (pm20) cc_final: 0.6766 (mp0) REVERT: D 100 GLN cc_start: 0.9309 (OUTLIER) cc_final: 0.9106 (pt0) REVERT: D 108 LYS cc_start: 0.8612 (tptp) cc_final: 0.8229 (tppt) REVERT: D 134 LYS cc_start: 0.7974 (pttp) cc_final: 0.7406 (pttm) REVERT: D 150 MET cc_start: 0.8051 (ttt) cc_final: 0.7600 (tpp) REVERT: D 179 MET cc_start: 0.8039 (pp-130) cc_final: 0.6893 (ppp) REVERT: D 198 ASN cc_start: 0.9228 (m110) cc_final: 0.8735 (m-40) REVERT: D 199 GLU cc_start: 0.8213 (pt0) cc_final: 0.7904 (tp30) REVERT: D 202 GLN cc_start: 0.8546 (pp30) cc_final: 0.8051 (pp30) REVERT: D 205 LYS cc_start: 0.9078 (mtpp) cc_final: 0.8433 (ttmm) REVERT: D 214 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8115 (tm-30) REVERT: D 244 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8293 (mt) REVERT: D 245 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8230 (mm) REVERT: D 261 ASP cc_start: 0.8984 (m-30) cc_final: 0.8775 (m-30) REVERT: D 319 ASP cc_start: 0.8569 (m-30) cc_final: 0.8366 (m-30) REVERT: D 327 SER cc_start: 0.8607 (p) cc_final: 0.8401 (p) REVERT: D 352 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8566 (tm-30) REVERT: D 353 TYR cc_start: 0.8993 (t80) cc_final: 0.8750 (t80) REVERT: D 412 ARG cc_start: 0.8007 (ttp80) cc_final: 0.7501 (ptt90) REVERT: D 420 MET cc_start: 0.6741 (mtm) cc_final: 0.6514 (mtm) REVERT: D 455 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8626 (mmmm) REVERT: D 474 LYS cc_start: 0.8847 (mtpt) cc_final: 0.8602 (mtpt) REVERT: D 507 HIS cc_start: 0.8812 (t-90) cc_final: 0.8387 (t-90) REVERT: E 25 ASN cc_start: 0.8925 (m-40) cc_final: 0.8632 (p0) REVERT: E 26 CYS cc_start: 0.8981 (m) cc_final: 0.8619 (t) REVERT: E 75 GLU cc_start: 0.7227 (pm20) cc_final: 0.6818 (mp0) REVERT: E 108 LYS cc_start: 0.8641 (tptp) cc_final: 0.8208 (tppt) REVERT: E 150 MET cc_start: 0.8027 (ttt) cc_final: 0.7382 (tpp) REVERT: E 179 MET cc_start: 0.7660 (pp-130) cc_final: 0.6398 (ppp) REVERT: E 198 ASN cc_start: 0.9200 (m110) cc_final: 0.8632 (m-40) REVERT: E 199 GLU cc_start: 0.8133 (pt0) cc_final: 0.7679 (tp30) REVERT: E 202 GLN cc_start: 0.8524 (pp30) cc_final: 0.8086 (pp30) REVERT: E 203 ARG cc_start: 0.8747 (tpp-160) cc_final: 0.8119 (mtp-110) REVERT: E 209 LEU cc_start: 0.8086 (tt) cc_final: 0.7842 (tt) REVERT: E 214 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8088 (tm-30) REVERT: E 245 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8125 (mm) REVERT: E 261 ASP cc_start: 0.9104 (m-30) cc_final: 0.8788 (m-30) REVERT: E 319 ASP cc_start: 0.8619 (m-30) cc_final: 0.8347 (m-30) REVERT: E 327 SER cc_start: 0.8667 (p) cc_final: 0.8035 (p) REVERT: E 352 GLU cc_start: 0.9117 (tm-30) cc_final: 0.8590 (tm-30) REVERT: E 412 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7493 (ptt90) REVERT: E 455 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8596 (mmmm) REVERT: E 507 HIS cc_start: 0.8828 (t-90) cc_final: 0.8445 (t-90) REVERT: F 16 ASP cc_start: 0.8509 (t0) cc_final: 0.8244 (t0) REVERT: F 34 ASP cc_start: 0.9190 (t0) cc_final: 0.8930 (t0) REVERT: F 75 GLU cc_start: 0.7205 (pm20) cc_final: 0.6866 (pm20) REVERT: F 92 HIS cc_start: 0.9069 (p90) cc_final: 0.8774 (p-80) REVERT: F 108 LYS cc_start: 0.8591 (tptp) cc_final: 0.8157 (tppt) REVERT: F 150 MET cc_start: 0.8068 (ttt) cc_final: 0.7593 (tpp) REVERT: F 174 PHE cc_start: 0.8060 (m-80) cc_final: 0.7860 (m-80) REVERT: F 179 MET cc_start: 0.7954 (pp-130) cc_final: 0.6828 (ppp) REVERT: F 198 ASN cc_start: 0.9215 (m110) cc_final: 0.8704 (m-40) REVERT: F 199 GLU cc_start: 0.8178 (pt0) cc_final: 0.7693 (tp30) REVERT: F 202 GLN cc_start: 0.8479 (pp30) cc_final: 0.8027 (pp30) REVERT: F 203 ARG cc_start: 0.8690 (tpp-160) cc_final: 0.8075 (mtp-110) REVERT: F 214 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8050 (tm-30) REVERT: F 245 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8117 (mm) REVERT: F 261 ASP cc_start: 0.9025 (m-30) cc_final: 0.8763 (m-30) REVERT: F 286 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.8888 (tmt) REVERT: F 300 ILE cc_start: 0.8513 (mm) cc_final: 0.8262 (mm) REVERT: F 319 ASP cc_start: 0.8531 (m-30) cc_final: 0.8282 (m-30) REVERT: F 327 SER cc_start: 0.8645 (p) cc_final: 0.8126 (p) REVERT: F 352 GLU cc_start: 0.9104 (tm-30) cc_final: 0.8567 (tm-30) REVERT: F 353 TYR cc_start: 0.8988 (t80) cc_final: 0.8769 (t80) REVERT: F 412 ARG cc_start: 0.8012 (ttp80) cc_final: 0.7513 (ptt90) REVERT: F 420 MET cc_start: 0.6687 (mtm) cc_final: 0.6481 (mtm) REVERT: F 455 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8600 (mmmm) REVERT: F 474 LYS cc_start: 0.8770 (mtpt) cc_final: 0.8522 (mtpt) REVERT: F 507 HIS cc_start: 0.8851 (t-90) cc_final: 0.8439 (t-90) REVERT: G 34 ASP cc_start: 0.9247 (t0) cc_final: 0.8897 (t0) REVERT: G 75 GLU cc_start: 0.7297 (pm20) cc_final: 0.6787 (mp0) REVERT: G 94 ASN cc_start: 0.9160 (t0) cc_final: 0.8840 (t0) REVERT: G 108 LYS cc_start: 0.8640 (tptp) cc_final: 0.8241 (tppt) REVERT: G 179 MET cc_start: 0.7764 (pp-130) cc_final: 0.6481 (ppp) REVERT: G 198 ASN cc_start: 0.9221 (m110) cc_final: 0.8734 (m-40) REVERT: G 199 GLU cc_start: 0.8202 (pt0) cc_final: 0.7822 (tp30) REVERT: G 202 GLN cc_start: 0.8548 (pp30) cc_final: 0.8212 (pp30) REVERT: G 203 ARG cc_start: 0.8844 (tpp-160) cc_final: 0.8051 (mtp-110) REVERT: G 214 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8031 (tm-30) REVERT: G 245 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8112 (mm) REVERT: G 259 ARG cc_start: 0.8578 (mtp85) cc_final: 0.8112 (mtp180) REVERT: G 300 ILE cc_start: 0.8628 (mm) cc_final: 0.8402 (mm) REVERT: G 319 ASP cc_start: 0.8540 (m-30) cc_final: 0.8265 (m-30) REVERT: G 327 SER cc_start: 0.8554 (p) cc_final: 0.8284 (p) REVERT: G 352 GLU cc_start: 0.9085 (tm-30) cc_final: 0.8533 (tm-30) REVERT: G 353 TYR cc_start: 0.8927 (t80) cc_final: 0.8725 (t80) REVERT: G 412 ARG cc_start: 0.8105 (ttp80) cc_final: 0.7569 (ptt90) REVERT: G 420 MET cc_start: 0.6939 (mtm) cc_final: 0.6728 (mtm) REVERT: G 455 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8607 (mmmm) REVERT: G 474 LYS cc_start: 0.8876 (mtpt) cc_final: 0.8628 (mtpt) REVERT: G 487 GLU cc_start: 0.9020 (tt0) cc_final: 0.8658 (tt0) REVERT: G 507 HIS cc_start: 0.8818 (t-90) cc_final: 0.8397 (t-90) REVERT: H 75 GLU cc_start: 0.7267 (pm20) cc_final: 0.6816 (mp0) REVERT: H 100 GLN cc_start: 0.9317 (OUTLIER) cc_final: 0.9117 (pt0) REVERT: H 179 MET cc_start: 0.8055 (pp-130) cc_final: 0.6886 (ppp) REVERT: H 194 LEU cc_start: 0.8765 (mm) cc_final: 0.8371 (mm) REVERT: H 198 ASN cc_start: 0.9232 (m110) cc_final: 0.8694 (m-40) REVERT: H 199 GLU cc_start: 0.8200 (pt0) cc_final: 0.7855 (tp30) REVERT: H 202 GLN cc_start: 0.8507 (pp30) cc_final: 0.7979 (pp30) REVERT: H 214 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8107 (tm-30) REVERT: H 245 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8121 (mm) REVERT: H 286 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8743 (tmt) REVERT: H 300 ILE cc_start: 0.8742 (mm) cc_final: 0.8466 (mm) REVERT: H 319 ASP cc_start: 0.8575 (m-30) cc_final: 0.8306 (m-30) REVERT: H 327 SER cc_start: 0.8572 (p) cc_final: 0.8218 (p) REVERT: H 412 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7533 (ptt90) REVERT: H 420 MET cc_start: 0.6768 (mtm) cc_final: 0.6530 (mtm) REVERT: H 455 LYS cc_start: 0.8906 (mmmm) cc_final: 0.8694 (mmmm) REVERT: H 507 HIS cc_start: 0.8805 (t-90) cc_final: 0.8403 (t-90) outliers start: 168 outliers final: 91 residues processed: 1016 average time/residue: 0.1938 time to fit residues: 321.0100 Evaluate side-chains 902 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 790 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 496 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 38 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 311 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 39 optimal weight: 0.0670 chunk 129 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 304 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 303 optimal weight: 0.9980 chunk 248 optimal weight: 0.9980 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 198 ASN A 303 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN B 198 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 HIS C 102 ASN C 303 ASN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS D 198 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN E 198 ASN ** E 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN F 198 ASN F 303 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 ASN G 198 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 HIS H 198 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.134547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.101585 restraints weight = 54490.812| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 3.66 r_work: 0.3062 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 32096 Z= 0.168 Angle : 0.717 7.971 43488 Z= 0.368 Chirality : 0.048 0.152 4968 Planarity : 0.004 0.040 5448 Dihedral : 14.146 74.302 5406 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 5.59 % Allowed : 21.67 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -1.85 (0.13), residues: 3968 helix: -0.42 (0.14), residues: 1288 sheet: -1.50 (0.20), residues: 600 loop : -1.65 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 493 TYR 0.011 0.001 TYR G 348 PHE 0.015 0.001 PHE A 24 HIS 0.003 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00392 (32072) covalent geometry : angle 0.71673 (43488) hydrogen bonds : bond 0.03300 ( 1009) hydrogen bonds : angle 5.09660 ( 2835) Misc. bond : bond 0.00158 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1061 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 878 time to evaluate : 1.237 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: A 25 ASN cc_start: 0.8915 (m-40) cc_final: 0.8600 (p0) REVERT: A 75 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6759 (mp0) REVERT: A 94 ASN cc_start: 0.9193 (t0) cc_final: 0.8937 (t0) REVERT: A 136 ARG cc_start: 0.8566 (ptm-80) cc_final: 0.8272 (ptt180) REVERT: A 150 MET cc_start: 0.7985 (ttt) cc_final: 0.7471 (tpp) REVERT: A 179 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.6525 (ppp) REVERT: A 198 ASN cc_start: 0.9273 (m-40) cc_final: 0.8705 (m-40) REVERT: A 199 GLU cc_start: 0.8251 (pt0) cc_final: 0.7876 (tp30) REVERT: A 202 GLN cc_start: 0.8584 (pp30) cc_final: 0.8106 (pp30) REVERT: A 203 ARG cc_start: 0.8831 (tpp-160) cc_final: 0.8200 (mtp-110) REVERT: A 214 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8129 (tm-30) REVERT: A 231 ARG cc_start: 0.8450 (mmm160) cc_final: 0.8219 (mmp80) REVERT: A 245 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8111 (mm) REVERT: A 319 ASP cc_start: 0.8488 (m-30) cc_final: 0.8198 (m-30) REVERT: A 325 MET cc_start: 0.8122 (ptm) cc_final: 0.7916 (ptm) REVERT: A 353 TYR cc_start: 0.8921 (t80) cc_final: 0.8699 (t80) REVERT: A 369 ASN cc_start: 0.8355 (p0) cc_final: 0.8111 (p0) REVERT: A 385 MET cc_start: 0.8973 (ttp) cc_final: 0.8478 (ttp) REVERT: A 412 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7411 (ptt90) REVERT: A 420 MET cc_start: 0.6940 (mtm) cc_final: 0.6722 (mtm) REVERT: A 455 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8542 (mmmm) REVERT: A 474 LYS cc_start: 0.8903 (mtpt) cc_final: 0.8631 (mtpt) REVERT: A 507 HIS cc_start: 0.8819 (t-90) cc_final: 0.8412 (t-90) REVERT: B 16 ASP cc_start: 0.8493 (t0) cc_final: 0.8228 (t0) REVERT: B 25 ASN cc_start: 0.8802 (m-40) cc_final: 0.8572 (p0) REVERT: B 34 ASP cc_start: 0.9245 (t0) cc_final: 0.8908 (t0) REVERT: B 75 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6709 (mp0) REVERT: B 94 ASN cc_start: 0.9218 (t0) cc_final: 0.8965 (t0) REVERT: B 134 LYS cc_start: 0.8056 (pttp) cc_final: 0.7644 (pttm) REVERT: B 150 MET cc_start: 0.7965 (ttt) cc_final: 0.7474 (tpp) REVERT: B 174 PHE cc_start: 0.7973 (m-80) cc_final: 0.7521 (m-80) REVERT: B 179 MET cc_start: 0.7974 (pp-130) cc_final: 0.6809 (ppp) REVERT: B 198 ASN cc_start: 0.9259 (m-40) cc_final: 0.8665 (m-40) REVERT: B 199 GLU cc_start: 0.8149 (pt0) cc_final: 0.7842 (tp30) REVERT: B 202 GLN cc_start: 0.8651 (pp30) cc_final: 0.8226 (pp30) REVERT: B 205 LYS cc_start: 0.9122 (mtpp) cc_final: 0.8537 (ttmm) REVERT: B 214 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8220 (tm-30) REVERT: B 245 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8103 (mm) REVERT: B 300 ILE cc_start: 0.8629 (mm) cc_final: 0.8357 (mm) REVERT: B 319 ASP cc_start: 0.8480 (m-30) cc_final: 0.8235 (m-30) REVERT: B 327 SER cc_start: 0.8820 (p) cc_final: 0.8538 (p) REVERT: B 353 TYR cc_start: 0.9008 (t80) cc_final: 0.8793 (t80) REVERT: B 385 MET cc_start: 0.8794 (ttp) cc_final: 0.8283 (ttp) REVERT: B 412 ARG cc_start: 0.7986 (ttp80) cc_final: 0.7443 (ptt90) REVERT: B 420 MET cc_start: 0.6806 (mtm) cc_final: 0.6592 (mtm) REVERT: B 448 GLN cc_start: 0.8269 (pt0) cc_final: 0.8043 (pt0) REVERT: B 507 HIS cc_start: 0.8818 (t-90) cc_final: 0.8407 (t-90) REVERT: C 75 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6726 (mp0) REVERT: C 134 LYS cc_start: 0.8083 (pttp) cc_final: 0.7644 (pttm) REVERT: C 136 ARG cc_start: 0.8591 (ptm-80) cc_final: 0.8310 (ptt180) REVERT: C 150 MET cc_start: 0.8086 (ttt) cc_final: 0.7485 (tpp) REVERT: C 174 PHE cc_start: 0.8428 (m-80) cc_final: 0.8212 (t80) REVERT: C 179 MET cc_start: 0.7650 (pp-130) cc_final: 0.6389 (ppp) REVERT: C 199 GLU cc_start: 0.8170 (pt0) cc_final: 0.7776 (tp30) REVERT: C 202 GLN cc_start: 0.8571 (pp30) cc_final: 0.8242 (pp30) REVERT: C 203 ARG cc_start: 0.8861 (tpp-160) cc_final: 0.8188 (mtp-110) REVERT: C 205 LYS cc_start: 0.9075 (mtpp) cc_final: 0.8534 (ttmm) REVERT: C 209 LEU cc_start: 0.8149 (tt) cc_final: 0.7931 (tt) REVERT: C 214 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8079 (tm-30) REVERT: C 245 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8072 (mm) REVERT: C 261 ASP cc_start: 0.9159 (m-30) cc_final: 0.8749 (m-30) REVERT: C 319 ASP cc_start: 0.8575 (m-30) cc_final: 0.8288 (m-30) REVERT: C 325 MET cc_start: 0.8107 (ptm) cc_final: 0.7893 (ptm) REVERT: C 352 GLU cc_start: 0.9131 (tm-30) cc_final: 0.8585 (tm-30) REVERT: C 353 TYR cc_start: 0.8944 (t80) cc_final: 0.8708 (t80) REVERT: C 385 MET cc_start: 0.8949 (ttp) cc_final: 0.8411 (ttp) REVERT: C 412 ARG cc_start: 0.7993 (ttp80) cc_final: 0.7445 (ptt90) REVERT: C 420 MET cc_start: 0.6559 (mtm) cc_final: 0.6315 (mtm) REVERT: C 455 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8553 (mmmm) REVERT: C 474 LYS cc_start: 0.8874 (mtpt) cc_final: 0.8615 (mtpt) REVERT: C 507 HIS cc_start: 0.8822 (t-90) cc_final: 0.8393 (t-90) REVERT: D 16 ASP cc_start: 0.8511 (t0) cc_final: 0.8254 (t0) REVERT: D 34 ASP cc_start: 0.9303 (t0) cc_final: 0.8960 (t0) REVERT: D 75 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6788 (mp0) REVERT: D 134 LYS cc_start: 0.7930 (pttp) cc_final: 0.7598 (pttm) REVERT: D 150 MET cc_start: 0.8041 (ttt) cc_final: 0.7614 (tpp) REVERT: D 179 MET cc_start: 0.7995 (pp-130) cc_final: 0.6853 (ppp) REVERT: D 198 ASN cc_start: 0.9289 (m-40) cc_final: 0.8761 (m-40) REVERT: D 199 GLU cc_start: 0.8262 (pt0) cc_final: 0.7931 (tp30) REVERT: D 202 GLN cc_start: 0.8634 (pp30) cc_final: 0.8179 (pp30) REVERT: D 205 LYS cc_start: 0.9058 (mtpp) cc_final: 0.8498 (ttmm) REVERT: D 214 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8112 (tm-30) REVERT: D 245 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8214 (mm) REVERT: D 261 ASP cc_start: 0.9019 (m-30) cc_final: 0.8818 (m-30) REVERT: D 300 ILE cc_start: 0.8847 (mm) cc_final: 0.8558 (mm) REVERT: D 319 ASP cc_start: 0.8602 (m-30) cc_final: 0.8321 (m-30) REVERT: D 327 SER cc_start: 0.8809 (p) cc_final: 0.8571 (p) REVERT: D 352 GLU cc_start: 0.9108 (tm-30) cc_final: 0.8552 (tm-30) REVERT: D 353 TYR cc_start: 0.9007 (t80) cc_final: 0.8748 (t80) REVERT: D 385 MET cc_start: 0.9004 (ttp) cc_final: 0.8510 (ttp) REVERT: D 412 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7473 (ptt90) REVERT: D 455 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8615 (mmmm) REVERT: D 474 LYS cc_start: 0.8839 (mtpt) cc_final: 0.8563 (mtpt) REVERT: D 507 HIS cc_start: 0.8821 (t-90) cc_final: 0.8388 (t-90) REVERT: E 25 ASN cc_start: 0.8913 (m-40) cc_final: 0.8623 (p0) REVERT: E 26 CYS cc_start: 0.9029 (m) cc_final: 0.8654 (t) REVERT: E 75 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6816 (mp0) REVERT: E 94 ASN cc_start: 0.9212 (t0) cc_final: 0.8936 (t0) REVERT: E 134 LYS cc_start: 0.8109 (pttp) cc_final: 0.7739 (pttm) REVERT: E 136 ARG cc_start: 0.8567 (ptm-80) cc_final: 0.8327 (ptt180) REVERT: E 150 MET cc_start: 0.8038 (ttt) cc_final: 0.7424 (tpp) REVERT: E 174 PHE cc_start: 0.8438 (m-80) cc_final: 0.7995 (t80) REVERT: E 175 LEU cc_start: 0.8361 (mt) cc_final: 0.7926 (mt) REVERT: E 179 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.6418 (ppp) REVERT: E 198 ASN cc_start: 0.9233 (m-40) cc_final: 0.8596 (m-40) REVERT: E 199 GLU cc_start: 0.8141 (pt0) cc_final: 0.7748 (tp30) REVERT: E 202 GLN cc_start: 0.8609 (pp30) cc_final: 0.8251 (pp30) REVERT: E 203 ARG cc_start: 0.8713 (tpp-160) cc_final: 0.8102 (ttp-110) REVERT: E 209 LEU cc_start: 0.8042 (tt) cc_final: 0.7788 (tt) REVERT: E 214 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8102 (tm-30) REVERT: E 231 ARG cc_start: 0.8437 (mmm160) cc_final: 0.8178 (mmp80) REVERT: E 245 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8015 (mm) REVERT: E 261 ASP cc_start: 0.9171 (m-30) cc_final: 0.8721 (m-30) REVERT: E 319 ASP cc_start: 0.8562 (m-30) cc_final: 0.8280 (m-30) REVERT: E 352 GLU cc_start: 0.9106 (tm-30) cc_final: 0.8552 (tm-30) REVERT: E 369 ASN cc_start: 0.8436 (p0) cc_final: 0.8210 (p0) REVERT: E 412 ARG cc_start: 0.8016 (ttp80) cc_final: 0.7477 (ptt90) REVERT: E 420 MET cc_start: 0.6816 (mtm) cc_final: 0.6566 (mtm) REVERT: E 455 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8603 (mmmm) REVERT: E 507 HIS cc_start: 0.8841 (t-90) cc_final: 0.8456 (t-90) REVERT: F 16 ASP cc_start: 0.8498 (t0) cc_final: 0.8222 (t0) REVERT: F 25 ASN cc_start: 0.8824 (m-40) cc_final: 0.8573 (p0) REVERT: F 34 ASP cc_start: 0.9212 (t0) cc_final: 0.8898 (t0) REVERT: F 75 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6829 (mp0) REVERT: F 94 ASN cc_start: 0.9226 (t0) cc_final: 0.8987 (t0) REVERT: F 134 LYS cc_start: 0.8004 (pttp) cc_final: 0.7630 (pttm) REVERT: F 136 ARG cc_start: 0.8625 (ptm-80) cc_final: 0.8386 (ptt180) REVERT: F 150 MET cc_start: 0.8047 (ttt) cc_final: 0.7596 (tpp) REVERT: F 174 PHE cc_start: 0.8028 (m-80) cc_final: 0.7652 (m-80) REVERT: F 179 MET cc_start: 0.7972 (pp-130) cc_final: 0.6835 (ppp) REVERT: F 198 ASN cc_start: 0.9284 (m-40) cc_final: 0.8729 (m-40) REVERT: F 199 GLU cc_start: 0.8261 (pt0) cc_final: 0.7762 (tp30) REVERT: F 202 GLN cc_start: 0.8530 (pp30) cc_final: 0.8113 (pp30) REVERT: F 203 ARG cc_start: 0.8720 (tpp-160) cc_final: 0.8056 (mtp-110) REVERT: F 214 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8054 (tm-30) REVERT: F 245 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8107 (mm) REVERT: F 261 ASP cc_start: 0.9125 (m-30) cc_final: 0.8745 (m-30) REVERT: F 285 ASN cc_start: 0.8585 (m110) cc_final: 0.8334 (m110) REVERT: F 286 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8886 (tmt) REVERT: F 319 ASP cc_start: 0.8486 (m-30) cc_final: 0.8234 (m-30) REVERT: F 325 MET cc_start: 0.8103 (ptm) cc_final: 0.7886 (ptm) REVERT: F 352 GLU cc_start: 0.9108 (tm-30) cc_final: 0.8561 (tm-30) REVERT: F 353 TYR cc_start: 0.9008 (t80) cc_final: 0.8778 (t80) REVERT: F 369 ASN cc_start: 0.8434 (p0) cc_final: 0.8213 (p0) REVERT: F 385 MET cc_start: 0.8914 (ttp) cc_final: 0.8343 (ttp) REVERT: F 412 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7464 (ptt90) REVERT: F 420 MET cc_start: 0.6508 (mtm) cc_final: 0.6291 (mtm) REVERT: F 455 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8610 (mmmm) REVERT: F 474 LYS cc_start: 0.8815 (mtpt) cc_final: 0.8545 (mtpt) REVERT: F 507 HIS cc_start: 0.8859 (t-90) cc_final: 0.8450 (t-90) REVERT: G 25 ASN cc_start: 0.8878 (m-40) cc_final: 0.8572 (p0) REVERT: G 75 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6887 (mp0) REVERT: G 94 ASN cc_start: 0.9247 (t0) cc_final: 0.8854 (t0) REVERT: G 132 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8480 (pp20) REVERT: G 150 MET cc_start: 0.7998 (ttt) cc_final: 0.7471 (tpp) REVERT: G 179 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.6470 (ppp) REVERT: G 198 ASN cc_start: 0.9249 (m-40) cc_final: 0.8731 (m-40) REVERT: G 199 GLU cc_start: 0.8230 (pt0) cc_final: 0.7839 (tp30) REVERT: G 202 GLN cc_start: 0.8599 (pp30) cc_final: 0.8236 (pp30) REVERT: G 203 ARG cc_start: 0.8871 (tpp-160) cc_final: 0.8077 (mtp-110) REVERT: G 214 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8182 (tm-30) REVERT: G 231 ARG cc_start: 0.8409 (mmm160) cc_final: 0.8005 (mmm160) REVERT: G 245 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8082 (mm) REVERT: G 256 ASP cc_start: 0.8408 (p0) cc_final: 0.8045 (p0) REVERT: G 259 ARG cc_start: 0.8676 (mtp85) cc_final: 0.8184 (mtp180) REVERT: G 279 ASN cc_start: 0.8554 (t0) cc_final: 0.8193 (t0) REVERT: G 300 ILE cc_start: 0.8638 (mm) cc_final: 0.8352 (mm) REVERT: G 319 ASP cc_start: 0.8498 (m-30) cc_final: 0.8214 (m-30) REVERT: G 369 ASN cc_start: 0.8383 (p0) cc_final: 0.8173 (p0) REVERT: G 412 ARG cc_start: 0.8027 (ttp80) cc_final: 0.7461 (ptt90) REVERT: G 420 MET cc_start: 0.6830 (mtm) cc_final: 0.6574 (mtm) REVERT: G 455 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8574 (mmmm) REVERT: G 474 LYS cc_start: 0.8910 (mtpt) cc_final: 0.8640 (mtpt) REVERT: G 487 GLU cc_start: 0.9017 (tt0) cc_final: 0.8590 (tt0) REVERT: G 507 HIS cc_start: 0.8828 (t-90) cc_final: 0.8414 (t-90) REVERT: H 34 ASP cc_start: 0.9240 (t0) cc_final: 0.8903 (t0) REVERT: H 75 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6745 (mp0) REVERT: H 134 LYS cc_start: 0.7976 (pttp) cc_final: 0.7509 (pttm) REVERT: H 150 MET cc_start: 0.7980 (ttt) cc_final: 0.7501 (tpp) REVERT: H 174 PHE cc_start: 0.7955 (m-80) cc_final: 0.7507 (m-80) REVERT: H 179 MET cc_start: 0.8030 (pp-130) cc_final: 0.6902 (ppp) REVERT: H 199 GLU cc_start: 0.8222 (pt0) cc_final: 0.7868 (tp30) REVERT: H 202 GLN cc_start: 0.8612 (pp30) cc_final: 0.8074 (pp30) REVERT: H 214 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8122 (tm-30) REVERT: H 245 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8084 (mm) REVERT: H 286 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8717 (tmt) REVERT: H 319 ASP cc_start: 0.8486 (m-30) cc_final: 0.8229 (m-30) REVERT: H 335 GLU cc_start: 0.8727 (tt0) cc_final: 0.8383 (tt0) REVERT: H 412 ARG cc_start: 0.7993 (ttp80) cc_final: 0.7474 (ptt90) REVERT: H 441 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: H 507 HIS cc_start: 0.8827 (t-90) cc_final: 0.8429 (t-90) outliers start: 183 outliers final: 112 residues processed: 993 average time/residue: 0.1836 time to fit residues: 298.9623 Evaluate side-chains 952 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 811 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 26 CYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 102 ASN Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 496 SER Chi-restraints excluded: chain H residue 499 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 363 optimal weight: 2.9990 chunk 274 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 261 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 328 optimal weight: 0.9980 chunk 250 optimal weight: 1.9990 chunk 312 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 285 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 HIS E 102 ASN E 285 ASN ** E 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 ASN G 285 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** 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 = 0.3696 r_free = 0.3696 target = 0.134709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.101354 restraints weight = 54104.739| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.65 r_work: 0.3074 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 32096 Z= 0.187 Angle : 0.726 8.220 43488 Z= 0.373 Chirality : 0.048 0.150 4968 Planarity : 0.004 0.053 5448 Dihedral : 13.803 77.191 5398 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 6.30 % Allowed : 21.55 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -1.76 (0.13), residues: 3968 helix: -0.17 (0.14), residues: 1256 sheet: -1.81 (0.19), residues: 680 loop : -1.55 (0.15), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 128 TYR 0.011 0.001 TYR G 348 PHE 0.016 0.001 PHE B 24 HIS 0.004 0.001 HIS H 92 Details of bonding type rmsd covalent geometry : bond 0.00439 (32072) covalent geometry : angle 0.72638 (43488) hydrogen bonds : bond 0.03323 ( 1009) hydrogen bonds : angle 5.02366 ( 2835) Misc. bond : bond 0.00160 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 852 time to evaluate : 1.226 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 25 ASN cc_start: 0.8933 (m-40) cc_final: 0.8638 (p0) REVERT: A 75 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6637 (mp0) REVERT: A 94 ASN cc_start: 0.9228 (t0) cc_final: 0.8953 (t0) REVERT: A 136 ARG cc_start: 0.8561 (ptm-80) cc_final: 0.8137 (ptt180) REVERT: A 150 MET cc_start: 0.7871 (ttt) cc_final: 0.7291 (tpp) REVERT: A 179 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.6497 (ppp) REVERT: A 198 ASN cc_start: 0.9267 (m-40) cc_final: 0.8773 (m-40) REVERT: A 199 GLU cc_start: 0.8283 (pt0) cc_final: 0.7895 (tp30) REVERT: A 202 GLN cc_start: 0.8649 (pp30) cc_final: 0.8185 (pp30) REVERT: A 203 ARG cc_start: 0.8852 (tpp-160) cc_final: 0.8199 (mtp-110) REVERT: A 214 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8123 (tm-30) REVERT: A 231 ARG cc_start: 0.8430 (mmm160) cc_final: 0.8209 (mmp80) REVERT: A 245 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8147 (mm) REVERT: A 259 ARG cc_start: 0.9006 (ttm170) cc_final: 0.8771 (ttm170) REVERT: A 319 ASP cc_start: 0.8486 (m-30) cc_final: 0.8194 (m-30) REVERT: A 353 TYR cc_start: 0.8976 (t80) cc_final: 0.8757 (t80) REVERT: A 385 MET cc_start: 0.9105 (ttp) cc_final: 0.8685 (ttp) REVERT: A 412 ARG cc_start: 0.7945 (ttp80) cc_final: 0.7395 (ptt90) REVERT: A 455 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8579 (mmmm) REVERT: A 474 LYS cc_start: 0.8881 (mtpt) cc_final: 0.8650 (mtpt) REVERT: A 507 HIS cc_start: 0.8835 (t-90) cc_final: 0.8457 (t-90) REVERT: B 16 ASP cc_start: 0.8439 (t0) cc_final: 0.8204 (t0) REVERT: B 25 ASN cc_start: 0.8831 (m-40) cc_final: 0.8578 (p0) REVERT: B 34 ASP cc_start: 0.9269 (t0) cc_final: 0.8931 (t0) REVERT: B 75 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6754 (mp0) REVERT: B 94 ASN cc_start: 0.9225 (t0) cc_final: 0.8913 (t0) REVERT: B 134 LYS cc_start: 0.8060 (pttp) cc_final: 0.7705 (pttm) REVERT: B 136 ARG cc_start: 0.8604 (ptm160) cc_final: 0.7931 (ptt90) REVERT: B 150 MET cc_start: 0.8060 (ttt) cc_final: 0.7513 (tpp) REVERT: B 179 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.6894 (ppp) REVERT: B 198 ASN cc_start: 0.9289 (m-40) cc_final: 0.8682 (m-40) REVERT: B 199 GLU cc_start: 0.8223 (pt0) cc_final: 0.7917 (tp30) REVERT: B 202 GLN cc_start: 0.8654 (pp30) cc_final: 0.8184 (pp30) REVERT: B 205 LYS cc_start: 0.9119 (mtpp) cc_final: 0.8550 (ttmm) REVERT: B 214 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8183 (tm-30) REVERT: B 245 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8112 (mm) REVERT: B 300 ILE cc_start: 0.8638 (mm) cc_final: 0.8355 (mm) REVERT: B 319 ASP cc_start: 0.8479 (m-30) cc_final: 0.8224 (m-30) REVERT: B 353 TYR cc_start: 0.9057 (t80) cc_final: 0.8845 (t80) REVERT: B 385 MET cc_start: 0.8976 (ttp) cc_final: 0.8409 (ttp) REVERT: B 412 ARG cc_start: 0.7986 (ttp80) cc_final: 0.7427 (ptt90) REVERT: B 507 HIS cc_start: 0.8826 (t-90) cc_final: 0.8422 (t-90) REVERT: C 75 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6736 (mp0) REVERT: C 134 LYS cc_start: 0.8096 (pttp) cc_final: 0.7806 (pttm) REVERT: C 136 ARG cc_start: 0.8566 (ptm-80) cc_final: 0.8166 (ptt180) REVERT: C 150 MET cc_start: 0.8086 (ttt) cc_final: 0.7637 (tpp) REVERT: C 174 PHE cc_start: 0.8312 (m-80) cc_final: 0.7939 (t80) REVERT: C 175 LEU cc_start: 0.8352 (mt) cc_final: 0.7846 (mt) REVERT: C 179 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.6508 (ppp) REVERT: C 199 GLU cc_start: 0.8217 (pt0) cc_final: 0.7815 (tp30) REVERT: C 202 GLN cc_start: 0.8564 (pp30) cc_final: 0.8252 (pp30) REVERT: C 203 ARG cc_start: 0.8880 (tpp-160) cc_final: 0.8214 (mtp-110) REVERT: C 205 LYS cc_start: 0.9074 (mtpp) cc_final: 0.8581 (ttmm) REVERT: C 209 LEU cc_start: 0.8137 (tt) cc_final: 0.7881 (tt) REVERT: C 214 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8057 (tm-30) REVERT: C 231 ARG cc_start: 0.8324 (mmm160) cc_final: 0.7990 (mmm160) REVERT: C 245 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8007 (mm) REVERT: C 261 ASP cc_start: 0.9187 (m-30) cc_final: 0.8712 (m-30) REVERT: C 325 MET cc_start: 0.8118 (ptm) cc_final: 0.7898 (ptm) REVERT: C 352 GLU cc_start: 0.9144 (tm-30) cc_final: 0.8601 (tm-30) REVERT: C 353 TYR cc_start: 0.8997 (t80) cc_final: 0.8756 (t80) REVERT: C 385 MET cc_start: 0.9089 (ttp) cc_final: 0.8639 (ttp) REVERT: C 412 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7417 (ptt90) REVERT: C 420 MET cc_start: 0.6830 (mtm) cc_final: 0.6629 (mtm) REVERT: C 455 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8585 (mmmm) REVERT: C 474 LYS cc_start: 0.8867 (mtpt) cc_final: 0.8637 (mtpt) REVERT: C 507 HIS cc_start: 0.8869 (t-90) cc_final: 0.8460 (t-90) REVERT: D 16 ASP cc_start: 0.8489 (t0) cc_final: 0.8250 (t0) REVERT: D 75 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6675 (mp0) REVERT: D 150 MET cc_start: 0.8142 (ttt) cc_final: 0.7694 (tpp) REVERT: D 179 MET cc_start: 0.8105 (pp-130) cc_final: 0.6932 (ppp) REVERT: D 198 ASN cc_start: 0.9310 (m-40) cc_final: 0.8765 (m-40) REVERT: D 199 GLU cc_start: 0.8286 (pt0) cc_final: 0.7952 (tp30) REVERT: D 202 GLN cc_start: 0.8694 (pp30) cc_final: 0.8235 (pp30) REVERT: D 205 LYS cc_start: 0.9059 (mtpp) cc_final: 0.8464 (ttmm) REVERT: D 214 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8154 (tm-30) REVERT: D 245 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8200 (mm) REVERT: D 261 ASP cc_start: 0.9079 (m-30) cc_final: 0.8755 (m-30) REVERT: D 300 ILE cc_start: 0.8815 (mm) cc_final: 0.8518 (mm) REVERT: D 353 TYR cc_start: 0.9048 (t80) cc_final: 0.8830 (t80) REVERT: D 385 MET cc_start: 0.9193 (ttp) cc_final: 0.8788 (ttp) REVERT: D 412 ARG cc_start: 0.7936 (ttp80) cc_final: 0.7428 (ptt90) REVERT: D 420 MET cc_start: 0.6816 (mtm) cc_final: 0.6555 (mtm) REVERT: D 455 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8624 (mmmm) REVERT: D 474 LYS cc_start: 0.8832 (mtpt) cc_final: 0.8593 (mtpt) REVERT: D 507 HIS cc_start: 0.8878 (t-90) cc_final: 0.8465 (t-90) REVERT: E 25 ASN cc_start: 0.8942 (m-40) cc_final: 0.8639 (p0) REVERT: E 26 CYS cc_start: 0.8971 (m) cc_final: 0.8555 (t) REVERT: E 75 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6794 (mp0) REVERT: E 94 ASN cc_start: 0.9241 (t0) cc_final: 0.9011 (t0) REVERT: E 100 GLN cc_start: 0.9257 (OUTLIER) cc_final: 0.8948 (pt0) REVERT: E 134 LYS cc_start: 0.8100 (pttp) cc_final: 0.7783 (pttm) REVERT: E 136 ARG cc_start: 0.8554 (ptm-80) cc_final: 0.8251 (ptt180) REVERT: E 174 PHE cc_start: 0.8492 (m-80) cc_final: 0.8130 (t80) REVERT: E 179 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.6518 (ppp) REVERT: E 198 ASN cc_start: 0.9213 (m-40) cc_final: 0.8671 (m-40) REVERT: E 199 GLU cc_start: 0.8200 (pt0) cc_final: 0.7781 (tp30) REVERT: E 202 GLN cc_start: 0.8661 (pp30) cc_final: 0.8299 (pp30) REVERT: E 203 ARG cc_start: 0.8717 (tpp-160) cc_final: 0.8110 (ttp-110) REVERT: E 214 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8166 (tm-30) REVERT: E 245 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7967 (mm) REVERT: E 261 ASP cc_start: 0.9176 (m-30) cc_final: 0.8675 (m-30) REVERT: E 369 ASN cc_start: 0.8516 (p0) cc_final: 0.8271 (p0) REVERT: E 412 ARG cc_start: 0.7976 (ttp80) cc_final: 0.7488 (ptt90) REVERT: E 420 MET cc_start: 0.6717 (mtm) cc_final: 0.6468 (mtm) REVERT: E 455 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8616 (mmmm) REVERT: E 507 HIS cc_start: 0.8878 (t-90) cc_final: 0.8490 (t-90) REVERT: F 16 ASP cc_start: 0.8450 (t0) cc_final: 0.8203 (t0) REVERT: F 25 ASN cc_start: 0.8825 (m-40) cc_final: 0.8564 (p0) REVERT: F 34 ASP cc_start: 0.9241 (t0) cc_final: 0.8916 (t0) REVERT: F 75 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6570 (pm20) REVERT: F 92 HIS cc_start: 0.9057 (p90) cc_final: 0.8800 (p-80) REVERT: F 94 ASN cc_start: 0.9236 (t0) cc_final: 0.8779 (t0) REVERT: F 134 LYS cc_start: 0.8043 (pttp) cc_final: 0.7731 (pttm) REVERT: F 150 MET cc_start: 0.8065 (ttt) cc_final: 0.7570 (tpp) REVERT: F 179 MET cc_start: 0.8033 (pp-130) cc_final: 0.6910 (ppp) REVERT: F 198 ASN cc_start: 0.9292 (m-40) cc_final: 0.8749 (m-40) REVERT: F 199 GLU cc_start: 0.8288 (pt0) cc_final: 0.7786 (tp30) REVERT: F 202 GLN cc_start: 0.8621 (pp30) cc_final: 0.8205 (pp30) REVERT: F 203 ARG cc_start: 0.8739 (tpp-160) cc_final: 0.8062 (mtp-110) REVERT: F 214 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8037 (tm-30) REVERT: F 245 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8100 (mm) REVERT: F 261 ASP cc_start: 0.9123 (m-30) cc_final: 0.8840 (m-30) REVERT: F 285 ASN cc_start: 0.8613 (m110) cc_final: 0.8355 (m110) REVERT: F 286 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8883 (tmt) REVERT: F 312 ASN cc_start: 0.8761 (OUTLIER) cc_final: 0.8259 (t0) REVERT: F 325 MET cc_start: 0.8135 (ptm) cc_final: 0.7916 (ptm) REVERT: F 343 GLN cc_start: 0.8993 (tp40) cc_final: 0.8742 (tp40) REVERT: F 369 ASN cc_start: 0.8490 (p0) cc_final: 0.8253 (p0) REVERT: F 385 MET cc_start: 0.9076 (ttp) cc_final: 0.8507 (ttp) REVERT: F 412 ARG cc_start: 0.7994 (ttp80) cc_final: 0.7527 (ptt90) REVERT: F 420 MET cc_start: 0.6638 (mtm) cc_final: 0.6371 (mtm) REVERT: F 455 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8657 (mmmm) REVERT: F 474 LYS cc_start: 0.8823 (mtpt) cc_final: 0.8608 (mtpt) REVERT: F 507 HIS cc_start: 0.8903 (t-90) cc_final: 0.8502 (t-90) REVERT: G 25 ASN cc_start: 0.8861 (m-40) cc_final: 0.8591 (p0) REVERT: G 34 ASP cc_start: 0.9376 (t0) cc_final: 0.9039 (t0) REVERT: G 75 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: G 94 ASN cc_start: 0.9251 (t0) cc_final: 0.8832 (t0) REVERT: G 132 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8536 (pp20) REVERT: G 134 LYS cc_start: 0.8056 (pttp) cc_final: 0.7675 (pttm) REVERT: G 150 MET cc_start: 0.8105 (ttt) cc_final: 0.7544 (tpp) REVERT: G 179 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.6502 (ppp) REVERT: G 198 ASN cc_start: 0.9267 (m-40) cc_final: 0.8750 (m-40) REVERT: G 199 GLU cc_start: 0.8282 (pt0) cc_final: 0.7872 (tp30) REVERT: G 202 GLN cc_start: 0.8641 (pp30) cc_final: 0.8291 (pp30) REVERT: G 203 ARG cc_start: 0.8888 (tpp-160) cc_final: 0.8098 (mtp-110) REVERT: G 214 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8078 (tm-30) REVERT: G 231 ARG cc_start: 0.8369 (mmm160) cc_final: 0.8098 (mmp80) REVERT: G 245 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8075 (mm) REVERT: G 279 ASN cc_start: 0.8638 (t0) cc_final: 0.8203 (t0) REVERT: G 369 ASN cc_start: 0.8454 (p0) cc_final: 0.8210 (p0) REVERT: G 412 ARG cc_start: 0.8000 (ttp80) cc_final: 0.7477 (ptt90) REVERT: G 420 MET cc_start: 0.6958 (mtm) cc_final: 0.6676 (mtm) REVERT: G 455 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8571 (mmmm) REVERT: G 474 LYS cc_start: 0.8909 (mtpt) cc_final: 0.8681 (mtpt) REVERT: G 487 GLU cc_start: 0.8985 (tt0) cc_final: 0.8582 (tt0) REVERT: G 507 HIS cc_start: 0.8866 (t-90) cc_final: 0.8489 (t-90) REVERT: H 34 ASP cc_start: 0.9259 (t0) cc_final: 0.8925 (t0) REVERT: H 75 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6703 (mp0) REVERT: H 134 LYS cc_start: 0.7944 (pttp) cc_final: 0.7633 (pttm) REVERT: H 150 MET cc_start: 0.8070 (ttt) cc_final: 0.7538 (tpp) REVERT: H 179 MET cc_start: 0.8089 (pp-130) cc_final: 0.6938 (ppp) REVERT: H 199 GLU cc_start: 0.8242 (pt0) cc_final: 0.7789 (tp30) REVERT: H 202 GLN cc_start: 0.8660 (pp30) cc_final: 0.8279 (pp30) REVERT: H 203 ARG cc_start: 0.8761 (tpp-160) cc_final: 0.8094 (mtp-110) REVERT: H 214 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8171 (tm-30) REVERT: H 245 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8104 (mm) REVERT: H 259 ARG cc_start: 0.8965 (ttm170) cc_final: 0.8744 (ttm170) REVERT: H 286 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8715 (tmt) REVERT: H 319 ASP cc_start: 0.8503 (m-30) cc_final: 0.8251 (m-30) REVERT: H 335 GLU cc_start: 0.8814 (tt0) cc_final: 0.8489 (tt0) REVERT: H 385 MET cc_start: 0.8464 (ttp) cc_final: 0.8195 (ttp) REVERT: H 390 LEU cc_start: 0.8361 (mt) cc_final: 0.7466 (mt) REVERT: H 412 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7454 (ptt90) REVERT: H 507 HIS cc_start: 0.8842 (t-90) cc_final: 0.8448 (t-90) outliers start: 206 outliers final: 130 residues processed: 972 average time/residue: 0.1878 time to fit residues: 298.1742 Evaluate side-chains 977 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 815 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 26 CYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 312 ASN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 102 ASN Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 496 SER Chi-restraints excluded: chain H residue 499 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 300 optimal weight: 0.0870 chunk 212 optimal weight: 7.9990 chunk 220 optimal weight: 0.9980 chunk 340 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 255 optimal weight: 0.7980 chunk 369 optimal weight: 8.9990 chunk 181 optimal weight: 0.5980 chunk 152 optimal weight: 0.6980 chunk 257 optimal weight: 5.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS B 102 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 HIS C 102 ASN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 HIS E 102 ASN ** E 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 HIS ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.137606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.105125 restraints weight = 53475.639| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.63 r_work: 0.3111 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32096 Z= 0.134 Angle : 0.690 8.927 43488 Z= 0.354 Chirality : 0.047 0.155 4968 Planarity : 0.004 0.034 5448 Dihedral : 13.389 80.432 5398 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 5.13 % Allowed : 23.04 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -1.61 (0.14), residues: 3968 helix: -0.06 (0.15), residues: 1256 sheet: -1.59 (0.19), residues: 664 loop : -1.51 (0.15), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 128 TYR 0.012 0.001 TYR E 110 PHE 0.011 0.001 PHE B 24 HIS 0.003 0.000 HIS G 92 Details of bonding type rmsd covalent geometry : bond 0.00307 (32072) covalent geometry : angle 0.68966 (43488) hydrogen bonds : bond 0.03141 ( 1009) hydrogen bonds : angle 4.96214 ( 2835) Misc. bond : bond 0.00107 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1070 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 902 time to evaluate : 1.130 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: A 25 ASN cc_start: 0.8863 (m-40) cc_final: 0.8606 (p0) REVERT: A 75 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6644 (mp0) REVERT: A 94 ASN cc_start: 0.9144 (t0) cc_final: 0.8871 (t0) REVERT: A 136 ARG cc_start: 0.8559 (ptm-80) cc_final: 0.8146 (ptt180) REVERT: A 150 MET cc_start: 0.7841 (ttt) cc_final: 0.7303 (tpp) REVERT: A 174 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7815 (t80) REVERT: A 179 MET cc_start: 0.7857 (pp-130) cc_final: 0.6593 (ppp) REVERT: A 198 ASN cc_start: 0.9283 (m-40) cc_final: 0.8826 (m-40) REVERT: A 199 GLU cc_start: 0.8235 (pt0) cc_final: 0.7876 (tp30) REVERT: A 202 GLN cc_start: 0.8657 (pp30) cc_final: 0.8221 (pp30) REVERT: A 203 ARG cc_start: 0.8861 (tpp-160) cc_final: 0.8164 (mtp-110) REVERT: A 214 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8195 (tm-30) REVERT: A 245 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8147 (mm) REVERT: A 319 ASP cc_start: 0.8486 (m-30) cc_final: 0.8187 (m-30) REVERT: A 343 GLN cc_start: 0.8606 (tp40) cc_final: 0.8367 (tp-100) REVERT: A 353 TYR cc_start: 0.8913 (t80) cc_final: 0.8687 (t80) REVERT: A 379 LEU cc_start: 0.9575 (mt) cc_final: 0.9372 (mt) REVERT: A 385 MET cc_start: 0.9046 (ttp) cc_final: 0.8545 (ttp) REVERT: A 412 ARG cc_start: 0.7802 (ttp80) cc_final: 0.7283 (ptt90) REVERT: A 420 MET cc_start: 0.6733 (mtm) cc_final: 0.6527 (mtm) REVERT: A 455 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8568 (mmmm) REVERT: A 474 LYS cc_start: 0.8898 (mtpt) cc_final: 0.8687 (mtpt) REVERT: A 507 HIS cc_start: 0.8791 (t-90) cc_final: 0.8417 (t-90) REVERT: B 16 ASP cc_start: 0.8433 (t0) cc_final: 0.8183 (t0) REVERT: B 25 ASN cc_start: 0.8832 (m-40) cc_final: 0.8603 (p0) REVERT: B 75 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6699 (mp0) REVERT: B 94 ASN cc_start: 0.9177 (t0) cc_final: 0.8696 (t0) REVERT: B 134 LYS cc_start: 0.7952 (pttp) cc_final: 0.7679 (pttm) REVERT: B 136 ARG cc_start: 0.8582 (ptm160) cc_final: 0.8080 (ptt180) REVERT: B 150 MET cc_start: 0.8028 (ttt) cc_final: 0.7446 (tpp) REVERT: B 179 MET cc_start: 0.7907 (pp-130) cc_final: 0.6716 (ppp) REVERT: B 198 ASN cc_start: 0.9280 (m-40) cc_final: 0.8738 (m-40) REVERT: B 199 GLU cc_start: 0.8120 (pt0) cc_final: 0.7502 (tp30) REVERT: B 202 GLN cc_start: 0.8696 (pp30) cc_final: 0.8177 (pp30) REVERT: B 203 ARG cc_start: 0.8838 (tpp-160) cc_final: 0.8070 (mtp-110) REVERT: B 205 LYS cc_start: 0.9104 (mtpp) cc_final: 0.8540 (ttmm) REVERT: B 209 LEU cc_start: 