Starting phenix.real_space_refine on Tue May 27 20:18:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c0b_16357/05_2025/8c0b_16357.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c0b_16357/05_2025/8c0b_16357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c0b_16357/05_2025/8c0b_16357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c0b_16357/05_2025/8c0b_16357.map" model { file = "/net/cci-nas-00/data/ceres_data/8c0b_16357/05_2025/8c0b_16357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c0b_16357/05_2025/8c0b_16357.cif" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.041 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: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 18928 2.51 5 N 5208 2.21 5 O 5576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29816 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3727 Classifications: {'peptide': 471} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 447} Chain breaks: 2 Chain: "B" Number of atoms: 3727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3727 Classifications: {'peptide': 471} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 447} Chain breaks: 2 Chain: "C" Number of atoms: 3727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3727 Classifications: {'peptide': 471} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 447} Chain breaks: 2 Chain: "D" Number of atoms: 3727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3727 Classifications: {'peptide': 471} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 447} Chain breaks: 2 Chain: "E" Number of atoms: 3727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3727 Classifications: {'peptide': 471} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 447} Chain breaks: 2 Chain: "F" Number of atoms: 3727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3727 Classifications: {'peptide': 471} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 447} Chain breaks: 2 Chain: "G" Number of atoms: 3727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3727 Classifications: {'peptide': 471} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 447} Chain breaks: 2 Chain: "H" Number of atoms: 3727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3727 Classifications: {'peptide': 471} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 447} Chain breaks: 2 Time building chain proxies: 16.50, per 1000 atoms: 0.55 Number of scatterers: 29816 At special positions: 0 Unit cell: (153.69, 152.6, 138.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 104 16.00 O 5576 8.00 N 5208 7.00 C 18928 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.60 Conformation dependent library (CDL) restraints added in 3.5 seconds 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7072 Finding SS restraints... Secondary structure from input PDB file: 191 helices and 60 sheets defined 42.1% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.19 Creating SS restraints... Processing helix chain 'A' and resid 32 through 51 Processing helix chain 'A' and resid 54 through 82 removed outlier: 3.738A pdb=" N PHE A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 69 " --> pdb=" O MET A 65 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 109 through 114 removed outlier: 3.769A pdb=" N ASN A 114 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 134 through 137 Processing helix chain 'A' and resid 146 through 162 removed outlier: 3.549A pdb=" N SER A 150 " --> pdb=" O PHE A 146 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 184 through 187 Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 230 through 238 Processing helix chain 'A' and resid 239 through 246 Processing helix chain 'A' and resid 265 through 276 removed outlier: 4.216A pdb=" N LEU A 269 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS A 271 " --> pdb=" O ARG A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 291 removed outlier: 4.089A pdb=" N VAL A 291 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 320 removed outlier: 4.764A pdb=" N ASN A 317 " --> pdb=" O LYS A 313 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLU A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 346 Processing helix chain 'A' and resid 380 through 386 removed outlier: 3.749A pdb=" N ARG A 384 " --> pdb=" O ALA A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 404 through 413 removed outlier: 3.542A pdb=" N LEU A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 443 removed outlier: 3.807A pdb=" N LYS A 443 " --> pdb=" O SER A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 443' Processing helix chain 'A' and resid 444 through 452 removed outlier: 4.058A pdb=" N GLN A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 51 Processing helix chain 'B' and resid 54 through 82 removed outlier: 3.565A pdb=" N PHE B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 109 through 114 removed outlier: 3.790A pdb=" N ASN B 114 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 130 Processing helix chain 'B' and resid 134 through 137 Processing helix chain 'B' and resid 146 through 162 removed outlier: 3.587A pdb=" N SER B 150 " --> pdb=" O PHE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 183 removed outlier: 4.779A pdb=" N GLN B 177 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ASP B 178 " --> pdb=" O ASN B 174 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 181 " --> pdb=" O GLN B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 187 Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 230 through 238 Processing helix chain 'B' and resid 239 through 246 Processing helix chain 'B' and resid 265 through 276 removed outlier: 4.057A pdb=" N LEU B 269 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS B 271 " --> pdb=" O ARG B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 291 removed outlier: 4.152A pdb=" N VAL B 291 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 320 Processing helix chain 'B' and resid 337 through 346 Processing helix chain 'B' and resid 380 through 386 removed outlier: 3.606A pdb=" N ARG B 384 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 399 Processing helix chain 'B' and resid 404 through 413 removed outlier: 3.558A pdb=" N LEU B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 443 removed outlier: 3.795A pdb=" N LYS B 443 " --> pdb=" O SER B 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 440 through 443' Processing helix chain 'B' and resid 444 through 452 removed outlier: 4.041A pdb=" N GLN B 449 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 51 Processing helix chain 'C' and resid 54 through 82 removed outlier: 3.650A pdb=" N PHE C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 109 through 114 removed outlier: 3.649A pdb=" N ASN C 114 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 Processing helix chain 'C' and resid 134 through 137 Processing helix chain 'C' and resid 146 through 162 removed outlier: 3.589A pdb=" N SER C 150 " --> pdb=" O PHE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 183 removed outlier: 3.538A pdb=" N SER C 181 " --> pdb=" O GLN C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 187 Processing helix chain 'C' and resid 219 through 221 No H-bonds generated for 'chain 'C' and resid 219 through 221' Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 230 through 238 Processing helix chain 'C' and resid 239 through 246 Processing helix chain 'C' and resid 265 through 276 removed outlier: 4.015A pdb=" N LEU C 269 " --> pdb=" O ASP C 265 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN C 270 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS C 271 " --> pdb=" O ARG C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 291 removed outlier: 4.129A pdb=" N VAL C 291 " --> pdb=" O LYS C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 320 Processing helix chain 'C' and resid 337 through 346 Processing helix chain 'C' and resid 380 through 386 removed outlier: 3.713A pdb=" N ARG C 384 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 399 Processing helix chain 'C' and resid 404 through 413 removed outlier: 3.581A pdb=" N LEU C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 409 " --> pdb=" O CYS C 405 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 443 removed outlier: 3.788A pdb=" N LYS C 443 " --> pdb=" O SER C 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 440 through 443' Processing helix chain 'C' and resid 444 through 452 removed outlier: 4.070A pdb=" N GLN C 449 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS C 450 " --> pdb=" O SER C 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 51 Processing helix chain 'D' and resid 54 through 82 removed outlier: 3.599A pdb=" N PHE D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 94 through 96 No H-bonds generated for 'chain 'D' and resid 94 through 96' Processing helix chain 'D' and resid 109 through 114 removed outlier: 3.882A pdb=" N ASN D 114 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 130 Processing helix chain 'D' and resid 134 through 137 Processing helix chain 'D' and resid 146 through 160 removed outlier: 3.514A pdb=" N SER D 150 " --> pdb=" O PHE D 146 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR D 160 " --> pdb=" O HIS D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 183 removed outlier: 4.766A pdb=" N GLN D 177 " --> pdb=" O PHE D 173 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASP D 178 " --> pdb=" O ASN D 174 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER D 181 " --> pdb=" O GLN D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 187 Processing helix chain 'D' and resid 219 through 221 No H-bonds generated for 'chain 'D' and resid 219 through 221' Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'D' and resid 230 through 238 Processing helix chain 'D' and resid 239 through 246 Processing helix chain 'D' and resid 265 through 276 removed outlier: 4.080A pdb=" N LEU D 269 " --> pdb=" O ASP D 265 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS D 271 " --> pdb=" O ARG D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 291 removed outlier: 4.103A pdb=" N VAL D 291 " --> pdb=" O LYS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 320 Processing helix chain 'D' and resid 337 through 346 Processing helix chain 'D' and resid 380 through 386 removed outlier: 3.724A pdb=" N ARG D 384 " --> pdb=" O ALA D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 399 Processing helix chain 'D' and resid 404 through 413 removed outlier: 3.544A pdb=" N LEU D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 443 removed outlier: 3.805A pdb=" N LYS D 443 " --> pdb=" O SER D 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 440 through 443' Processing helix chain 'D' and resid 444 through 452 removed outlier: 4.051A pdb=" N GLN D 449 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS D 450 " --> pdb=" O SER D 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 51 Processing helix chain 'E' and resid 54 through 82 removed outlier: 3.629A pdb=" N PHE E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA E 70 " --> pdb=" O ASP E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 94 through 96 No H-bonds generated for 'chain 'E' and resid 94 through 96' Processing helix chain 'E' and resid 102 through 104 No H-bonds generated for 'chain 'E' and resid 102 through 104' Processing helix chain 'E' and resid 109 through 114 removed outlier: 3.893A pdb=" N ASN E 114 " --> pdb=" O GLU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 130 Processing helix chain 'E' and resid 134 through 137 Processing helix chain 'E' and resid 146 through 162 removed outlier: 3.624A pdb=" N SER E 150 " --> pdb=" O PHE E 146 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 183 removed outlier: 4.752A pdb=" N GLN E 177 " --> pdb=" O PHE E 173 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ASP E 178 " --> pdb=" O ASN E 174 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER E 181 " --> pdb=" O GLN E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 187 Processing helix chain 'E' and resid 219 through 221 No H-bonds generated for 'chain 'E' and resid 219 through 221' Processing helix chain 'E' and resid 227 through 229 No H-bonds generated for 'chain 'E' and resid 227 through 229' Processing helix chain 'E' and resid 230 through 238 removed outlier: 3.503A pdb=" N TYR E 236 " --> pdb=" O PHE E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 246 Processing helix chain 'E' and resid 265 through 276 removed outlier: 4.039A pdb=" N LEU E 269 " --> pdb=" O ASP E 265 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN E 270 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS E 271 " --> pdb=" O ARG E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 291 removed outlier: 4.138A pdb=" N VAL E 291 " --> pdb=" O LYS E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 320 Processing helix chain 'E' and resid 337 through 346 Processing helix chain 'E' and resid 380 through 386 removed outlier: 3.659A pdb=" N ARG E 384 " --> pdb=" O ALA E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 399 Processing helix chain 'E' and resid 404 through 413 removed outlier: 3.589A pdb=" N LEU E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 443 removed outlier: 3.835A pdb=" N LYS E 443 " --> pdb=" O SER E 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 440 through 443' Processing helix chain 'E' and resid 444 through 452 removed outlier: 4.069A pdb=" N GLN E 449 " --> pdb=" O VAL E 445 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS E 450 " --> pdb=" O SER E 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 51 Processing helix chain 'F' and resid 54 through 82 removed outlier: 3.569A pdb=" N PHE F 68 " --> pdb=" O GLU F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'F' and resid 94 through 96 No H-bonds generated for 'chain 'F' and resid 94 through 96' Processing helix chain 'F' and resid 102 through 104 No H-bonds generated for 'chain 'F' and resid 102 through 104' Processing helix chain 'F' and resid 109 through 114 removed outlier: 3.853A pdb=" N ASN F 114 " --> pdb=" O GLU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 130 Processing helix chain 'F' and resid 134 through 137 Processing helix chain 'F' and resid 146 through 162 removed outlier: 3.566A pdb=" N SER F 150 " --> pdb=" O PHE F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 183 removed outlier: 4.789A pdb=" N GLN F 177 " --> pdb=" O PHE F 173 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ASP F 178 " --> pdb=" O ASN F 174 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER F 181 " --> pdb=" O GLN F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 187 Processing helix chain 'F' and resid 219 through 221 No H-bonds generated for 'chain 'F' and resid 219 through 221' Processing helix chain 'F' and resid 227 through 229 No H-bonds generated for 'chain 'F' and resid 227 through 229' Processing helix chain 'F' and resid 230 through 238 removed outlier: 3.536A pdb=" N TYR F 236 " --> pdb=" O PHE F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 246 Processing helix chain 'F' and resid 265 through 276 removed outlier: 4.081A pdb=" N LEU F 269 " --> pdb=" O ASP F 265 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN F 270 " --> pdb=" O THR F 266 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS F 271 " --> pdb=" O ARG F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 291 removed outlier: 4.084A pdb=" N VAL F 291 " --> pdb=" O LYS F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 320 Processing helix chain 'F' and resid 337 through 346 Processing helix chain 'F' and resid 380 through 386 removed outlier: 3.728A pdb=" N ARG F 384 " --> pdb=" O ALA F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 399 Processing helix chain 'F' and resid 404 through 413 removed outlier: 3.583A pdb=" N LEU F 408 " --> pdb=" O THR F 404 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU F 410 " --> pdb=" O SER F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 443 removed outlier: 3.814A pdb=" N LYS F 443 " --> pdb=" O SER F 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 440 through 443' Processing helix chain 'F' and resid 444 through 452 removed outlier: 4.029A pdb=" N GLN F 449 " --> pdb=" O VAL F 445 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS F 450 " --> pdb=" O SER F 446 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 51 Processing helix chain 'G' and resid 54 through 82 removed outlier: 3.673A pdb=" N PHE G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 90 Processing helix chain 'G' and resid 94 through 96 No H-bonds generated for 'chain 'G' and resid 94 through 96' Processing helix chain 'G' and resid 102 through 104 No H-bonds generated for 'chain 'G' and resid 102 through 104' Processing helix chain 'G' and resid 109 through 114 removed outlier: 3.758A pdb=" N ASN G 114 " --> pdb=" O GLU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 130 Processing helix chain 'G' and resid 134 through 137 Processing helix chain 'G' and resid 146 through 162 removed outlier: 3.588A pdb=" N SER G 150 " --> pdb=" O PHE G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 183 removed outlier: 4.751A pdb=" N GLN G 177 " --> pdb=" O PHE G 173 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ASP G 178 " --> pdb=" O ASN G 174 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER G 181 " --> pdb=" O GLN G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 187 Processing helix chain 'G' and resid 219 through 221 No H-bonds generated for 'chain 'G' and resid 219 through 221' Processing helix chain 'G' and resid 227 through 229 No H-bonds generated for 'chain 'G' and resid 227 through 229' Processing helix chain 'G' and resid 230 through 238 Processing helix chain 'G' and resid 239 through 246 Processing helix chain 'G' and resid 265 through 276 removed outlier: 4.051A pdb=" N LEU G 269 " --> pdb=" O ASP G 265 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN G 270 " --> pdb=" O THR G 266 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N HIS G 271 " --> pdb=" O ARG G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 291 removed outlier: 4.087A pdb=" N VAL G 291 " --> pdb=" O LYS G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 315 through 320 Processing helix chain 'G' and resid 337 through 346 Processing helix chain 'G' and resid 380 through 386 removed outlier: 3.720A pdb=" N ARG G 384 " --> pdb=" O ALA G 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 395 through 399 Processing helix chain 'G' and resid 404 through 413 removed outlier: 3.559A pdb=" N LEU G 408 " --> pdb=" O THR G 404 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU G 410 " --> pdb=" O SER G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 443 removed outlier: 3.836A pdb=" N LYS G 443 " --> pdb=" O SER G 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 440 through 443' Processing helix chain 'G' and resid 444 through 452 removed outlier: 4.030A pdb=" N GLN G 449 " --> pdb=" O VAL G 445 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS G 450 " --> pdb=" O SER G 446 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 51 Processing helix chain 'H' and resid 54 through 82 removed outlier: 3.581A pdb=" N PHE H 68 " --> pdb=" O GLU H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 94 through 96 No H-bonds generated for 'chain 'H' and resid 94 through 96' Processing helix chain 'H' and resid 102 through 104 No H-bonds generated for 'chain 'H' and resid 102 through 104' Processing helix chain 'H' and resid 109 through 114 removed outlier: 3.775A pdb=" N ASN H 114 " --> pdb=" O GLU H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 130 Processing helix chain 'H' and resid 134 through 137 Processing helix chain 'H' and resid 146 through 162 removed outlier: 3.561A pdb=" N SER H 150 " --> pdb=" O PHE H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 183 removed outlier: 4.737A pdb=" N GLN H 177 " --> pdb=" O PHE H 173 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ASP H 178 " --> pdb=" O ASN H 174 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER H 181 " --> pdb=" O GLN H 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 187 Processing helix chain 'H' and resid 219 through 221 No H-bonds generated for 'chain 'H' and resid 219 through 221' Processing helix chain 'H' and resid 227 through 229 No H-bonds generated for 'chain 'H' and resid 227 through 229' Processing helix chain 'H' and resid 230 through 238 Processing helix chain 'H' and resid 239 through 246 Processing helix chain 'H' and resid 265 through 276 removed outlier: 4.069A pdb=" N LEU H 269 " --> pdb=" O ASP H 265 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN H 270 " --> pdb=" O THR H 266 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS H 271 " --> pdb=" O ARG H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 291 removed outlier: 4.091A pdb=" N VAL H 291 " --> pdb=" O LYS H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 315 through 320 Processing helix chain 'H' and resid 337 through 346 Processing helix chain 'H' and resid 380 through 386 removed outlier: 3.724A pdb=" N ARG H 384 " --> pdb=" O ALA H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 395 through 399 Processing helix chain 'H' and resid 404 through 413 removed outlier: 3.591A pdb=" N LEU H 408 " --> pdb=" O THR H 404 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU H 410 " --> pdb=" O SER H 406 " (cutoff:3.500A) Processing helix chain 'H' and resid 440 through 443 removed outlier: 3.823A pdb=" N LYS H 443 " --> pdb=" O SER H 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 440 through 443' Processing helix chain 'H' and resid 444 through 452 removed outlier: 4.051A pdb=" N GLN H 449 " --> pdb=" O VAL H 445 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS H 450 " --> pdb=" O SER H 446 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 98 through 100 removed outlier: 6.847A pdb=" N VAL A 99 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET A 281 " --> pdb=" O HIS A 390 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASN A 332 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR A 284 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR A 330 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N ASN A 331 " --> pdb=" O ASN A 256 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ASN A 256 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 255 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 121 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N VAL A 168 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL A 118 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N MET A 170 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS A 120 " --> pdb=" O MET A 170 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE A 194 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 169 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 196 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 139 through 141 removed outlier: 3.897A pdb=" N ARG A 141 " --> pdb=" O MET A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 201 through 202 removed outlier: 3.656A pdb=" N TYR A 201 " --> pdb=" O TYR A 224 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 204 through 205 removed outlier: 3.793A pdb=" N ILE A 204 " --> pdb=" O TYR A 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 295 through 297 Processing sheet with id=AA6, first strand: chain 'A' and resid 416 through 419 removed outlier: 4.125A pdb=" N ARG A 417 " --> pdb=" O VAL A 424 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 424 " --> pdb=" O ARG A 417 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 435 through 438 removed outlier: 6.511A pdb=" N VAL A 435 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ILE A 466 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LYS A 437 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N VAL A 482 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU A 464 " --> pdb=" O VAL A 482 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE A 484 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE A 466 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ALA A 486 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR A 477 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N GLU A 501 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LYS A 479 " --> pdb=" O GLU A 501 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N CYS A 503 " --> pdb=" O LYS A 479 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR A 481 " --> pdb=" O CYS A 503 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N VAL A 505 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE A 483 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N GLY A 507 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL A 485 " --> pdb=" O GLY A 507 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N LEU A 509 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR H 477 " --> pdb=" O VAL H 499 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLU H 501 " --> pdb=" O THR H 477 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYS H 479 " --> pdb=" O GLU H 501 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N CYS H 503 " --> pdb=" O LYS H 479 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR H 481 " --> pdb=" O CYS H 503 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL H 505 " --> pdb=" O THR H 481 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE H 483 " --> pdb=" O VAL H 505 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N GLY H 507 " --> pdb=" O ILE H 483 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL H 485 " --> pdb=" O GLY H 507 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N LEU H 509 " --> pdb=" O VAL H 485 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL H 482 " --> pdb=" O ASP H 462 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU H 464 " --> pdb=" O VAL H 482 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE H 484 " --> pdb=" O LEU H 464 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE H 466 " --> pdb=" O ILE H 484 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ALA H 486 " --> pdb=" O ILE H 466 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL H 435 " --> pdb=" O LEU H 464 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ILE H 466 " --> pdb=" O VAL H 435 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS H 437 " --> pdb=" O ILE H 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 469 through 472 Processing sheet with id=AA9, first strand: chain 'B' and resid 98 through 100 removed outlier: 6.866A pdb=" N VAL B 99 " --> pdb=" O ASN B 393 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET B 281 " --> pdb=" O HIS B 390 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN B 332 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N THR B 284 " --> pdb=" O THR B 330 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR B 330 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N ASN B 331 " --> pdb=" O ASN B 256 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ASN B 256 " --> pdb=" O ASN B 331 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 121 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N VAL B 168 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL B 118 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N MET B 170 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LYS B 120 " --> pdb=" O MET B 170 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE B 194 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE B 196 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 139 through 141 removed outlier: 3.839A pdb=" N ARG B 141 " --> pdb=" O MET B 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 201 through 202 removed outlier: 3.649A pdb=" N TYR B 201 " --> pdb=" O TYR B 224 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 204 through 205 removed outlier: 3.964A pdb=" N ILE B 204 " --> pdb=" O TYR B 373 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 295 through 297 Processing sheet with id=AB5, first strand: chain 'B' and resid 416 through 419 removed outlier: 4.245A pdb=" N ARG B 417 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL B 424 " --> pdb=" O ARG B 417 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 435 through 438 removed outlier: 6.534A pdb=" N VAL B 435 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ILE B 466 " --> pdb=" O VAL B 435 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS B 437 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL B 482 " --> pdb=" O ASP B 462 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU B 464 " --> pdb=" O VAL B 482 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE B 484 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE B 466 " --> pdb=" O ILE B 484 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ALA B 486 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR B 477 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N GLU B 501 " --> pdb=" O THR B 477 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LYS B 479 " --> pdb=" O GLU B 501 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N CYS B 503 " --> pdb=" O LYS B 479 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR B 481 " --> pdb=" O CYS B 503 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL B 505 " --> pdb=" O THR B 481 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE B 483 " --> pdb=" O VAL B 505 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N GLY B 507 " --> pdb=" O ILE B 483 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL B 485 " --> pdb=" O GLY B 507 " (cutoff:3.500A) removed outlier: 9.201A pdb=" N LEU B 509 " --> pdb=" O VAL B 485 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR G 477 " --> pdb=" O VAL G 499 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N GLU G 501 " --> pdb=" O THR G 477 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS G 479 " --> pdb=" O GLU G 501 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N CYS G 503 " --> pdb=" O LYS G 479 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR G 481 " --> pdb=" O CYS G 503 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL G 505 " --> pdb=" O THR G 481 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE G 483 " --> pdb=" O VAL G 505 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N GLY G 507 " --> pdb=" O ILE G 483 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL G 485 " --> pdb=" O GLY G 507 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N LEU G 509 " --> pdb=" O VAL G 485 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL G 482 " --> pdb=" O ASP G 462 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU G 464 " --> pdb=" O VAL G 482 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE G 484 " --> pdb=" O LEU G 464 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE G 466 " --> pdb=" O ILE G 484 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ALA G 486 " --> pdb=" O ILE G 466 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL G 435 " --> pdb=" O LEU G 464 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ILE G 466 " --> pdb=" O VAL G 435 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LYS G 437 " --> pdb=" O ILE G 466 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 469 through 472 Processing sheet with id=AB8, first strand: chain 'C' and resid 98 through 100 removed outlier: 6.782A pdb=" N VAL C 99 " --> pdb=" O ASN C 393 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET C 281 " --> pdb=" O HIS C 390 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASN C 332 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N THR C 284 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR C 330 " --> pdb=" O THR C 284 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N ASN C 331 " --> pdb=" O ASN C 256 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASN C 256 " --> pdb=" O ASN C 331 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C 121 " --> pdb=" O SER C 255 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N VAL C 168 " --> pdb=" O LEU C 116 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL C 118 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N MET C 170 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LYS C 120 " --> pdb=" O MET C 170 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE C 194 " --> pdb=" O PHE C 167 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE C 196 " --> pdb=" O LEU C 169 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 139 through 141 removed outlier: 3.847A pdb=" N ARG C 141 " --> pdb=" O MET C 144 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 201 through 202 removed outlier: 3.691A pdb=" N TYR C 201 " --> pdb=" O TYR C 224 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 204 through 205 removed outlier: 3.902A pdb=" N ILE C 204 " --> pdb=" O TYR C 373 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 295 through 297 Processing sheet with id=AC4, first strand: chain 'C' and resid 416 through 419 removed outlier: 4.089A pdb=" N ARG C 417 " --> pdb=" O VAL C 424 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL C 424 " --> pdb=" O ARG C 417 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 435 through 438 removed outlier: 6.552A pdb=" N VAL C 435 " --> pdb=" O LEU C 464 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ILE C 466 " --> pdb=" O VAL C 435 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS C 437 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL C 482 " --> pdb=" O ASP C 462 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU C 464 " --> pdb=" O VAL C 482 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ILE C 484 " --> pdb=" O LEU C 464 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE C 466 " --> pdb=" O ILE C 484 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ALA C 486 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR C 477 " --> pdb=" O VAL C 499 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLU C 501 " --> pdb=" O THR C 477 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LYS C 479 " --> pdb=" O GLU C 501 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N CYS C 503 " --> pdb=" O LYS C 479 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR C 481 " --> pdb=" O CYS C 503 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL C 505 " --> pdb=" O THR C 481 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE C 483 " --> pdb=" O VAL C 505 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N GLY C 507 " --> pdb=" O ILE C 483 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL C 485 " --> pdb=" O GLY C 507 " (cutoff:3.500A) removed outlier: 9.265A pdb=" N LEU C 509 " --> pdb=" O VAL C 485 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR F 477 " --> pdb=" O VAL F 499 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLU F 501 " --> pdb=" O THR F 477 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LYS F 479 " --> pdb=" O GLU F 501 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N CYS F 503 " --> pdb=" O LYS F 479 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR F 481 " --> pdb=" O CYS F 503 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N VAL F 505 " --> pdb=" O THR F 481 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE F 483 " --> pdb=" O VAL F 505 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N GLY F 507 " --> pdb=" O ILE F 483 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL F 485 " --> pdb=" O GLY F 507 " (cutoff:3.500A) removed outlier: 9.245A pdb=" N LEU F 509 " --> pdb=" O VAL F 485 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL F 482 " --> pdb=" O ASP F 462 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU F 464 " --> pdb=" O VAL F 482 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILE F 484 " --> pdb=" O LEU F 464 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE F 466 " --> pdb=" O ILE F 484 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ALA F 486 " --> pdb=" O ILE F 466 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL F 435 " --> pdb=" O LEU F 464 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ILE F 466 " --> pdb=" O VAL F 435 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LYS F 437 " --> pdb=" O ILE F 466 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 469 through 472 Processing sheet with id=AC7, first strand: chain 'D' and resid 98 through 100 removed outlier: 6.910A pdb=" N VAL D 99 " --> pdb=" O ASN D 393 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET D 281 " --> pdb=" O HIS D 390 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN D 332 " --> pdb=" O GLU D 282 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N THR D 284 " --> pdb=" O THR D 330 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR D 330 " --> pdb=" O THR D 284 " (cutoff:3.500A) removed outlier: 9.198A pdb=" N ASN D 331 " --> pdb=" O ASN D 256 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ASN D 256 " --> pdb=" O ASN D 331 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA D 117 " --> pdb=" O PHE D 253 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N SER D 255 " --> pdb=" O ALA D 117 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL D 119 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N VAL D 168 " --> pdb=" O LEU D 116 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL D 118 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N MET D 170 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LYS D 120 " --> pdb=" O MET D 170 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE D 194 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE D 196 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 139 through 141 removed outlier: 3.879A pdb=" N ARG D 141 " --> pdb=" O MET D 144 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 201 through 202 removed outlier: 3.613A pdb=" N TYR D 201 " --> pdb=" O TYR D 224 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 204 through 205 removed outlier: 3.982A pdb=" N ILE D 204 " --> pdb=" O TYR D 373 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 295 through 297 Processing sheet with id=AD3, first strand: chain 'D' and resid 416 through 419 removed outlier: 4.098A pdb=" N ARG D 417 " --> pdb=" O VAL D 424 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL D 424 " --> pdb=" O ARG D 417 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 435 through 438 removed outlier: 6.508A pdb=" N VAL D 435 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ILE D 466 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LYS D 437 " --> pdb=" O ILE D 466 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL D 482 " --> pdb=" O ASP D 462 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU D 464 " --> pdb=" O VAL D 482 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE D 484 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE D 466 " --> pdb=" O ILE D 484 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ALA D 486 " --> pdb=" O ILE D 466 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR D 477 " --> pdb=" O VAL D 499 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLU D 501 " --> pdb=" O THR D 477 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LYS D 479 " --> pdb=" O GLU D 501 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N CYS D 503 " --> pdb=" O LYS D 479 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR D 481 " --> pdb=" O CYS D 503 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL D 505 " --> pdb=" O THR D 481 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE D 483 " --> pdb=" O VAL D 505 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N GLY D 507 " --> pdb=" O ILE D 483 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL D 485 " --> pdb=" O GLY D 507 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N LEU D 509 " --> pdb=" O VAL D 485 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR E 477 " --> pdb=" O VAL E 499 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N GLU E 501 " --> pdb=" O THR E 477 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LYS E 479 " --> pdb=" O GLU E 501 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N CYS E 503 " --> pdb=" O LYS E 479 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR E 481 " --> pdb=" O CYS E 503 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL E 505 " --> pdb=" O THR E 481 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE E 483 " --> pdb=" O VAL E 505 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N GLY E 507 " --> pdb=" O ILE E 483 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL E 485 " --> pdb=" O GLY E 507 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N LEU E 509 " --> pdb=" O VAL E 485 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL E 482 " --> pdb=" O ASP E 462 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU E 464 " --> pdb=" O VAL E 482 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE E 484 " --> pdb=" O LEU E 464 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE E 466 " --> pdb=" O ILE E 484 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ALA E 486 " --> pdb=" O ILE E 466 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL E 435 " --> pdb=" O LEU E 464 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ILE E 466 " --> pdb=" O VAL E 435 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS E 437 " --> pdb=" O ILE E 466 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 469 through 472 Processing sheet with id=AD6, first strand: chain 'E' and resid 98 through 100 removed outlier: 6.849A pdb=" N VAL E 99 " --> pdb=" O ASN E 393 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET E 281 " --> pdb=" O HIS E 390 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASN E 332 " --> pdb=" O GLU E 282 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N THR E 284 " --> pdb=" O THR E 330 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR E 330 " --> pdb=" O THR E 284 " (cutoff:3.500A) removed outlier: 9.180A pdb=" N ASN E 331 " --> pdb=" O ASN E 256 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ASN E 256 " --> pdb=" O ASN E 331 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER E 255 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU E 121 " --> pdb=" O SER E 255 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N VAL E 168 " --> pdb=" O LEU E 116 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL E 118 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N MET E 170 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS E 120 " --> pdb=" O MET E 170 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE E 194 " --> pdb=" O PHE E 167 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU E 169 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE E 196 " --> pdb=" O LEU E 169 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 139 through 141 removed outlier: 3.858A pdb=" N ARG E 141 " --> pdb=" O MET E 144 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 201 through 202 removed outlier: 3.618A pdb=" N TYR E 201 " --> pdb=" O TYR E 224 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 204 