0.8315 (tt) cc_final: 0.8088 (tt) REVERT: B 214 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8142 (tm-30) REVERT: B 224 ARG cc_start: 0.8280 (tpp80) cc_final: 0.7459 (ttm170) REVERT: B 245 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8076 (mm) REVERT: B 300 ILE cc_start: 0.8618 (mm) cc_final: 0.8345 (mm) REVERT: B 319 ASP cc_start: 0.8458 (m-30) cc_final: 0.8193 (m-30) REVERT: B 353 TYR cc_start: 0.8941 (t80) cc_final: 0.8716 (t80) REVERT: B 385 MET cc_start: 0.9024 (ttp) cc_final: 0.8433 (ttp) REVERT: B 412 ARG cc_start: 0.7839 (ttp80) cc_final: 0.7357 (ptt90) REVERT: B 474 LYS cc_start: 0.8809 (mttt) cc_final: 0.8478 (mmmt) REVERT: B 507 HIS cc_start: 0.8803 (t-90) cc_final: 0.8413 (t-90) REVERT: C 75 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6747 (mp0) REVERT: C 136 ARG cc_start: 0.8550 (ptm-80) cc_final: 0.8132 (ptt180) REVERT: C 150 MET cc_start: 0.8046 (ttt) cc_final: 0.7516 (tpp) REVERT: C 174 PHE cc_start: 0.8421 (m-80) cc_final: 0.8049 (t80) REVERT: C 179 MET cc_start: 0.7696 (pp-130) cc_final: 0.6420 (ppp) REVERT: C 199 GLU cc_start: 0.8173 (pt0) cc_final: 0.7835 (tp30) REVERT: C 202 GLN cc_start: 0.8655 (pp30) cc_final: 0.8372 (pp30) REVERT: C 203 ARG cc_start: 0.8859 (tpp-160) cc_final: 0.8185 (ttp-110) REVERT: C 205 LYS cc_start: 0.9068 (mtpp) cc_final: 0.8521 (ttmm) REVERT: C 214 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8118 (tm-30) REVERT: C 245 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7995 (mm) REVERT: C 261 ASP cc_start: 0.9198 (m-30) cc_final: 0.8681 (m-30) REVERT: C 353 TYR cc_start: 0.8902 (t80) cc_final: 0.8693 (t80) REVERT: C 385 MET cc_start: 0.8996 (ttp) cc_final: 0.8472 (ttp) REVERT: C 412 ARG cc_start: 0.7801 (ttp80) cc_final: 0.7344 (ptt90) REVERT: C 420 MET cc_start: 0.6900 (mtm) cc_final: 0.6678 (mtm) REVERT: C 455 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8576 (mmmm) REVERT: C 474 LYS cc_start: 0.8873 (mtpt) cc_final: 0.8647 (mtpt) REVERT: C 507 HIS cc_start: 0.8818 (t-90) cc_final: 0.8409 (t-90) REVERT: D 16 ASP cc_start: 0.8492 (t0) cc_final: 0.8231 (t0) REVERT: D 25 ASN cc_start: 0.8855 (m-40) cc_final: 0.8534 (p0) REVERT: D 34 ASP cc_start: 0.9323 (t0) cc_final: 0.9061 (t0) REVERT: D 75 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6656 (pm20) REVERT: D 94 ASN cc_start: 0.9140 (t0) cc_final: 0.8731 (t0) REVERT: D 150 MET cc_start: 0.8080 (ttt) cc_final: 0.7545 (tpp) REVERT: D 179 MET cc_start: 0.8054 (pp-130) cc_final: 0.6904 (ppp) REVERT: D 198 ASN cc_start: 0.9281 (m-40) cc_final: 0.8801 (m-40) REVERT: D 199 GLU cc_start: 0.8224 (pt0) cc_final: 0.7857 (tp30) REVERT: D 202 GLN cc_start: 0.8741 (pp30) cc_final: 0.8167 (pp30) REVERT: D 205 LYS cc_start: 0.9050 (mtpp) cc_final: 0.8470 (ttmm) REVERT: D 214 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8222 (tm-30) REVERT: D 245 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8146 (mm) REVERT: D 259 ARG cc_start: 0.8888 (ttm170) cc_final: 0.8645 (ttm170) REVERT: D 261 ASP cc_start: 0.9070 (m-30) cc_final: 0.8690 (m-30) REVERT: D 300 ILE cc_start: 0.8785 (mm) cc_final: 0.8565 (mm) REVERT: D 327 SER cc_start: 0.8840 (p) cc_final: 0.8588 (p) REVERT: D 353 TYR cc_start: 0.8977 (t80) cc_final: 0.8764 (t80) REVERT: D 369 ASN cc_start: 0.8263 (p0) cc_final: 0.7999 (p0) REVERT: D 385 MET cc_start: 0.9176 (ttp) cc_final: 0.8746 (ttp) REVERT: D 412 ARG cc_start: 0.7788 (ttp80) cc_final: 0.7338 (ptt90) REVERT: D 420 MET cc_start: 0.6646 (mtm) cc_final: 0.6373 (mtm) REVERT: D 455 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8668 (mmmm) REVERT: D 474 LYS cc_start: 0.8812 (mtpt) cc_final: 0.8586 (mtpt) REVERT: D 507 HIS cc_start: 0.8817 (t-90) cc_final: 0.8401 (t-90) REVERT: E 25 ASN cc_start: 0.8862 (m-40) cc_final: 0.8597 (p0) REVERT: E 26 CYS cc_start: 0.9007 (m) cc_final: 0.8543 (t) REVERT: E 75 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6782 (mp0) REVERT: E 94 ASN cc_start: 0.9221 (t0) cc_final: 0.8894 (t0) REVERT: E 100 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8906 (pt0) REVERT: E 134 LYS cc_start: 0.7984 (pttp) cc_final: 0.7733 (pttm) REVERT: E 136 ARG cc_start: 0.8566 (ptm-80) cc_final: 0.8172 (ptt180) REVERT: E 174 PHE cc_start: 0.8485 (m-80) cc_final: 0.8096 (t80) REVERT: E 175 LEU cc_start: 0.8357 (mt) cc_final: 0.7899 (mt) REVERT: E 179 MET cc_start: 0.7787 (pp-130) cc_final: 0.6513 (ppp) REVERT: E 194 LEU cc_start: 0.8812 (mm) cc_final: 0.8336 (mm) REVERT: E 198 ASN cc_start: 0.9231 (m-40) cc_final: 0.8706 (m-40) REVERT: E 199 GLU cc_start: 0.8140 (pt0) cc_final: 0.7707 (tp30) REVERT: E 202 GLN cc_start: 0.8669 (pp30) cc_final: 0.8251 (pp30) REVERT: E 203 ARG cc_start: 0.8745 (tpp-160) cc_final: 0.8033 (mtp-110) REVERT: E 214 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8253 (tm-30) REVERT: E 245 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7897 (mm) REVERT: E 261 ASP cc_start: 0.9187 (m-30) cc_final: 0.8803 (m-30) REVERT: E 312 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8079 (t0) REVERT: E 369 ASN cc_start: 0.8369 (p0) cc_final: 0.8090 (p0) REVERT: E 412 ARG cc_start: 0.7825 (ttp80) cc_final: 0.7365 (ptt90) REVERT: E 420 MET cc_start: 0.6794 (mtm) cc_final: 0.6546 (mtm) REVERT: E 455 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8601 (mmmm) REVERT: E 507 HIS cc_start: 0.8852 (t-90) cc_final: 0.8475 (t-90) REVERT: F 16 ASP cc_start: 0.8445 (t0) cc_final: 0.8198 (t0) REVERT: F 25 ASN cc_start: 0.8795 (m-40) cc_final: 0.8552 (p0) REVERT: F 75 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6776 (pm20) REVERT: F 92 HIS cc_start: 0.9002 (p90) cc_final: 0.8743 (p-80) REVERT: F 94 ASN cc_start: 0.9165 (t0) cc_final: 0.8733 (t0) REVERT: F 134 LYS cc_start: 0.7971 (pttp) cc_final: 0.7641 (pttm) REVERT: F 136 ARG cc_start: 0.8539 (ptm-80) cc_final: 0.8054 (ptt180) REVERT: F 150 MET cc_start: 0.8043 (ttt) cc_final: 0.7459 (tpp) REVERT: F 179 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.6863 (ppp) REVERT: F 198 ASN cc_start: 0.9268 (m-40) cc_final: 0.8787 (m-40) REVERT: F 199 GLU cc_start: 0.8220 (pt0) cc_final: 0.7785 (tp30) REVERT: F 202 GLN cc_start: 0.8655 (pp30) cc_final: 0.8248 (pp30) REVERT: F 203 ARG cc_start: 0.8754 (tpp-160) cc_final: 0.8104 (mtp-110) REVERT: F 214 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8073 (tm-30) REVERT: F 245 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8105 (mm) REVERT: F 261 ASP cc_start: 0.9152 (m-30) cc_final: 0.8659 (m-30) REVERT: F 285 ASN cc_start: 0.8616 (m110) cc_final: 0.8369 (m110) REVERT: F 369 ASN cc_start: 0.8403 (p0) cc_final: 0.8131 (p0) REVERT: F 385 MET cc_start: 0.9100 (ttp) cc_final: 0.8525 (ttp) REVERT: F 412 ARG cc_start: 0.7853 (ttp80) cc_final: 0.7446 (ptt90) REVERT: F 420 MET cc_start: 0.6833 (mtm) cc_final: 0.6627 (mtm) REVERT: F 474 LYS cc_start: 0.8819 (mtpt) cc_final: 0.8615 (mtpt) REVERT: F 507 HIS cc_start: 0.8831 (t-90) cc_final: 0.8436 (t-90) REVERT: G 34 ASP cc_start: 0.9235 (t0) cc_final: 0.8929 (t0) REVERT: G 75 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6722 (pm20) REVERT: G 94 ASN cc_start: 0.9128 (t0) cc_final: 0.8698 (t0) REVERT: G 132 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8516 (pp20) REVERT: G 134 LYS cc_start: 0.7981 (pttp) cc_final: 0.7676 (pttm) REVERT: G 136 ARG cc_start: 0.8504 (ptm-80) cc_final: 0.7993 (ptt90) REVERT: G 150 MET cc_start: 0.8021 (ttt) cc_final: 0.7476 (tpp) REVERT: G 179 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.6485 (ppp) REVERT: G 198 ASN cc_start: 0.9251 (m-40) cc_final: 0.8756 (m-40) REVERT: G 199 GLU cc_start: 0.8237 (pt0) cc_final: 0.7645 (tp30) REVERT: G 202 GLN cc_start: 0.8666 (pp30) cc_final: 0.7778 (pp30) REVERT: G 203 ARG cc_start: 0.8917 (tpp-160) cc_final: 0.8068 (mtp-110) REVERT: G 214 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8124 (tm-30) REVERT: G 231 ARG cc_start: 0.8375 (mmm160) cc_final: 0.8153 (mmp80) REVERT: G 245 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8053 (mm) REVERT: G 412 ARG cc_start: 0.7819 (ttp80) cc_final: 0.7436 (ptt90) REVERT: G 420 MET cc_start: 0.6822 (mtm) cc_final: 0.6546 (mtm) REVERT: G 455 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8578 (mmmm) REVERT: G 474 LYS cc_start: 0.8897 (mtpt) cc_final: 0.8684 (mtpt) REVERT: G 487 GLU cc_start: 0.8980 (tt0) cc_final: 0.8530 (tt0) REVERT: G 507 HIS cc_start: 0.8808 (t-90) cc_final: 0.8438 (t-90) REVERT: H 25 ASN cc_start: 0.8928 (m-40) cc_final: 0.8560 (p0) REVERT: H 75 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6663 (pm20) REVERT: H 94 ASN cc_start: 0.9227 (t0) cc_final: 0.8805 (t0) REVERT: H 134 LYS cc_start: 0.7898 (pttp) cc_final: 0.7619 (pttm) REVERT: H 150 MET cc_start: 0.8000 (ttt) cc_final: 0.7431 (tpp) REVERT: H 179 MET cc_start: 0.7982 (pp-130) cc_final: 0.6820 (ppp) REVERT: H 194 LEU cc_start: 0.8854 (mm) cc_final: 0.8422 (mm) REVERT: H 198 ASN cc_start: 0.9289 (m-40) cc_final: 0.8793 (m-40) REVERT: H 199 GLU cc_start: 0.8204 (pt0) cc_final: 0.7810 (tp30) REVERT: H 202 GLN cc_start: 0.8714 (pp30) cc_final: 0.8331 (pp30) REVERT: H 203 ARG cc_start: 0.8803 (tpp-160) cc_final: 0.8160 (mtp-110) REVERT: H 214 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8161 (tm-30) REVERT: H 259 ARG cc_start: 0.8866 (ttm170) cc_final: 0.8582 (ttm170) REVERT: H 285 ASN cc_start: 0.8680 (m110) cc_final: 0.8379 (m110) REVERT: H 286 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8747 (tmt) REVERT: H 300 ILE cc_start: 0.8734 (mm) cc_final: 0.8420 (mm) REVERT: H 319 ASP cc_start: 0.8444 (m-30) cc_final: 0.8189 (m-30) REVERT: H 335 GLU cc_start: 0.8762 (tt0) cc_final: 0.8399 (tt0) REVERT: H 369 ASN cc_start: 0.8264 (p0) cc_final: 0.7998 (p0) REVERT: H 379 LEU cc_start: 0.9543 (mt) cc_final: 0.9328 (mt) REVERT: H 385 MET cc_start: 0.8478 (ttp) cc_final: 0.8230 (ttp) REVERT: H 409 LYS cc_start: 0.8364 (ttmm) cc_final: 0.8092 (tppt) REVERT: H 412 ARG cc_start: 0.7847 (ttp80) cc_final: 0.7446 (ptt90) REVERT: H 507 HIS cc_start: 0.8822 (t-90) cc_final: 0.8440 (t-90) outliers start: 168 outliers final: 106 residues processed: 992 average time/residue: 0.1797 time to fit residues: 291.8096 Evaluate side-chains 963 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 830 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 26 CYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 312 ASN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 102 ASN Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 496 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 271 optimal weight: 0.4980 chunk 220 optimal weight: 0.9980 chunk 358 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 chunk 288 optimal weight: 0.8980 chunk 388 optimal weight: 0.7980 chunk 195 optimal weight: 0.5980 chunk 218 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 369 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 102 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 HIS C 102 ASN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN D 285 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN E 213 ASN E 303 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.137947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.104639 restraints weight = 54255.888| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.72 r_work: 0.3115 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32096 Z= 0.141 Angle : 0.700 8.354 43488 Z= 0.360 Chirality : 0.047 0.162 4968 Planarity : 0.004 0.034 5448 Dihedral : 13.131 81.097 5398 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 4.89 % Allowed : 25.37 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -1.53 (0.14), residues: 3968 helix: -0.11 (0.15), residues: 1280 sheet: -1.20 (0.20), residues: 584 loop : -1.53 (0.14), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 231 TYR 0.010 0.001 TYR G 348 PHE 0.009 0.001 PHE B 24 HIS 0.004 0.000 HIS G 92 Details of bonding type rmsd covalent geometry : bond 0.00323 (32072) covalent geometry : angle 0.69980 (43488) hydrogen bonds : bond 0.03110 ( 1009) hydrogen bonds : angle 4.89018 ( 2835) Misc. bond : bond 0.00125 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1031 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 871 time to evaluate : 1.145 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: A 25 ASN cc_start: 0.8882 (m-40) cc_final: 0.8609 (p0) REVERT: A 36 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8278 (pp) REVERT: A 75 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6674 (mp0) REVERT: A 94 ASN cc_start: 0.9176 (t0) cc_final: 0.8674 (t0) REVERT: A 136 ARG cc_start: 0.8568 (ptm-80) cc_final: 0.8260 (ptt180) REVERT: A 150 MET cc_start: 0.7790 (ttt) cc_final: 0.7287 (tpp) REVERT: A 174 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7682 (t80) REVERT: A 179 MET cc_start: 0.7795 (pp-130) cc_final: 0.6501 (ppp) REVERT: A 198 ASN cc_start: 0.9295 (m-40) cc_final: 0.8828 (m-40) REVERT: A 199 GLU cc_start: 0.8231 (pt0) cc_final: 0.7879 (tp30) REVERT: A 202 GLN cc_start: 0.8651 (pp30) cc_final: 0.8194 (pp30) REVERT: A 203 ARG cc_start: 0.8883 (tpp-160) cc_final: 0.8190 (mtp-110) REVERT: A 214 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8202 (tm-30) REVERT: A 245 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8174 (mm) REVERT: A 319 ASP cc_start: 0.8493 (m-30) cc_final: 0.8186 (m-30) REVERT: A 353 TYR cc_start: 0.8930 (t80) cc_final: 0.8719 (t80) REVERT: A 385 MET cc_start: 0.9108 (ttp) cc_final: 0.8661 (ttp) REVERT: A 409 LYS cc_start: 0.8451 (ttmm) cc_final: 0.8251 (tppt) REVERT: A 412 ARG cc_start: 0.7746 (ttp80) cc_final: 0.7260 (ptt90) REVERT: A 420 MET cc_start: 0.6753 (mtm) cc_final: 0.6548 (mtm) REVERT: A 455 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8570 (mmmm) REVERT: A 474 LYS cc_start: 0.8906 (mtpt) cc_final: 0.8695 (mtpt) REVERT: A 507 HIS cc_start: 0.8792 (t-90) cc_final: 0.8419 (t-90) REVERT: B 16 ASP cc_start: 0.8418 (t0) cc_final: 0.8179 (t0) REVERT: B 25 ASN cc_start: 