through 205 removed outlier: 3.848A pdb=" N ILE E 204 " --> pdb=" O TYR E 373 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 295 through 297 Processing sheet with id=AE2, first strand: chain 'E' and resid 416 through 419 removed outlier: 4.336A pdb=" N ARG E 417 " --> pdb=" O VAL E 424 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL E 424 " --> pdb=" O ARG E 417 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 469 through 472 Processing sheet with id=AE4, first strand: chain 'F' and resid 98 through 100 removed outlier: 6.872A pdb=" N VAL F 99 " --> pdb=" O ASN F 393 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET F 281 " --> pdb=" O HIS F 390 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ASN F 332 " --> pdb=" O GLU F 282 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N THR F 284 " --> pdb=" O THR F 330 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR F 330 " --> pdb=" O THR F 284 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N ASN F 331 " --> pdb=" O ASN F 256 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN F 256 " --> pdb=" O ASN F 331 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA F 117 " --> pdb=" O PHE F 253 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N SER F 255 " --> pdb=" O ALA F 117 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL F 119 " --> pdb=" O SER F 255 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N VAL F 168 " --> pdb=" O LEU F 116 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL F 118 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N MET F 170 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS F 120 " --> pdb=" O MET F 170 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE F 194 " --> pdb=" O PHE F 167 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU F 169 " --> pdb=" O ILE F 194 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE F 196 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 139 through 141 removed outlier: 3.914A pdb=" N ARG F 141 " --> pdb=" O MET F 144 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 201 through 202 removed outlier: 3.540A pdb=" N TYR F 201 " --> pdb=" O TYR F 224 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 204 through 205 removed outlier: 3.764A pdb=" N ILE F 204 " --> pdb=" O TYR F 373 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 295 through 297 Processing sheet with id=AE9, first strand: chain 'F' and resid 416 through 419 removed outlier: 3.795A pdb=" N ARG F 417 " --> pdb=" O VAL F 424 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL F 424 " --> pdb=" O ARG F 417 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 469 through 472 Processing sheet with id=AF2, first strand: chain 'G' and resid 98 through 100 removed outlier: 6.813A pdb=" N VAL G 99 " --> pdb=" O ASN G 393 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET G 281 " --> pdb=" O HIS G 390 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASN G 332 " --> pdb=" O GLU G 282 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N THR G 284 " --> pdb=" O THR G 330 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR G 330 " --> pdb=" O THR G 284 " (cutoff:3.500A) removed outlier: 9.200A pdb=" N ASN G 331 " --> pdb=" O ASN G 256 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ASN G 256 " --> pdb=" O ASN G 331 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA G 117 " --> pdb=" O PHE G 253 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N SER G 255 " --> pdb=" O ALA G 117 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL G 119 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N VAL G 168 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL G 118 " --> pdb=" O VAL G 168 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N MET G 170 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS G 120 " --> pdb=" O MET G 170 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE G 194 " --> pdb=" O PHE G 167 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU G 169 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE G 196 " --> pdb=" O LEU G 169 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 139 through 141 removed outlier: 3.871A pdb=" N ARG G 141 " --> pdb=" O MET G 144 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 201 through 202 removed outlier: 3.564A pdb=" N TYR G 201 " --> pdb=" O TYR G 224 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 204 through 205 removed outlier: 3.766A pdb=" N ILE G 204 " --> pdb=" O TYR G 373 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 295 through 297 Processing sheet with id=AF7, first strand: chain 'G' and resid 416 through 419 removed outlier: 4.185A pdb=" N ARG G 417 " --> pdb=" O VAL G 424 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL G 424 " --> pdb=" O ARG G 417 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 469 through 472 Processing sheet with id=AF9, first strand: chain 'H' and resid 98 through 100 removed outlier: 6.895A pdb=" N VAL H 99 " --> pdb=" O ASN H 393 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET H 281 " --> pdb=" O HIS H 390 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASN H 332 " --> pdb=" O GLU H 282 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N THR H 284 " --> pdb=" O THR H 330 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR H 330 " --> pdb=" O THR H 284 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N ASN H 331 " --> pdb=" O ASN H 256 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASN H 256 " --> pdb=" O ASN H 331 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA H 117 " --> pdb=" O PHE H 253 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N SER H 255 " --> pdb=" O ALA H 117 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL H 119 " --> pdb=" O SER H 255 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N VAL H 168 " --> pdb=" O LEU H 116 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL H 118 " --> pdb=" O VAL H 168 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N MET H 170 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS H 120 " --> pdb=" O MET H 170 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE H 194 " --> pdb=" O PHE H 167 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU H 169 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE H 196 " --> pdb=" O LEU H 169 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 139 through 141 removed outlier: 3.869A pdb=" N ARG H 141 " --> pdb=" O MET H 144 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 201 through 202 removed outlier: 3.537A pdb=" N TYR H 201 " --> pdb=" O TYR H 224 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 204 through 205 removed outlier: 3.743A pdb=" N ILE H 204 " --> pdb=" O TYR H 373 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 295 through 297 Processing sheet with id=AG5, first strand: chain 'H' and resid 416 through 419 removed outlier: 4.201A pdb=" N ARG H 417 " --> pdb=" O VAL H 424 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL H 424 " --> pdb=" O ARG H 417 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 469 through 472 1087 hydrogen bonds defined for protein. 2733 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: 13.01 Time building geometry restraints manager: 7.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9969 1.34 - 1.46: 4508 1.46 - 1.57: 15707 1.57 - 1.69: 0 1.69 - 1.81: 184 Bond restraints: 30368 Sorted by residual: bond pdb=" CA PRO E 92 " pdb=" C PRO E 92 " ideal model delta sigma weight residual 1.514 1.504 0.010 5.50e-03 3.31e+04 3.34e+00 bond pdb=" CA PHE G 325 " pdb=" CB PHE G 325 " ideal model delta sigma weight residual 1.539 1.491 0.049 4.88e-02 4.20e+02 9.96e-01 bond pdb=" CA PHE E 325 " pdb=" CB PHE E 325 " ideal model delta sigma weight residual 1.539 1.493 0.047 4.88e-02 4.20e+02 9.08e-01 bond pdb=" CA PHE F 325 " pdb=" CB PHE F 325 " ideal model delta sigma weight residual 1.539 1.493 0.046 4.88e-02 4.20e+02 9.05e-01 bond pdb=" CB PHE C 328 " pdb=" CG PHE C 328 " ideal model delta sigma weight residual 1.502 1.481 0.021 2.30e-02 1.89e+03 8.46e-01 ... (remaining 30363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 38300 1.46 - 2.92: 2300 2.92 - 4.38: 410 4.38 - 5.83: 69 5.83 - 7.29: 9 Bond angle restraints: 41088 Sorted by residual: angle pdb=" C SER F 109 " pdb=" N VAL F 110 " pdb=" CA VAL F 110 " ideal model delta sigma weight residual 120.53 126.10 -5.57 1.41e+00 5.03e-01 1.56e+01 angle pdb=" C SER B 109 " pdb=" N VAL B 110 " pdb=" CA VAL B 110 " ideal model delta sigma weight residual 120.53 125.97 -5.44 1.41e+00 5.03e-01 1.49e+01 angle pdb=" N ILE C 383 " pdb=" CA ILE C 383 " pdb=" C ILE C 383 " ideal model delta sigma weight residual 110.62 114.67 -4.05 1.14e+00 7.69e-01 1.26e+01 angle pdb=" C GLY G 105 " pdb=" N LYS G 106 " pdb=" CA LYS G 106 " ideal model delta sigma weight residual 120.87 125.99 -5.12 1.69e+00 3.50e-01 9.17e+00 angle pdb=" C ASN A 164 " pdb=" N VAL A 165 " pdb=" CA VAL A 165 " ideal model delta sigma weight residual 121.23 125.40 -4.17 1.38e+00 5.25e-01 9.12e+00 ... (remaining 41083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.47: 16923 15.47 - 30.95: 1165 30.95 - 46.42: 305 46.42 - 61.89: 119 61.89 - 77.36: 48 Dihedral angle restraints: 18560 sinusoidal: 7648 harmonic: 10912 Sorted by residual: dihedral pdb=" CD ARG E 342 " pdb=" NE ARG E 342 " pdb=" CZ ARG E 342 " pdb=" NH1 ARG E 342 " ideal model delta sinusoidal sigma weight residual 0.00 -36.57 36.57 1 1.00e+01 1.00e-02 1.89e+01 dihedral pdb=" CD ARG F 342 " pdb=" NE ARG F 342 " pdb=" CZ ARG F 342 " pdb=" NH1 ARG F 342 " ideal model delta sinusoidal sigma weight residual 0.00 -35.41 35.41 1 1.00e+01 1.00e-02 1.78e+01 dihedral pdb=" CD ARG D 342 " pdb=" NE ARG D 342 " pdb=" CZ ARG D 342 " pdb=" NH1 ARG D 342 " ideal model delta sinusoidal sigma weight residual 0.00 -34.84 34.84 1 1.00e+01 1.00e-02 1.72e+01 ... (remaining 18557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2735 0.035 - 0.070: 1172 0.070 - 0.106: 454 0.106 - 0.141: 274 0.141 - 0.176: 37 Chirality restraints: 4672 Sorted by residual: chirality pdb=" CA ILE E 252 " pdb=" N ILE E 252 " pdb=" C ILE E 252 " pdb=" CB ILE E 252 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" CA ILE F 252 " pdb=" N ILE F 252 " pdb=" C ILE F 252 " pdb=" CB ILE F 252 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CA ILE G 252 " pdb=" N ILE G 252 " pdb=" C ILE G 252 " pdb=" CB ILE G 252 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 4669 not shown) Planarity restraints: 5352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 342 " 0.501 9.50e-02 1.11e+02 2.26e-01 3.92e+01 pdb=" NE ARG E 342 " -0.047 2.00e-02 2.50e+03 pdb=" CZ ARG E 342 " 0.044 2.00e-02 2.50e+03 pdb=" NH1 ARG E 342 " -0.020 2.00e-02 2.50e+03 pdb=" NH2 ARG E 342 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 342 " -0.487 9.50e-02 1.11e+02 2.20e-01 3.70e+01 pdb=" NE ARG F 342 " 0.046 2.00e-02 2.50e+03 pdb=" CZ ARG F 342 " -0.043 2.00e-02 2.50e+03 pdb=" NH1 ARG F 342 " 0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG F 342 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 342 " -0.479 9.50e-02 1.11e+02 2.16e-01 3.59e+01 pdb=" NE ARG D 342 " 0.045 2.00e-02 2.50e+03 pdb=" CZ ARG D 342 " -0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG D 342 " 0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG D 342 " -0.000 2.00e-02 2.50e+03 ... (remaining 5349 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1016 2.72 - 3.26: 32063 3.26 - 3.81: 45017 3.81 - 4.35: 58351 4.35 - 4.90: 94600 Nonbonded interactions: 231047 Sorted by model distance: nonbonded pdb=" NE2 GLN E 97 " pdb=" OD2 ASP E 298 " model vdw 2.172 3.120 nonbonded pdb=" NE2 GLN C 97 " pdb=" OD2 ASP C 298 " model vdw 2.177 3.120 nonbonded pdb=" NE2 GLN A 97 " pdb=" OD2 ASP A 298 " model vdw 2.181 3.120 nonbonded pdb=" NE2 GLN B 97 " pdb=" OD1 ASP B 298 " model vdw 2.196 3.120 nonbonded pdb=" NE2 GLN G 97 " pdb=" OD1 ASP G 298 " model vdw 2.198 3.120 ... (remaining 231042 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.890 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: 1.080 Check model and map are aligned: 0.210 Set scattering table: 0.280 Process input model: 64.910 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.180 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 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 : 0.003 0.049 30368 Z= 0.165 Angle : 0.787 7.293 41088 Z= 0.463 Chirality : 0.052 0.176 4672 Planarity : 0.011 0.226 5352 Dihedral : 12.770 77.363 11488 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.92 % Favored : 95.86 % Rotamer: Outliers : 0.51 % Allowed : 4.58 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.13), residues: 3720 helix: -1.06 (0.14), residues: 1064 sheet: 0.08 (0.21), residues: 656 loop : -0.53 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 87 HIS 0.009 0.002 HIS E 463 PHE 0.021 0.002 PHE D 167 TYR 0.029 0.005 TYR F 373 ARG 0.050 0.004 ARG E 342 Details of bonding type rmsd hydrogen bonds : bond 0.26007 ( 1087) hydrogen bonds : angle 7.30303 ( 2733) covalent geometry : bond 0.00347 (30368) covalent geometry : angle 0.78687 (41088) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 1078 time to evaluate : 3.174 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7518 (mt-10) REVERT: A 72 PHE cc_start: 0.8715 (t80) cc_final: 0.8252 (t80) REVERT: A 102 ASP cc_start: 0.8144 (m-30) cc_final: 0.7710 (p0) REVERT: A 121 LEU cc_start: 0.7966 (mt) cc_final: 0.7737 (mt) REVERT: A 129 MET cc_start: 0.7087 (mtm) cc_final: 0.6641 (mtm) REVERT: A 135 LYS cc_start: 0.7783 (ttmt) cc_final: 0.7482 (ttmm) REVERT: A 147 LEU cc_start: 0.8444 (tp) cc_final: 0.8096 (tp) REVERT: A 170 MET cc_start: 0.7716 (ttt) cc_final: 0.7116 (ptp) REVERT: A 180 GLN cc_start: 0.8311 (mt0) cc_final: 0.8023 (mt0) REVERT: A 251 TYR cc_start: 0.6325 (m-80) cc_final: 0.6123 (m-80) REVERT: A 270 GLN cc_start: 0.8443 (tp40) cc_final: 0.8068 (tp-100) REVERT: A 280 ILE cc_start: 0.6182 (mt) cc_final: 0.5961 (mm) REVERT: A 327 TYR cc_start: 0.7280 (m-80) cc_final: 0.6922 (m-80) REVERT: A 386 PHE cc_start: 0.7591 (m-80) cc_final: 0.7171 (m-80) REVERT: A 418 LEU cc_start: 0.8284 (tp) cc_final: 0.7992 (pp) REVERT: A 425 MET cc_start: 0.7592 (ttp) cc_final: 0.7230 (ttp) REVERT: A 426 ASP cc_start: 0.8540 (t0) cc_final: 0.8135 (t0) REVERT: A 448 PHE cc_start: 0.8403 (t80) cc_final: 0.7893 (t80) REVERT: A 450 LYS cc_start: 0.8495 (ttpp) cc_final: 0.8152 (ttpp) REVERT: A 481 THR cc_start: 0.8317 (m) cc_final: 0.7878 (p) REVERT: A 491 THR cc_start: 0.8362 (m) cc_final: 0.7998 (t) REVERT: A 501 GLU cc_start: 0.7109 (tt0) cc_final: 0.6699 (tt0) REVERT: A 503 CYS cc_start: 0.7398 (p) cc_final: 0.7169 (p) REVERT: B 72 PHE cc_start: 0.8451 (t80) cc_final: 0.7806 (t80) REVERT: B 76 LEU cc_start: 0.8372 (mt) cc_final: 0.8112 (mt) REVERT: B 94 GLN cc_start: 0.7689 (mm-40) cc_final: 0.7271 (mm-40) REVERT: B 121 LEU cc_start: 0.8028 (mt) cc_final: 0.7757 (mt) REVERT: B 147 LEU cc_start: 0.8608 (tp) cc_final: 0.8274 (tp) REVERT: B 170 MET cc_start: 0.7698 (ttt) cc_final: 0.7154 (ptp) REVERT: B 185 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8246 (tmtt) REVERT: B 201 TYR cc_start: 0.8266 (m-80) cc_final: 0.7857 (m-80) REVERT: B 253 PHE cc_start: 0.7211 (t80) cc_final: 0.6945 (t80) REVERT: B 259 ASN cc_start: 0.7400 (t0) cc_final: 0.7110 (t0) REVERT: B 260 LEU cc_start: 0.8333 (mt) cc_final: 0.8122 (mp) REVERT: B 265 ASP cc_start: 0.6604 (t0) cc_final: 0.6397 (t70) REVERT: B 272 MET cc_start: 0.7739 (tpp) cc_final: 0.7442 (tpp) REVERT: B 340 ILE cc_start: 0.8870 (mt) cc_final: 0.8502 (mt) REVERT: B 386 PHE cc_start: 0.7617 (m-80) cc_final: 0.7213 (m-80) REVERT: B 387 LYS cc_start: 0.8381 (mttt) cc_final: 0.8143 (mttt) REVERT: B 415 LEU cc_start: 0.8534 (tp) cc_final: 0.8146 (tt) REVERT: B 418 LEU cc_start: 0.8369 (tp) cc_final: 0.8100 (pp) REVERT: B 425 MET cc_start: 0.7249 (ttp) cc_final: 0.6846 (ttp) REVERT: B 426 ASP cc_start: 0.8477 (t0) cc_final: 0.8043 (t0) REVERT: B 441 ASP cc_start: 0.7286 (m-30) cc_final: 0.6895 (m-30) REVERT: B 443 LYS cc_start: 0.7938 (mtpp) cc_final: 0.7645 (mttm) REVERT: B 447 ASP cc_start: 0.7116 (m-30) cc_final: 0.6912 (m-30) REVERT: B 448 PHE cc_start: 0.8420 (t80) cc_final: 0.7730 (t80) REVERT: B 450 LYS cc_start: 0.8309 (ttpp) cc_final: 0.8087 (ttpp) REVERT: B 481 THR cc_start: 0.8264 (m) cc_final: 0.7775 (p) REVERT: B 491 THR cc_start: 0.8302 (m) cc_final: 0.7886 (t) REVERT: C 72 PHE cc_start: 0.8583 (t80) cc_final: 0.7974 (t80) REVERT: C 94 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7460 (mm-40) REVERT: C 115 LYS cc_start: 0.7931 (ptpt) cc_final: 0.6890 (ptpt) REVERT: C 129 MET cc_start: 0.6927 (mtm) cc_final: 0.6535 (mtm) REVERT: C 135 LYS cc_start: 0.8078 (ttmt) cc_final: 0.7736 (ttmt) REVERT: C 153 GLN cc_start: 0.7962 (mt0) cc_final: 0.7745 (mt0) REVERT: C 170 MET cc_start: 0.7611 (ttt) cc_final: 0.6984 (ptp) REVERT: C 171 ASN cc_start: 0.7692 (m-40) cc_final: 0.7484 (p0) REVERT: C 180 GLN cc_start: 0.8216 (mt0) cc_final: 0.7869 (mt0) REVERT: C 201 TYR cc_start: 0.8249 (m-80) cc_final: 0.7496 (m-80) REVERT: C 251 TYR cc_start: 0.6629 (m-80) cc_final: 0.6083 (m-80) REVERT: C 253 PHE cc_start: 0.7537 (t80) cc_final: 0.7334 (t80) REVERT: C 259 ASN cc_start: 0.7432 (t0) cc_final: 0.7074 (t0) REVERT: C 282 GLU cc_start: 0.6668 (mt-10) cc_final: 0.6415 (mt-10) REVERT: C 340 ILE cc_start: 0.8952 (mt) cc_final: 0.8192 (mt) REVERT: C 386 PHE cc_start: 0.7788 (m-80) cc_final: 0.7532 (m-80) REVERT: C 425 MET cc_start: 0.7547 (ttp) cc_final: 0.7218 (ttp) REVERT: C 426 ASP cc_start: 0.8568 (t0) cc_final: 0.8245 (t0) REVERT: C 447 ASP cc_start: 0.7286 (m-30) cc_final: 0.7041 (m-30) REVERT: C 450 LYS cc_start: 0.8414 (ttpp) cc_final: 0.8119 (ttpp) REVERT: C 479 LYS cc_start: 0.7033 (mttt) cc_final: 0.6680 (mttm) REVERT: C 481 THR cc_start: 0.7947 (m) cc_final: 0.7493 (p) REVERT: C 501 GLU cc_start: 0.7131 (tt0) cc_final: 0.6816 (tt0) REVERT: C 503 CYS cc_start: 0.7474 (p) cc_final: 0.7261 (p) REVERT: D 72 PHE cc_start: 0.8526 (t80) cc_final: 0.7985 (t80) REVERT: D 94 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7199 (mm-40) REVERT: D 121 LEU cc_start: 0.7964 (mt) cc_final: 0.7720 (mt) REVERT: D 129 MET cc_start: 0.6917 (mtm) cc_final: 0.6526 (mtm) REVERT: D 135 LYS cc_start: 0.7926 (ttmt) cc_final: 0.7684 (tptm) REVERT: D 147 LEU cc_start: 0.8517 (tp) cc_final: 0.8033 (tp) REVERT: D 169 LEU cc_start: 0.8222 (mt) cc_final: 0.7995 (mt) REVERT: D 170 MET cc_start: 0.7552 (ttt) cc_final: 0.7074 (ptp) REVERT: D 180 GLN cc_start: 0.8149 (mt0) cc_final: 0.7774 (mt0) REVERT: D 201 TYR cc_start: 0.8210 (m-80) cc_final: 0.7479 (m-80) REVERT: D 243 LYS cc_start: 0.8962 (mttt) cc_final: 0.8710 (mttt) REVERT: D 253 PHE cc_start: 0.7571 (t80) cc_final: 0.7282 (t80) REVERT: D 260 LEU cc_start: 0.8271 (mt) cc_final: 0.7917 (mm) REVERT: D 327 TYR cc_start: 0.7383 (m-80) cc_final: 0.7077 (m-80) REVERT: D 340 ILE cc_start: 0.8926 (mt) cc_final: 0.8307 (mt) REVERT: D 374 GLN cc_start: 0.7418 (mt0) cc_final: 0.7088 (pp30) REVERT: D 386 PHE cc_start: 0.7569 (m-80) cc_final: 0.7363 (m-80) REVERT: D 387 LYS cc_start: 0.8192 (mttt) cc_final: 0.7955 (mttt) REVERT: D 425 MET cc_start: 0.7438 (ttp) cc_final: 0.7108 (ttp) REVERT: D 426 ASP cc_start: 0.8635 (t0) cc_final: 0.7712 (t0) REVERT: D 436 ILE cc_start: 0.8201 (mt) cc_final: 0.7385 (mt) REVERT: D 448 PHE cc_start: 0.8540 (t80) cc_final: 0.7970 (t80) REVERT: D 452 ILE cc_start: 0.9029 (mt) cc_final: 0.8788 (mm) REVERT: D 479 LYS cc_start: 0.7051 (mttt) cc_final: 0.6798 (mttm) REVERT: D 481 THR cc_start: 0.8169 (m) cc_final: 0.7719 (p) REVERT: D 491 THR cc_start: 0.8321 (m) cc_final: 0.7948 (p) REVERT: D 492 ILE cc_start: 0.7947 (mt) cc_final: 0.7373 (tt) REVERT: E 41 MET cc_start: 0.8051 (tpp) cc_final: 0.7803 (mmm) REVERT: E 72 PHE cc_start: 0.8561 (t80) cc_final: 0.7852 (t80) REVERT: E 76 LEU cc_start: 0.8427 (mt) cc_final: 0.8128 (mt) REVERT: E 116 LEU cc_start: 0.8407 (tp) cc_final: 0.8121 (tp) REVERT: E 121 LEU cc_start: 0.8121 (mt) cc_final: 0.7579 (mt) REVERT: E 129 MET cc_start: 0.7185 (mtm) cc_final: 0.6539 (mtm) REVERT: E 135 LYS cc_start: 0.7842 (ttmt) cc_final: 0.7495 (tptm) REVERT: E 170 MET cc_start: 0.7718 (ttt) cc_final: 0.7082 (ptp) REVERT: E 180 GLN cc_start: 0.8255 (mt0) cc_final: 0.7671 (mt0) REVERT: E 201 TYR cc_start: 0.8098 (m-80) cc_final: 0.7610 (m-80) REVERT: E 242 ASP cc_start: 0.8852 (m-30) cc_final: 0.8558 (t0) REVERT: E 253 PHE cc_start: 0.7433 (t80) cc_final: 0.7095 (t80) REVERT: E 259 ASN cc_start: 0.7632 (t0) cc_final: 0.7357 (t0) REVERT: E 270 GLN cc_start: 0.8549 (tp40) cc_final: 0.8320 (tp-100) REVERT: E 272 MET cc_start: 0.7843 (tpp) cc_final: 0.7599 (tpp) REVERT: E 340 ILE cc_start: 0.8986 (mt) cc_final: 0.8394 (mt) REVERT: E 386 PHE cc_start: 0.7574 (m-80) cc_final: 0.7198 (m-80) REVERT: E 425 MET cc_start: 0.7291 (ttp) cc_final: 0.6921 (ttp) REVERT: E 426 ASP cc_start: 0.8559 (t0) cc_final: 0.8040 (t0) REVERT: E 441 ASP cc_start: 0.7212 (m-30) cc_final: 0.6747 (m-30) REVERT: E 443 LYS cc_start: 0.7957 (mtpp) cc_final: 0.7544 (mttm) REVERT: E 450 LYS cc_start: 0.8391 (ttpp) cc_final: 0.8162 (ttpp) REVERT: E 474 ARG cc_start: 0.7120 (ptp-110) cc_final: 0.6881 (ptp-110) REVERT: E 481 THR cc_start: 0.8204 (m) cc_final: 0.7683 (p) REVERT: E 491 THR cc_start: 0.8234 (m) cc_final: 0.7910 (t) REVERT: E 501 GLU cc_start: 0.7140 (tt0) cc_final: 0.6773 (tt0) REVERT: E 503 CYS cc_start: 0.7471 (p) cc_final: 0.7220 (p) REVERT: F 72 PHE cc_start: 0.8470 (t80) cc_final: 0.7631 (t80) REVERT: F 102 ASP cc_start: 0.7943 (m-30) cc_final: 0.7545 (p0) REVERT: F 115 LYS cc_start: 0.8024 (ptpt) cc_final: 0.6546 (ptpt) REVERT: F 116 LEU cc_start: 0.8450 (tp) cc_final: 0.8149 (tp) REVERT: F 121 LEU cc_start: 0.7997 (mt) cc_final: 0.7610 (mt) REVERT: F 129 MET cc_start: 0.7136 (mtm) cc_final: 0.6801 (mtm) REVERT: F 167 PHE cc_start: 0.7539 (t80) cc_final: 0.7246 (t80) REVERT: F 170 MET cc_start: 0.7640 (ttt) cc_final: 0.7149 (ptp) REVERT: F 171 ASN cc_start: 0.7665 (m-40) cc_final: 0.7299 (p0) REVERT: F 180 GLN cc_start: 0.8414 (mt0) cc_final: 0.7861 (mt0) REVERT: F 201 TYR cc_start: 0.8214 (m-80) cc_final: 0.7438 (m-80) REVERT: F 251 TYR cc_start: 0.6463 (m-80) cc_final: 0.5718 (m-80) REVERT: F 253 PHE cc_start: 0.7649 (t80) cc_final: 0.7275 (t80) REVERT: F 259 ASN cc_start: 0.7612 (t0) cc_final: 0.7272 (t0) REVERT: F 286 LYS cc_start: 0.7458 (mttm) cc_final: 0.7173 (mttm) REVERT: F 340 ILE cc_start: 0.8761 (mt) cc_final: 0.8521 (mt) REVERT: F 374 GLN cc_start: 0.7304 (mt0) cc_final: 0.6747 (pp30) REVERT: F 386 PHE cc_start: 0.7480 (m-80) cc_final: 0.7234 (m-80) REVERT: F 387 LYS cc_start: 0.8011 (mttt) cc_final: 0.7782 (mttt) REVERT: F 425 MET cc_start: 0.7606 (ttp) cc_final: 0.7177 (ttp) REVERT: F 426 ASP cc_start: 0.8598 (t0) cc_final: 0.8372 (t0) REVERT: F 441 ASP cc_start: 0.7128 (m-30) cc_final: 0.6622 (m-30) REVERT: F 443 LYS cc_start: 0.7936 (mtpp) cc_final: 0.7654 (mttm) REVERT: F 444 LYS cc_start: 0.7646 (mtpt) cc_final: 0.7045 (ptpp) REVERT: F 447 ASP cc_start: 0.7645 (m-30) cc_final: 0.7313 (m-30) REVERT: F 450 LYS cc_start: 0.8385 (ttpp) cc_final: 0.8048 (ttpp) REVERT: F 481 THR cc_start: 0.7989 (m) cc_final: 0.7482 (p) REVERT: F 491 THR cc_start: 0.8295 (m) cc_final: 0.7980 (t) REVERT: F 501 GLU cc_start: 0.6926 (tt0) cc_final: 0.6498 (tt0) REVERT: F 503 CYS cc_start: 0.7450 (p) cc_final: 0.7235 (p) REVERT: G 72 PHE cc_start: 0.8558 (t80) cc_final: 0.7813 (t80) REVERT: G 121 LEU cc_start: 0.8115 (mt) cc_final: 0.7863 (mt) REVERT: G 129 MET cc_start: 0.6910 (mtm) cc_final: 0.6281 (mtm) REVERT: G 146 PHE cc_start: 0.7567 (m-80) cc_final: 0.7336 (m-10) REVERT: G 147 LEU cc_start: 0.8562 (tp) cc_final: 0.8178 (tp) REVERT: G 170 MET cc_start: 0.7695 (ttt) cc_final: 0.7215 (ptp) REVERT: G 180 GLN cc_start: 0.8199 (mt0) cc_final: 0.7832 (mt0) REVERT: G 201 TYR cc_start: 0.8264 (m-80) cc_final: 0.7397 (m-80) REVERT: G 243 LYS cc_start: 0.8896 (mttt) cc_final: 0.8609 (mttt) REVERT: G 253 PHE cc_start: 0.7707 (t80) cc_final: 0.7505 (t80) REVERT: G 259 ASN cc_start: 0.7668 (t0) cc_final: 0.7375 (t0) REVERT: G 272 MET cc_start: 0.7682 (tpp) cc_final: 0.7334 (tpp) REVERT: G 326 LYS cc_start: 0.7670 (ptpt) cc_final: 0.7069 (mmtm) REVERT: G 340 ILE cc_start: 0.9084 (mt) cc_final: 0.8280 (mt) REVERT: G 386 PHE cc_start: 0.7293 (m-80) cc_final: 0.6840 (m-80) REVERT: G 387 LYS cc_start: 0.7955 (mttt) cc_final: 0.7695 (mtmm) REVERT: G 403 LYS cc_start: 0.7806 (mmtt) cc_final: 0.7332 (tppt) REVERT: G 425 MET cc_start: 0.7442 (ttp) cc_final: 0.7027 (ttp) REVERT: G 426 ASP cc_start: 0.8627 (t0) cc_final: 0.8300 (t0) REVERT: G 443 LYS cc_start: 0.8001 (mtpp) cc_final: 0.7743 (mtmm) REVERT: G 444 LYS cc_start: 0.7585 (mtpt) cc_final: 0.6933 (ptpp) REVERT: G 447 ASP cc_start: 0.7722 (m-30) cc_final: 0.7464 (m-30) REVERT: G 481 THR cc_start: 0.8168 (m) cc_final: 0.7661 (p) REVERT: G 491 THR cc_start: 0.8293 (m) cc_final: 0.8001 (p) REVERT: G 501 GLU cc_start: 0.6906 (tt0) cc_final: 0.6493 (tt0) REVERT: G 503 CYS cc_start: 0.7400 (p) cc_final: 0.7118 (p) REVERT: H 41 MET cc_start: 0.7526 (tpp) cc_final: 0.7259 (tpp) REVERT: H 72 PHE cc_start: 0.8804 (t80) cc_final: 0.8082 (t80) REVERT: H 74 ARG cc_start: 0.8664 (mtm-85) cc_final: 0.8449 (mtm180) REVERT: H 116 LEU cc_start: 0.8445 (tp) cc_final: 0.8237 (tp) REVERT: H 121 LEU cc_start: 0.7989 (mt) cc_final: 0.7638 (mt) REVERT: H 129 MET cc_start: 0.7169 (mtm) cc_final: 0.6646 (mtm) REVERT: H 169 LEU cc_start: 0.8257 (mt) cc_final: 0.8033 (mt) REVERT: H 170 MET cc_start: 0.7667 (ttt) cc_final: 0.7308 (ptp) REVERT: H 180 GLN cc_start: 0.8197 (mt0) cc_final: 0.7872 (mt0) REVERT: H 184 LYS cc_start: 0.8560 (mttp) cc_final: 0.8359 (mmtm) REVERT: H 185 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7976 (ptmt) REVERT: H 201 TYR cc_start: 0.8310 (m-80) cc_final: 0.7971 (m-80) REVERT: H 259 ASN cc_start: 0.7633 (t0) cc_final: 0.7307 (t0) REVERT: H 272 MET cc_start: 0.7688 (tpp) cc_final: 0.7357 (tpp) REVERT: H 327 TYR cc_start: 0.7333 (m-80) cc_final: 0.7009 (m-80) REVERT: H 340 ILE cc_start: 0.9035 (mt) cc_final: 0.8626 (mt) REVERT: H 403 LYS cc_start: 0.7781 (mmtt) cc_final: 0.7483 (mmmt) REVERT: H 415 LEU cc_start: 0.8444 (tp) cc_final: 0.8091 (tp) REVERT: H 418 LEU cc_start: 0.8395 (tp) cc_final: 0.8183 (tp) REVERT: H 425 MET cc_start: 0.7379 (ttp) cc_final: 0.6920 (ttp) REVERT: H 426 ASP cc_start: 0.8594 (t0) cc_final: 0.7458 (t0) REVERT: H 444 LYS cc_start: 0.7731 (mtpt) cc_final: 0.7455 (mtmm) REVERT: H 450 LYS cc_start: 0.8349 (ttpp) cc_final: 0.7966 (ttpp) REVERT: H 481 THR cc_start: 0.8317 (m) cc_final: 0.7834 (p) REVERT: H 491 THR cc_start: 0.8379 (m) cc_final: 0.8141 (t) outliers start: 17 outliers final: 9 residues processed: 1080 average time/residue: 0.5014 time to fit residues: 816.1472 Evaluate side-chains 992 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 981 time to evaluate : 3.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 185 LYS Chi-restraints excluded: chain E residue 161 TYR Chi-restraints excluded: chain F residue 161 TYR Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain G residue 161 TYR Chi-restraints excluded: chain G residue 185 LYS Chi-restraints excluded: chain H residue 185 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 5.9990 chunk 284 optimal weight: 8.9990 chunk 158 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 294 optimal weight: 0.2980 chunk 114 optimal weight: 0.9990 chunk 179 optimal weight: 0.7980 chunk 219 optimal weight: 5.9990 chunk 341 optimal weight: 0.6980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 GLN A 463 HIS B 153 GLN B 463 HIS C 374 GLN C 463 HIS D 153 GLN D 374 GLN D 463 HIS E 374 GLN E 463 HIS F 259 ASN F 374 GLN F 463 HIS G 158 ASN G 190 ASN G 259 ASN G 374 GLN G 385 HIS G 463 HIS H 374 GLN H 385 HIS H 463 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.185119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.143950 restraints weight = 55268.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.149538 restraints weight = 30648.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.153160 restraints weight = 19810.340| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30368 Z= 0.144 Angle : 0.697 10.211 41088 Z= 0.361 Chirality : 0.048 0.169 4672 Planarity : 0.005 0.056 5352 Dihedral : 4.813 48.105 4090 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.54 % Allowed : 11.72 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.14), residues: 3720 helix: -0.18 (0.15), residues: 1144 sheet: 0.32 (0.20), residues: 696 loop : 0.25 (0.15), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP F 87 HIS 0.006 0.001 HIS F 315 PHE 0.030 0.002 PHE G 232 TYR 0.024 0.002 TYR B 224 ARG 0.008 0.001 ARG B 60 Details of bonding type rmsd hydrogen bonds : bond 0.06189 ( 1087) hydrogen bonds : angle 5.46748 ( 2733) covalent geometry : bond 0.00293 (30368) covalent geometry : angle 0.69720 (41088) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 1047 time to evaluate : 2.944 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: 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: 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 58 ARG cc_start: 0.8122 (mtt-85) cc_final: 0.7896 (mpt-90) REVERT: A 64 GLU cc_start: 0.8339 (tt0) cc_final: 0.7999 (tt0) REVERT: A 72 PHE cc_start: 0.8627 (t80) cc_final: 0.8230 (t80) REVERT: A 78 ASP cc_start: 0.7279 (m-30) cc_final: 0.6739 (m-30) REVERT: A 89 ARG cc_start: 0.8673 (mmm-85) cc_final: 0.8418 (mtp85) REVERT: A 115 LYS cc_start: 0.8080 (mtmm) cc_final: 0.7799 (mtmm) REVERT: A 129 MET cc_start: 0.6924 (mtm) cc_final: 0.6467 (mtm) REVERT: A 135 LYS cc_start: 0.7621 (ttmt) cc_final: 0.7406 (ttmm) REVERT: A 179 THR cc_start: 0.8504 (m) cc_final: 0.8123 (p) REVERT: A 185 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8258 (tmmt) REVERT: A 222 ASP cc_start: 0.8155 (m-30) cc_final: 0.7824 (m-30) REVERT: A 253 PHE cc_start: 0.7290 (t80) cc_final: 0.6946 (t80) REVERT: A 259 ASN cc_start: 0.7562 (t0) cc_final: 0.7266 (t0) REVERT: A 280 ILE cc_start: 0.6081 (mt) cc_final: 0.5835 (mm) REVERT: A 341 LYS cc_start: 0.9057 (tttt) cc_final: 0.8777 (ttpp) REVERT: A 386 PHE cc_start: 0.7474 (m-80) cc_final: 0.7233 (m-80) REVERT: A 400 LEU cc_start: 0.8299 (tp) cc_final: 0.8052 (tt) REVERT: A 410 LEU cc_start: 0.8128 (tp) cc_final: 0.7928 (tt) REVERT: A 425 MET cc_start: 0.7499 (ttp) cc_final: 0.7163 (ttp) REVERT: A 426 ASP cc_start: 0.8623 (t0) cc_final: 0.8047 (t0) REVERT: A 491 THR cc_start: 0.8200 (m) cc_final: 0.7919 (t) REVERT: A 501 GLU cc_start: 0.7155 (tt0) cc_final: 0.6755 (tt0) REVERT: B 41 MET cc_start: 0.8519 (mmm) cc_final: 0.8307 (mmm) REVERT: B 50 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7279 (mt-10) REVERT: B 54 ASP cc_start: 0.7826 (t0) cc_final: 0.7585 (t0) REVERT: B 64 GLU cc_start: 0.8467 (tt0) cc_final: 0.7800 (tt0) REVERT: B 72 PHE cc_start: 0.8449 (t80) cc_final: 0.7841 (t80) REVERT: B 89 ARG cc_start: 0.8510 (mmm-85) cc_final: 0.8033 (mmm-85) REVERT: B 94 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7127 (mm-40) REVERT: B 178 ASP cc_start: 0.7313 (p0) cc_final: 0.7092 (p0) REVERT: B 201 TYR cc_start: 0.8030 (m-80) cc_final: 0.7729 (m-80) REVERT: B 224 TYR cc_start: 0.6572 (p90) cc_final: 0.6209 (p90) REVERT: B 232 PHE cc_start: 0.6789 (m-10) cc_final: 0.6438 (m-80) REVERT: B 253 PHE cc_start: 0.7235 (t80) cc_final: 0.6871 (t80) REVERT: B 259 ASN cc_start: 0.7342 (t0) cc_final: 0.7118 (t0) REVERT: B 260 LEU cc_start: 0.8239 (mt) cc_final: 0.7930 (mm) REVERT: B 272 MET cc_start: 0.7519 (tpp) cc_final: 0.7138 (tpp) REVERT: B 281 MET cc_start: 0.6628 (ttm) cc_final: 0.6070 (ttm) REVERT: B 286 LYS cc_start: 0.8071 (mttm) cc_final: 0.7747 (tttm) REVERT: B 304 ARG cc_start: 0.8004 (ttt180) cc_final: 0.7665 (ttt180) REVERT: B 318 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7206 (mt-10) REVERT: B 340 ILE cc_start: 0.9002 (mt) cc_final: 0.8414 (mt) REVERT: B 400 LEU cc_start: 0.8278 (tp) cc_final: 0.8062 (tt) REVERT: B 415 LEU cc_start: 0.8403 (tp) cc_final: 0.8052 (tt) REVERT: B 425 MET cc_start: 0.7237 (ttp) cc_final: 0.6946 (ttp) REVERT: B 426 ASP cc_start: 0.8477 (t0) cc_final: 0.7954 (t0) REVERT: B 441 ASP cc_start: 0.7228 (m-30) cc_final: 0.7019 (m-30) REVERT: B 443 LYS cc_start: 0.7819 (mtpp) cc_final: 0.7600 (mtmm) REVERT: B 447 ASP cc_start: 0.6922 (m-30) cc_final: 0.6698 (m-30) REVERT: B 450 LYS cc_start: 0.8105 (ttpp) cc_final: 0.7805 (ttpp) REVERT: B 491 THR cc_start: 0.8092 (m) cc_final: 0.7779 (t) REVERT: C 41 MET cc_start: 0.8577 (mmm) cc_final: 0.8306 (mmm) REVERT: C 64 GLU cc_start: 0.8049 (tt0) cc_final: 0.7282 (tt0) REVERT: C 72 PHE cc_start: 0.8569 (t80) cc_final: 0.7910 (t80) REVERT: C 89 ARG cc_start: 0.8878 (mmm-85) cc_final: 0.8405 (mmm-85) REVERT: C 102 ASP cc_start: 0.8030 (m-30) cc_final: 0.7611 (p0) REVERT: C 115 LYS cc_start: 0.8381 (ptpt) cc_final: 0.6967 (ptpt) REVERT: C 116 LEU cc_start: 0.7781 (tp) cc_final: 0.7371 (mm) REVERT: C 127 THR cc_start: 0.7321 (p) cc_final: 0.7049 (t) REVERT: C 129 MET cc_start: 0.6839 (mtm) cc_final: 0.6567 (mtm) REVERT: C 135 LYS cc_start: 0.7779 (ttmt) cc_final: 0.7443 (ttmt) REVERT: C 180 GLN cc_start: 0.8477 (mt0) cc_final: 0.8194 (mt0) REVERT: C 201 TYR cc_start: 0.7886 (m-80) cc_final: 0.7279 (m-80) REVERT: C 251 TYR cc_start: 0.5593 (m-80) cc_final: 0.5279 (m-80) REVERT: C 253 PHE cc_start: 0.7478 (t80) cc_final: 0.7192 (t80) REVERT: C 259 ASN cc_start: 0.7414 (t0) cc_final: 0.7145 (t0) REVERT: C 282 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6184 (mt-10) REVERT: C 283 LEU cc_start: 0.7614 (mt) cc_final: 0.7241 (mm) REVERT: C 425 MET cc_start: 0.7540 (ttp) cc_final: 0.7318 (ttp) REVERT: C 426 ASP cc_start: 0.8639 (t0) cc_final: 0.8391 (t0) REVERT: C 450 LYS cc_start: 0.8227 (ttpp) cc_final: 0.7978 (ttpp) REVERT: C 479 LYS cc_start: 0.6956 (mttt) cc_final: 0.6644 (mttm) REVERT: C 481 THR cc_start: 0.8011 (m) cc_final: 0.7520 (p) REVERT: C 501 GLU cc_start: 0.7256 (tt0) cc_final: 0.6921 (tt0) REVERT: C 511 ILE cc_start: 0.8423 (mt) cc_final: 0.7979 (tt) REVERT: D 50 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7380 (mt-10) REVERT: D 64 GLU cc_start: 0.8251 (tt0) cc_final: 0.7376 (tt0) REVERT: D 72 PHE cc_start: 0.8557 (t80) cc_final: 0.7974 (t80) REVERT: D 94 GLN cc_start: 0.7649 (mm-40) cc_final: 0.7091 (mm-40) REVERT: D 121 LEU cc_start: 0.8046 (mt) cc_final: 0.7639 (mt) REVERT: D 147 LEU cc_start: 0.8300 (tp) cc_final: 0.7866 (tp) REVERT: D 170 MET cc_start: 0.7775 (ttt) cc_final: 0.7575 (ptp) REVERT: D 185 LYS cc_start: 0.8517 (ptmt) cc_final: 0.8088 (ptmt) REVERT: D 201 TYR cc_start: 0.8017 (m-80) cc_final: 0.7339 (m-80) REVERT: D 243 LYS cc_start: 0.8834 (mttt) cc_final: 0.8589 (mttt) REVERT: D 260 LEU cc_start: 0.8196 (mt) cc_final: 0.7972 (mm) REVERT: D 270 GLN cc_start: 0.8277 (tp40) cc_final: 0.7992 (tp40) REVERT: D 272 MET cc_start: 0.7563 (tpp) cc_final: 0.7066 (tpp) REVERT: D 304 ARG cc_start: 0.7522 (mtp180) cc_final: 0.6869 (mtt180) REVERT: D 327 TYR cc_start: 0.7547 (m-80) cc_final: 0.7290 (m-80) REVERT: D 387 LYS cc_start: 0.8255 (mttt) cc_final: 0.8045 (mttt) REVERT: D 403 LYS cc_start: 0.7761 (mmtt) cc_final: 0.7232 (tptt) REVERT: D 425 MET cc_start: 0.7494 (ttp) cc_final: 0.7193 (ttp) REVERT: D 443 LYS cc_start: 0.7729 (mtpp) cc_final: 0.7528 (mttm) REVERT: D 481 THR cc_start: 0.8170 (m) cc_final: 0.7730 (p) REVERT: D 491 THR cc_start: 0.8112 (m) cc_final: 0.7689 (t) REVERT: E 41 MET cc_start: 0.8042 (tpp) cc_final: 0.7813 (mmm) REVERT: E 72 PHE cc_start: 0.8612 (t80) cc_final: 0.7816 (t80) REVERT: E 76 LEU cc_start: 0.8432 (mt) cc_final: 0.8135 (mt) REVERT: E 89 ARG cc_start: 0.8595 (mmm-85) cc_final: 0.8182 (mmm-85) REVERT: E 121 LEU cc_start: 0.8213 (mt) cc_final: 0.7676 (mt) REVERT: E 129 MET cc_start: 0.7055 (mtm) cc_final: 0.6396 (mtm) REVERT: E 135 LYS cc_start: 0.7647 (ttmt) cc_final: 0.7393 (tptm) REVERT: E 170 MET cc_start: 0.7601 (ttt) cc_final: 0.7378 (ptp) REVERT: E 180 GLN cc_start: 0.8399 (mt0) cc_final: 0.8062 (mt0) REVERT: E 201 TYR cc_start: 0.7868 (m-80) cc_final: 0.7493 (m-80) REVERT: E 242 ASP cc_start: 0.8638 (m-30) cc_final: 0.8432 (t0) REVERT: E 243 LYS cc_start: 0.8236 (mttt) cc_final: 0.7991 (mttt) REVERT: E 253 PHE cc_start: 0.7269 (t80) cc_final: 0.7051 (t80) REVERT: E 259 ASN cc_start: 0.7519 (t0) cc_final: 0.7230 (t0) REVERT: E 272 MET cc_start: 0.7386 (tpp) cc_final: 0.7139 (tpp) REVERT: E 281 MET cc_start: 0.6727 (ttm) cc_final: 0.6216 (ttm) REVERT: E 282 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6747 (mt-10) REVERT: E 326 LYS cc_start: 0.7730 (ptpt) cc_final: 0.7083 (mptt) REVERT: E 398 ARG cc_start: 0.8506 (tpp-160) cc_final: 0.8161 (tpp-160) REVERT: E 425 MET cc_start: 0.7339 (ttp) cc_final: 0.7107 (ttp) REVERT: E 426 ASP cc_start: 0.8529 (t0) cc_final: 0.8096 (t0) REVERT: E 441 ASP cc_start: 0.7089 (m-30) cc_final: 0.6631 (m-30) REVERT: E 443 LYS cc_start: 0.7731 (mtpp) cc_final: 0.7430 (mttm) REVERT: E 474 ARG cc_start: 0.6883 (ptp-110) cc_final: 0.6669 (ptp-110) REVERT: E 491 THR cc_start: 0.8129 (m) cc_final: 0.7891 (t) REVERT: E 501 GLU cc_start: 0.7066 (tt0) cc_final: 0.6700 (tt0) REVERT: F 72 PHE cc_start: 0.8456 (t80) cc_final: 0.7552 (t80) REVERT: F 87 TRP cc_start: 0.5712 (t-100) cc_final: 0.5251 (t-100) REVERT: F 102 ASP cc_start: 0.7979 (m-30) cc_final: 0.7547 (p0) REVERT: F 170 MET cc_start: 0.7846 (ttt) cc_final: 0.7479 (ptp) REVERT: F 171 ASN cc_start: 0.7663 (m-40) cc_final: 0.7307 (p0) REVERT: F 180 GLN cc_start: 0.8563 (mt0) cc_final: 0.8127 (mt0) REVERT: F 201 TYR cc_start: 0.7962 (m-80) cc_final: 0.7196 (m-80) REVERT: F 232 PHE cc_start: 0.7064 (m-80) cc_final: 0.6836 (m-80) REVERT: F 258 ASP cc_start: 0.5379 (p0) cc_final: 0.4943 (t70) REVERT: F 281 MET cc_start: 0.6704 (ttm) cc_final: 0.6151 (ttm) REVERT: F 304 ARG cc_start: 0.7223 (mtt180) cc_final: 0.6833 (mtp180) REVERT: F 340 ILE cc_start: 0.8921 (mt) cc_final: 0.8709 (mt) REVERT: F 373 TYR cc_start: 0.7893 (m-80) cc_final: 0.7576 (m-80) REVERT: F 387 LYS cc_start: 0.8077 (mttt) cc_final: 0.7842 (mttt) REVERT: F 418 LEU cc_start: 0.8546 (tp) cc_final: 0.8331 (tp) REVERT: F 425 MET cc_start: 0.7413 (ttp) cc_final: 0.7168 (ttp) REVERT: F 426 ASP cc_start: 0.8609 (t0) cc_final: 0.8273 (t0) REVERT: F 441 ASP cc_start: 0.7050 (m-30) cc_final: 0.6518 (m-30) REVERT: F 481 THR cc_start: 0.7972 (m) cc_final: 0.7483 (p) REVERT: F 491 THR cc_start: 0.8050 (m) cc_final: 0.7754 (t) REVERT: F 501 GLU cc_start: 0.7027 (tt0) cc_final: 0.6643 (tt0) REVERT: G 41 MET cc_start: 0.7979 (mmm) cc_final: 0.7704 (mmm) REVERT: G 72 PHE cc_start: 0.8600 (t80) cc_final: 0.7842 (t80) REVERT: G 89 ARG cc_start: 0.8834 (mmm-85) cc_final: 0.8371 (mmm-85) REVERT: G 102 ASP cc_start: 0.8062 (m-30) cc_final: 0.7854 (p0) REVERT: G 129 MET cc_start: 0.6761 (mtm) cc_final: 0.6552 (mtm) REVERT: G 147 LEU cc_start: 0.8511 (tp) cc_final: 0.8243 (tp) REVERT: G 170 MET cc_start: 0.7655 (ttt) cc_final: 0.7422 (ptp) REVERT: G 180 GLN cc_start: 0.8464 (mt0) cc_final: 0.7958 (mt0) REVERT: G 185 LYS cc_start: 0.8636 (ptmt) cc_final: 0.8114 (ptmt) REVERT: G 186 TYR cc_start: 0.7227 (m-80) cc_final: 0.6863 (m-80) REVERT: G 200 ARG cc_start: 0.6877 (mtp-110) cc_final: 0.6334 (ttp80) REVERT: G 242 ASP cc_start: 0.8639 (m-30) cc_final: 0.8311 (t0) REVERT: G 243 LYS cc_start: 0.8837 (mttt) cc_final: 0.8543 (mttt) REVERT: G 259 ASN cc_start: 0.7641 (t0) cc_final: 0.7326 (t0) REVERT: G 304 ARG cc_start: 0.8138 (ttt180) cc_final: 0.7900 (ttt180) REVERT: G 387 LYS cc_start: 0.7984 (mttt) cc_final: 0.7779 (mtmm) REVERT: G 414 ASP cc_start: 0.8034 (p0) cc_final: 0.7781 (t0) REVERT: G 417 ARG cc_start: 0.6321 (mtt-85) cc_final: 0.6081 (mtt-85) REVERT: G 425 MET cc_start: 0.7400 (ttp) cc_final: 0.7094 (ttp) REVERT: G 426 ASP cc_start: 0.8638 (t0) cc_final: 0.8180 (t0) REVERT: G 481 THR cc_start: 0.8171 (m) cc_final: 0.7664 (p) REVERT: G 491 THR cc_start: 0.8023 (m) cc_final: 0.7706 (p) REVERT: G 501 GLU cc_start: 0.7067 (tt0) cc_final: 0.6627 (tt0) REVERT: H 41 MET cc_start: 0.7645 (tpp) cc_final: 0.7323 (tpp) REVERT: H 72 PHE cc_start: 0.8844 (t80) cc_final: 0.8124 (t80) REVERT: H 74 ARG cc_start: 0.8734 (mtm-85) cc_final: 0.8395 (mtm110) REVERT: H 89 ARG cc_start: 0.8693 (mmm-85) cc_final: 0.8198 (mmm-85) REVERT: H 102 ASP cc_start: 0.8164 (m-30) cc_final: 0.7508 (p0) REVERT: H 121 LEU cc_start: 0.8125 (mt) cc_final: 0.7699 (mt) REVERT: H 141 ARG cc_start: 0.7633 (mtp85) cc_final: 0.7276 (ttm-80) REVERT: H 168 VAL cc_start: 0.9008 (t) cc_final: 0.8685 (p) REVERT: H 170 MET cc_start: 0.7941 (ttt) cc_final: 0.7359 (ptp) REVERT: H 171 ASN cc_start: 0.7842 (m-40) cc_final: 0.7310 (p0) REVERT: H 180 GLN cc_start: 0.8469 (mt0) cc_final: 0.8146 (mt0) REVERT: H 185 LYS cc_start: 0.8507 (ptmt) cc_final: 0.8073 (ptmt) REVERT: H 201 TYR cc_start: 0.8081 (m-80) cc_final: 0.7786 (m-80) REVERT: H 232 PHE cc_start: 0.7096 (m-10) cc_final: 0.6854 (m-80) REVERT: H 272 MET cc_start: 0.7500 (tpp) cc_final: 0.7152 (tpp) REVERT: H 281 MET cc_start: 0.6740 (ttm) cc_final: 0.6531 (ttm) REVERT: H 304 ARG cc_start: 0.7993 (mtt180) cc_final: 0.7788 (mtt180) REVERT: H 340 ILE cc_start: 0.9117 (mt) cc_final: 0.8842 (mt) REVERT: H 403 LYS cc_start: 0.7881 (mmtt) cc_final: 0.7569 (mmmt) REVERT: H 425 MET cc_start: 0.7467 (ttp) cc_final: 0.7138 (ttp) REVERT: H 426 ASP cc_start: 0.8302 (t0) cc_final: 0.7963 (t0) REVERT: H 450 LYS cc_start: 0.8146 (ttpp) cc_final: 0.7908 (ttpp) REVERT: H 481 THR cc_start: 0.8305 (m) cc_final: 0.7787 (p) outliers start: 51 outliers final: 22 residues processed: 1070 average time/residue: 0.4460 time to fit residues: 712.6189 Evaluate side-chains 989 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 966 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 258 ASP Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 270 GLN Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain G residue 351 MET Chi-restraints excluded: chain H residue 181 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 328 optimal weight: 1.9990 chunk 238 optimal weight: 0.9990 chunk 254 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 316 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 150 optimal weight: 0.1980 chunk 143 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN C 374 GLN D 180 GLN D 463 HIS E 153 GLN F 153 GLN F 259 ASN G 153 GLN G 259 ASN H 259 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.184020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.142904 restraints weight = 54988.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.148434 restraints weight = 30301.