0.8821 (m-40) cc_final: 0.8601 (p0) REVERT: B 36 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8295 (pp) REVERT: B 75 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6634 (mp0) REVERT: B 94 ASN cc_start: 0.9144 (t0) cc_final: 0.8658 (t0) REVERT: B 134 LYS cc_start: 0.7920 (pttp) cc_final: 0.7704 (pttm) REVERT: B 136 ARG cc_start: 0.8648 (ptm160) cc_final: 0.8163 (ptt180) REVERT: B 150 MET cc_start: 0.7974 (ttt) cc_final: 0.7457 (tpp) REVERT: B 179 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.6761 (ppp) REVERT: B 198 ASN cc_start: 0.9285 (m-40) cc_final: 0.8739 (m-40) REVERT: B 199 GLU cc_start: 0.8112 (pt0) cc_final: 0.7511 (tp30) REVERT: B 202 GLN cc_start: 0.8713 (pp30) cc_final: 0.8183 (pp30) REVERT: B 203 ARG cc_start: 0.8787 (tpp-160) cc_final: 0.7986 (mtp-110) REVERT: B 205 LYS cc_start: 0.9097 (mtpp) cc_final: 0.8581 (ttmm) REVERT: B 209 LEU cc_start: 0.8333 (tt) cc_final: 0.8106 (tt) REVERT: B 214 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8193 (tm-30) REVERT: B 224 ARG cc_start: 0.8293 (tpp80) cc_final: 0.7418 (ttm170) REVERT: B 245 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8143 (mm) REVERT: B 300 ILE cc_start: 0.8625 (mm) cc_final: 0.8356 (mm) REVERT: B 319 ASP cc_start: 0.8476 (m-30) cc_final: 0.8215 (m-30) REVERT: B 353 TYR cc_start: 0.8974 (t80) cc_final: 0.8766 (t80) REVERT: B 385 MET cc_start: 0.9072 (ttp) cc_final: 0.8540 (ttp) REVERT: B 412 ARG cc_start: 0.7771 (ttp80) cc_final: 0.7315 (ptt90) REVERT: B 474 LYS cc_start: 0.8849 (mttt) cc_final: 0.8527 (mmmt) REVERT: B 483 MET cc_start: 0.9295 (tmm) cc_final: 0.8739 (tmm) REVERT: B 507 HIS cc_start: 0.8813 (t-90) cc_final: 0.8409 (t-90) REVERT: C 75 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6699 (mp0) REVERT: C 136 ARG cc_start: 0.8560 (ptm-80) cc_final: 0.8147 (ptt180) REVERT: C 150 MET cc_start: 0.7956 (ttt) cc_final: 0.7501 (tpp) REVERT: C 174 PHE cc_start: 0.8402 (m-80) cc_final: 0.8004 (t80) REVERT: C 179 MET cc_start: 0.7825 (pp-130) cc_final: 0.6544 (ppp) REVERT: C 199 GLU cc_start: 0.8149 (pt0) cc_final: 0.7812 (tp30) REVERT: C 202 GLN cc_start: 0.8657 (pp30) cc_final: 0.8355 (pp30) REVERT: C 203 ARG cc_start: 0.8892 (tpp-160) cc_final: 0.8241 (ttp-110) REVERT: C 205 LYS cc_start: 0.9063 (mtpp) cc_final: 0.8530 (ttmm) REVERT: C 214 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8118 (tm-30) REVERT: C 245 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8100 (mm) REVERT: C 261 ASP cc_start: 0.9178 (m-30) cc_final: 0.8636 (m-30) REVERT: C 279 ASN cc_start: 0.8551 (t0) cc_final: 0.8319 (t0) REVERT: C 353 TYR cc_start: 0.8940 (t80) cc_final: 0.8736 (t80) REVERT: C 385 MET cc_start: 0.9072 (ttp) cc_final: 0.8622 (ttp) REVERT: C 412 ARG cc_start: 0.7798 (ttp80) cc_final: 0.7324 (ptt90) REVERT: C 455 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8567 (mmmm) REVERT: C 474 LYS cc_start: 0.8879 (mtpt) cc_final: 0.8662 (mtpt) REVERT: C 507 HIS cc_start: 0.8811 (t-90) cc_final: 0.8398 (t-90) REVERT: D 16 ASP cc_start: 0.8431 (t0) cc_final: 0.8183 (t0) REVERT: D 25 ASN cc_start: 0.8873 (m-40) cc_final: 0.8556 (p0) REVERT: D 34 ASP cc_start: 0.9298 (t0) cc_final: 0.9058 (t0) REVERT: D 75 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6637 (pm20) REVERT: D 94 ASN cc_start: 0.9120 (t0) cc_final: 0.8673 (t0) REVERT: D 136 ARG cc_start: 0.8592 (ptm-80) cc_final: 0.8056 (ptt90) REVERT: D 150 MET cc_start: 0.7957 (ttt) cc_final: 0.7557 (tpp) REVERT: D 179 MET cc_start: 0.8060 (pp-130) cc_final: 0.6911 (ppp) REVERT: D 198 ASN cc_start: 0.9293 (m-40) cc_final: 0.8826 (m-40) REVERT: D 199 GLU cc_start: 0.8202 (pt0) cc_final: 0.7847 (tp30) REVERT: D 202 GLN cc_start: 0.8741 (pp30) cc_final: 0.8155 (pp30) REVERT: D 205 LYS cc_start: 0.9044 (mtpp) cc_final: 0.8438 (ttmm) REVERT: D 214 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8111 (tm-30) REVERT: D 245 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8194 (mm) REVERT: D 261 ASP cc_start: 0.9062 (m-30) cc_final: 0.8647 (m-30) REVERT: D 353 TYR cc_start: 0.8992 (t80) cc_final: 0.8785 (t80) REVERT: D 369 ASN cc_start: 0.8351 (p0) cc_final: 0.8097 (p0) REVERT: D 385 MET cc_start: 0.9212 (ttp) cc_final: 0.8748 (ttp) REVERT: D 412 ARG cc_start: 0.7785 (ttp80) cc_final: 0.7280 (ptt90) REVERT: D 420 MET cc_start: 0.6706 (mtm) cc_final: 0.6439 (mtm) REVERT: D 455 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8607 (mmmm) REVERT: D 474 LYS cc_start: 0.8816 (mtpt) cc_final: 0.8584 (mtpt) REVERT: D 507 HIS cc_start: 0.8796 (t-90) cc_final: 0.8378 (t-90) REVERT: E 25 ASN cc_start: 0.8863 (m-40) cc_final: 0.8609 (p0) REVERT: E 26 CYS cc_start: 0.9029 (m) cc_final: 0.8570 (t) REVERT: E 75 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6830 (mp0) REVERT: E 94 ASN cc_start: 0.9105 (t0) cc_final: 0.8784 (t0) REVERT: E 136 ARG cc_start: 0.8567 (ptm-80) cc_final: 0.8271 (ptt180) REVERT: E 174 PHE cc_start: 0.8493 (m-80) cc_final: 0.8149 (t80) REVERT: E 179 MET cc_start: 0.7790 (pp-130) cc_final: 0.6521 (ppp) REVERT: E 194 LEU cc_start: 0.8784 (mm) cc_final: 0.8303 (mm) REVERT: E 198 ASN cc_start: 0.9254 (m-40) cc_final: 0.8722 (m-40) REVERT: E 199 GLU cc_start: 0.8184 (pt0) cc_final: 0.7730 (tp30) REVERT: E 202 GLN cc_start: 0.8700 (pp30) cc_final: 0.8265 (pp30) REVERT: E 203 ARG cc_start: 0.8760 (tpp-160) cc_final: 0.8045 (mtp-110) REVERT: E 214 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8245 (tm-30) REVERT: E 245 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8036 (mm) REVERT: E 261 ASP cc_start: 0.9210 (m-30) cc_final: 0.8820 (m-30) REVERT: E 312 ASN cc_start: 0.8582 (OUTLIER) cc_final: 0.8185 (t0) REVERT: E 369 ASN cc_start: 0.8440 (p0) cc_final: 0.8168 (p0) REVERT: E 379 LEU cc_start: 0.9547 (mt) cc_final: 0.9328 (mt) REVERT: E 412 ARG cc_start: 0.7731 (ttp80) cc_final: 0.7341 (ptt90) REVERT: E 420 MET cc_start: 0.6855 (mtm) cc_final: 0.6570 (mtm) REVERT: E 455 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8589 (mmmm) REVERT: E 507 HIS cc_start: 0.8851 (t-90) cc_final: 0.8469 (t-90) REVERT: F 16 ASP cc_start: 0.8424 (t0) cc_final: 0.8182 (t0) REVERT: F 25 ASN cc_start: 0.8822 (m-40) cc_final: 0.8563 (p0) REVERT: F 75 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6793 (pm20) REVERT: F 92 HIS cc_start: 0.9011 (p90) cc_final: 0.8719 (p-80) REVERT: F 94 ASN cc_start: 0.9176 (t0) cc_final: 0.8711 (t0) REVERT: F 134 LYS cc_start: 0.7906 (pttp) cc_final: 0.7603 (pttm) REVERT: F 136 ARG cc_start: 0.8544 (ptm-80) cc_final: 0.8072 (ptt180) REVERT: F 150 MET cc_start: 0.8039 (ttt) cc_final: 0.7553 (tpp) REVERT: F 179 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.6848 (ppp) REVERT: F 198 ASN cc_start: 0.9275 (m-40) cc_final: 0.8792 (m-40) REVERT: F 199 GLU cc_start: 0.8153 (pt0) cc_final: 0.7678 (tp30) REVERT: F 202 GLN cc_start: 0.8650 (pp30) cc_final: 0.8245 (pp30) REVERT: F 203 ARG cc_start: 0.8766 (tpp-160) cc_final: 0.8056 (mtp-110) REVERT: F 214 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8105 (tm-30) REVERT: F 245 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8197 (mm) REVERT: F 261 ASP cc_start: 0.9136 (m-30) cc_final: 0.8629 (m-30) REVERT: F 283 GLN cc_start: 0.8908 (mt0) cc_final: 0.8627 (tt0) REVERT: F 285 ASN cc_start: 0.8579 (m110) cc_final: 0.8324 (m110) REVERT: F 300 ILE cc_start: 0.8605 (mm) cc_final: 0.8323 (mm) REVERT: F 312 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8310 (t0) REVERT: F 369 ASN cc_start: 0.8474 (p0) cc_final: 0.8173 (p0) REVERT: F 385 MET cc_start: 0.9107 (ttp) cc_final: 0.8648 (ttp) REVERT: F 412 ARG cc_start: 0.7846 (ttp80) cc_final: 0.7402 (ptt90) REVERT: F 420 MET cc_start: 0.6884 (mtm) cc_final: 0.6672 (mtm) REVERT: F 474 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8624 (mtpt) REVERT: F 483 MET cc_start: 0.9335 (tmm) cc_final: 0.8725 (tmm) REVERT: F 507 HIS cc_start: 0.8835 (t-90) cc_final: 0.8450 (t-90) REVERT: G 25 ASN cc_start: 0.8889 (m-40) cc_final: 0.8582 (p0) REVERT: G 34 ASP cc_start: 0.9180 (t0) cc_final: 0.8914 (t0) REVERT: G 75 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6756 (pm20) REVERT: G 94 ASN cc_start: 0.9124 (t0) cc_final: 0.8729 (t0) REVERT: G 132 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8469 (pp20) REVERT: G 134 LYS cc_start: 0.7941 (pttp) cc_final: 0.7708 (pttm) REVERT: G 136 ARG cc_start: 0.8534 (ptm-80) cc_final: 0.8091 (ptt180) REVERT: G 150 MET cc_start: 0.8027 (ttt) cc_final: 0.7516 (tpp) REVERT: G 179 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.6513 (ppp) REVERT: G 198 ASN cc_start: 0.9246 (m-40) cc_final: 0.8787 (m-40) REVERT: G 199 GLU cc_start: 0.8130 (pt0) cc_final: 0.7764 (tp30) REVERT: G 202 GLN cc_start: 0.8655 (pp30) cc_final: 0.8257 (pp30) REVERT: G 203 ARG cc_start: 0.8929 (tpp-160) cc_final: 0.8146 (mtp-110) REVERT: G 214 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8261 (tm-30) REVERT: G 245 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8131 (mm) REVERT: G 279 ASN cc_start: 0.8606 (t0) cc_final: 0.8303 (t0) REVERT: G 369 ASN cc_start: 0.8429 (p0) cc_final: 0.8137 (p0) REVERT: G 412 ARG cc_start: 0.7792 (ttp80) cc_final: 0.7370 (ptt90) REVERT: G 420 MET cc_start: 0.6831 (mtm) cc_final: 0.6548 (mtm) REVERT: G 455 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8588 (mmmm) REVERT: G 474 LYS cc_start: 0.8898 (mtpt) cc_final: 0.8681 (mtpt) REVERT: G 487 GLU cc_start: 0.8974 (tt0) cc_final: 0.8573 (tt0) REVERT: G 507 HIS cc_start: 0.8824 (t-90) cc_final: 0.8463 (t-90) REVERT: H 25 ASN cc_start: 0.8892 (m-40) cc_final: 0.8570 (p0) REVERT: H 75 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6760 (pm20) REVERT: H 94 ASN cc_start: 0.9166 (t0) cc_final: 0.8767 (t0) REVERT: H 134 LYS cc_start: 0.7870 (pttp) cc_final: 0.7655 (pttm) REVERT: H 136 ARG cc_start: 0.8554 (ptm-80) cc_final: 0.8052 (ptt90) REVERT: H 150 MET cc_start: 0.7937 (ttt) cc_final: 0.7435 (tpp) REVERT: H 179 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.6798 (ppp) REVERT: H 194 LEU cc_start: 0.8785 (mm) cc_final: 0.8354 (mm) REVERT: H 198 ASN cc_start: 0.9297 (m-40) cc_final: 0.8795 (m-40) REVERT: H 199 GLU cc_start: 0.8216 (pt0) cc_final: 0.7824 (tp30) REVERT: H 202 GLN cc_start: 0.8724 (pp30) cc_final: 0.8326 (pp30) REVERT: H 203 ARG cc_start: 0.8811 (tpp-160) cc_final: 0.8172 (mtp-110) REVERT: H 214 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8117 (tm-30) REVERT: H 259 ARG cc_start: 0.8853 (ttm170) cc_final: 0.8562 (ttm170) REVERT: H 279 ASN cc_start: 0.8537 (t0) cc_final: 0.8005 (t0) REVERT: H 285 ASN cc_start: 0.8697 (m110) cc_final: 0.8416 (m110) REVERT: H 286 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8728 (tmt) REVERT: H 300 ILE cc_start: 0.8746 (mm) cc_final: 0.8485 (mm) REVERT: H 319 ASP cc_start: 0.8444 (m-30) cc_final: 0.8186 (m-30) REVERT: H 335 GLU cc_start: 0.8791 (tt0) cc_final: 0.8458 (tt0) REVERT: H 369 ASN cc_start: 0.8306 (p0) cc_final: 0.8050 (p0) REVERT: H 379 LEU cc_start: 0.9528 (mt) cc_final: 0.9246 (mt) REVERT: H 385 MET cc_start: 0.8609 (ttp) cc_final: 0.8351 (ttp) REVERT: H 412 ARG cc_start: 0.7822 (ttp80) cc_final: 0.7381 (ptt90) REVERT: H 441 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.8000 (tt0) REVERT: H 483 MET cc_start: 0.9299 (tmm) cc_final: 0.8701 (tmm) REVERT: H 507 HIS cc_start: 0.8824 (t-90) cc_final: 0.8441 (t-90) outliers start: 160 outliers final: 108 residues processed: 950 average time/residue: 0.1913 time to fit residues: 297.7570 Evaluate side-chains 970 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 830 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 26 CYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 312 ASN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 312 ASN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain H residue 496 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 293 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 63 optimal weight: 0.0030 chunk 188 optimal weight: 0.9990 chunk 324 optimal weight: 3.9990 chunk 219 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 307 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 29 optimal weight: 0.0470 chunk 352 optimal weight: 2.9990 overall best weight: 0.5690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS B 102 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.139195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.105724 restraints weight = 53971.351| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.72 r_work: 0.3133 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32096 Z= 0.132 Angle : 0.698 9.468 43488 Z= 0.358 Chirality : 0.047 0.190 4968 Planarity : 0.004 0.035 5448 Dihedral : 12.836 82.640 5397 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 4.74 % Allowed : 26.19 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -1.41 (0.14), residues: 3968 helix: -0.05 (0.15), residues: 1264 sheet: -1.23 (0.21), residues: 544 loop : -1.39 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 231 TYR 0.013 0.001 TYR D 110 PHE 0.008 0.001 PHE B 24 HIS 0.004 0.000 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00302 (32072) covalent geometry : angle 0.69755 (43488) hydrogen bonds : bond 0.03085 ( 1009) hydrogen bonds : angle 4.90316 ( 2835) Misc. bond : bond 0.00119 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 856 time to evaluate : 1.158 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 25 ASN cc_start: 0.8843 (m-40) cc_final: 0.8584 (p0) REVERT: A 36 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8159 (pp) REVERT: A 75 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6617 (mp0) REVERT: A 94 ASN cc_start: 0.9068 (t0) cc_final: 0.8612 (t0) REVERT: A 136 ARG cc_start: 0.8571 (ptm-80) cc_final: 0.8277 (ptt180) REVERT: A 150 MET cc_start: 0.7822 (ttt) cc_final: 0.7331 (tpp) REVERT: A 174 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7727 (t80) REVERT: A 179 MET cc_start: 0.7713 (pp-130) cc_final: 0.6435 (ppp) REVERT: A 