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.151999 restraints weight = 19498.772| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30368 Z= 0.138 Angle : 0.651 10.418 41088 Z= 0.333 Chirality : 0.047 0.198 4672 Planarity : 0.005 0.057 5352 Dihedral : 4.453 46.602 4062 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.50 % Allowed : 14.31 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.14), residues: 3720 helix: -0.02 (0.15), residues: 1136 sheet: 0.18 (0.20), residues: 704 loop : 0.37 (0.15), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP G 87 HIS 0.007 0.001 HIS H 315 PHE 0.018 0.002 PHE B 325 TYR 0.024 0.002 TYR C 327 ARG 0.005 0.001 ARG D 200 Details of bonding type rmsd hydrogen bonds : bond 0.05456 ( 1087) hydrogen bonds : angle 5.27690 ( 2733) covalent geometry : bond 0.00296 (30368) covalent geometry : angle 0.65135 (41088) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 991 time to evaluate : 3.159 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: 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: 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 64 GLU cc_start: 0.8414 (tt0) cc_final: 0.7973 (tt0) REVERT: A 72 PHE cc_start: 0.8620 (t80) cc_final: 0.8203 (t80) REVERT: A 78 ASP cc_start: 0.7194 (m-30) cc_final: 0.6991 (m-30) REVERT: A 102 ASP cc_start: 0.8146 (m-30) cc_final: 0.7719 (p0) REVERT: A 129 MET cc_start: 0.7030 (mtm) cc_final: 0.6389 (mtm) REVERT: A 170 MET cc_start: 0.7661 (ptp) cc_final: 0.7443 (ptp) REVERT: A 179 THR cc_start: 0.8512 (m) cc_final: 0.8279 (p) REVERT: A 180 GLN cc_start: 0.8154 (mt0) cc_final: 0.7841 (mp10) REVERT: A 222 ASP cc_start: 0.8216 (m-30) cc_final: 0.8012 (m-30) REVERT: A 224 TYR cc_start: 0.6863 (p90) cc_final: 0.6537 (p90) REVERT: A 253 PHE cc_start: 0.7445 (t80) cc_final: 0.6919 (t80) REVERT: A 254 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.6897 (tp) REVERT: A 259 ASN cc_start: 0.7618 (t0) cc_final: 0.7328 (t0) REVERT: A 280 ILE cc_start: 0.6159 (mt) cc_final: 0.5902 (mm) REVERT: A 341 LYS cc_start: 0.9030 (tttt) cc_final: 0.8506 (ttpp) REVERT: A 386 PHE cc_start: 0.7497 (m-80) cc_final: 0.7255 (m-80) REVERT: A 400 LEU cc_start: 0.8289 (tp) cc_final: 0.8083 (tt) REVERT: A 425 MET cc_start: 0.7519 (ttp) cc_final: 0.7170 (ttp) REVERT: A 426 ASP cc_start: 0.8229 (t0) cc_final: 0.7740 (t0) REVERT: A 448 PHE cc_start: 0.8163 (t80) cc_final: 0.7443 (t80) REVERT: B 41 MET cc_start: 0.8516 (mmm) cc_final: 0.8234 (mmm) REVERT: B 50 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7130 (mt-10) REVERT: B 64 GLU cc_start: 0.8457 (tt0) cc_final: 0.7808 (tt0) REVERT: B 72 PHE cc_start: 0.8494 (t80) cc_final: 0.7924 (t80) REVERT: B 94 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7183 (mm-40) REVERT: B 170 MET cc_start: 0.7861 (ptp) cc_final: 0.7628 (ptp) REVERT: B 180 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7594 (mp10) REVERT: B 181 SER cc_start: 0.9035 (OUTLIER) cc_final: 0.8717 (p) REVERT: B 182 ILE cc_start: 0.9220 (pp) cc_final: 0.8981 (pp) REVERT: B 224 TYR cc_start: 0.5662 (p90) cc_final: 0.5310 (p90) REVERT: B 232 PHE cc_start: 0.6835 (m-10) cc_final: 0.6486 (m-80) REVERT: B 260 LEU cc_start: 0.8293 (mt) cc_final: 0.7946 (mm) REVERT: B 272 MET cc_start: 0.7575 (tpp) cc_final: 0.7264 (tpp) REVERT: B 281 MET cc_start: 0.6728 (ttm) cc_final: 0.6149 (ttm) REVERT: B 282 GLU cc_start: 0.6951 (mt-10) cc_final: 0.6416 (mt-10) REVERT: B 286 LYS cc_start: 0.8209 (mttm) cc_final: 0.7667 (tttm) REVERT: B 304 ARG cc_start: 0.8040 (ttt180) cc_final: 0.7718 (ttt180) REVERT: B 318 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8000 (mt-10) REVERT: B 340 ILE cc_start: 0.9070 (mt) cc_final: 0.8383 (mt) REVERT: B 374 GLN cc_start: 0.6669 (mm110) cc_final: 0.6083 (mm-40) REVERT: B 400 LEU cc_start: 0.8200 (tp) cc_final: 0.7968 (tt) REVERT: B 415 LEU cc_start: 0.8422 (tp) cc_final: 0.8179 (tt) REVERT: B 425 MET cc_start: 0.7413 (ttp) cc_final: 0.6999 (ttp) REVERT: B 426 ASP cc_start: 0.8474 (t0) cc_final: 0.7978 (t0) REVERT: B 441 ASP cc_start: 0.7209 (m-30) cc_final: 0.6933 (m-30) REVERT: B 443 LYS cc_start: 0.7840 (mtpp) cc_final: 0.7573 (mtmm) REVERT: B 448 PHE cc_start: 0.8118 (t80) cc_final: 0.7511 (t80) REVERT: B 450 LYS cc_start: 0.8125 (ttpp) cc_final: 0.7804 (ttpp) REVERT: B 481 THR cc_start: 0.8230 (m) cc_final: 0.7737 (p) REVERT: B 491 THR cc_start: 0.8131 (m) cc_final: 0.7780 (t) REVERT: C 41 MET cc_start: 0.8599 (mmm) cc_final: 0.8287 (mmm) REVERT: C 64 GLU cc_start: 0.8255 (tt0) cc_final: 0.7423 (tt0) REVERT: C 72 PHE cc_start: 0.8619 (t80) cc_final: 0.7970 (t80) REVERT: C 89 ARG cc_start: 0.8837 (mmm-85) cc_final: 0.8376 (mmm-85) REVERT: C 94 GLN cc_start: 0.7818 (mm-40) cc_final: 0.7400 (mm-40) REVERT: C 102 ASP cc_start: 0.8040 (m-30) cc_final: 0.7695 (p0) REVERT: C 115 LYS cc_start: 0.8361 (ptpt) cc_final: 0.7928 (mtmm) REVERT: C 116 LEU cc_start: 0.7884 (tp) cc_final: 0.7489 (mm) REVERT: C 119 VAL cc_start: 0.6321 (OUTLIER) cc_final: 0.5935 (m) REVERT: C 127 THR cc_start: 0.7372 (p) cc_final: 0.7087 (t) REVERT: C 135 LYS cc_start: 0.7865 (ttmt) cc_final: 0.7512 (mtpp) REVERT: C 141 ARG cc_start: 0.7347 (ttm-80) cc_final: 0.7034 (ttt90) REVERT: C 170 MET cc_start: 0.7469 (ptp) cc_final: 0.7116 (ptp) REVERT: C 181 SER cc_start: 0.8819 (OUTLIER) cc_final: 0.8532 (p) REVERT: C 201 TYR cc_start: 0.7986 (m-80) cc_final: 0.7235 (m-80) REVERT: C 224 TYR cc_start: 0.6742 (p90) cc_final: 0.6426 (p90) REVERT: C 243 LYS cc_start: 0.8455 (mttt) cc_final: 0.8103 (mttt) REVERT: C 259 ASN cc_start: 0.7569 (t0) cc_final: 0.7304 (t0) REVERT: C 272 MET cc_start: 0.7483 (tpp) cc_final: 0.7058 (tpp) REVERT: C 282 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6165 (mt-10) REVERT: C 283 LEU cc_start: 0.7684 (mt) cc_final: 0.7321 (mm) REVERT: C 425 MET cc_start: 0.7620 (ttp) cc_final: 0.7363 (ttp) REVERT: C 426 ASP cc_start: 0.8578 (t0) cc_final: 0.8095 (t0) REVERT: C 447 ASP cc_start: 0.7322 (p0) cc_final: 0.7070 (p0) REVERT: C 450 LYS cc_start: 0.8296 (ttpp) cc_final: 0.8038 (ttpp) REVERT: C 479 LYS cc_start: 0.6954 (mttt) cc_final: 0.6679 (mttm) REVERT: C 481 THR cc_start: 0.8057 (m) cc_final: 0.7591 (p) REVERT: C 511 ILE cc_start: 0.8443 (mt) cc_final: 0.8052 (tt) REVERT: D 50 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7318 (mt-10) REVERT: D 64 GLU cc_start: 0.8329 (tt0) cc_final: 0.7498 (tt0) REVERT: D 72 PHE cc_start: 0.8594 (t80) cc_final: 0.8004 (t80) REVERT: D 94 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7087 (mm-40) REVERT: D 121 LEU cc_start: 0.8052 (mt) cc_final: 0.7501 (mt) REVERT: D 144 MET cc_start: 0.7442 (mtp) cc_final: 0.7182 (ttp) REVERT: D 147 LEU cc_start: 0.8346 (tp) cc_final: 0.7944 (tp) REVERT: D 170 MET cc_start: 0.7793 (ttt) cc_final: 0.7476 (ptp) REVERT: D 185 LYS cc_start: 0.8530 (ptmt) cc_final: 0.8100 (ptmt) REVERT: D 201 TYR cc_start: 0.8038 (m-80) cc_final: 0.7385 (m-80) REVERT: D 241 LEU cc_start: 0.7498 (pt) cc_final: 0.7161 (pp) REVERT: D 243 LYS cc_start: 0.8755 (mttt) cc_final: 0.8505 (mttt) REVERT: D 270 GLN cc_start: 0.8204 (tp40) cc_final: 0.7793 (tp40) REVERT: D 272 MET cc_start: 0.7781 (tpp) cc_final: 0.7206 (tpp) REVERT: D 283 LEU cc_start: 0.7876 (mt) cc_final: 0.7555 (mm) REVERT: D 304 ARG cc_start: 0.7548 (mtp180) cc_final: 0.6863 (mtt180) REVERT: D 387 LYS cc_start: 0.8386 (mttt) cc_final: 0.8171 (mttt) REVERT: D 398 ARG cc_start: 0.8225 (tpp-160) cc_final: 0.7680 (tpt170) REVERT: D 403 LYS cc_start: 0.7914 (mmtt) cc_final: 0.7233 (tptt) REVERT: D 425 MET cc_start: 0.7468 (ttp) cc_final: 0.7153 (ttp) REVERT: D 448 PHE cc_start: 0.8339 (t80) cc_final: 0.7428 (t80) REVERT: D 481 THR cc_start: 0.8233 (m) cc_final: 0.7786 (p) REVERT: D 491 THR cc_start: 0.8122 (m) cc_final: 0.7691 (t) REVERT: E 41 MET cc_start: 0.8067 (tpp) cc_final: 0.7809 (mmm) REVERT: E 50 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7611 (mt-10) REVERT: E 72 PHE cc_start: 0.8674 (t80) cc_final: 0.8080 (t80) REVERT: E 89 ARG cc_start: 0.8646 (mmm-85) cc_final: 0.8202 (mmp80) REVERT: E 121 LEU cc_start: 0.8248 (mt) cc_final: 0.7692 (mt) REVERT: E 129 MET cc_start: 0.7072 (mtm) cc_final: 0.6537 (mtm) REVERT: E 135 LYS cc_start: 0.7777 (ttmt) cc_final: 0.7476 (tptm) REVERT: E 170 MET cc_start: 0.7633 (ttt) cc_final: 0.7410 (ptp) REVERT: E 173 PHE cc_start: 0.8106 (p90) cc_final: 0.7871 (p90) REVERT: E 180 GLN cc_start: 0.8514 (mt0) cc_final: 0.7906 (mt0) REVERT: E 201 TYR cc_start: 0.7915 (m-80) cc_final: 0.7525 (m-80) REVERT: E 243 LYS cc_start: 0.8299 (mttt) cc_final: 0.8027 (mttt) REVERT: E 259 ASN cc_start: 0.7659 (t0) cc_final: 0.7459 (t0) REVERT: E 272 MET cc_start: 0.7483 (tpp) cc_final: 0.7276 (tpp) REVERT: E 281 MET cc_start: 0.6824 (ttm) cc_final: 0.6238 (ttm) REVERT: E 282 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6670 (mt-10) REVERT: E 387 LYS cc_start: 0.8377 (mppt) cc_final: 0.7932 (mtmm) REVERT: E 414 ASP cc_start: 0.8062 (t0) cc_final: 0.7711 (t0) REVERT: E 425 MET cc_start: 0.7341 (ttp) cc_final: 0.7120 (ttp) REVERT: E 426 ASP cc_start: 0.8531 (t0) cc_final: 0.8107 (t70) REVERT: E 441 ASP cc_start: 0.6928 (m-30) cc_final: 0.6694 (m-30) REVERT: E 443 LYS cc_start: 0.7701 (mtpp) cc_final: 0.7491 (mtmm) REVERT: E 474 ARG cc_start: 0.6952 (ptp-110) cc_final: 0.6742 (ptp-110) REVERT: E 481 THR cc_start: 0.8260 (m) cc_final: 0.7807 (p) REVERT: E 501 GLU cc_start: 0.6959 (tt0) cc_final: 0.6685 (tt0) REVERT: F 72 PHE cc_start: 0.8506 (t80) cc_final: 0.7578 (t80) REVERT: F 87 TRP cc_start: 0.5806 (t-100) cc_final: 0.5319 (t-100) REVERT: F 129 MET cc_start: 0.7162 (mtm) cc_final: 0.6682 (mtm) REVERT: F 148 ASP cc_start: 0.6873 (m-30) cc_final: 0.6566 (m-30) REVERT: F 168 VAL cc_start: 0.9072 (t) cc_final: 0.8768 (p) REVERT: F 170 MET cc_start: 0.7790 (ttt) cc_final: 0.7480 (ptp) REVERT: F 171 ASN cc_start: 0.7800 (m-40) cc_final: 0.7525 (p0) REVERT: F 180 GLN cc_start: 0.8605 (mt0) cc_final: 0.8216 (mt0) REVERT: F 189 HIS cc_start: 0.7693 (m-70) cc_final: 0.7478 (m-70) REVERT: F 201 TYR cc_start: 0.7989 (m-80) cc_final: 0.7175 (m-80) REVERT: F 232 PHE cc_start: 0.7144 (m-80) cc_final: 0.6909 (m-80) REVERT: F 253 PHE cc_start: 0.7343 (t80) cc_final: 0.7141 (t80) REVERT: F 286 LYS cc_start: 0.8301 (mttm) cc_final: 0.8088 (mttm) REVERT: F 304 ARG cc_start: 0.7321 (mtt180) cc_final: 0.6680 (mtt180) REVERT: F 340 ILE cc_start: 0.9021 (mt) cc_final: 0.8643 (tt) REVERT: F 398 ARG cc_start: 0.8529 (tpp-160) cc_final: 0.8032 (tpt170) REVERT: F 425 MET cc_start: 0.7477 (ttp) cc_final: 0.7249 (ttp) REVERT: F 426 ASP cc_start: 0.8460 (t0) cc_final: 0.8019 (t70) REVERT: F 481 THR cc_start: 0.8046 (m) cc_final: 0.7575 (p) REVERT: F 491 THR cc_start: 0.8144 (m) cc_final: 0.7835 (t) REVERT: G 41 MET cc_start: 0.7936 (mmm) cc_final: 0.7640 (mmm) REVERT: G 72 PHE cc_start: 0.8662 (t80) cc_final: 0.7855 (t80) REVERT: G 89 ARG cc_start: 0.8844 (mmm-85) cc_final: 0.8392 (mmm-85) REVERT: G 102 ASP cc_start: 0.8084 (m-30) cc_final: 0.7787 (p0) REVERT: G 129 MET cc_start: 0.6821 (mtm) cc_final: 0.6360 (mtm) REVERT: G 135 LYS cc_start: 0.7920 (ttmm) cc_final: 0.6966 (tptm) REVERT: G 147 LEU cc_start: 0.8497 (tp) cc_final: 0.8150 (tp) REVERT: G 180 GLN cc_start: 0.8529 (mt0) cc_final: 0.8061 (mt0) REVERT: G 242 ASP cc_start: 0.8757 (m-30) cc_final: 0.8360 (t0) REVERT: G 243 LYS cc_start: 0.8842 (mttt) cc_final: 0.8538 (mttt) REVERT: G 254 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6833 (tp) REVERT: G 259 ASN cc_start: 0.7727 (t0) cc_final: 0.7391 (t0) REVERT: G 272 MET cc_start: 0.7672 (tpp) cc_final: 0.7175 (tpp) REVERT: G 282 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6369 (mt-10) REVERT: G 283 LEU cc_start: 0.7686 (mt) cc_final: 0.7353 (mm) REVERT: G 304 ARG cc_start: 0.8165 (ttt180) cc_final: 0.7514 (mtt180) REVERT: G 414 ASP cc_start: 0.7944 (p0) cc_final: 0.7701 (t0) REVERT: G 425 MET cc_start: 0.7521 (ttp) cc_final: 0.7202 (ttp) REVERT: G 426 ASP cc_start: 0.8642 (t0) cc_final: 0.8165 (t0) REVERT: G 443 LYS cc_start: 0.7958 (mtmm) cc_final: 0.7434 (mttm) REVERT: G 481 THR cc_start: 0.8194 (m) cc_final: 0.7753 (p) REVERT: G 491 THR cc_start: 0.8165 (m) cc_final: 0.7764 (p) REVERT: G 501 GLU cc_start: 0.6956 (tt0) cc_final: 0.6726 (tt0) REVERT: H 41 MET cc_start: 0.7764 (tpp) cc_final: 0.7482 (tpp) REVERT: H 72 PHE cc_start: 0.8774 (t80) cc_final: 0.8082 (t80) REVERT: H 74 ARG cc_start: 0.8724 (mtm-85) cc_final: 0.8371 (mtm110) REVERT: H 89 ARG cc_start: 0.8674 (mmm-85) cc_final: 0.8183 (mmm-85) REVERT: H 102 ASP cc_start: 0.8131 (m-30) cc_final: 0.7421 (p0) REVERT: H 121 LEU cc_start: 0.8130 (mt) cc_final: 0.7652 (mt) REVERT: H 129 MET cc_start: 0.7114 (mtm) cc_final: 0.6868 (mtm) REVERT: H 141 ARG cc_start: 0.7651 (mtp85) cc_final: 0.7169 (ttm-80) REVERT: H 168 VAL cc_start: 0.9115 (t) cc_final: 0.8793 (p) REVERT: H 170 MET cc_start: 0.7908 (ttt) cc_final: 0.7347 (ptp) REVERT: H 171 ASN cc_start: 0.7922 (m-40) cc_final: 0.7522 (p0) REVERT: H 180 GLN cc_start: 0.8564 (mt0) cc_final: 0.8127 (mt0) REVERT: H 185 LYS cc_start: 0.8520 (ptmt) cc_final: 0.8081 (ptmt) REVERT: H 201 TYR cc_start: 0.8161 (m-80) cc_final: 0.7467 (m-80) REVERT: H 232 PHE cc_start: 0.7204 (m-10) cc_final: 0.6832 (m-80) REVERT: H 254 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6612 (tp) REVERT: H 267 ARG cc_start: 0.8637 (tpp80) cc_final: 0.8209 (tpp80) REVERT: H 272 MET cc_start: 0.7397 (tpp) cc_final: 0.7093 (tpp) REVERT: H 281 MET cc_start: 0.6754 (ttm) cc_final: 0.6421 (ttm) REVERT: H 283 LEU cc_start: 0.7998 (mt) cc_final: 0.7640 (mm) REVERT: H 304 ARG cc_start: 0.8009 (mtt180) cc_final: 0.7377 (mtt180) REVERT: H 340 ILE cc_start: 0.9145 (mt) cc_final: 0.8665 (mt) REVERT: H 403 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7630 (mmmt) REVERT: H 425 MET cc_start: 0.7460 (ttp) cc_final: 0.7172 (ttp) REVERT: H 426 ASP cc_start: 0.8239 (t0) cc_final: 0.7820 (t0) REVERT: H 443 LYS cc_start: 0.7901 (mtmm) cc_final: 0.7663 (mtmm) REVERT: H 444 LYS cc_start: 0.6561 (mtpt) cc_final: 0.6296 (ttmm) REVERT: H 481 THR cc_start: 0.8321 (m) cc_final: 0.7860 (p) outliers start: 83 outliers final: 51 residues processed: 1027 average time/residue: 0.4761 time to fit residues: 725.4485 Evaluate side-chains 1003 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 945 time to evaluate : 3.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 503 CYS Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 503 CYS Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 503 CYS Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 258 ASP Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 503 CYS Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 503 CYS Chi-restraints excluded: chain E residue 513 GLU Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 449 GLN Chi-restraints excluded: chain F residue 474 ARG Chi-restraints excluded: chain F residue 503 CYS Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 351 MET Chi-restraints excluded: chain G residue 449 GLN Chi-restraints excluded: chain G residue 503 CYS Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 307 GLU Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain H residue 503 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 65 optimal weight: 0.9980 chunk 268 optimal weight: 2.9990 chunk 295 optimal weight: 0.9990 chunk 302 optimal weight: 7.9990 chunk 361 optimal weight: 1.9990 chunk 243 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 chunk 98 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 chunk 249 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 HIS C 153 GLN C 180 GLN ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN H 153 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.183506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.142154 restraints weight = 55207.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.147662 restraints weight = 30410.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.151257 restraints weight = 19510.855| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30368 Z= 0.144 Angle : 0.628 12.606 41088 Z= 0.322 Chirality : 0.047 0.204 4672 Planarity : 0.005 0.051 5352 Dihedral : 4.415 38.740 4058 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.86 % Allowed : 15.60 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.14), residues: 3720 helix: 0.14 (0.16), residues: 1120 sheet: 0.07 (0.20), residues: 704 loop : 0.35 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP E 87 HIS 0.004 0.001 HIS D 463 PHE 0.022 0.002 PHE C 232 TYR 0.024 0.002 TYR E 327 ARG 0.007 0.001 ARG G 267 Details of bonding type rmsd hydrogen bonds : bond 0.05054 ( 1087) hydrogen bonds : angle 5.18417 ( 2733) covalent geometry : bond 0.00310 (30368) covalent geometry : angle 0.62759 (41088) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1084 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 989 time to evaluate : 3.367 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: 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: 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 64 GLU cc_start: 0.8445 (tt0) cc_final: 0.7947 (tt0) REVERT: A 65 MET cc_start: 0.8367 (mmm) cc_final: 0.7948 (mmm) REVERT: A 72 PHE cc_start: 0.8642 (t80) cc_final: 0.8197 (t80) REVERT: A 102 ASP cc_start: 0.8112 (m-30) cc_final: 0.7768 (p0) REVERT: A 170 MET cc_start: 0.7536 (ptp) cc_final: 0.7223 (ptp) REVERT: A 179 THR cc_start: 0.8705 (m) cc_final: 0.8474 (p) REVERT: A 180 GLN cc_start: 0.7941 (mt0) cc_final: 0.7485 (mp10) REVERT: A 185 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8176 (ptmt) REVERT: A 224 TYR cc_start: 0.6214 (p90) cc_final: 0.5611 (p90) REVERT: A 232 PHE cc_start: 0.6929 (m-10) cc_final: 0.6666 (m-80) REVERT: A 254 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.6954 (tp) REVERT: A 259 ASN cc_start: 0.7653 (t0) cc_final: 0.7450 (t0) REVERT: A 280 ILE cc_start: 0.6225 (mt) cc_final: 0.5948 (mm) REVERT: A 282 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6609 (mt-10) REVERT: A 304 ARG cc_start: 0.8070 (ttt180) cc_final: 0.7835 (mtt180) REVERT: A 341 LYS cc_start: 0.9059 (tttt) cc_final: 0.8795 (ttpp) REVERT: A 374 GLN cc_start: 0.6837 (OUTLIER) cc_final: 0.5978 (mm-40) REVERT: A 386 PHE cc_start: 0.7523 (m-80) cc_final: 0.7234 (m-80) REVERT: A 400 LEU cc_start: 0.8293 (tp) cc_final: 0.8066 (tt) REVERT: A 425 MET cc_start: 0.7512 (ttp) cc_final: 0.7173 (ttp) REVERT: A 426 ASP cc_start: 0.8240 (t0) cc_final: 0.7777 (t0) REVERT: A 481 THR cc_start: 0.8425 (m) cc_final: 0.8017 (p) REVERT: B 41 MET cc_start: 0.8623 (mmm) cc_final: 0.8291 (mmm) REVERT: B 50 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7094 (mt-10) REVERT: B 64 GLU cc_start: 0.8502 (tt0) cc_final: 0.7815 (tt0) REVERT: B 72 PHE cc_start: 0.8461 (t80) cc_final: 0.7975 (t80) REVERT: B 74 ARG cc_start: 0.8242 (ttm110) cc_final: 0.7759 (ptp-170) REVERT: B 89 ARG cc_start: 0.8497 (mmm-85) cc_final: 0.8045 (mmm-85) REVERT: B 94 GLN cc_start: 0.7738 (mm-40) cc_final: 0.7196 (mm-40) REVERT: B 170 MET cc_start: 0.7782 (ptp) cc_final: 0.7444 (ptp) REVERT: B 180 GLN cc_start: 0.7900 (mp10) cc_final: 0.7583 (mp10) REVERT: B 197 ASN cc_start: 0.7160 (t0) cc_final: 0.6852 (t0) REVERT: B 232 PHE cc_start: 0.6868 (m-10) cc_final: 0.6380 (m-80) REVERT: B 259 ASN cc_start: 0.7264 (t0) cc_final: 0.6346 (p0) REVERT: B 260 LEU cc_start: 0.8276 (mt) cc_final: 0.7906 (mm) REVERT: B 272 MET cc_start: 0.7530 (tpp) cc_final: 0.7205 (tpp) REVERT: B 281 MET cc_start: 0.6750 (ttm) cc_final: 0.6189 (ttm) REVERT: B 282 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6451 (mt-10) REVERT: B 304 ARG cc_start: 0.8067 (ttt180) cc_final: 0.7762 (ttt180) REVERT: B 318 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7889 (mt-10) REVERT: B 340 ILE cc_start: 0.9083 (mt) cc_final: 0.8664 (mt) REVERT: B 341 LYS cc_start: 0.9181 (pttm) cc_final: 0.8972 (pmtt) REVERT: B 374 GLN cc_start: 0.6710 (mm110) cc_final: 0.6458 (mm110) REVERT: B 415 LEU cc_start: 0.8458 (tp) cc_final: 0.8254 (tt) REVERT: B 425 MET cc_start: 0.7391 (ttp) cc_final: 0.7010 (ttp) REVERT: B 426 ASP cc_start: 0.8451 (t0) cc_final: 0.7941 (t0) REVERT: B 441 ASP cc_start: 0.7067 (m-30) cc_final: 0.6788 (m-30) REVERT: B 443 LYS cc_start: 0.7853 (mtpp) cc_final: 0.7573 (mtmm) REVERT: B 481 THR cc_start: 0.8261 (m) cc_final: 0.7826 (p) REVERT: B 491 THR cc_start: 0.8133 (m) cc_final: 0.7720 (t) REVERT: C 41 MET cc_start: 0.8591 (mmm) cc_final: 0.8263 (mmm) REVERT: C 64 GLU cc_start: 0.8336 (tt0) cc_final: 0.7426 (tt0) REVERT: C 72 PHE cc_start: 0.8627 (t80) cc_final: 0.8015 (t80) REVERT: C 89 ARG cc_start: 0.8843 (mmm-85) cc_final: 0.8381 (mmm-85) REVERT: C 94 GLN cc_start: 0.7840 (mm-40) cc_final: 0.7420 (mm-40) REVERT: C 102 ASP cc_start: 0.8091 (m-30) cc_final: 0.7767 (p0) REVERT: C 115 LYS cc_start: 0.8098 (ptpt) cc_final: 0.7716 (ptpt) REVERT: C 119 VAL cc_start: 0.6577 (OUTLIER) cc_final: 0.6206 (m) REVERT: C 127 THR cc_start: 0.7430 (p) cc_final: 0.7158 (t) REVERT: C 135 LYS cc_start: 0.7985 (ttmt) cc_final: 0.7587 (mtpp) REVERT: C 141 ARG cc_start: 0.7328 (ttm-80) cc_final: 0.7104 (ptm160) REVERT: C 170 MET cc_start: 0.7657 (ptp) cc_final: 0.7428 (ptp) REVERT: C 180 GLN cc_start: 0.8149 (mt0) cc_final: 0.7837 (mt0) REVERT: C 181 SER cc_start: 0.8811 (OUTLIER) cc_final: 0.8480 (p) REVERT: C 201 TYR cc_start: 0.7945 (m-80) cc_final: 0.7269 (m-80) REVERT: C 221 GLN cc_start: 0.7961 (tp40) cc_final: 0.7701 (tp40) REVERT: C 232 PHE cc_start: 0.7019 (m-80) cc_final: 0.6666 (m-80) REVERT: C 243 LYS cc_start: 0.8536 (mttt) cc_final: 0.8168 (mttt) REVERT: C 272 MET cc_start: 0.7633 (tpp) cc_final: 0.7333 (tpp) REVERT: C 282 GLU cc_start: 0.6802 (mt-10) cc_final: 0.6230 (mt-10) REVERT: C 410 LEU cc_start: 0.7964 (tp) cc_final: 0.7697 (tt) REVERT: C 425 MET cc_start: 0.7640 (ttp) cc_final: 0.7402 (ttp) REVERT: C 426 ASP cc_start: 0.8543 (t0) cc_final: 0.8147 (t70) REVERT: C 443 LYS cc_start: 0.7831 (mttm) cc_final: 0.7433 (mttp) REVERT: C 447 ASP cc_start: 0.7385 (p0) cc_final: 0.7123 (p0) REVERT: C 450 LYS cc_start: 0.8323 (ttpp) cc_final: 0.8032 (ttpp) REVERT: C 479 LYS cc_start: 0.6995 (mttt) cc_final: 0.6675 (mttm) REVERT: C 481 THR cc_start: 0.8009 (m) cc_final: 0.7605 (p) REVERT: C 498 SER cc_start: 0.8390 (m) cc_final: 0.7994 (p) REVERT: C 511 ILE cc_start: 0.8449 (mt) cc_final: 0.8088 (tt) REVERT: D 41 MET cc_start: 0.8710 (mmm) cc_final: 0.8374 (tpp) REVERT: D 50 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7199 (mt-10) REVERT: D 64 GLU cc_start: 0.8418 (tt0) cc_final: 0.7560 (tt0) REVERT: D 72 PHE cc_start: 0.8574 (t80) cc_final: 0.7934 (t80) REVERT: D 94 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7089 (mm-40) REVERT: D 121 LEU cc_start: 0.8222 (mt) cc_final: 0.7947 (mt) REVERT: D 147 LEU cc_start: 0.8406 (tp) cc_final: 0.8043 (tp) REVERT: D 170 MET cc_start: 0.7798 (ttt) cc_final: 0.7566 (ptp) REVERT: D 185 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8105 (ptmt) REVERT: D 201 TYR cc_start: 0.8045 (m-80) cc_final: 0.7418 (m-80) REVERT: D 232 PHE cc_start: 0.7274 (m-80) cc_final: 0.6941 (m-80) REVERT: D 243 LYS cc_start: 0.8779 (mttt) cc_final: 0.8501 (mttt) REVERT: D 270 GLN cc_start: 0.8139 (tp40) cc_final: 0.7772 (tp40) REVERT: D 272 MET cc_start: 0.7755 (tpp) cc_final: 0.7509 (tpp) REVERT: D 304 ARG cc_start: 0.7568 (mtp180) cc_final: 0.7217 (mtp180) REVERT: D 387 LYS cc_start: 0.8419 (mttt) cc_final: 0.8192 (mttt) REVERT: D 403 LYS cc_start: 0.7977 (mmtt) cc_final: 0.7312 (tptt) REVERT: D 425 MET cc_start: 0.7464 (ttp) cc_final: 0.7199 (ttp) REVERT: D 426 ASP cc_start: 0.8402 (t0) cc_final: 0.8005 (t0) REVERT: D 444 LYS cc_start: 0.6387 (mtpt) cc_final: 0.5514 (ttmm) REVERT: D 447 ASP cc_start: 0.7306 (p0) cc_final: 0.6994 (p0) REVERT: D 448 PHE cc_start: 0.8185 (t80) cc_final: 0.7692 (t80) REVERT: D 474 ARG cc_start: 0.7653 (ptm-80) cc_final: 0.7073 (ptt90) REVERT: D 481 THR cc_start: 0.8281 (m) cc_final: 0.7867 (p) REVERT: D 491 THR cc_start: 0.8150 (m) cc_final: 0.7776 (p) REVERT: E 50 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7514 (mt-10) REVERT: E 64 GLU cc_start: 0.8577 (tt0) cc_final: 0.7836 (tt0) REVERT: E 72 PHE cc_start: 0.8621 (t80) cc_final: 0.8034 (t80) REVERT: E 89 ARG cc_start: 0.8619 (mmm-85) cc_final: 0.8258 (mmm-85) REVERT: E 121 LEU cc_start: 0.8325 (mt) cc_final: 0.7588 (mt) REVERT: E 129 MET cc_start: 0.7074 (mtm) cc_final: 0.6404 (mtm) REVERT: E 135 LYS cc_start: 0.7784 (ttmt) cc_final: 0.7484 (tptm) REVERT: E 170 MET cc_start: 0.7620 (ttt) cc_final: 0.7398 (ptp) REVERT: E 180 GLN cc_start: 0.8506 (mt0) cc_final: 0.7923 (mt0) REVERT: E 181 SER cc_start: 0.8838 (OUTLIER) cc_final: 0.8611 (p) REVERT: E 201 TYR cc_start: 0.7936 (m-80) cc_final: 0.7616 (m-80) REVERT: E 243 LYS cc_start: 0.8366 (mttt) cc_final: 0.8049 (mttt) REVERT: E 259 ASN cc_start: 0.7730 (t0) cc_final: 0.7506 (t0) REVERT: E 281 MET cc_start: 0.6894 (ttm) cc_final: 0.6346 (ttm) REVERT: E 282 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6780 (mt-10) REVERT: E 387 LYS cc_start: 0.8410 (mppt) cc_final: 0.7947 (mtmm) REVERT: E 425 MET cc_start: 0.7406 (ttp) cc_final: 0.7148 (ttp) REVERT: E 426 ASP cc_start: 0.8609 (t0) cc_final: 0.7923 (t70) REVERT: E 474 ARG cc_start: 0.7010 (ptp-110) cc_final: 0.6798 (ptp-110) REVERT: E 481 THR cc_start: 0.8320 (m) cc_final: 0.7848 (p) REVERT: E 501 GLU cc_start: 0.7038 (tt0) cc_final: 0.6708 (tt0) REVERT: F 72 PHE cc_start: 0.8515 (t80) cc_final: 0.7592 (t80) REVERT: F 87 TRP cc_start: 0.5879 (t-100) cc_final: 0.5519 (m-90) REVERT: F 89 ARG cc_start: 0.8447 (mmm-85) cc_final: 0.7935 (ttt90) REVERT: F 129 MET cc_start: 0.7154 (mtm) cc_final: 0.6923 (mtm) REVERT: F 135 LYS cc_start: 0.8388 (tptp) cc_final: 0.7933 (tptp) REVERT: F 168 VAL cc_start: 0.9079 (t) cc_final: 0.8724 (p) REVERT: F 170 MET cc_start: 0.7839 (ttt) cc_final: 0.7491 (ptp) REVERT: F 171 ASN cc_start: 0.7801 (m-40) cc_final: 0.7573 (p0) REVERT: F 181 SER cc_start: 0.9023 (OUTLIER) cc_final: 0.8756 (p) REVERT: F 185 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8088 (ptmm) REVERT: F 201 TYR cc_start: 0.7980 (m-80) cc_final: 0.7291 (m-80) REVERT: F 232 PHE cc_start: 0.7109 (m-80) cc_final: 0.6810 (m-80) REVERT: F 243 LYS cc_start: 0.8483 (mttt) cc_final: 0.8236 (mttt) REVERT: F 272 MET cc_start: 0.7196 (tpp) cc_final: 0.6975 (tpp) REVERT: F 281 MET cc_start: 0.6734 (ttm) cc_final: 0.6272 (ttm) REVERT: F 282 GLU cc_start: 0.7316 (mt-10) cc_final: 0.7038 (mt-10) REVERT: F 286 LYS cc_start: 0.8232 (mttm) cc_final: 0.8012 (mttm) REVERT: F 340 ILE cc_start: 0.9025 (mt) cc_final: 0.8718 (mt) REVERT: F 398 ARG cc_start: 0.8541 (tpp-160) cc_final: 0.8030 (tpt170) REVERT: F 425 MET cc_start: 0.7426 (ttp) cc_final: 0.7188 (ttp) REVERT: F 426 ASP cc_start: 0.8441 (t0) cc_final: 0.8018 (t70) REVERT: F 443 LYS cc_start: 0.7861 (mttm) cc_final: 0.7197 (mptp) REVERT: F 444 LYS cc_start: 0.6463 (mtpt) cc_final: 0.6168 (ttmm) REVERT: F 450 LYS cc_start: 0.8282 (ttpp) cc_final: 0.8080 (ttpp) REVERT: F 481 THR cc_start: 0.8031 (m) cc_final: 0.7551 (p) REVERT: F 491 THR cc_start: 0.8124 (m) cc_final: 0.7803 (t) REVERT: G 41 MET cc_start: 0.7929 (mmm) cc_final: 0.7698 (mmm) REVERT: G 64 GLU cc_start: 0.8520 (tt0) cc_final: 0.7805 (tt0) REVERT: G 72 PHE cc_start: 0.8627 (t80) cc_final: 0.7866 (t80) REVERT: G 89 ARG cc_start: 0.8838 (mmm-85) cc_final: 0.8402 (mmm-85) REVERT: G 102 ASP cc_start: 0.8065 (m-30) cc_final: 0.7807 (p0) REVERT: G 129 MET cc_start: 0.6827 (mtm) cc_final: 0.6379 (mtm) REVERT: G 135 LYS cc_start: 0.8010 (ttmm) cc_final: 0.7220 (tptm) REVERT: G 147 LEU cc_start: 0.8545 (tp) cc_final: 0.8292 (tp) REVERT: G 170 MET cc_start: 0.7847 (ptp) cc_final: 0.7531 (ptp) REVERT: G 180 GLN cc_start: 0.8551 (mt0) cc_final: 0.8117 (mt0) REVERT: G 232 PHE cc_start: 0.7111 (m-80) cc_final: 0.6697 (m-80) REVERT: G 242 ASP cc_start: 0.8775 (m-30) cc_final: 0.8394 (t0) REVERT: G 243 LYS cc_start: 0.8856 (mttt) cc_final: 0.8528 (mttt) REVERT: G 259 ASN cc_start: 0.7901 (t0) cc_final: 0.7600 (t0) REVERT: G 272 MET cc_start: 0.7599 (tpp) cc_final: 0.7131 (tpp) REVERT: G 282 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6426 (mt-10) REVERT: G 283 LEU cc_start: 0.7798 (mt) cc_final: 0.7440 (mm) REVERT: G 304 ARG cc_start: 0.8123 (ttt180) cc_final: 0.7841 (mtp180) REVERT: G 414 ASP cc_start: 0.7879 (p0) cc_final: 0.7542 (t0) REVERT: G 417 ARG cc_start: 0.6272 (mtt-85) cc_final: 0.5807 (mtm-85) REVERT: G 425 MET cc_start: 0.7518 (ttp) cc_final: 0.7240 (ttp) REVERT: G 426 ASP cc_start: 0.8641 (t0) cc_final: 0.8154 (t70) REVERT: G 443 LYS cc_start: 0.7992 (mtmm) cc_final: 0.7452 (mttm) REVERT: G 481 THR cc_start: 0.8245 (m) cc_final: 0.7811 (p) REVERT: G 501 GLU cc_start: 0.7005 (tt0) cc_final: 0.6768 (tt0) REVERT: H 41 MET cc_start: 0.7796 (tpp) cc_final: 0.7528 (tpp) REVERT: H 72 PHE cc_start: 0.8788 (t80) cc_final: 0.8059 (t80) REVERT: H 89 ARG cc_start: 0.8665 (mmm-85) cc_final: 0.8221 (mmm-85) REVERT: H 102 ASP cc_start: 0.8113 (m-30) cc_final: 0.7384 (p0) REVERT: H 121 LEU cc_start: 0.8231 (mt) cc_final: 0.7541 (mt) REVERT: H 129 MET cc_start: 0.7219 (mtm) cc_final: 0.6469 (mtm) REVERT: H 141 ARG cc_start: 0.7623 (mtp85) cc_final: 0.7263 (ttm-80) REVERT: H 168 VAL cc_start: 0.9114 (t) cc_final: 0.8785 (p) REVERT: H 170 MET cc_start: 0.7904 (ttt) cc_final: 0.7365 (ptp) REVERT: H 171 ASN cc_start: 0.7919 (m-40) cc_final: 0.7408 (p0) REVERT: H 180 GLN cc_start: 0.8568 (mt0) cc_final: 0.8168 (mt0) REVERT: H 185 LYS cc_start: 0.8498 (ptmt) cc_final: 0.8104 (ptmt) REVERT: H 201 TYR cc_start: 0.8166 (m-80) cc_final: 0.7605 (m-80) REVERT: H 232 PHE cc_start: 0.7217 (m-10) cc_final: 0.6909 (m-80) REVERT: H 254 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6493 (tp) REVERT: H 267 ARG cc_start: 0.8574 (tpp80) cc_final: 0.8127 (tpt90) REVERT: H 272 MET cc_start: 0.7462 (tpp) cc_final: 0.7162 (tpp) REVERT: H 281 MET cc_start: 0.6794 (ttm) cc_final: 0.6543 (ttm) REVERT: H 282 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6429 (mt-10) REVERT: H 283 LEU cc_start: 0.8018 (mt) cc_final: 0.7639 (mm) REVERT: H 304 ARG cc_start: 0.8033 (mtt180) cc_final: 0.7401 (mtt180) REVERT: H 403 LYS cc_start: 0.8085 (mmtt) cc_final: 0.7881 (mmtt) REVERT: H 425 MET cc_start: 0.7474 (ttp) cc_final: 0.7209 (ttp) REVERT: H 426 ASP cc_start: 0.8277 (t0) cc_final: 0.7985 (t0) REVERT: H 443 LYS cc_start: 0.7907 (mtmm) cc_final: 0.7557 (mtmm) REVERT: H 481 THR cc_start: 0.8353 (m) cc_final: 0.7880 (p) outliers start: 95 outliers final: 66 residues processed: 1033 average time/residue: 0.4794 time to fit residues: 736.4105 Evaluate side-chains 1023 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 947 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 503 CYS Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 503 CYS Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 503 CYS Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 185 LYS Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 503 CYS Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 161 TYR Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 503 CYS Chi-restraints excluded: chain E residue 513 GLU Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 449 GLN Chi-restraints excluded: chain F residue 474 ARG Chi-restraints excluded: chain F residue 503 CYS Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain G residue 503 CYS Chi-restraints excluded: chain G residue 504 VAL Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 307 GLU Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 503 CYS Chi-restraints excluded: chain H residue 504 VAL Chi-restraints excluded: chain H residue 513 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 67 optimal weight: 1.9990 chunk 268 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 272 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 171 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.179608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.138857 restraints weight = 54574.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.144267 restraints weight = 30190.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.147714 restraints weight = 19392.078| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30368 Z= 0.151 Angle : 0.632 14.809 41088 Z= 0.323 Chirality : 0.047 0.251 4672 Planarity : 0.005 0.057 5352 Dihedral : 4.457 39.636 4058 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.58 % Allowed : 16.14 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3720 helix: 0.27 (0.16), residues: 1120 sheet: -0.05 (0.20), residues: 704 loop : 0.33 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 87 HIS 0.005 0.001 HIS C 463 PHE 0.019 0.001 PHE C 232 TYR 0.030 0.002 TYR B 224 ARG 0.011 0.001 ARG F 304 Details of bonding type rmsd hydrogen bonds : bond 0.04897 ( 1087) hydrogen bonds : angle 5.15358 ( 2733) covalent geometry : bond 0.00327 (30368) covalent geometry : angle 0.63164 (41088) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 974 time to evaluate : 3.245 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8487 (tt0) cc_final: 0.7937 (tt0) REVERT: A 65 MET cc_start: 0.8339 (mmm) cc_final: 0.7904 (mmm) REVERT: A 72 PHE cc_start: 0.8545 (t80) cc_final: 0.8129 (t80) REVERT: A 89 ARG cc_start: 0.8664 (mtp85) cc_final: 0.8429 (mmm-85) REVERT: A 102 ASP cc_start: 0.8101 (m-30) cc_final: 0.7844 (p0) REVERT: A 170 MET cc_start: 0.7501 (ptp) cc_final: 0.7266 (ptp) REVERT: A 180 GLN cc_start: 0.7917 (mt0) cc_final: 0.7532 (mp10) REVERT: A 185 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8149 (ptmt) REVERT: A 201 TYR cc_start: 0.7947 (m-80) cc_final: 0.7655 (m-80) REVERT: A 280 ILE cc_start: 0.6399 (mt) cc_final: 0.6118 (mm) REVERT: A 282 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6644 (mt-10) REVERT: A 341 LYS cc_start: 0.9088 (tttt) cc_final: 0.8771 (ttpp) REVERT: A 374 GLN cc_start: 0.6679 (mm110) cc_final: 0.6469 (mm-40) REVERT: A 386 PHE cc_start: 0.7525 (m-80) cc_final: 0.7315 (m-80) REVERT: A 400 LEU cc_start: 0.8281 (tp) cc_final: 0.8064 (tt) REVERT: A 425 MET cc_start: 0.7510 (ttp) cc_final: 0.7284 (ttp) REVERT: A 426 ASP cc_start: 0.8257 (t0) cc_final: 0.7800 (t0) REVERT: A 481 THR cc_start: 0.8435 (m) cc_final: 0.8054 (p) REVERT: A 498 SER cc_start: 0.8220 (m) cc_final: 0.7777 (p) REVERT: B 41 MET cc_start: 0.8628 (mmm) cc_final: 0.8373 (mmm) REVERT: B 50 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7102 (mt-10) REVERT: B 64 GLU cc_start: 0.8506 (tt0) cc_final: 0.7804 (tt0) REVERT: B 72 PHE cc_start: 0.8417 (t80) cc_final: 0.7879 (t80) REVERT: B 94 GLN cc_start: 0.7738 (mm-40) cc_final: 0.7228 (mm-40) REVERT: B 141 ARG cc_start: 0.7505 (ttm-80) cc_final: 0.7202 (ptm160) REVERT: B 170 MET cc_start: 0.7698 (ptp) cc_final: 0.7358 (ptp) REVERT: B 181 SER cc_start: 0.9006 (OUTLIER) cc_final: 0.8684 (p) REVERT: B 184 LYS cc_start: 0.8460 (mttp) cc_final: 0.8246 (mmtm) REVERT: B 200 ARG cc_start: 0.6505 (mtp-110) cc_final: 0.6218 (ttp80) REVERT: B 232 PHE cc_start: 0.6817 (m-10) cc_final: 0.6347 (m-80) REVERT: B 259 ASN cc_start: 0.7341 (t0) cc_final: 0.6717 (p0) REVERT: B 260 LEU cc_start: 0.8311 (mt) cc_final: 0.8001 (mm) REVERT: B 267 ARG cc_start: 0.8452 (ttm170) cc_final: 0.8205 (tpt-90) REVERT: B 270 GLN cc_start: 0.8726 (tp-100) cc_final: 0.8502 (tp-100) REVERT: B 282 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6567 (mt-10) REVERT: B 318 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7975 (mt-10) REVERT: B 340 ILE cc_start: 0.9084 (mt) cc_final: 0.8636 (mt) REVERT: B 341 LYS cc_start: 0.9210 (pttm) cc_final: 0.8948 (pttt) REVERT: B 374 GLN cc_start: 0.6920 (mm110) cc_final: 0.6698 (mm-40) REVERT: B 415 LEU cc_start: 0.8492 (tp) cc_final: 0.8252 (tt) REVERT: B 425 MET cc_start: 0.7444 (ttp) cc_final: 0.7012 (ttp) REVERT: B 426 ASP cc_start: 0.8450 (t0) cc_final: 0.7924 (t0) REVERT: B 443 LYS cc_start: 0.7863 (mtpp) cc_final: 0.7557 (mtmm) REVERT: B 450 LYS cc_start: 0.8207 (ttpp) cc_final: 0.7871 (ttpp) REVERT: B 479 LYS cc_start: 0.7105 (mttt) cc_final: 0.6753 (mttp) REVERT: B 481 THR cc_start: 0.8284 (m) cc_final: 0.7871 (p) REVERT: B 491 THR cc_start: 0.8024 (m) cc_final: 0.7716 (t) REVERT: C 41 MET cc_start: 0.8546 (mmm) cc_final: 0.8199 (mmm) REVERT: C 64 GLU cc_start: 0.8367 (tt0) cc_final: 0.7492 (tt0) REVERT: C 72 PHE cc_start: 0.8645 (t80) cc_final: 0.8085 (t80) REVERT: C 74 ARG cc_start: 0.8435 (ttm110) cc_final: 0.7869 (ptp-170) REVERT: C 94 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7421 (mm-40) REVERT: C 135 LYS cc_start: 0.8006 (ttmt) cc_final: 0.7582 (mtpp) REVERT: C 180 GLN cc_start: 0.8018 (mt0) cc_final: 0.7744 (mt0) REVERT: C 181 SER cc_start: 0.8720 (OUTLIER) cc_final: 0.8494 (p) REVERT: C 201 TYR cc_start: 0.7907 (m-80) cc_final: 0.7129 (m-80) REVERT: C 221 GLN cc_start: 0.7933 (tp40) cc_final: 0.7683 (tp40) REVERT: C 232 PHE cc_start: 0.7037 (m-80) cc_final: 0.6551 (m-80) REVERT: C 243 LYS cc_start: 0.8553 (mttt) cc_final: 0.8270 (mttt) REVERT: C 272 MET cc_start: 0.7557 (tpp) cc_final: 0.7328 (tpp) REVERT: C 282 GLU cc_start: 0.6725 (mt-10) cc_final: 0.6152 (mt-10) REVERT: C 283 LEU cc_start: 0.7706 (mt) cc_final: 0.7355 (mm) REVERT: C 304 ARG cc_start: 0.8127 (mmt180) cc_final: 0.7900 (mmt180) REVERT: C 335 MET cc_start: 0.4399 (mtt) cc_final: 0.3459 (mtt) REVERT: C 425 MET cc_start: 0.7620 (ttp) cc_final: 0.7393 (ttp) REVERT: C 426 ASP cc_start: 0.8562 (t0) cc_final: 0.8205 (t70) REVERT: C 443 LYS cc_start: 0.7855 (mttm) cc_final: 0.7499 (mttm) REVERT: C 447 ASP cc_start: 0.7419 (p0) cc_final: 0.7198 (p0) REVERT: C 450 LYS cc_start: 0.8323 (ttpp) cc_final: 0.8101 (ttpp) REVERT: C 479 LYS cc_start: 0.6990 (mttt) cc_final: 0.6676 (mtmm) REVERT: C 481 THR cc_start: 0.8014 (m) cc_final: 0.7599 (p) REVERT: C 498 SER cc_start: 0.8434 (m) cc_final: 0.8005 (p) REVERT: C 511 ILE cc_start: 0.8466 (mt) cc_final: 0.8108 (tt) REVERT: D 50 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7133 (mt-10) REVERT: D 64 GLU cc_start: 0.8450 (tt0) cc_final: 0.7573 (tt0) REVERT: D 72 PHE cc_start: 0.8601 (t80) cc_final: 0.8010 (t80) REVERT: D 94 GLN cc_start: 0.7697 (mm-40) cc_final: 0.7092 (mm-40) REVERT: D 121 LEU cc_start: 0.8284 (mt) cc_final: 0.7877 (mt) REVERT: D 147 LEU cc_start: 0.8446 (tp) cc_final: 0.8149 (tp) REVERT: D 185 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8111 (ptmt) REVERT: D 201 TYR cc_start: 0.8059 (m-80) cc_final: 0.7366 (m-80) REVERT: D 232 PHE cc_start: 0.7269 (m-80) cc_final: 0.6945 (m-80) REVERT: D 243 LYS cc_start: 0.8789 (mttt) cc_final: 0.8484 (mttt) REVERT: D 267 ARG cc_start: 0.8200 (ttt180) cc_final: 0.7884 (ttt-90) REVERT: D 270 GLN cc_start: 0.8129 (tp40) cc_final: 0.7769 (tp40) REVERT: D 326 LYS cc_start: 0.7768 (ptpt) cc_final: 0.7190 (mmtt) REVERT: D 341 LYS cc_start: 0.8914 (pttp) cc_final: 0.8690 (ptpp) REVERT: D 387 LYS cc_start: 0.8437 (mttt) cc_final: 0.8198 (mttt) REVERT: D 398 ARG cc_start: 0.8294 (tpp-160) cc_final: 0.7633 (tpt170) REVERT: D 403 LYS cc_start: 0.7962 (mmtt) cc_final: 0.7310 (tptt) REVERT: D 425 MET cc_start: 0.7477 (ttp) cc_final: 0.7228 (ttp) REVERT: D 426 ASP cc_start: 0.8394 (t0) cc_final: 0.8007 (t0) REVERT: D 443 LYS cc_start: 0.7640 (mtpp) cc_final: 0.7375 (mttm) REVERT: D 447 ASP cc_start: 0.7384 (p0) cc_final: 0.7109 (p0) REVERT: D 448 PHE cc_start: 0.8224 (t80) cc_final: 0.7668 (t80) REVERT: D 481 THR cc_start: 0.8288 (m) cc_final: 0.7906 (p) REVERT: D 491 THR cc_start: 0.8169 (m) cc_final: 0.7787 (p) REVERT: E 41 MET cc_start: 0.8385 (mmm) cc_final: 0.8034 (mmm) REVERT: E 50 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7508 (mt-10) REVERT: E 64 GLU cc_start: 0.8582 (tt0) cc_final: 0.7833 (tt0) REVERT: E 72 PHE cc_start: 0.8614 (t80) cc_final: 0.7947 (t80) REVERT: E 89 ARG cc_start: 0.8560 (mmm-85) cc_final: 0.8208 (mmm-85) REVERT: E 121 LEU cc_start: 0.8340 (mt) cc_final: 0.7344 (mt) REVERT: E 129 MET cc_start: 0.7056 (mtm) cc_final: 0.6364 (mtm) REVERT: E 135 LYS cc_start: 0.7833 (ttmt) cc_final: 0.7528 (tptm) REVERT: E 180 GLN cc_start: 0.8442 (mt0) cc_final: 0.7972 (mt0) REVERT: E 201 TYR cc_start: 0.7943 (m-80) cc_final: 0.7559 (m-80) REVERT: E 224 TYR cc_start: 0.6886 (p90) cc_final: 0.6420 (p90) REVERT: E 243 LYS cc_start: 0.8369 (mttt) cc_final: 0.8026 (mttt) REVERT: E 281 MET cc_start: 0.6968 (ttm) cc_final: 0.6411 (ttm) REVERT: E 282 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6732 (mt-10) REVERT: E 304 ARG cc_start: 0.8012 (mmt180) cc_final: 0.7757 (mmt180) REVERT: E 387 LYS cc_start: 0.8384 (mppt) cc_final: 0.8007 (mtmm) REVERT: E 425 MET cc_start: 0.7372 (ttp) cc_final: 0.7147 (ttp) REVERT: E 474 ARG cc_start: 0.7018 (ptp-110) cc_final: 0.6813 (ptp-110) REVERT: E 481 THR cc_start: 0.8371 (m) cc_final: 0.7897 (p) REVERT: E 501 GLU cc_start: 0.7066 (tt0) cc_final: 0.6723 (tt0) REVERT: F 72 PHE cc_start: 0.8506 (t80) cc_final: 0.7578 (t80) REVERT: F 89 ARG cc_start: 0.8427 (mmm-85) cc_final: 0.7933 (ttt90) REVERT: F 129 MET cc_start: 0.7267 (mtm) cc_final: 0.6919 (mtm) REVERT: F 135 LYS cc_start: 0.8436 (tptp) cc_final: 0.7935 (tptm) REVERT: F 168 VAL cc_start: 0.9069 (t) cc_final: 0.8777 (p) REVERT: F 170 MET cc_start: 0.7863 (ttt) cc_final: 0.7526 (ptp) REVERT: F 171 ASN cc_start: 0.7847 (m-40) cc_final: 0.7425 (p0) REVERT: F 185 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7962 (ptmm) REVERT: F 201 TYR cc_start: 0.7958 (m-80) cc_final: 0.7214 (m-80) REVERT: F 224 TYR cc_start: 0.6783 (p90) cc_final: 0.6156 (p90) REVERT: F 232 PHE cc_start: 0.7135 (m-80) cc_final: 0.6842 (m-80) REVERT: F 243 LYS cc_start: 0.8516 (mttt) cc_final: 0.8260 (mttt) REVERT: F 272 MET cc_start: 0.7157 (tpp) cc_final: 0.6748 (tpp) REVERT: F 281 MET cc_start: 0.6722 (ttm) cc_final: 0.6091 (ttm) REVERT: F 282 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7022 (mt-10) REVERT: F 283 LEU cc_start: 0.7986 (mt) cc_final: 0.7665 (mm) REVERT: F 286 LYS cc_start: 0.8273 (mttm) cc_final: 0.8010 (mttm) REVERT: F 304 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6815 (mtt90) REVERT: F 326 LYS cc_start: 0.7884 (ptpt) cc_final: 0.7286 (mptt) REVERT: F 340 ILE cc_start: 0.9027 (mt) cc_final: 0.8805 (mt) REVERT: F 341 LYS cc_start: 0.9140 (pttt) cc_final: 0.8788 (pmtt) REVERT: F 425 MET cc_start: 0.7428 (ttp) cc_final: 0.7150 (ttp) REVERT: F 426 ASP cc_start: 0.8461 (t0) cc_final: 0.8199 (t70) REVERT: F 443 LYS cc_start: 0.7896 (mttm) cc_final: 0.7425 (mptp) REVERT: F 481 THR cc_start: 0.8059 (m) cc_final: 0.7574 (p) REVERT: G 41 MET cc_start: 0.7930 (mmm) cc_final: 0.7687 (mmm) REVERT: G 50 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7428 (mt-10) REVERT: G 64 GLU cc_start: 0.8534 (tt0) cc_final: 0.7944 (tt0) REVERT: G 72 PHE cc_start: 0.8625 (t80) cc_final: 0.7860 (t80) REVERT: G 89 ARG cc_start: 0.8802 (mmm-85) cc_final: 0.8379 (mmm-85) REVERT: G 102 ASP cc_start: 0.8076 (m-30) cc_final: 0.7735 (p0) REVERT: G 129 MET cc_start: 0.6855 (mtm) cc_final: 0.6500 (mtm) REVERT: G 135 LYS cc_start: 0.8117 (ttmm) cc_final: 0.7167 (tptm) REVERT: G 180 GLN cc_start: 0.8540 (mt0) cc_final: 0.8130 (mt0) REVERT: G 200 ARG cc_start: 0.6877 (mtp-110) cc_final: 0.6464 (ttp80) REVERT: G 232 PHE cc_start: 0.7043 (m-10) cc_final: 0.6605 (m-80) REVERT: G 243 LYS cc_start: 0.8856 (mttt) cc_final: 0.8534 (mttt) REVERT: G 259 ASN cc_start: 0.7932 (t0) cc_final: 0.7648 (t0) REVERT: G 272 MET cc_start: 0.7546 (tpp) cc_final: 0.7136 (tpp) REVERT: G 282 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6604 (mt-10) REVERT: G 304 ARG cc_start: 0.8144 (ttt180) cc_final: 0.7476 (mtt180) REVERT: G 326 LYS cc_start: 0.7886 (ptpt) cc_final: 0.7276 (mptt) REVERT: G 414 ASP cc_start: 0.7792 (p0) cc_final: 0.7555 (t0) REVERT: G 417 ARG cc_start: 0.6262 (mtt-85) cc_final: 0.5790 (mtm-85) REVERT: G 425 MET cc_start: 0.7540 (ttp) cc_final: 0.7269 (ttp) REVERT: G 426 ASP cc_start: 0.8623 (t0) cc_final: 0.8207 (t0) REVERT: G 443 LYS cc_start: 0.8046 (mtmm) cc_final: 0.7530 (mttm) REVERT: G 444 LYS cc_start: 0.6386 (mtpt) cc_final: 0.6029 (ttmm) REVERT: G 481 THR cc_start: 0.8303 (m) cc_final: 0.7845 (p) REVERT: G 501 GLU cc_start: 0.7058 (tt0) cc_final: 0.6672 (tt0) REVERT: H 41 MET cc_start: 0.7853 (tpp) cc_final: 0.7578 (tpp) REVERT: H 64 GLU cc_start: 0.8572 (tt0) cc_final: 0.7859 (tt0) REVERT: H 72 PHE cc_start: 0.8775 (t80) cc_final: 0.8060 (t80) REVERT: H 74 ARG cc_start: 0.8686 (mtm-85) cc_final: 0.8360 (ttm110) REVERT: H 89 ARG cc_start: 0.8633 (mmm-85) cc_final: 0.8240 (mmm-85) REVERT: H 102 ASP cc_start: 0.8133 (m-30) cc_final: 0.7500 (p0) REVERT: H 121 LEU cc_start: 0.8256 (mt) cc_final: 0.7298 (mt) REVERT: H 141 ARG cc_start: 0.7628 (mtp85) cc_final: 0.7291 (ttm-80) REVERT: H 168 VAL cc_start: 0.9188 (t) cc_final: 0.8837 (p) REVERT: H 170 MET cc_start: 0.7876 (ttt) cc_final: 0.7437 (ptp) REVERT: H 171 ASN cc_start: 0.7947 (m-40) cc_final: 0.7440 (p0) REVERT: H 180 GLN cc_start: 0.8565 (mt0) cc_final: 0.8167 (mt0) REVERT: H 185 LYS cc_start: 0.8500 (ptmt) cc_final: 0.8068 (ptmt) REVERT: H 201 TYR cc_start: 0.8164 (m-80) cc_final: 0.7552 (m-80) REVERT: H 232 PHE cc_start: 0.7167 (m-10) cc_final: 0.6781 (m-80) REVERT: H 254 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6451 (tp) REVERT: H 267 ARG cc_start: 0.8614 (tpp80) cc_final: 0.8278 (tpp80) REVERT: H 272 MET cc_start: 0.7446 (tpp) cc_final: 0.7185 (tpp) REVERT: H 282 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6378 (mt-10) REVERT: H 283 LEU cc_start: 0.7932 (mt) cc_final: 0.7610 (mm) REVERT: H 304 ARG cc_start: 0.8041 (mtt180) cc_final: 0.7446 (mtt180) REVERT: H 340 ILE cc_start: 0.9190 (mt) cc_final: 0.8688 (mt) REVERT: H 398 ARG cc_start: 0.8605 (tpp-160) cc_final: 0.8345 (tpp-160) REVERT: H 426 ASP cc_start: 0.8283 (t0) cc_final: 0.7838 (t0) REVERT: H 481 THR cc_start: 0.8386 (m) cc_final: 0.7917 (p) outliers start: 119 outliers final: 77 residues processed: 1027 average time/residue: 0.4605 time to fit residues: 706.0527 Evaluate side-chains 1025 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 941 time to evaluate : 2.