198 ASN cc_start: 0.9313 (m-40) cc_final: 0.8838 (m-40) REVERT: A 199 GLU cc_start: 0.8225 (pt0) cc_final: 0.7901 (tp30) REVERT: A 202 GLN cc_start: 0.8681 (pp30) cc_final: 0.8200 (pp30) REVERT: A 203 ARG cc_start: 0.8870 (tpp-160) cc_final: 0.8228 (mtp-110) REVERT: A 214 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8221 (tm-30) REVERT: A 245 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8232 (mm) REVERT: A 319 ASP cc_start: 0.8486 (m-30) cc_final: 0.8175 (m-30) REVERT: A 353 TYR cc_start: 0.8886 (t80) cc_final: 0.8668 (t80) REVERT: A 385 MET cc_start: 0.9076 (ttp) cc_final: 0.8642 (ttp) REVERT: A 412 ARG cc_start: 0.7600 (ttp80) cc_final: 0.7148 (ptt90) REVERT: A 420 MET cc_start: 0.6768 (mtm) cc_final: 0.6549 (mtm) REVERT: A 455 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8546 (mmmm) REVERT: A 474 LYS cc_start: 0.8882 (mtpt) cc_final: 0.8664 (mtpt) REVERT: A 483 MET cc_start: 0.9270 (tmm) cc_final: 0.8542 (tmm) REVERT: A 507 HIS cc_start: 0.8808 (t-90) cc_final: 0.8448 (t-90) REVERT: B 16 ASP cc_start: 0.8380 (t0) cc_final: 0.8165 (t0) REVERT: B 25 ASN cc_start: 0.8803 (m-40) cc_final: 0.8569 (p0) REVERT: B 36 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8149 (pp) REVERT: B 94 ASN cc_start: 0.9170 (t0) cc_final: 0.8673 (t0) REVERT: B 136 ARG cc_start: 0.8554 (ptm160) cc_final: 0.8109 (ptt180) REVERT: B 150 MET cc_start: 0.7900 (ttt) cc_final: 0.7475 (tpp) REVERT: B 179 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.6707 (ppp) REVERT: B 198 ASN cc_start: 0.9280 (m-40) cc_final: 0.8759 (m-40) REVERT: B 199 GLU cc_start: 0.8093 (pt0) cc_final: 0.7498 (tp30) REVERT: B 202 GLN cc_start: 0.8702 (pp30) cc_final: 0.8160 (pp30) REVERT: B 203 ARG cc_start: 0.8775 (tpp-160) cc_final: 0.7973 (mtp-110) REVERT: B 205 LYS cc_start: 0.9108 (mtpp) cc_final: 0.8631 (ttmm) REVERT: B 214 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8196 (tm-30) REVERT: B 224 ARG cc_start: 0.8273 (tpp80) cc_final: 0.7394 (ttm170) REVERT: B 245 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8152 (mm) REVERT: B 300 ILE cc_start: 0.8577 (mm) cc_final: 0.8145 (mm) REVERT: B 319 ASP cc_start: 0.8465 (m-30) cc_final: 0.8184 (m-30) REVERT: B 353 TYR cc_start: 0.8931 (t80) cc_final: 0.8730 (t80) REVERT: B 385 MET cc_start: 0.9072 (ttp) cc_final: 0.8561 (ttp) REVERT: B 412 ARG cc_start: 0.7634 (ttp80) cc_final: 0.7333 (ptt90) REVERT: B 474 LYS cc_start: 0.8842 (mttt) cc_final: 0.8517 (mmmt) REVERT: B 507 HIS cc_start: 0.8807 (t-90) cc_final: 0.8418 (t-90) REVERT: C 75 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6709 (mp0) REVERT: C 136 ARG cc_start: 0.8569 (ptm-80) cc_final: 0.8268 (ptt180) REVERT: C 150 MET cc_start: 0.8056 (ttt) cc_final: 0.7596 (tpp) REVERT: C 174 PHE cc_start: 0.8295 (m-80) cc_final: 0.7880 (t80) REVERT: C 179 MET cc_start: 0.7725 (pp-130) cc_final: 0.6429 (ppp) REVERT: C 199 GLU cc_start: 0.8182 (pt0) cc_final: 0.7609 (tp30) REVERT: C 202 GLN cc_start: 0.8706 (pp30) cc_final: 0.8138 (pp30) REVERT: C 203 ARG cc_start: 0.8905 (tpp-160) cc_final: 0.8160 (ttp-110) REVERT: C 205 LYS cc_start: 0.9042 (mtpp) cc_final: 0.8488 (ttmm) REVERT: C 214 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8138 (tm-30) REVERT: C 245 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8137 (mm) REVERT: C 261 ASP cc_start: 0.9165 (m-30) cc_final: 0.8819 (m-30) REVERT: C 353 TYR cc_start: 0.8906 (t80) cc_final: 0.8702 (t80) REVERT: C 385 MET cc_start: 0.9055 (ttp) cc_final: 0.8619 (ttp) REVERT: C 395 GLU cc_start: 0.8283 (pm20) cc_final: 0.7853 (pm20) REVERT: C 412 ARG cc_start: 0.7637 (ttp80) cc_final: 0.7203 (ptt90) REVERT: C 455 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8575 (mmmm) REVERT: C 474 LYS cc_start: 0.8864 (mtpt) cc_final: 0.8641 (mtpt) REVERT: C 496 SER cc_start: 0.9267 (OUTLIER) cc_final: 0.8977 (p) REVERT: C 507 HIS cc_start: 0.8811 (t-90) cc_final: 0.8404 (t-90) REVERT: D 16 ASP cc_start: 0.8434 (t0) cc_final: 0.8202 (t0) REVERT: D 25 ASN cc_start: 0.8866 (m-40) cc_final: 0.8549 (p0) REVERT: D 36 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8014 (pp) REVERT: D 75 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6713 (pm20) REVERT: D 94 ASN cc_start: 0.9136 (t0) cc_final: 0.8689 (t0) REVERT: D 136 ARG cc_start: 0.8598 (ptm-80) cc_final: 0.8310 (ptt180) REVERT: D 150 MET cc_start: 0.7911 (ttt) cc_final: 0.7590 (tpp) REVERT: D 179 MET cc_start: 0.8024 (pp-130) cc_final: 0.6869 (ppp) REVERT: D 198 ASN cc_start: 0.9287 (m-40) cc_final: 0.8828 (m-40) REVERT: D 199 GLU cc_start: 0.8113 (pt0) cc_final: 0.7788 (tp30) REVERT: D 202 GLN cc_start: 0.8745 (pp30) cc_final: 0.8382 (pp30) REVERT: D 203 ARG cc_start: 0.8861 (tpp-160) cc_final: 0.8170 (mtp180) REVERT: D 205 LYS cc_start: 0.9041 (mtpp) cc_final: 0.8445 (ttmm) REVERT: D 214 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8194 (tm-30) REVERT: D 261 ASP cc_start: 0.9068 (m-30) cc_final: 0.8624 (m-30) REVERT: D 353 TYR cc_start: 0.8948 (t80) cc_final: 0.8734 (t80) REVERT: D 369 ASN cc_start: 0.8331 (p0) cc_final: 0.8067 (p0) REVERT: D 379 LEU cc_start: 0.9454 (mt) cc_final: 0.9191 (mt) REVERT: D 385 MET cc_start: 0.9135 (ttp) cc_final: 0.8680 (ttp) REVERT: D 412 ARG cc_start: 0.7620 (ttp80) cc_final: 0.7271 (ptt90) REVERT: D 420 MET cc_start: 0.6659 (mtm) cc_final: 0.6384 (mtm) REVERT: D 455 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8618 (mmmm) REVERT: D 474 LYS cc_start: 0.8808 (mtpt) cc_final: 0.8572 (mtpt) REVERT: D 507 HIS cc_start: 0.8821 (t-90) cc_final: 0.8419 (t-90) REVERT: E 25 ASN cc_start: 0.8846 (m-40) cc_final: 0.8602 (p0) REVERT: E 26 CYS cc_start: 0.9016 (m) cc_final: 0.8573 (t) REVERT: E 75 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6697 (mp0) REVERT: E 94 ASN cc_start: 0.9094 (t0) cc_final: 0.8751 (t0) REVERT: E 136 ARG cc_start: 0.8577 (ptm-80) cc_final: 0.8282 (ptt180) REVERT: E 174 PHE cc_start: 0.8397 (m-80) cc_final: 0.8065 (t80) REVERT: E 179 MET cc_start: 0.7724 (pp-130) cc_final: 0.6442 (ppp) REVERT: E 194 LEU cc_start: 0.8700 (mm) cc_final: 0.8220 (mm) REVERT: E 198 ASN cc_start: 0.9261 (m-40) cc_final: 0.8731 (m-40) REVERT: E 199 GLU cc_start: 0.8120 (pt0) cc_final: 0.7691 (tp30) REVERT: E 202 GLN cc_start: 0.8694 (pp30) cc_final: 0.8256 (pp30) REVERT: E 203 ARG cc_start: 0.8768 (tpp-160) cc_final: 0.8032 (mtp-110) REVERT: E 214 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8309 (tm-30) REVERT: E 245 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8087 (mm) REVERT: E 261 ASP cc_start: 0.9202 (m-30) cc_final: 0.8800 (m-30) REVERT: E 312 ASN cc_start: 0.8519 (OUTLIER) cc_final: 0.8203 (t0) REVERT: E 369 ASN cc_start: 0.8420 (p0) cc_final: 0.8136 (p0) REVERT: E 379 LEU cc_start: 0.9473 (mt) cc_final: 0.9160 (mt) REVERT: E 412 ARG cc_start: 0.7594 (ttp80) cc_final: 0.7217 (ptt90) REVERT: E 420 MET cc_start: 0.6844 (mtm) cc_final: 0.6556 (mtm) REVERT: E 455 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8587 (mmmm) REVERT: E 483 MET cc_start: 0.9289 (tmm) cc_final: 0.8578 (tmm) REVERT: E 507 HIS cc_start: 0.8858 (t-90) cc_final: 0.8485 (t-90) REVERT: F 16 ASP cc_start: 0.8327 (t0) cc_final: 0.8104 (t0) REVERT: F 25 ASN cc_start: 0.8799 (m-40) cc_final: 0.8547 (p0) REVERT: F 36 LEU cc_start: 0.8485 (pp) cc_final: 0.8221 (pp) REVERT: F 75 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6809 (pm20) REVERT: F 92 HIS cc_start: 0.9024 (p90) cc_final: 0.8744 (p-80) REVERT: F 94 ASN cc_start: 0.9155 (t0) cc_final: 0.8690 (t0) REVERT: F 136 ARG cc_start: 0.8585 (ptm-80) cc_final: 0.8134 (ptt180) REVERT: F 150 MET cc_start: 0.8000 (ttt) cc_final: 0.7593 (tpp) REVERT: F 174 PHE cc_start: 0.8228 (m-80) cc_final: 0.7597 (t80) REVERT: F 179 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.6785 (ppp) REVERT: F 198 ASN cc_start: 0.9264 (m-40) cc_final: 0.8813 (m-40) REVERT: F 199 GLU cc_start: 0.8165 (pt0) cc_final: 0.7708 (tp30) REVERT: F 202 GLN cc_start: 0.8710 (pp30) cc_final: 0.8306 (pp30) REVERT: F 203 ARG cc_start: 0.8767 (tpp-160) cc_final: 0.8061 (mtp-110) REVERT: F 214 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8120 (tm-30) REVERT: F 261 ASP cc_start: 0.9164 (m-30) cc_final: 0.8647 (m-30) REVERT: F 283 GLN cc_start: 0.8898 (mt0) cc_final: 0.8651 (tt0) REVERT: F 300 ILE cc_start: 0.8618 (mm) cc_final: 0.8333 (mm) REVERT: F 312 ASN cc_start: 0.8631 (OUTLIER) cc_final: 0.8245 (t0) REVERT: F 369 ASN cc_start: 0.8409 (p0) cc_final: 0.8109 (p0) REVERT: F 379 LEU cc_start: 0.9503 (mt) cc_final: 0.9292 (mt) REVERT: F 385 MET cc_start: 0.9125 (ttp) cc_final: 0.8635 (ttp) REVERT: F 412 ARG cc_start: 0.7698 (ttp80) cc_final: 0.7385 (ptt90) REVERT: F 420 MET cc_start: 0.6846 (mtm) cc_final: 0.6636 (mtm) REVERT: F 474 LYS cc_start: 0.8815 (mtpt) cc_final: 0.8600 (mtpt) REVERT: F 507 HIS cc_start: 0.8850 (t-90) cc_final: 0.8467 (t-90) REVERT: G 25 ASN cc_start: 0.8875 (m-40) cc_final: 0.8574 (p0) REVERT: G 34 ASP cc_start: 0.9170 (t0) cc_final: 0.8903 (t0) REVERT: G 75 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6689 (pm20) REVERT: G 94 ASN cc_start: 0.9130 (t0) cc_final: 0.8765 (t0) REVERT: G 132 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8451 (pp20) REVERT: G 136 ARG cc_start: 0.8520 (ptm-80) cc_final: 0.8069 (ptt180) REVERT: G 150 MET cc_start: 0.7993 (ttt) cc_final: 0.7571 (tpp) REVERT: G 179 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.6433 (ppp) REVERT: G 198 ASN cc_start: 0.9253 (m-40) cc_final: 0.8826 (m-40) REVERT: G 199 GLU cc_start: 0.8187 (pt0) cc_final: 0.7820 (tp30) REVERT: G 202 GLN cc_start: 0.8709 (pp30) cc_final: 0.8299 (pp30) REVERT: G 203 ARG cc_start: 0.8919 (tpp-160) cc_final: 0.8145 (mtp-110) REVERT: G 214 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8201 (tm-30) REVERT: G 245 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8207 (mm) REVERT: G 369 ASN cc_start: 0.8436 (p0) cc_final: 0.8121 (p0) REVERT: G 395 GLU cc_start: 0.8299 (pm20) cc_final: 0.7934 (pm20) REVERT: G 412 ARG cc_start: 0.7635 (ttp80) cc_final: 0.7279 (ptt90) REVERT: G 420 MET cc_start: 0.6824 (mtm) cc_final: 0.6539 (mtm) REVERT: G 455 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8584 (mmmm) REVERT: G 474 LYS cc_start: 0.8890 (mtpt) cc_final: 0.8671 (mtpt) REVERT: G 487 GLU cc_start: 0.8971 (tt0) cc_final: 0.8590 (tt0) REVERT: G 496 SER cc_start: 0.9247 (OUTLIER) cc_final: 0.8941 (p) REVERT: G 507 HIS cc_start: 0.8812 (t-90) cc_final: 0.8450 (t-90) REVERT: H 25 ASN cc_start: 0.8889 (m-40) cc_final: 0.8566 (p0) REVERT: H 75 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6720 (pm20) REVERT: H 94 ASN cc_start: 0.9080 (t0) cc_final: 0.8650 (t0) REVERT: H 136 ARG cc_start: 0.8532 (ptm-80) cc_final: 0.8058 (ptt180) REVERT: H 150 MET cc_start: 0.7848 (ttt) cc_final: 0.7408 (tpp) REVERT: H 179 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.6736 (ppp) REVERT: H 194 LEU cc_start: 0.8795 (mm) cc_final: 0.8361 (mm) REVERT: H 198 ASN cc_start: 0.9303 (m-40) cc_final: 0.8785 (m-40) REVERT: H 199 GLU cc_start: 0.8094 (pt0) cc_final: 0.7694 (tp30) REVERT: H 202 GLN cc_start: 0.8738 (pp30) cc_final: 0.8330 (pp30) REVERT: H 203 ARG cc_start: 0.8794 (tpp-160) cc_final: 0.8108 (mtp-110) REVERT: H 214 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8143 (tm-30) REVERT: H 259 ARG cc_start: 0.8681 (ttm170) cc_final: 0.8378 (ttm170) REVERT: H 285 ASN cc_start: 0.8701 (m110) cc_final: 0.8404 (m110) REVERT: H 286 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8678 (tmt) REVERT: H 300 ILE cc_start: 0.8754 (mm) cc_final: 0.8466 (mm) REVERT: H 335 GLU cc_start: 0.8806 (tt0) cc_final: 0.8478 (tt0) REVERT: H 369 ASN cc_start: 0.8240 (p0) cc_final: 0.7980 (p0) REVERT: H 385 MET cc_start: 0.8587 (ttp) cc_final: 0.8280 (ttp) REVERT: H 412 ARG cc_start: 0.7674 (ttp80) cc_final: 0.7250 (ptt90) REVERT: H 441 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: H 507 HIS cc_start: 0.8802 (t-90) cc_final: 0.8426 (t-90) outliers start: 155 outliers final: 99 residues processed: 931 average time/residue: 0.1869 time to fit residues: 286.4625 Evaluate side-chains 936 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 805 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 26 CYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 312 ASN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 312 ASN Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain H residue 496 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 155 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 383 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 102 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN C 102 ASN D 213 ASN E 92 HIS ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN F 213 ASN F 285 ASN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** 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 = 0.3731 r_free = 0.3731 target = 0.137353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.104839 restraints weight = 53601.346| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.63 r_work: 0.3121 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32096 Z= 0.156 Angle : 0.715 9.134 43488 Z= 0.367 Chirality : 0.048 0.213 4968 Planarity : 0.004 0.040 5448 Dihedral : 12.748 81.824 5397 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 4.28 % Allowed : 27.60 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -1.39 (0.14), residues: 3968 helix: -0.10 (0.14), residues: 1280 sheet: -1.22 (0.21), residues: 544 loop : -1.34 (0.14), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 231 TYR 0.010 0.001 TYR H 348 PHE 0.010 0.001 PHE B 24 HIS 0.004 0.000 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00365 (32072) covalent geometry : angle 0.71450 (43488) hydrogen bonds : bond 0.03149 ( 1009) hydrogen bonds : angle 4.92978 ( 2835) Misc. bond : bond 0.00143 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 806 time to evaluate : 0.823 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 25 ASN cc_start: 0.8879 (m-40) cc_final: 0.8606 (p0) REVERT: A 36 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8211 (pp) REVERT: A 75 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6953 (mm-30) REVERT: A 94 ASN cc_start: 0.9186 (t0) cc_final: 0.8731 (t0) REVERT: A 136 ARG cc_start: 0.8564 (ptm-80) cc_final: 0.8269 (ptt180) REVERT: A 150 MET cc_start: 0.7865 (ttt) cc_final: 0.7336 (tpp) REVERT: A 174 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7761 (t80) REVERT: A 179 MET cc_start: 0.7730 (pp-130) cc_final: 0.6447 (ppp) REVERT: A 198 ASN cc_start: 0.9320 (m-40) cc_final: 0.8820 (m-40) REVERT: A 199 GLU cc_start: 0.8229 (pt0) cc_final: 0.7898 (tp30) REVERT: A 202 GLN cc_start: 0.8680 (pp30) cc_final: 0.8193 (pp30) REVERT: A 203 ARG cc_start: 0.8894 (tpp-160) cc_final: 0.8254 (mtp-110) REVERT: A 214 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8267 (tm-30) REVERT: A 319 ASP cc_start: 0.8471 (m-30) cc_final: 0.8144 (m-30) REVERT: A 353 TYR cc_start: 0.8897 (t80) cc_final: 0.8656 (t80) REVERT: A 385 MET cc_start: 0.9178 (ttp) cc_final: 0.8665 (ttp) REVERT: A 412 ARG cc_start: 0.7642 (ttp80) cc_final: 0.7202 (ptt90) REVERT: A 420 MET cc_start: 0.6789 (mtm) cc_final: 0.6526 (mtm) REVERT: A 455 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8535 (mmmm) REVERT: A 474 LYS cc_start: 0.8895 (mtpt) cc_final: 0.8671 (mtpt) REVERT: A 507 HIS cc_start: 0.8769 (t-90) cc_final: 0.8427 (t-90) REVERT: B 25 ASN cc_start: 0.8836 (m-40) cc_final: 0.8594 (p0) REVERT: B 36 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8267 (pp) REVERT: B 94 ASN cc_start: 0.9045 (t0) cc_final: 0.8649 (t0) REVERT: B 136 ARG cc_start: 0.8547 (ptm160) cc_final: 0.8108 (ptt180) REVERT: B 150 MET cc_start: 0.7997 (ttt) cc_final: 0.7397 (tpp) REVERT: B 179 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.6882 (ppp) REVERT: B 198 ASN cc_start: 0.9289 (m-40) cc_final: 0.8761 (m-40) REVERT: B 199 GLU cc_start: 0.8112 (pt0) cc_final: 0.7505 (tp30) REVERT: B 202 GLN cc_start: 0.8712 (pp30) cc_final: 0.8154 (pp30) REVERT: B 203 ARG cc_start: 0.8772 (tpp-160) cc_final: 0.7957 (mtp-110) REVERT: B 205 LYS cc_start: 0.9078 (mtpp) cc_final: 0.8637 (ttmm) REVERT: B 214 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8214 (tm-30) REVERT: B 224 ARG cc_start: 0.8292 (tpp80) cc_final: 0.7395 (ttm170) REVERT: B 300 ILE cc_start: 0.8585 (mm) cc_final: 0.8309 (mm) REVERT: B 319 ASP cc_start: 0.8473 (m-30) cc_final: 0.8184 (m-30) REVERT: B 353 TYR cc_start: 0.8928 (t80) cc_final: 0.8701 (t80) REVERT: B 385 MET cc_start: 0.9094 (ttp) cc_final: 0.8609 (ttp) REVERT: B 412 ARG cc_start: 0.7735 (ttp80) cc_final: 0.7337 (ptt90) REVERT: B 474 LYS cc_start: 0.8871 (mttt) cc_final: 0.8557 (mmmt) REVERT: B 507 HIS cc_start: 0.8844 (t-90) cc_final: 0.8448 (t-90) REVERT: C 75 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6756 (pm20) REVERT: C 136 ARG cc_start: 0.8576 (ptm-80) cc_final: 0.8279 (ptt180) REVERT: C 150 MET cc_start: 0.8046 (ttt) cc_final: 0.7537 (tpp) REVERT: C 174 PHE cc_start: 0.8256 (m-80) cc_final: 0.7904 (t80) REVERT: C 179 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.6698 (ppp) REVERT: C 199 GLU cc_start: 0.8141 (pt0) cc_final: 0.7794 (tp30) REVERT: C 202 GLN cc_start: 0.8696 (pp30) cc_final: 0.8367 (pp30) REVERT: C 203 ARG cc_start: 0.8904 (tpp-160) cc_final: 0.8186 (mtp180) REVERT: C 205 LYS cc_start: 0.9047 (mtpp) cc_final: 0.8494 (ttmm) REVERT: C 214 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8128 (tm-30) REVERT: C 245 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8152 (mm) REVERT: C 261 ASP cc_start: 0.9183 (m-30) cc_final: 0.8829 (m-30) REVERT: C 300 ILE cc_start: 0.8193 (mm) cc_final: 0.7507 (mt) REVERT: C 353 TYR cc_start: 0.8910 (t80) cc_final: 0.8686 (t80) REVERT: C 385 MET cc_start: 0.9108 (ttp) cc_final: 0.8708 (ttp) REVERT: C 412 ARG cc_start: 0.7677 (ttp80) cc_final: 0.7226 (ptt90) REVERT: C 455 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8556 (mmmm) REVERT: C 474 LYS cc_start: 0.8859 (mtpt) cc_final: 0.8626 (mtpt) REVERT: C 507 HIS cc_start: 0.8837 (t-90) cc_final: 0.8444 (t-90) REVERT: D 25 ASN cc_start: 0.8880 (m-40) cc_final: 0.8553 (p0) REVERT: D 36 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8190 (pp) REVERT: D 75 GLU cc_start: 0.7296 (pm20) cc_final: 0.6705 (pm20) REVERT: D 94 ASN cc_start: 0.9242 (t0) cc_final: 0.8779 (t0) REVERT: D 136 ARG cc_start: 0.8609 (ptm-80) cc_final: 0.8323 (ptt180) REVERT: D 150 MET cc_start: 0.7909 (ttt) cc_final: 0.7527 (tpp) REVERT: D 174 PHE cc_start: 0.8123 (m-80) cc_final: 0.7825 (t80) REVERT: D 179 MET cc_start: 0.8058 (pp-130) cc_final: 0.6905 (ppp) REVERT: D 198 ASN cc_start: 0.9298 (m-40) cc_final: 0.8823 (m-40) REVERT: D 199 GLU cc_start: 0.8143 (pt0) cc_final: 0.7781 (tp30) REVERT: D 202 GLN cc_start: 0.8787 (pp30) cc_final: 0.8408 (pp30) REVERT: D 203 ARG cc_start: 0.8873 (tpp-160) cc_final: 0.8120 (mtp-110) REVERT: D 205 LYS cc_start: 0.9016 (mtpp) cc_final: 0.8385 (ttmm) REVERT: D 214 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8185 (tm-30) REVERT: D 261 ASP cc_start: 0.9088 (m-30) cc_final: 0.8634 (m-30) REVERT: D 353 TYR cc_start: 0.8945 (t80) cc_final: 0.8725 (t80) REVERT: D 379 LEU cc_start: 0.9478 (mt) cc_final: 0.9213 (mt) REVERT: D 385 MET cc_start: 0.9157 (ttp) cc_final: 0.8722 (ttp) REVERT: D 412 ARG cc_start: 0.7675 (ttp80) cc_final: 0.7310 (ptt90) REVERT: D 420 MET cc_start: 0.6726 (mtm) cc_final: 0.6442 (mtm) REVERT: D 455 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8620 (mmmm) REVERT: D 474 LYS cc_start: 0.8819 (mtpt) cc_final: 0.8587 (mtpt) REVERT: D 507 HIS cc_start: 0.8820 (t-90) cc_final: 0.8430 (t-90) REVERT: E 25 ASN cc_start: 0.8881 (m-40) cc_final: 0.8621 (p0) REVERT: E 26 CYS cc_start: 0.9024 (m) cc_final: 0.8583 (t) REVERT: E 75 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7049 (mm-30) REVERT: E 136 ARG cc_start: 0.8587 (ptm-80) cc_final: 0.8294 (ptt180) REVERT: E 174 PHE cc_start: 0.8320 (m-80) cc_final: 0.7974 (t80) REVERT: E 179 MET cc_start: 0.7841 (pp-130) cc_final: 0.6635 (ppp) REVERT: E 198 ASN cc_start: 0.9273 (m-40) cc_final: 0.8726 (m-40) REVERT: E 199 GLU cc_start: 0.8140 (pt0) cc_final: 0.7695 (tp30) REVERT: E 202 GLN cc_start: 0.8690 (pp30) cc_final: 0.8271 (pp30) REVERT: E 203 ARG cc_start: 0.8769 (tpp-160) cc_final: 0.8017 (mtp-110) REVERT: E 214 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8319 (tm-30) REVERT: E 231 ARG cc_start: 0.8370 (mmm160) cc_final: 0.8120 (mmp80) REVERT: E 245 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8159 (mm) REVERT: E 261 ASP cc_start: 0.9204 (m-30) cc_final: 0.8781 (m-30) REVERT: E 312 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.8198 (t0) REVERT: E 379 LEU cc_start: 0.9506 (mt) cc_final: 0.9270 (mt) REVERT: E 412 ARG cc_start: 0.7650 (ttp80) cc_final: 0.7247 (ptt90) REVERT: E 420 MET cc_start: 0.6921 (mtm) cc_final: 0.6614 (mtm) REVERT: E 455 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8563 (mmmm) REVERT: E 507 HIS cc_start: 0.8848 (t-90) cc_final: 0.8488 (t-90) REVERT: F 25 ASN cc_start: 0.8824 (m-40) cc_final: 0.8558 (p0) REVERT: F 75 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6832 (pm20) REVERT: F 92 HIS cc_start: 0.9003 (p90) cc_final: 0.8687 (p-80) REVERT: F 94 ASN cc_start: 0.9184 (t0) cc_final: 0.8728 (t0) REVERT: F 136 ARG cc_start: 0.8569 (ptm-80) cc_final: 0.8118 (ptt180) REVERT: F 150 MET cc_start: 0.8000 (ttt) cc_final: 0.7560 (tpp) REVERT: F 174 PHE cc_start: 0.8227 (m-80) cc_final: 0.7600 (t80) REVERT: F 179 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.6819 (ppp) REVERT: F 198 ASN cc_start: 0.9275 (m-40) cc_final: 0.8837 (m-40) REVERT: F 199 GLU cc_start: 0.8092 (pt0) cc_final: 0.7634 (tp30) REVERT: F 202 GLN cc_start: 0.8691 (pp30) cc_final: 0.8278 (pp30) REVERT: F 203 ARG cc_start: 0.8768 (tpp-160) cc_final: 0.8060 (mtp-110) REVERT: F 214 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8158 (tm-30) REVERT: F 261 ASP cc_start: 0.9175 (m-30) cc_final: 0.8665 (m-30) REVERT: F 300 ILE cc_start: 0.8639 (mm) cc_final: 0.8359 (mm) REVERT: F 312 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8313 (t0) REVERT: F 369 ASN cc_start: 0.8466 (p0) cc_final: 0.8163 (p0) REVERT: F 385 MET cc_start: 0.9147 (ttp) cc_final: 0.8671 (ttp) REVERT: F 412 ARG cc_start: 0.7760 (ttp80) cc_final: 0.7398 (ptt90) REVERT: F 420 MET cc_start: 0.6918 (mtm) cc_final: 0.6710 (mtm) REVERT: F 474 LYS cc_start: 0.8811 (mtpt) cc_final: 0.8587 (mtpt) REVERT: F 507 HIS cc_start: 0.8858 (t-90) cc_final: 0.8488 (t-90) REVERT: G 25 ASN cc_start: 0.8893 (m-40) cc_final: 0.8588 (p0) REVERT: G 34 ASP cc_start: 0.9218 (t0) cc_final: 0.8933 (t0) REVERT: G 75 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6862 (pm20) REVERT: G 94 ASN cc_start: 0.9161 (t0) cc_final: 0.8726 (t0) REVERT: G 132 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8522 (pp20) REVERT: G 134 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7442 (pttm) REVERT: G 136 ARG cc_start: 0.8540 (ptm-80) cc_final: 0.8006 (ptt90) REVERT: G 150 MET cc_start: 0.7992 (ttt) cc_final: 0.7516 (tpp) REVERT: G 179 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.6484 (ppp) REVERT: G 198 ASN cc_start: 0.9280 (m-40) cc_final: 0.8825 (m-40) REVERT: G 199 GLU cc_start: 0.8217 (pt0) cc_final: 0.7834 (tp30) REVERT: G 202 GLN cc_start: 0.8697 (pp30) cc_final: 0.8276 (pp30) REVERT: G 203 ARG cc_start: 0.8931 (tpp-160) cc_final: 0.8155 (mtp-110) REVERT: G 213 ASN cc_start: 0.8633 (t0) cc_final: 0.8405 (t0) REVERT: G 279 ASN cc_start: 0.8756 (t0) cc_final: 0.7915 (t0) REVERT: G 369 ASN cc_start: 0.8424 (p0) cc_final: 0.8147 (p0) REVERT: G 385 MET cc_start: 0.8834 (ttm) cc_final: 0.8401 (ttp) REVERT: G 412 ARG cc_start: 0.7681 (ttp80) cc_final: 0.7310 (ptt90) REVERT: G 420 MET cc_start: 0.6878 (mtm) cc_final: 0.6582 (mtm) REVERT: G 455 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8558 (mmmm) REVERT: G 474 LYS cc_start: 0.8884 (mtpt) cc_final: 0.8652 (mtpt) REVERT: G 487 GLU cc_start: 0.8964 (tt0) cc_final: 0.8562 (tt0) REVERT: G 496 SER cc_start: 0.9262 (OUTLIER) cc_final: 0.8975 (p) REVERT: G 507 HIS cc_start: 0.8828 (t-90) cc_final: 0.8470 (t-90) REVERT: H 25 ASN cc_start: 0.8914 (m-40) cc_final: 0.8570 (p0) REVERT: H 36 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8337 (pp) REVERT: H 75 GLU cc_start: 0.7445 (pm20) cc_final: 0.6950 (pm20) REVERT: H 94 ASN cc_start: 0.9198 (t0) cc_final: 0.8777 (t0) REVERT: H 134 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7364 (pttm) REVERT: H 136 ARG cc_start: 0.8551 (ptm-80) cc_final: 0.8067 (ptt90) REVERT: H 150 MET cc_start: 0.7861 (ttt) cc_final: 0.7413 (tpp) REVERT: H 179 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.6894 (ppp) REVERT: H 194 LEU cc_start: 0.8823 (mm) cc_final: 0.8390 (mm) REVERT: H 198 ASN cc_start: 0.9304 (m-40) cc_final: 0.8784 (m-40) REVERT: H 199 GLU cc_start: 0.8193 (pt0) cc_final: 0.7761 (tp30) REVERT: H 202 GLN cc_start: 0.8750 (pp30) cc_final: 0.8334 (pp30) REVERT: H 203 ARG cc_start: 0.8806 (tpp-160) cc_final: 0.8112 (mtp-110) REVERT: H 214 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8161 (tm-30) REVERT: H 259 ARG cc_start: 0.8766 (ttm170) cc_final: 0.8436 (ttm170) REVERT: H 285 ASN cc_start: 0.8695 (m110) cc_final: 0.8392 (m110) REVERT: H 286 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8630 (tmt) REVERT: H 300 ILE cc_start: 0.8723 (mm) cc_final: 0.8437 (mm) REVERT: H 319 ASP cc_start: 0.8439 (m-30) cc_final: 0.8192 (m-30) REVERT: H 369 ASN cc_start: 0.8291 (p0) cc_final: 0.7994 (p0) REVERT: H 379 LEU cc_start: 0.9498 (mt) cc_final: 0.9277 (mt) REVERT: H 385 MET cc_start: 0.8604 (ttp) cc_final: 0.8364 (ttp) REVERT: H 412 ARG cc_start: 0.7714 (ttp80) cc_final: 0.7271 (ptt90) REVERT: H 507 HIS cc_start: 0.8827 (t-90) cc_final: 0.8467 (t-90) outliers start: 140 outliers final: 96 residues processed: 870 average time/residue: 0.1846 time to fit residues: 264.6064 Evaluate side-chains 912 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 787 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 26 CYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 312 ASN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 312 ASN Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 134 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 496 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 380 optimal weight: 0.9980 chunk 384 optimal weight: 1.9990 chunk 269 optimal weight: 0.0000 chunk 201 optimal weight: 0.6980 chunk 378 optimal weight: 0.0270 chunk 105 optimal weight: 2.9990 chunk 387 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 195 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 368 optimal weight: 0.6980 overall best weight: 0.