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 503 CYS Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 503 CYS Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 503 CYS Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 185 LYS Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 503 CYS Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 420 HIS Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 503 CYS Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 513 GLU Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 304 ARG Chi-restraints excluded: chain F residue 387 LYS Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 474 ARG Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 503 CYS Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain G residue 284 THR Chi-restraints excluded: chain G residue 315 HIS Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 449 GLN Chi-restraints excluded: chain G residue 503 CYS Chi-restraints excluded: chain G residue 504 VAL Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 307 GLU Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain H residue 423 LEU Chi-restraints excluded: chain H residue 503 CYS Chi-restraints excluded: chain H residue 504 VAL Chi-restraints excluded: chain H residue 513 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 18 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 284 optimal weight: 6.9990 chunk 229 optimal weight: 1.9990 chunk 155 optimal weight: 0.4980 chunk 85 optimal weight: 8.9990 chunk 243 optimal weight: 4.9990 chunk 222 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 259 ASN ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 HIS A 514 HIS B 463 HIS ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 HIS E 259 ASN E 374 GLN E 463 HIS F 374 GLN H 463 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.179160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.137811 restraints weight = 54692.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.143172 restraints weight = 30256.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.146707 restraints weight = 19497.328| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 30368 Z= 0.238 Angle : 0.696 13.911 41088 Z= 0.359 Chirality : 0.049 0.298 4672 Planarity : 0.005 0.073 5352 Dihedral : 4.980 48.551 4058 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.01 % Allowed : 17.05 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.14), residues: 3720 helix: 0.10 (0.16), residues: 1120 sheet: -0.62 (0.22), residues: 592 loop : 0.12 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP G 87 HIS 0.007 0.002 HIS D 463 PHE 0.021 0.002 PHE F 325 TYR 0.028 0.002 TYR D 327 ARG 0.008 0.001 ARG G 60 Details of bonding type rmsd hydrogen bonds : bond 0.05425 ( 1087) hydrogen bonds : angle 5.32974 ( 2733) covalent geometry : bond 0.00515 (30368) covalent geometry : angle 0.69559 (41088) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1144 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 1011 time to evaluate : 3.872 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8686 (mmm) cc_final: 0.8446 (mmm) REVERT: A 64 GLU cc_start: 0.8579 (tt0) cc_final: 0.8054 (tt0) REVERT: A 65 MET cc_start: 0.8331 (mmm) cc_final: 0.7947 (mmm) REVERT: A 72 PHE cc_start: 0.8649 (t80) cc_final: 0.8217 (t80) REVERT: A 102 ASP cc_start: 0.8207 (m-30) cc_final: 0.7845 (p0) REVERT: A 170 MET cc_start: 0.7394 (ptp) cc_final: 0.7066 (ptp) REVERT: A 180 GLN cc_start: 0.7914 (mt0) cc_final: 0.7500 (mp10) REVERT: A 185 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8164 (ptmt) REVERT: A 197 ASN cc_start: 0.7085 (t0) cc_final: 0.6844 (t0) REVERT: A 228 HIS cc_start: 0.6747 (m170) cc_final: 0.6483 (m170) REVERT: A 259 ASN cc_start: 0.7542 (OUTLIER) cc_final: 0.7136 (p0) REVERT: A 280 ILE cc_start: 0.6821 (mt) cc_final: 0.6508 (mm) REVERT: A 282 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7040 (mt-10) REVERT: A 341 LYS cc_start: 0.9127 (tttt) cc_final: 0.8770 (ttpp) REVERT: A 386 PHE cc_start: 0.7564 (m-80) cc_final: 0.7137 (m-80) REVERT: A 398 ARG cc_start: 0.8532 (tpp-160) cc_final: 0.7843 (ttp-110) REVERT: A 400 LEU cc_start: 0.8236 (tp) cc_final: 0.8000 (tt) REVERT: A 412 LYS cc_start: 0.7774 (mttt) cc_final: 0.7405 (mttp) REVERT: A 425 MET cc_start: 0.7551 (ttp) cc_final: 0.7287 (ttp) REVERT: A 426 ASP cc_start: 0.8313 (t0) cc_final: 0.7859 (t0) REVERT: A 438 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7717 (mp) REVERT: A 481 THR cc_start: 0.8617 (m) cc_final: 0.8177 (p) REVERT: B 41 MET cc_start: 0.8676 (mmm) cc_final: 0.8419 (mmm) REVERT: B 54 ASP cc_start: 0.8074 (t70) cc_final: 0.7850 (t70) REVERT: B 64 GLU cc_start: 0.8645 (tt0) cc_final: 0.7901 (tt0) REVERT: B 72 PHE cc_start: 0.8459 (t80) cc_final: 0.7939 (t80) REVERT: B 74 ARG cc_start: 0.8221 (ttm110) cc_final: 0.7774 (ptp-170) REVERT: B 89 ARG cc_start: 0.8543 (mmm-85) cc_final: 0.8163 (mmm-85) REVERT: B 94 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7249 (mm-40) REVERT: B 147 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8431 (tp) REVERT: B 168 VAL cc_start: 0.9194 (t) cc_final: 0.8929 (p) REVERT: B 200 ARG cc_start: 0.6657 (mtp-110) cc_final: 0.6313 (ttp80) REVERT: B 232 PHE cc_start: 0.6896 (m-10) cc_final: 0.6424 (m-80) REVERT: B 259 ASN cc_start: 0.7442 (t0) cc_final: 0.6866 (p0) REVERT: B 260 LEU cc_start: 0.8333 (mt) cc_final: 0.8008 (mm) REVERT: B 267 ARG cc_start: 0.8390 (ttm170) cc_final: 0.8172 (tpt-90) REVERT: B 270 GLN cc_start: 0.8753 (tp-100) cc_final: 0.8542 (tp-100) REVERT: B 280 ILE cc_start: 0.7163 (mm) cc_final: 0.6883 (mm) REVERT: B 282 GLU cc_start: 0.7308 (mt-10) cc_final: 0.6618 (mt-10) REVERT: B 318 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8055 (mt-10) REVERT: B 340 ILE cc_start: 0.9068 (mt) cc_final: 0.8613 (mt) REVERT: B 341 LYS cc_start: 0.9267 (pttm) cc_final: 0.9000 (pttt) REVERT: B 374 GLN cc_start: 0.6829 (mm110) cc_final: 0.6367 (mm-40) REVERT: B 386 PHE cc_start: 0.7691 (m-80) cc_final: 0.7489 (m-80) REVERT: B 398 ARG cc_start: 0.8667 (tpp-160) cc_final: 0.8368 (tpp-160) REVERT: B 415 LEU cc_start: 0.8596 (tp) cc_final: 0.8266 (tt) REVERT: B 425 MET cc_start: 0.7491 (ttp) cc_final: 0.7080 (ttp) REVERT: B 426 ASP cc_start: 0.8503 (t0) cc_final: 0.8071 (t0) REVERT: B 437 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7507 (mtmt) REVERT: B 443 LYS cc_start: 0.7812 (mtpp) cc_final: 0.7393 (mttm) REVERT: B 444 LYS cc_start: 0.6727 (mtpt) cc_final: 0.6272 (ttmm) REVERT: B 479 LYS cc_start: 0.7240 (mttt) cc_final: 0.6936 (mtmm) REVERT: B 481 THR cc_start: 0.8352 (m) cc_final: 0.7940 (p) REVERT: B 491 THR cc_start: 0.8104 (m) cc_final: 0.7722 (t) REVERT: C 41 MET cc_start: 0.8561 (mmm) cc_final: 0.8257 (mmm) REVERT: C 64 GLU cc_start: 0.8448 (tt0) cc_final: 0.7854 (tt0) REVERT: C 72 PHE cc_start: 0.8693 (t80) cc_final: 0.8106 (t80) REVERT: C 89 ARG cc_start: 0.8908 (mmm-85) cc_final: 0.8561 (mmm-85) REVERT: C 115 LYS cc_start: 0.8028 (mtmm) cc_final: 0.7260 (mmmt) REVERT: C 119 VAL cc_start: 0.6870 (OUTLIER) cc_final: 0.6554 (m) REVERT: C 135 LYS cc_start: 0.8171 (ttmt) cc_final: 0.7855 (ttmt) REVERT: C 139 GLU cc_start: 0.7023 (tm-30) cc_final: 0.6799 (tm-30) REVERT: C 168 VAL cc_start: 0.9104 (t) cc_final: 0.8895 (p) REVERT: C 179 THR cc_start: 0.8477 (m) cc_final: 0.8169 (p) REVERT: C 180 GLN cc_start: 0.8071 (mt0) cc_final: 0.7654 (mt0) REVERT: C 181 SER cc_start: 0.8745 (OUTLIER) cc_final: 0.8490 (p) REVERT: C 221 GLN cc_start: 0.8020 (tp40) cc_final: 0.7758 (tp40) REVERT: C 232 PHE cc_start: 0.7264 (m-80) cc_final: 0.6798 (m-80) REVERT: C 272 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7448 (tpp) REVERT: C 282 GLU cc_start: 0.6948 (mt-10) cc_final: 0.6286 (mt-10) REVERT: C 283 LEU cc_start: 0.7824 (mt) cc_final: 0.7451 (mm) REVERT: C 425 MET cc_start: 0.7619 (ttp) cc_final: 0.7302 (ttp) REVERT: C 443 LYS cc_start: 0.7886 (mttm) cc_final: 0.7449 (mttm) REVERT: C 448 PHE cc_start: 0.8103 (t80) cc_final: 0.7553 (t80) REVERT: C 450 LYS cc_start: 0.8400 (ttpp) cc_final: 0.8183 (ttpp) REVERT: C 479 LYS cc_start: 0.7120 (mttt) cc_final: 0.6766 (mtmm) REVERT: C 481 THR cc_start: 0.8088 (m) cc_final: 0.7655 (p) REVERT: C 499 VAL cc_start: 0.8492 (t) cc_final: 0.8169 (m) REVERT: D 64 GLU cc_start: 0.8495 (tt0) cc_final: 0.7702 (tt0) REVERT: D 65 MET cc_start: 0.8161 (mmm) cc_final: 0.7860 (mmm) REVERT: D 72 PHE cc_start: 0.8657 (t80) cc_final: 0.8058 (t80) REVERT: D 170 MET cc_start: 0.7923 (ptp) cc_final: 0.7602 (ptp) REVERT: D 179 THR cc_start: 0.8355 (m) cc_final: 0.8073 (p) REVERT: D 185 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8120 (ptmt) REVERT: D 201 TYR cc_start: 0.8119 (m-80) cc_final: 0.7574 (m-80) REVERT: D 232 PHE cc_start: 0.7399 (m-80) cc_final: 0.7047 (m-80) REVERT: D 270 GLN cc_start: 0.8171 (tp40) cc_final: 0.7788 (tp40) REVERT: D 272 MET cc_start: 0.7474 (tpp) cc_final: 0.7133 (tpp) REVERT: D 304 ARG cc_start: 0.7675 (mtp180) cc_final: 0.7355 (mtt180) REVERT: D 318 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7978 (mt-10) REVERT: D 341 LYS cc_start: 0.8978 (pttp) cc_final: 0.8710 (ptpp) REVERT: D 387 LYS cc_start: 0.8465 (mttt) cc_final: 0.8204 (mttt) REVERT: D 398 ARG cc_start: 0.8366 (tpp-160) cc_final: 0.8134 (tpp-160) REVERT: D 403 LYS cc_start: 0.7858 (mmtt) cc_final: 0.7238 (tptt) REVERT: D 426 ASP cc_start: 0.8400 (t0) cc_final: 0.8021 (t0) REVERT: D 437 LYS cc_start: 0.7684 (mptt) cc_final: 0.7442 (mptt) REVERT: D 443 LYS cc_start: 0.7646 (mtpp) cc_final: 0.7227 (mttm) REVERT: D 444 LYS cc_start: 0.6676 (mtpt) cc_final: 0.6385 (mtmm) REVERT: D 448 PHE cc_start: 0.8370 (t80) cc_final: 0.7846 (t80) REVERT: D 479 LYS cc_start: 0.7380 (mttt) cc_final: 0.6895 (mtmm) REVERT: D 481 THR cc_start: 0.8389 (m) cc_final: 0.7988 (p) REVERT: D 499 VAL cc_start: 0.8443 (t) cc_final: 0.8099 (p) REVERT: E 41 MET cc_start: 0.8387 (mmm) cc_final: 0.8183 (mmm) REVERT: E 64 GLU cc_start: 0.8664 (tt0) cc_final: 0.7957 (tt0) REVERT: E 72 PHE cc_start: 0.8643 (t80) cc_final: 0.7959 (t80) REVERT: E 89 ARG cc_start: 0.8626 (mmm-85) cc_final: 0.8329 (mmm-85) REVERT: E 129 MET cc_start: 0.7009 (mtm) cc_final: 0.6427 (mtm) REVERT: E 135 LYS cc_start: 0.8013 (ttmt) cc_final: 0.7718 (tptm) REVERT: E 147 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8263 (tp) REVERT: E 168 VAL cc_start: 0.9106 (t) cc_final: 0.8760 (p) REVERT: E 180 GLN cc_start: 0.8498 (mt0) cc_final: 0.7872 (mt0) REVERT: E 201 TYR cc_start: 0.7992 (m-80) cc_final: 0.7596 (m-80) REVERT: E 224 TYR cc_start: 0.6420 (p90) cc_final: 0.5961 (p90) REVERT: E 243 LYS cc_start: 0.8404 (mttt) cc_final: 0.8046 (mttt) REVERT: E 259 ASN cc_start: 0.7690 (OUTLIER) cc_final: 0.7049 (p0) REVERT: E 280 ILE cc_start: 0.7509 (mm) cc_final: 0.7233 (mm) REVERT: E 281 MET cc_start: 0.7159 (ttm) cc_final: 0.6296 (ttm) REVERT: E 283 LEU cc_start: 0.8038 (mt) cc_final: 0.7723 (mm) REVERT: E 374 GLN cc_start: 0.6646 (mm110) cc_final: 0.5982 (mm-40) REVERT: E 387 LYS cc_start: 0.8392 (mppt) cc_final: 0.7977 (mtmm) REVERT: E 419 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7813 (tm-30) REVERT: E 425 MET cc_start: 0.7412 (ttp) cc_final: 0.7043 (ttp) REVERT: E 426 ASP cc_start: 0.8406 (t0) cc_final: 0.8026 (t70) REVERT: E 437 LYS cc_start: 0.7748 (mmtt) cc_final: 0.7276 (mppt) REVERT: E 438 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7781 (mp) REVERT: E 481 THR cc_start: 0.8435 (m) cc_final: 0.7887 (p) REVERT: E 501 GLU cc_start: 0.7196 (tt0) cc_final: 0.6603 (tt0) REVERT: E 503 CYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7092 (m) REVERT: F 72 PHE cc_start: 0.8549 (t80) cc_final: 0.7632 (t80) REVERT: F 89 ARG cc_start: 0.8452 (mmm-85) cc_final: 0.8205 (ttt90) REVERT: F 129 MET cc_start: 0.7310 (mtm) cc_final: 0.7060 (mtm) REVERT: F 135 LYS cc_start: 0.8445 (tptp) cc_final: 0.8140 (tptp) REVERT: F 141 ARG cc_start: 0.7552 (ttm-80) cc_final: 0.7046 (ttt90) REVERT: F 168 VAL cc_start: 0.9079 (t) cc_final: 0.8798 (p) REVERT: F 171 ASN cc_start: 0.7988 (m-40) cc_final: 0.7544 (p0) REVERT: F 179 THR cc_start: 0.8701 (m) cc_final: 0.8411 (p) REVERT: F 180 GLN cc_start: 0.8600 (mt0) cc_final: 0.8232 (mt0) REVERT: F 181 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.7957 (p) REVERT: F 184 LYS cc_start: 0.8636 (mttp) cc_final: 0.8367 (mttp) REVERT: F 185 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7918 (ptmm) REVERT: F 201 TYR cc_start: 0.8030 (m-80) cc_final: 0.7319 (m-80) REVERT: F 232 PHE cc_start: 0.7267 (m-80) cc_final: 0.6935 (m-80) REVERT: F 243 LYS cc_start: 0.8579 (mttt) cc_final: 0.8294 (mttt) REVERT: F 267 ARG cc_start: 0.8249 (ttt180) cc_final: 0.7826 (tpt-90) REVERT: F 272 MET cc_start: 0.7210 (tpp) cc_final: 0.6867 (tpp) REVERT: F 281 MET cc_start: 0.6902 (ttm) cc_final: 0.6552 (ttm) REVERT: F 282 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7191 (mt-10) REVERT: F 304 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7211 (mtt90) REVERT: F 326 LYS cc_start: 0.7950 (ptpt) cc_final: 0.7435 (mptt) REVERT: F 340 ILE cc_start: 0.9034 (mt) cc_final: 0.8732 (mt) REVERT: F 398 ARG cc_start: 0.8558 (tpp-160) cc_final: 0.8333 (tpp-160) REVERT: F 406 SER cc_start: 0.8968 (m) cc_final: 0.8670 (p) REVERT: F 425 MET cc_start: 0.7526 (ttp) cc_final: 0.7251 (ttp) REVERT: F 426 ASP cc_start: 0.8443 (t0) cc_final: 0.8198 (t70) REVERT: F 443 LYS cc_start: 0.8020 (mttm) cc_final: 0.7440 (mmtm) REVERT: G 41 MET cc_start: 0.7965 (mmm) cc_final: 0.7718 (mmm) REVERT: G 64 GLU cc_start: 0.8524 (tt0) cc_final: 0.8023 (tt0) REVERT: G 72 PHE cc_start: 0.8691 (t80) cc_final: 0.7975 (t80) REVERT: G 102 ASP cc_start: 0.8187 (m-30) cc_final: 0.7854 (p0) REVERT: G 135 LYS cc_start: 0.8266 (ttmm) cc_final: 0.7872 (tttp) REVERT: G 180 GLN cc_start: 0.8584 (mt0) cc_final: 0.8177 (mt0) REVERT: G 185 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8229 (ptmt) REVERT: G 232 PHE cc_start: 0.7214 (m-10) cc_final: 0.6797 (m-80) REVERT: G 243 LYS cc_start: 0.8900 (mttt) cc_final: 0.8582 (mttt) REVERT: G 259 ASN cc_start: 0.8005 (t0) cc_final: 0.7777 (t0) REVERT: G 267 ARG cc_start: 0.8517 (tpp80) cc_final: 0.8252 (tpp80) REVERT: G 272 MET cc_start: 0.7601 (tpp) cc_final: 0.7213 (tpp) REVERT: G 282 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6792 (mt-10) REVERT: G 286 LYS cc_start: 0.8287 (mttm) cc_final: 0.7789 (tttm) REVERT: G 304 ARG cc_start: 0.8205 (ttt180) cc_final: 0.7515 (mtt180) REVERT: G 326 LYS cc_start: 0.7959 (ptpt) cc_final: 0.7486 (mptt) REVERT: G 341 LYS cc_start: 0.9199 (pttp) cc_final: 0.8893 (ptpp) REVERT: G 347 ASN cc_start: 0.6713 (t0) cc_final: 0.6500 (t0) REVERT: G 417 ARG cc_start: 0.6305 (mtt-85) cc_final: 0.5840 (mtm-85) REVERT: G 425 MET cc_start: 0.7582 (ttp) cc_final: 0.7352 (ttp) REVERT: G 426 ASP cc_start: 0.8625 (t0) cc_final: 0.8373 (t70) REVERT: G 443 LYS cc_start: 0.7982 (mtmm) cc_final: 0.7522 (mttm) REVERT: G 444 LYS cc_start: 0.6767 (mtpt) cc_final: 0.6438 (ttmm) REVERT: G 481 THR cc_start: 0.8360 (m) cc_final: 0.7855 (p) REVERT: G 482 VAL cc_start: 0.8723 (t) cc_final: 0.8255 (p) REVERT: G 501 GLU cc_start: 0.7110 (tt0) cc_final: 0.6474 (tt0) REVERT: G 503 CYS cc_start: 0.7674 (OUTLIER) cc_final: 0.6966 (m) REVERT: H 41 MET cc_start: 0.7896 (tpp) cc_final: 0.7604 (tpp) REVERT: H 64 GLU cc_start: 0.8618 (tt0) cc_final: 0.8012 (tt0) REVERT: H 65 MET cc_start: 0.8358 (mmm) cc_final: 0.8112 (mmm) REVERT: H 72 PHE cc_start: 0.8827 (t80) cc_final: 0.8107 (t80) REVERT: H 89 ARG cc_start: 0.8714 (mmm-85) cc_final: 0.8448 (mmm-85) REVERT: H 102 ASP cc_start: 0.8264 (m-30) cc_final: 0.7528 (p0) REVERT: H 121 LEU cc_start: 0.8315 (mt) cc_final: 0.7697 (mt) REVERT: H 141 ARG cc_start: 0.7799 (mtp85) cc_final: 0.7249 (ttm-80) REVERT: H 168 VAL cc_start: 0.9152 (t) cc_final: 0.8730 (p) REVERT: H 170 MET cc_start: 0.7913 (ttt) cc_final: 0.7290 (ptp) REVERT: H 171 ASN cc_start: 0.8011 (m-40) cc_final: 0.7544 (p0) REVERT: H 180 GLN cc_start: 0.8608 (mt0) cc_final: 0.8228 (mt0) REVERT: H 185 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8041 (ptmt) REVERT: H 201 TYR cc_start: 0.8240 (m-80) cc_final: 0.7913 (m-80) REVERT: H 232 PHE cc_start: 0.7305 (m-10) cc_final: 0.6825 (m-80) REVERT: H 260 LEU cc_start: 0.8553 (mp) cc_final: 0.8349 (mt) REVERT: H 267 ARG cc_start: 0.8579 (tpp80) cc_final: 0.8137 (tpp80) REVERT: H 280 ILE cc_start: 0.6621 (mm) cc_final: 0.6278 (mm) REVERT: H 281 MET cc_start: 0.7116 (ttm) cc_final: 0.6790 (ttm) REVERT: H 282 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6461 (mt-10) REVERT: H 304 ARG cc_start: 0.8032 (mtt180) cc_final: 0.7394 (mtt180) REVERT: H 333 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7463 (mt) REVERT: H 340 ILE cc_start: 0.9155 (mt) cc_final: 0.8608 (mt) REVERT: H 341 LYS cc_start: 0.9301 (pttp) cc_final: 0.9095 (pttt) REVERT: H 481 THR cc_start: 0.8485 (m) cc_final: 0.7919 (p) REVERT: H 511 ILE cc_start: 0.8676 (mt) cc_final: 0.8247 (tt) outliers start: 133 outliers final: 90 residues processed: 1059 average time/residue: 0.4881 time to fit residues: 775.0887 Evaluate side-chains 1085 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 975 time to evaluate : 3.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 503 CYS Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 437 LYS Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 503 CYS Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 503 CYS Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 185 LYS Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 503 CYS Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 161 TYR Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 259 ASN Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 351 MET Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 420 HIS Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 503 CYS Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 513 GLU Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 265 ASP Chi-restraints excluded: chain F residue 304 ARG Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 387 LYS Chi-restraints excluded: chain F residue 474 ARG Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 503 CYS Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 513 GLU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain G residue 185 LYS Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 315 HIS Chi-restraints excluded: chain G residue 351 MET Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 474 ARG Chi-restraints excluded: chain G residue 488 GLU Chi-restraints excluded: chain G residue 503 CYS Chi-restraints excluded: chain G residue 504 VAL Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 185 LYS Chi-restraints excluded: chain H residue 307 GLU Chi-restraints excluded: chain H residue 333 ILE Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 423 LEU Chi-restraints excluded: chain H residue 449 GLN Chi-restraints excluded: chain H residue 488 GLU Chi-restraints excluded: chain H residue 503 CYS Chi-restraints excluded: chain H residue 504 VAL Chi-restraints excluded: chain H residue 513 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 266 optimal weight: 5.9990 chunk 308 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 193 optimal weight: 0.0000 chunk 142 optimal weight: 20.0000 chunk 352 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 275 optimal weight: 1.9990 chunk 297 optimal weight: 5.9990 chunk 192 optimal weight: 0.0050 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 HIS B 463 HIS C 270 GLN C 463 HIS ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 HIS F 315 HIS G 259 ASN H 256 ASN H 463 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.179500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.139404 restraints weight = 54179.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.144521 restraints weight = 30174.