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 GLN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.139727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.106139 restraints weight = 53954.539| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.76 r_work: 0.3144 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32096 Z= 0.130 Angle : 0.708 9.376 43488 Z= 0.362 Chirality : 0.047 0.222 4968 Planarity : 0.004 0.037 5448 Dihedral : 12.506 83.700 5397 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.85 % Allowed : 27.90 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -1.36 (0.14), residues: 3968 helix: -0.04 (0.15), residues: 1264 sheet: -1.15 (0.21), residues: 544 loop : -1.35 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 231 TYR 0.009 0.001 TYR H 348 PHE 0.008 0.001 PHE H 490 HIS 0.004 0.000 HIS G 92 Details of bonding type rmsd covalent geometry : bond 0.00295 (32072) covalent geometry : angle 0.70768 (43488) hydrogen bonds : bond 0.03096 ( 1009) hydrogen bonds : angle 4.94065 ( 2835) Misc. bond : bond 0.00103 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 977 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 851 time to evaluate : 1.169 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 25 ASN cc_start: 0.8811 (m-40) cc_final: 0.8569 (p0) REVERT: A 36 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8160 (pp) REVERT: A 75 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6930 (mm-30) REVERT: A 94 ASN cc_start: 0.9013 (t0) cc_final: 0.8528 (t0) REVERT: A 136 ARG cc_start: 0.8545 (ptm-80) cc_final: 0.8007 (ptt180) REVERT: A 150 MET cc_start: 0.7864 (ttt) cc_final: 0.7377 (tpp) REVERT: A 174 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7573 (t80) REVERT: A 179 MET cc_start: 0.7656 (pp-130) cc_final: 0.6376 (ppp) REVERT: A 194 LEU cc_start: 0.8727 (mm) cc_final: 0.8307 (mm) REVERT: A 198 ASN cc_start: 0.9320 (m-40) cc_final: 0.8808 (m-40) REVERT: A 199 GLU cc_start: 0.8215 (pt0) cc_final: 0.7908 (tp30) REVERT: A 202 GLN cc_start: 0.8690 (pp30) cc_final: 0.8244 (pp30) REVERT: A 203 ARG cc_start: 0.8877 (tpp-160) cc_final: 0.8219 (mtp-110) REVERT: A 214 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8280 (tm-30) REVERT: A 231 ARG cc_start: 0.8420 (mmm160) cc_final: 0.8191 (mmp80) REVERT: A 319 ASP cc_start: 0.8471 (m-30) cc_final: 0.8129 (m-30) REVERT: A 353 TYR cc_start: 0.8876 (t80) cc_final: 0.8655 (t80) REVERT: A 385 MET cc_start: 0.9156 (ttp) cc_final: 0.8665 (ttp) REVERT: A 412 ARG cc_start: 0.7543 (ttp80) cc_final: 0.7206 (ptt90) REVERT: A 420 MET cc_start: 0.6771 (mtm) cc_final: 0.6489 (mtm) REVERT: A 455 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8567 (mmmm) REVERT: A 474 LYS cc_start: 0.8887 (mtpt) cc_final: 0.8676 (mtpt) REVERT: A 483 MET cc_start: 0.9303 (tmm) cc_final: 0.8664 (tmm) REVERT: A 507 HIS cc_start: 0.8806 (t-90) cc_final: 0.8471 (t-90) REVERT: B 36 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8193 (pp) REVERT: B 94 ASN cc_start: 0.8984 (t0) cc_final: 0.8521 (t0) REVERT: B 136 ARG cc_start: 0.8562 (ptm160) cc_final: 0.8131 (ptt180) REVERT: B 150 MET cc_start: 0.7948 (ttt) cc_final: 0.7469 (tpp) REVERT: B 179 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.6757 (ppp) REVERT: B 198 ASN cc_start: 0.9262 (m-40) cc_final: 0.8728 (m-40) REVERT: B 199 GLU cc_start: 0.8087 (pt0) cc_final: 0.7493 (tp30) REVERT: B 202 GLN cc_start: 0.8713 (pp30) cc_final: 0.8151 (pp30) REVERT: B 203 ARG cc_start: 0.8782 (tpp-160) cc_final: 0.7953 (mtp-110) REVERT: B 205 LYS cc_start: 0.9100 (mtpp) cc_final: 0.8626 (ttmm) REVERT: B 214 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8291 (tm-30) REVERT: B 224 ARG cc_start: 0.8261 (tpp80) cc_final: 0.7361 (ttm170) REVERT: B 300 ILE cc_start: 0.8601 (mm) cc_final: 0.8388 (mm) REVERT: B 319 ASP cc_start: 0.8547 (m-30) cc_final: 0.8267 (m-30) REVERT: B 385 MET cc_start: 0.9035 (ttp) cc_final: 0.8511 (ttp) REVERT: B 412 ARG cc_start: 0.7617 (ttp80) cc_final: 0.7277 (ptt90) REVERT: B 474 LYS cc_start: 0.8885 (mttt) cc_final: 0.8529 (mmmt) REVERT: B 507 HIS cc_start: 0.8839 (t-90) cc_final: 0.8468 (t-90) REVERT: C 31 THR cc_start: 0.9128 (t) cc_final: 0.8876 (t) REVERT: C 75 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6888 (mm-30) REVERT: C 136 ARG cc_start: 0.8554 (ptm-80) cc_final: 0.8260 (ptt180) REVERT: C 150 MET cc_start: 0.8092 (ttt) cc_final: 0.7576 (tpp) REVERT: C 174 PHE cc_start: 0.8264 (m-80) cc_final: 0.7960 (t80) REVERT: C 179 MET cc_start: 0.7745 (pp-130) cc_final: 0.6537 (ppp) REVERT: C 199 GLU cc_start: 0.8128 (pt0) cc_final: 0.7560 (tp30) REVERT: C 202 GLN cc_start: 0.8715 (pp30) cc_final: 0.8120 (pp30) REVERT: C 203 ARG cc_start: 0.8921 (tpp-160) cc_final: 0.8108 (mtp180) REVERT: C 205 LYS cc_start: 0.9023 (mtpp) cc_final: 0.8464 (ttmm) REVERT: C 214 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8157 (tm-30) REVERT: C 245 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8223 (mm) REVERT: C 261 ASP cc_start: 0.9160 (m-30) cc_final: 0.8797 (m-30) REVERT: C 300 ILE cc_start: 0.8172 (mm) cc_final: 0.7550 (mt) REVERT: C 379 LEU cc_start: 0.9506 (mt) cc_final: 0.9191 (mt) REVERT: C 385 MET cc_start: 0.9040 (ttp) cc_final: 0.8618 (ttp) REVERT: C 412 ARG cc_start: 0.7587 (ttp80) cc_final: 0.7295 (ptt90) REVERT: C 455 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8555 (mmmm) REVERT: C 474 LYS cc_start: 0.8846 (mtpt) cc_final: 0.8610 (mtpt) REVERT: C 483 MET cc_start: 0.9240 (tmm) cc_final: 0.8469 (tmm) REVERT: C 496 SER cc_start: 0.9265 (OUTLIER) cc_final: 0.8964 (p) REVERT: C 507 HIS cc_start: 0.8799 (t-90) cc_final: 0.8415 (t-90) REVERT: D 25 ASN cc_start: 0.8840 (m-40) cc_final: 0.8546 (p0) REVERT: D 36 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8086 (pp) REVERT: D 75 GLU cc_start: 0.7239 (pm20) cc_final: 0.6706 (pm20) REVERT: D 94 ASN cc_start: 0.9083 (t0) cc_final: 0.8596 (t0) REVERT: D 136 ARG cc_start: 0.8594 (ptm-80) cc_final: 0.8307 (ptt180) REVERT: D 150 MET cc_start: 0.7897 (ttt) cc_final: 0.7534 (tpp) REVERT: D 174 PHE cc_start: 0.8073 (m-80) cc_final: 0.7837 (t80) REVERT: D 179 MET cc_start: 0.7936 (pp-130) cc_final: 0.6794 (ppp) REVERT: D 198 ASN cc_start: 0.9300 (m-40) cc_final: 0.8834 (m-40) REVERT: D 199 GLU cc_start: 0.8147 (pt0) cc_final: 0.7615 (tp30) REVERT: D 202 GLN cc_start: 0.8812 (pp30) cc_final: 0.8180 (pp30) REVERT: D 203 ARG cc_start: 0.8882 (tpp-160) cc_final: 0.8084 (mtp180) REVERT: D 205 LYS cc_start: 0.9010 (mtpp) cc_final: 0.8386 (ttmm) REVERT: D 214 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8209 (tm-30) REVERT: D 261 ASP cc_start: 0.9076 (m-30) cc_final: 0.8607 (m-30) REVERT: D 353 TYR cc_start: 0.8926 (t80) cc_final: 0.8718 (t80) REVERT: D 385 MET cc_start: 0.9089 (ttp) cc_final: 0.8553 (ttp) REVERT: D 411 TYR cc_start: 0.8461 (t80) cc_final: 0.7997 (t80) REVERT: D 420 MET cc_start: 0.6746 (mtm) cc_final: 0.6461 (mtm) REVERT: D 455 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8601 (mmmm) REVERT: D 474 LYS cc_start: 0.8798 (mtpt) cc_final: 0.8562 (mtpt) REVERT: D 507 HIS cc_start: 0.8836 (t-90) cc_final: 0.8463 (t-90) REVERT: E 25 ASN cc_start: 0.8854 (m-40) cc_final: 0.8611 (p0) REVERT: E 26 CYS cc_start: 0.8999 (m) cc_final: 0.8548 (t) REVERT: E 75 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6947 (mm-30) REVERT: E 94 ASN cc_start: 0.9058 (t0) cc_final: 0.8855 (t0) REVERT: E 136 ARG cc_start: 0.8576 (ptm-80) cc_final: 0.8291 (ptt180) REVERT: E 174 PHE cc_start: 0.8288 (m-80) cc_final: 0.7954 (t80) REVERT: E 179 MET cc_start: 0.7777 (pp-130) cc_final: 0.6583 (ppp) REVERT: E 194 LEU cc_start: 0.8713 (mm) cc_final: 0.8253 (mm) REVERT: E 198 ASN cc_start: 0.9258 (m-40) cc_final: 0.8711 (m-40) REVERT: E 199 GLU cc_start: 0.8121 (pt0) cc_final: 0.7686 (tp30) REVERT: E 202 GLN cc_start: 0.8694 (pp30) cc_final: 0.8274 (pp30) REVERT: E 203 ARG cc_start: 0.8795 (tpp-160) cc_final: 0.7994 (mtp-110) REVERT: E 214 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8346 (tm-30) REVERT: E 231 ARG cc_start: 0.8349 (mmm160) cc_final: 0.8128 (mmp80) REVERT: E 245 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8178 (mm) REVERT: E 261 ASP cc_start: 0.9195 (m-30) cc_final: 0.8768 (m-30) REVERT: E 369 ASN cc_start: 0.8465 (p0) cc_final: 0.8114 (p0) REVERT: E 379 LEU cc_start: 0.9497 (mt) cc_final: 0.9159 (mt) REVERT: E 412 ARG cc_start: 0.7542 (ttp80) cc_final: 0.7191 (ptt90) REVERT: E 420 MET cc_start: 0.6874 (mtm) cc_final: 0.6574 (mtm) REVERT: E 455 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8575 (mmmm) REVERT: E 483 MET cc_start: 0.9279 (tmm) cc_final: 0.8676 (tmm) REVERT: E 507 HIS cc_start: 0.8815 (t-90) cc_final: 0.8462 (t-90) REVERT: F 25 ASN cc_start: 0.8785 (m-40) cc_final: 0.8538 (p0) REVERT: F 75 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6765 (pm20) REVERT: F 92 HIS cc_start: 0.9014 (p90) cc_final: 0.8735 (p-80) REVERT: F 94 ASN cc_start: 0.9134 (t0) cc_final: 0.8642 (t0) REVERT: F 136 ARG cc_start: 0.8568 (ptm-80) cc_final: 0.8137 (ptt180) REVERT: F 150 MET cc_start: 0.7978 (ttt) cc_final: 0.7611 (tpp) REVERT: F 174 PHE cc_start: 0.8244 (m-80) cc_final: 0.7640 (t80) REVERT: F 179 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.6744 (ppp) REVERT: F 198 ASN cc_start: 0.9253 (m-40) cc_final: 0.8829 (m-40) REVERT: F 199 GLU cc_start: 0.8038 (pt0) cc_final: 0.7588 (tp30) REVERT: F 202 GLN cc_start: 0.8716 (pp30) cc_final: 0.8305 (pp30) REVERT: F 203 ARG cc_start: 0.8761 (tpp-160) cc_final: 0.8055 (mtp-110) REVERT: F 214 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8180 (tm-30) REVERT: F 261 ASP cc_start: 0.9179 (m-30) cc_final: 0.8662 (m-30) REVERT: F 283 GLN cc_start: 0.8878 (mt0) cc_final: 0.8622 (tt0) REVERT: F 300 ILE cc_start: 0.8635 (mm) cc_final: 0.8387 (mm) REVERT: F 369 ASN cc_start: 0.8414 (p0) cc_final: 0.8119 (p0) REVERT: F 379 LEU cc_start: 0.9487 (mt) cc_final: 0.9278 (mt) REVERT: F 385 MET cc_start: 0.9137 (ttp) cc_final: 0.8678 (ttp) REVERT: F 412 ARG cc_start: 0.7645 (ttp80) cc_final: 0.7319 (ptt90) REVERT: F 474 LYS cc_start: 0.8809 (mtpt) cc_final: 0.8593 (mtpt) REVERT: F 507 HIS cc_start: 0.8809 (t-90) cc_final: 0.8441 (t-90) REVERT: G 25 ASN cc_start: 0.8852 (m-40) cc_final: 0.8552 (p0) REVERT: G 75 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6710 (pm20) REVERT: G 94 ASN cc_start: 0.9083 (t0) cc_final: 0.8683 (t0) REVERT: G 134 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7435 (pttm) REVERT: G 136 ARG cc_start: 0.8519 (ptm-80) cc_final: 0.8242 (ptt90) REVERT: G 150 MET cc_start: 0.7995 (ttt) cc_final: 0.7540 (tpp) REVERT: G 174 PHE cc_start: 0.8085 (m-80) cc_final: 0.7682 (t80) REVERT: G 179 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.6316 (ppp) REVERT: G 198 ASN cc_start: 0.9281 (m-40) cc_final: 0.8809 (m-40) REVERT: G 199 GLU cc_start: 0.8100 (pt0) cc_final: 0.7741 (tp30) REVERT: G 202 GLN cc_start: 0.8684 (pp30) cc_final: 0.8282 (pp30) REVERT: G 203 ARG cc_start: 0.8910 (tpp-160) cc_final: 0.8140 (mtp-110) REVERT: G 232 ASP cc_start: 0.8509 (t70) cc_final: 0.8279 (t70) REVERT: G 279 ASN cc_start: 0.8721 (t0) cc_final: 0.7921 (t0) REVERT: G 369 ASN cc_start: 0.8315 (p0) cc_final: 0.8010 (p0) REVERT: G 379 LEU cc_start: 0.9516 (mt) cc_final: 0.9284 (mt) REVERT: G 385 MET cc_start: 0.8832 (ttm) cc_final: 0.8565 (ttp) REVERT: G 412 ARG cc_start: 0.7527 (ttp80) cc_final: 0.7293 (ptt90) REVERT: G 420 MET cc_start: 0.6899 (mtm) cc_final: 0.6605 (mtm) REVERT: G 455 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8577 (mmmm) REVERT: G 474 LYS cc_start: 0.8877 (mtpt) cc_final: 0.8653 (mtpt) REVERT: G 487 GLU cc_start: 0.8955 (tt0) cc_final: 0.8544 (tt0) REVERT: G 496 SER cc_start: 0.9251 (OUTLIER) cc_final: 0.8931 (p) REVERT: G 507 HIS cc_start: 0.8789 (t-90) cc_final: 0.8460 (t-90) REVERT: H 25 ASN cc_start: 0.8860 (m-40) cc_final: 0.8534 (p0) REVERT: H 36 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8275 (pp) REVERT: H 75 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6666 (pm20) REVERT: H 94 ASN cc_start: 0.9142 (t0) cc_final: 0.8713 (t0) REVERT: H 134 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7344 (pttm) REVERT: H 136 ARG cc_start: 0.8543 (ptm-80) cc_final: 0.8056 (ptt180) REVERT: H 150 MET cc_start: 0.7826 (ttt) cc_final: 0.7403 (tpp) REVERT: H 179 MET cc_start: 0.7943 (pp-130) cc_final: 0.6848 (ppp) REVERT: H 194 LEU cc_start: 0.8822 (mm) cc_final: 0.8396 (mm) REVERT: H 198 ASN cc_start: 0.9295 (m-40) cc_final: 0.8782 (m-40) REVERT: H 199 GLU cc_start: 0.8091 (pt0) cc_final: 0.7672 (tp30) REVERT: H 202 GLN cc_start: 0.8756 (pp30) cc_final: 0.8335 (pp30) REVERT: H 203 ARG cc_start: 0.8774 (tpp-160) cc_final: 0.8091 (mtp-110) REVERT: H 214 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8224 (tm-30) REVERT: H 285 ASN cc_start: 0.8708 (m110) cc_final: 0.8423 (m110) REVERT: H 286 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8612 (tmt) REVERT: H 300 ILE cc_start: 0.8722 (mm) cc_final: 0.8449 (mm) REVERT: H 319 ASP cc_start: 0.8491 (m-30) cc_final: 0.8243 (m-30) REVERT: H 369 ASN cc_start: 0.8186 (p0) cc_final: 0.7903 (p0) REVERT: H 412 ARG cc_start: 0.7607 (ttp80) cc_final: 0.7258 (ptt90) REVERT: H 507 HIS cc_start: 0.8824 (t-90) cc_final: 0.8450 (t-90) outliers start: 126 outliers final: 87 residues processed: 908 average time/residue: 0.1818 time to fit residues: 271.6457 Evaluate side-chains 898 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 785 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 26 CYS Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 134 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain H residue 496 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 236 optimal weight: 0.7980 chunk 244 optimal weight: 0.5980 chunk 139 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 223 optimal weight: 0.5980 chunk 346 optimal weight: 0.6980 chunk 326 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 GLN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.140122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106602 restraints weight = 53941.210| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.76 r_work: 0.3151 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 32096 Z= 0.172 Angle : 0.813 59.200 43488 Z= 0.440 Chirality : 0.048 0.320 4968 Planarity : 0.004 0.120 5448 Dihedral : 12.499 83.678 5396 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.82 % Allowed : 28.55 % Favored : 67.63 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -1.38 (0.14), residues: 3968 helix: -0.08 (0.14), residues: 1264 sheet: -1.15 (0.21), residues: 544 loop : -1.36 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.064 0.001 ARG G 259 TYR 0.013 0.001 TYR D 110 PHE 0.009 0.001 PHE G 131 HIS 0.004 0.000 HIS G 92 Details of bonding type rmsd covalent geometry : bond 0.00398 (32072) covalent geometry : angle 0.81311 (43488) hydrogen bonds : bond 0.03140 ( 1009) hydrogen bonds : angle 4.95495 ( 2835) Misc. bond : bond 0.00116 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8232.99 seconds wall clock time: 142 minutes 7.21 seconds (8527.21 seconds total)