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.147907 restraints weight = 19533.758| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30368 Z= 0.133 Angle : 0.649 15.911 41088 Z= 0.330 Chirality : 0.047 0.261 4672 Planarity : 0.005 0.067 5352 Dihedral : 4.658 44.967 4058 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.22 % Allowed : 19.55 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3720 helix: 0.28 (0.16), residues: 1120 sheet: -0.75 (0.21), residues: 664 loop : 0.37 (0.15), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 87 HIS 0.009 0.001 HIS A 271 PHE 0.021 0.001 PHE B 325 TYR 0.032 0.002 TYR F 224 ARG 0.008 0.001 ARG F 304 Details of bonding type rmsd hydrogen bonds : bond 0.04614 ( 1087) hydrogen bonds : angle 5.15737 ( 2733) covalent geometry : bond 0.00291 (30368) covalent geometry : angle 0.64897 (41088) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 964 time to evaluate : 3.545 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: 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: 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 64 GLU cc_start: 0.8554 (tt0) cc_final: 0.8031 (tt0) REVERT: A 65 MET cc_start: 0.8329 (mmm) cc_final: 0.7943 (mmm) REVERT: A 72 PHE cc_start: 0.8605 (t80) cc_final: 0.8166 (t80) REVERT: A 89 ARG cc_start: 0.8744 (mtp85) cc_final: 0.8498 (mmm-85) REVERT: A 102 ASP cc_start: 0.8137 (m-30) cc_final: 0.7829 (p0) REVERT: A 141 ARG cc_start: 0.7442 (ttm-80) cc_final: 0.7053 (ttt90) REVERT: A 170 MET cc_start: 0.7288 (ptp) cc_final: 0.6956 (ptp) REVERT: A 180 GLN cc_start: 0.7833 (mt0) cc_final: 0.7493 (mp10) REVERT: A 185 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8134 (ptmt) REVERT: A 197 ASN cc_start: 0.7102 (t0) cc_final: 0.6840 (t0) REVERT: A 271 HIS cc_start: 0.7468 (t70) cc_final: 0.6966 (t70) REVERT: A 280 ILE cc_start: 0.6728 (mt) cc_final: 0.6462 (mm) REVERT: A 282 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7137 (mt-10) REVERT: A 341 LYS cc_start: 0.9061 (tttt) cc_final: 0.8711 (ttpp) REVERT: A 386 PHE cc_start: 0.7569 (m-80) cc_final: 0.7242 (m-80) REVERT: A 400 LEU cc_start: 0.8241 (tp) cc_final: 0.8007 (tt) REVERT: A 425 MET cc_start: 0.7545 (ttp) cc_final: 0.7275 (ttp) REVERT: A 426 ASP cc_start: 0.8309 (t0) cc_final: 0.7873 (t0) REVERT: A 479 LYS cc_start: 0.7274 (mttt) cc_final: 0.6885 (mttm) REVERT: A 481 THR cc_start: 0.8560 (m) cc_final: 0.8160 (p) REVERT: B 41 MET cc_start: 0.8682 (mmm) cc_final: 0.8445 (mmm) REVERT: B 54 ASP cc_start: 0.8026 (t70) cc_final: 0.7806 (t70) REVERT: B 64 GLU cc_start: 0.8649 (tt0) cc_final: 0.8145 (tt0) REVERT: B 65 MET cc_start: 0.8071 (mmm) cc_final: 0.7816 (mmm) REVERT: B 72 PHE cc_start: 0.8408 (t80) cc_final: 0.7922 (t80) REVERT: B 74 ARG cc_start: 0.8202 (ttm110) cc_final: 0.7769 (ptp-170) REVERT: B 89 ARG cc_start: 0.8527 (mmm-85) cc_final: 0.8128 (mmm-85) REVERT: B 94 GLN cc_start: 0.7653 (mm-40) cc_final: 0.7128 (mm-40) REVERT: B 147 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8314 (tp) REVERT: B 168 VAL cc_start: 0.9157 (t) cc_final: 0.8926 (p) REVERT: B 170 MET cc_start: 0.7399 (ptp) cc_final: 0.7199 (ptp) REVERT: B 232 PHE cc_start: 0.6802 (m-10) cc_final: 0.6342 (m-80) REVERT: B 243 LYS cc_start: 0.8412 (mttt) cc_final: 0.8141 (mttt) REVERT: B 282 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6657 (mt-10) REVERT: B 304 ARG cc_start: 0.8069 (ttt180) cc_final: 0.7601 (ttt180) REVERT: B 318 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8049 (mt-10) REVERT: B 340 ILE cc_start: 0.9051 (mt) cc_final: 0.8615 (mt) REVERT: B 341 LYS cc_start: 0.9250 (pttm) cc_final: 0.8985 (pttt) REVERT: B 374 GLN cc_start: 0.6908 (mm110) cc_final: 0.6705 (mm-40) REVERT: B 398 ARG cc_start: 0.8570 (tpp-160) cc_final: 0.8217 (tpp-160) REVERT: B 415 LEU cc_start: 0.8544 (tp) cc_final: 0.8251 (tt) REVERT: B 425 MET cc_start: 0.7513 (ttp) cc_final: 0.7115 (ttp) REVERT: B 426 ASP cc_start: 0.8469 (t0) cc_final: 0.8027 (t0) REVERT: B 448 PHE cc_start: 0.8193 (t80) cc_final: 0.7986 (t80) REVERT: B 479 LYS cc_start: 0.7194 (mttt) cc_final: 0.6873 (mtmm) REVERT: B 481 THR cc_start: 0.8347 (m) cc_final: 0.7921 (p) REVERT: B 491 THR cc_start: 0.8047 (m) cc_final: 0.7696 (t) REVERT: B 503 CYS cc_start: 0.7638 (p) cc_final: 0.7121 (m) REVERT: C 41 MET cc_start: 0.8545 (mmm) cc_final: 0.8209 (mmm) REVERT: C 64 GLU cc_start: 0.8467 (tt0) cc_final: 0.7821 (tt0) REVERT: C 72 PHE cc_start: 0.8651 (t80) cc_final: 0.8080 (t80) REVERT: C 74 ARG cc_start: 0.8396 (ttm110) cc_final: 0.7868 (ptp-170) REVERT: C 89 ARG cc_start: 0.8985 (mmm-85) cc_final: 0.8567 (mmm-85) REVERT: C 119 VAL cc_start: 0.6852 (OUTLIER) cc_final: 0.6553 (m) REVERT: C 135 LYS cc_start: 0.8074 (ttmt) cc_final: 0.7743 (ttmt) REVERT: C 139 GLU cc_start: 0.6919 (tm-30) cc_final: 0.6711 (tm-30) REVERT: C 179 THR cc_start: 0.8405 (m) cc_final: 0.8059 (p) REVERT: C 180 GLN cc_start: 0.8040 (mt0) cc_final: 0.7720 (mt0) REVERT: C 181 SER cc_start: 0.8675 (OUTLIER) cc_final: 0.8399 (p) REVERT: C 221 GLN cc_start: 0.7905 (tp40) cc_final: 0.7683 (tp40) REVERT: C 232 PHE cc_start: 0.7051 (m-80) cc_final: 0.6690 (m-80) REVERT: C 282 GLU cc_start: 0.6920 (mt-10) cc_final: 0.6264 (mt-10) REVERT: C 283 LEU cc_start: 0.7735 (mt) cc_final: 0.7374 (mm) REVERT: C 304 ARG cc_start: 0.8163 (mmt180) cc_final: 0.7887 (mmt180) REVERT: C 425 MET cc_start: 0.7523 (ttp) cc_final: 0.7311 (ttp) REVERT: C 443 LYS cc_start: 0.7771 (mttm) cc_final: 0.7534 (mttm) REVERT: C 448 PHE cc_start: 0.8113 (t80) cc_final: 0.7502 (t80) REVERT: C 450 LYS cc_start: 0.8334 (ttpp) cc_final: 0.7981 (ttpp) REVERT: C 479 LYS cc_start: 0.7076 (mttt) cc_final: 0.6598 (mttm) REVERT: C 481 THR cc_start: 0.8084 (m) cc_final: 0.7682 (p) REVERT: C 499 VAL cc_start: 0.8501 (t) cc_final: 0.8220 (m) REVERT: C 511 ILE cc_start: 0.8494 (mt) cc_final: 0.8115 (tt) REVERT: D 50 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7185 (mt-10) REVERT: D 64 GLU cc_start: 0.8507 (tt0) cc_final: 0.7690 (tt0) REVERT: D 65 MET cc_start: 0.8085 (mmm) cc_final: 0.7872 (mmm) REVERT: D 72 PHE cc_start: 0.8641 (t80) cc_final: 0.8120 (t80) REVERT: D 74 ARG cc_start: 0.8372 (ttm110) cc_final: 0.7871 (ptp-170) REVERT: D 94 GLN cc_start: 0.7625 (mm-40) cc_final: 0.6994 (mm-40) REVERT: D 148 ASP cc_start: 0.7332 (m-30) cc_final: 0.6995 (m-30) REVERT: D 170 MET cc_start: 0.7815 (ptp) cc_final: 0.7567 (ptp) REVERT: D 179 THR cc_start: 0.8337 (m) cc_final: 0.8061 (p) REVERT: D 185 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8151 (ptmt) REVERT: D 200 ARG cc_start: 0.6614 (mtp-110) cc_final: 0.6190 (ttp-110) REVERT: D 201 TYR cc_start: 0.8037 (m-80) cc_final: 0.7402 (m-80) REVERT: D 232 PHE cc_start: 0.7185 (m-80) cc_final: 0.6903 (m-80) REVERT: D 243 LYS cc_start: 0.8721 (mttt) cc_final: 0.8402 (mttt) REVERT: D 272 MET cc_start: 0.7458 (tpp) cc_final: 0.6893 (tpp) REVERT: D 286 LYS cc_start: 0.8518 (mttm) cc_final: 0.8254 (tttm) REVERT: D 304 ARG cc_start: 0.7695 (mtp180) cc_final: 0.7340 (mtt180) REVERT: D 341 LYS cc_start: 0.8976 (pttp) cc_final: 0.8749 (ptpp) REVERT: D 387 LYS cc_start: 0.8441 (mttt) cc_final: 0.8179 (mttt) REVERT: D 398 ARG cc_start: 0.8273 (tpp-160) cc_final: 0.8073 (tpp-160) REVERT: D 403 LYS cc_start: 0.7818 (mmtt) cc_final: 0.7088 (tptp) REVERT: D 438 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7495 (mp) REVERT: D 443 LYS cc_start: 0.7600 (mtpp) cc_final: 0.7282 (mttm) REVERT: D 479 LYS cc_start: 0.7244 (mttt) cc_final: 0.6845 (mtmm) REVERT: D 481 THR cc_start: 0.8375 (m) cc_final: 0.8022 (p) REVERT: D 491 THR cc_start: 0.8246 (m) cc_final: 0.7864 (t) REVERT: D 499 VAL cc_start: 0.8503 (t) cc_final: 0.8168 (p) REVERT: E 41 MET cc_start: 0.8355 (mmm) cc_final: 0.8129 (mmm) REVERT: E 64 GLU cc_start: 0.8664 (tt0) cc_final: 0.7942 (tt0) REVERT: E 72 PHE cc_start: 0.8563 (t80) cc_final: 0.7884 (t80) REVERT: E 89 ARG cc_start: 0.8559 (mmm-85) cc_final: 0.8285 (mmm-85) REVERT: E 129 MET cc_start: 0.6970 (mtm) cc_final: 0.6431 (mtm) REVERT: E 135 LYS cc_start: 0.7921 (ttmt) cc_final: 0.7580 (tptm) REVERT: E 147 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8230 (tp) REVERT: E 168 VAL cc_start: 0.9052 (t) cc_final: 0.8798 (p) REVERT: E 179 THR cc_start: 0.8502 (m) cc_final: 0.8186 (p) REVERT: E 180 GLN cc_start: 0.8413 (mt0) cc_final: 0.7773 (mt0) REVERT: E 201 TYR cc_start: 0.7889 (m-80) cc_final: 0.7516 (m-80) REVERT: E 224 TYR cc_start: 0.6187 (p90) cc_final: 0.5736 (p90) REVERT: E 243 LYS cc_start: 0.8429 (mttt) cc_final: 0.8160 (mttt) REVERT: E 260 LEU cc_start: 0.8160 (mp) cc_final: 0.7641 (tt) REVERT: E 267 ARG cc_start: 0.8569 (tpt-90) cc_final: 0.8269 (tpp80) REVERT: E 280 ILE cc_start: 0.7333 (mm) cc_final: 0.7094 (mm) REVERT: E 281 MET cc_start: 0.6990 (ttm) cc_final: 0.6765 (ttm) REVERT: E 283 LEU cc_start: 0.8189 (mt) cc_final: 0.7976 (mm) REVERT: E 341 LYS cc_start: 0.9153 (pttt) cc_final: 0.8913 (ptpp) REVERT: E 374 GLN cc_start: 0.6535 (mm110) cc_final: 0.5892 (mm-40) REVERT: E 387 LYS cc_start: 0.8391 (mppt) cc_final: 0.8174 (mtmm) REVERT: E 501 GLU cc_start: 0.7112 (tt0) cc_final: 0.6547 (tt0) REVERT: E 503 CYS cc_start: 0.7610 (p) cc_final: 0.6996 (m) REVERT: F 72 PHE cc_start: 0.8519 (t80) cc_final: 0.7608 (t80) REVERT: F 135 LYS cc_start: 0.8455 (tptp) cc_final: 0.8113 (tptp) REVERT: F 168 VAL cc_start: 0.9081 (t) cc_final: 0.8841 (p) REVERT: F 170 MET cc_start: 0.7719 (ttt) cc_final: 0.7459 (ptp) REVERT: F 171 ASN cc_start: 0.7596 (m-40) cc_final: 0.7306 (p0) REVERT: F 179 THR cc_start: 0.8607 (m) cc_final: 0.8324 (p) REVERT: F 181 SER cc_start: 0.9031 (OUTLIER) cc_final: 0.8747 (p) REVERT: F 185 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.7994 (ptmm) REVERT: F 201 TYR cc_start: 0.7942 (m-80) cc_final: 0.7342 (m-80) REVERT: F 221 GLN cc_start: 0.7799 (tp40) cc_final: 0.7575 (tp40) REVERT: F 243 LYS cc_start: 0.8539 (mttt) cc_final: 0.8224 (mttt) REVERT: F 253 PHE cc_start: 0.7524 (t80) cc_final: 0.7024 (t80) REVERT: F 272 MET cc_start: 0.7119 (tpp) cc_final: 0.6779 (tpp) REVERT: F 281 MET cc_start: 0.6855 (ttm) cc_final: 0.6496 (ttm) REVERT: F 282 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7211 (mt-10) REVERT: F 304 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.6758 (mtt180) REVERT: F 341 LYS cc_start: 0.9151 (pttt) cc_final: 0.8873 (pmtt) REVERT: F 425 MET cc_start: 0.7498 (ttp) cc_final: 0.7210 (ttp) REVERT: F 426 ASP cc_start: 0.8423 (t0) cc_final: 0.8200 (t70) REVERT: F 443 LYS cc_start: 0.7844 (mttm) cc_final: 0.7397 (mptp) REVERT: F 503 CYS cc_start: 0.7622 (p) cc_final: 0.7031 (m) REVERT: G 41 MET cc_start: 0.7922 (mmm) cc_final: 0.7686 (mmm) REVERT: G 64 GLU cc_start: 0.8513 (tt0) cc_final: 0.8131 (tt0) REVERT: G 72 PHE cc_start: 0.8684 (t80) cc_final: 0.7996 (t80) REVERT: G 89 ARG cc_start: 0.8784 (mmm-85) cc_final: 0.8358 (mmm-85) REVERT: G 102 ASP cc_start: 0.8104 (m-30) cc_final: 0.7825 (p0) REVERT: G 115 LYS cc_start: 0.7898 (mtmm) cc_final: 0.7697 (ptpp) REVERT: G 129 MET cc_start: 0.7035 (mtm) cc_final: 0.6807 (mtm) REVERT: G 179 THR cc_start: 0.8414 (m) cc_final: 0.8177 (p) REVERT: G 180 GLN cc_start: 0.8551 (mt0) cc_final: 0.8089 (mt0) REVERT: G 185 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8399 (tmmt) REVERT: G 232 PHE cc_start: 0.7119 (m-10) cc_final: 0.6709 (m-80) REVERT: G 243 LYS cc_start: 0.8817 (mttt) cc_final: 0.8470 (tptp) REVERT: G 259 ASN cc_start: 0.7923 (t0) cc_final: 0.6937 (p0) REVERT: G 267 ARG cc_start: 0.8486 (tpp80) cc_final: 0.8114 (tpp80) REVERT: G 272 MET cc_start: 0.7527 (tpp) cc_final: 0.7161 (tpp) REVERT: G 282 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6693 (mt-10) REVERT: G 286 LYS cc_start: 0.8291 (mttm) cc_final: 0.7798 (tttm) REVERT: G 304 ARG cc_start: 0.8194 (ttt180) cc_final: 0.7540 (mtt180) REVERT: G 326 LYS cc_start: 0.7884 (ptpt) cc_final: 0.7271 (mttp) REVERT: G 341 LYS cc_start: 0.9174 (pttp) cc_final: 0.8833 (ptpp) REVERT: G 347 ASN cc_start: 0.6708 (t0) cc_final: 0.6382 (t0) REVERT: G 403 LYS cc_start: 0.7947 (mmtt) cc_final: 0.7499 (tptp) REVERT: G 412 LYS cc_start: 0.7309 (mttp) cc_final: 0.7109 (mttp) REVERT: G 425 MET cc_start: 0.7601 (ttp) cc_final: 0.7324 (ttp) REVERT: G 426 ASP cc_start: 0.8575 (t0) cc_final: 0.8358 (t70) REVERT: G 443 LYS cc_start: 0.7973 (mtmm) cc_final: 0.7642 (mttm) REVERT: G 444 LYS cc_start: 0.6574 (mtpt) cc_final: 0.6127 (ttmm) REVERT: G 479 LYS cc_start: 0.7208 (mttt) cc_final: 0.6888 (mtmm) REVERT: G 481 THR cc_start: 0.8353 (m) cc_final: 0.7802 (p) REVERT: G 501 GLU cc_start: 0.7065 (tt0) cc_final: 0.6481 (tt0) REVERT: G 503 CYS cc_start: 0.7591 (p) cc_final: 0.7038 (m) REVERT: H 41 MET cc_start: 0.7848 (tpp) cc_final: 0.7569 (tpp) REVERT: H 64 GLU cc_start: 0.8592 (tt0) cc_final: 0.8039 (tt0) REVERT: H 72 PHE cc_start: 0.8784 (t80) cc_final: 0.8053 (t80) REVERT: H 89 ARG cc_start: 0.8697 (mmm-85) cc_final: 0.8371 (mmm-85) REVERT: H 102 ASP cc_start: 0.8221 (m-30) cc_final: 0.7492 (p0) REVERT: H 115 LYS cc_start: 0.7353 (mtmm) cc_final: 0.7045 (pttm) REVERT: H 121 LEU cc_start: 0.8296 (mt) cc_final: 0.7681 (mt) REVERT: H 141 ARG cc_start: 0.7704 (mtp85) cc_final: 0.7238 (ttm-80) REVERT: H 168 VAL cc_start: 0.9179 (t) cc_final: 0.8832 (p) REVERT: H 170 MET cc_start: 0.7854 (ttt) cc_final: 0.7372 (ptp) REVERT: H 171 ASN cc_start: 0.7996 (m-40) cc_final: 0.7455 (p0) REVERT: H 180 GLN cc_start: 0.8598 (mt0) cc_final: 0.8177 (mt0) REVERT: H 185 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8253 (tptp) REVERT: H 201 TYR cc_start: 0.8138 (m-80) cc_final: 0.7835 (m-80) REVERT: H 232 PHE cc_start: 0.7163 (m-10) cc_final: 0.6705 (m-80) REVERT: H 243 LYS cc_start: 0.8645 (mttt) cc_final: 0.8327 (tptp) REVERT: H 267 ARG cc_start: 0.8515 (tpp80) cc_final: 0.8121 (tpp80) REVERT: H 280 ILE cc_start: 0.6572 (mm) cc_final: 0.6286 (mm) REVERT: H 281 MET cc_start: 0.7048 (ttm) cc_final: 0.6769 (ttm) REVERT: H 282 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6538 (mt-10) REVERT: H 304 ARG cc_start: 0.8058 (mtt180) cc_final: 0.7377 (mtt180) REVERT: H 333 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7264 (mt) REVERT: H 340 ILE cc_start: 0.9167 (mt) cc_final: 0.8599 (mt) REVERT: H 403 LYS cc_start: 0.8038 (mmtt) cc_final: 0.7333 (tptp) REVERT: H 443 LYS cc_start: 0.7569 (mtmm) cc_final: 0.7343 (mttp) REVERT: H 448 PHE cc_start: 0.8166 (t80) cc_final: 0.7741 (t80) REVERT: H 481 THR cc_start: 0.8482 (m) cc_final: 0.8018 (p) outliers start: 107 outliers final: 72 residues processed: 1000 average time/residue: 0.4721 time to fit residues: 700.3112 Evaluate side-chains 1037 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 952 time to evaluate : 2.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 185 LYS Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 161 TYR Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 259 ASN Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 420 HIS Chi-restraints excluded: chain E residue 474 ARG Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 513 GLU Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 265 ASP Chi-restraints excluded: chain F residue 304 ARG Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 387 LYS Chi-restraints excluded: chain F residue 474 ARG Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 513 GLU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain G residue 185 LYS Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 315 HIS Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 474 ARG Chi-restraints excluded: chain G residue 488 GLU Chi-restraints excluded: chain G residue 504 VAL Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 185 LYS Chi-restraints excluded: chain H residue 333 ILE Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 423 LEU Chi-restraints excluded: chain H residue 488 GLU Chi-restraints excluded: chain H residue 513 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 155 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 346 optimal weight: 0.0000 chunk 375 optimal weight: 0.9980 chunk 306 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 261 optimal weight: 6.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN A 374 GLN ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 ASN H 256 ASN H 315 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.181750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.141522 restraints weight = 54632.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.146764 restraints weight = 30189.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.150062 restraints weight = 19446.846| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 30368 Z= 0.118 Angle : 0.642 14.766 41088 Z= 0.325 Chirality : 0.047 0.234 4672 Planarity : 0.005 0.079 5352 Dihedral : 4.442 40.222 4058 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.74 % Allowed : 20.36 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.14), residues: 3720 helix: 0.26 (0.16), residues: 1152 sheet: -0.18 (0.20), residues: 784 loop : 0.35 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP H 87 HIS 0.007 0.001 HIS A 271 PHE 0.017 0.001 PHE E 325 TYR 0.028 0.002 TYR H 327 ARG 0.008 0.001 ARG G 74 Details of bonding type rmsd hydrogen bonds : bond 0.04223 ( 1087) hydrogen bonds : angle 5.04895 ( 2733) covalent geometry : bond 0.00261 (30368) covalent geometry : angle 0.64220 (41088) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 972 time to evaluate : 3.036 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: 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: 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 41 MET cc_start: 0.8714 (mmm) cc_final: 0.8248 (mmm) REVERT: A 60 ARG cc_start: 0.8329 (tpt170) cc_final: 0.7195 (tpt90) REVERT: A 64 GLU cc_start: 0.8625 (tt0) cc_final: 0.8393 (mt-10) REVERT: A 72 PHE cc_start: 0.8570 (t80) cc_final: 0.8100 (t80) REVERT: A 89 ARG cc_start: 0.8724 (mtp85) cc_final: 0.8472 (mmm-85) REVERT: A 102 ASP cc_start: 0.8134 (m-30) cc_final: 0.7821 (p0) REVERT: A 170 MET cc_start: 0.7278 (ptp) cc_final: 0.6942 (ptp) REVERT: A 180 GLN cc_start: 0.7819 (mt0) cc_final: 0.7524 (mp10) REVERT: A 185 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8106 (ptmt) REVERT: A 197 ASN cc_start: 0.7086 (t0) cc_final: 0.6840 (t0) REVERT: A 201 TYR cc_start: 0.7771 (m-80) cc_final: 0.7532 (m-80) REVERT: A 259 ASN cc_start: 0.7509 (OUTLIER) cc_final: 0.7037 (p0) REVERT: A 271 HIS cc_start: 0.7371 (t70) cc_final: 0.6897 (t70) REVERT: A 280 ILE cc_start: 0.6638 (mt) cc_final: 0.6357 (mm) REVERT: A 282 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7114 (mt-10) REVERT: A 335 MET cc_start: 0.3341 (mtt) cc_final: 0.2651 (mtt) REVERT: A 341 LYS cc_start: 0.9035 (tttt) cc_final: 0.8686 (ttpp) REVERT: A 386 PHE cc_start: 0.7522 (m-80) cc_final: 0.7252 (m-80) REVERT: A 387 LYS cc_start: 0.8280 (mppt) cc_final: 0.7985 (ptpp) REVERT: A 400 LEU cc_start: 0.8287 (tp) cc_final: 0.8020 (tt) REVERT: A 425 MET cc_start: 0.7495 (ttp) cc_final: 0.7244 (ttp) REVERT: A 426 ASP cc_start: 0.8320 (t0) cc_final: 0.7890 (t0) REVERT: A 479 LYS cc_start: 0.7273 (mttt) cc_final: 0.6885 (mttm) REVERT: A 481 THR cc_start: 0.8585 (m) cc_final: 0.8196 (p) REVERT: B 41 MET cc_start: 0.8705 (mmm) cc_final: 0.8464 (mmm) REVERT: B 64 GLU cc_start: 0.8641 (tt0) cc_final: 0.8182 (tt0) REVERT: B 72 PHE cc_start: 0.8413 (t80) cc_final: 0.7958 (t80) REVERT: B 74 ARG cc_start: 0.8155 (ttm110) cc_final: 0.7766 (ptp-170) REVERT: B 94 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7125 (mm-40) REVERT: B 147 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8314 (tp) REVERT: B 168 VAL cc_start: 0.9114 (t) cc_final: 0.8911 (p) REVERT: B 232 PHE cc_start: 0.6720 (m-10) cc_final: 0.6282 (m-80) REVERT: B 243 LYS cc_start: 0.8369 (mttt) cc_final: 0.8087 (mttt) REVERT: B 253 PHE cc_start: 0.7345 (t80) cc_final: 0.6989 (t80) REVERT: B 281 MET cc_start: 0.6910 (ttm) cc_final: 0.6630 (ttm) REVERT: B 282 GLU cc_start: 0.7416 (mt-10) cc_final: 0.6658 (mt-10) REVERT: B 304 ARG cc_start: 0.8047 (ttt180) cc_final: 0.7594 (ttt180) REVERT: B 318 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8055 (mt-10) REVERT: B 340 ILE cc_start: 0.9048 (mt) cc_final: 0.8658 (mt) REVERT: B 415 LEU cc_start: 0.8587 (tp) cc_final: 0.8272 (tt) REVERT: B 425 MET cc_start: 0.7516 (ttp) cc_final: 0.7077 (ttp) REVERT: B 426 ASP cc_start: 0.8428 (t0) cc_final: 0.7957 (t0) REVERT: B 443 LYS cc_start: 0.7847 (mtpp) cc_final: 0.7560 (mtmm) REVERT: B 448 PHE cc_start: 0.8170 (t80) cc_final: 0.7895 (t80) REVERT: B 479 LYS cc_start: 0.7177 (mttt) cc_final: 0.6876 (mtmm) REVERT: B 481 THR cc_start: 0.8409 (m) cc_final: 0.7997 (p) REVERT: B 491 THR cc_start: 0.8065 (m) cc_final: 0.7825 (t) REVERT: B 503 CYS cc_start: 0.7534 (p) cc_final: 0.7033 (m) REVERT: C 41 MET cc_start: 0.8502 (mmm) cc_final: 0.8228 (mmm) REVERT: C 64 GLU cc_start: 0.8494 (tt0) cc_final: 0.7916 (tt0) REVERT: C 72 PHE cc_start: 0.8617 (t80) cc_final: 0.8062 (t80) REVERT: C 74 ARG cc_start: 0.8344 (ttm110) cc_final: 0.7808 (ptp-170) REVERT: C 94 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7497 (mm-40) REVERT: C 115 LYS cc_start: 0.8139 (mtmm) cc_final: 0.7500 (mmmt) REVERT: C 119 VAL cc_start: 0.6358 (OUTLIER) cc_final: 0.5835 (p) REVERT: C 135 LYS cc_start: 0.8023 (ttmt) cc_final: 0.7667 (ttmt) REVERT: C 139 GLU cc_start: 0.6905 (tm-30) cc_final: 0.6679 (tm-30) REVERT: C 170 MET cc_start: 0.7619 (ptp) cc_final: 0.7417 (pmm) REVERT: C 181 SER cc_start: 0.8705 (OUTLIER) cc_final: 0.8413 (p) REVERT: C 221 GLN cc_start: 0.7928 (tp40) cc_final: 0.7685 (tp40) REVERT: C 232 PHE cc_start: 0.7060 (m-80) cc_final: 0.6732 (m-80) REVERT: C 282 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6009 (mt-10) REVERT: C 283 LEU cc_start: 0.7338 (mt) cc_final: 0.6968 (mm) REVERT: C 304 ARG cc_start: 0.8145 (mmt180) cc_final: 0.7035 (mmm-85) REVERT: C 426 ASP cc_start: 0.8444 (t0) cc_final: 0.8143 (t70) REVERT: C 443 LYS cc_start: 0.7754 (mttm) cc_final: 0.7525 (mttm) REVERT: C 450 LYS cc_start: 0.8292 (ttpp) cc_final: 0.8046 (ttpp) REVERT: C 479 LYS cc_start: 0.7040 (mttt) cc_final: 0.6668 (mttm) REVERT: C 481 THR cc_start: 0.8087 (m) cc_final: 0.7662 (p) REVERT: C 503 CYS cc_start: 0.7408 (p) cc_final: 0.6988 (m) REVERT: C 511 ILE cc_start: 0.8452 (mt) cc_final: 0.8064 (tt) REVERT: D 64 GLU cc_start: 0.8473 (tt0) cc_final: 0.7753 (tt0) REVERT: D 72 PHE cc_start: 0.8642 (t80) cc_final: 0.8094 (t80) REVERT: D 74 ARG cc_start: 0.8350 (ttm110) cc_final: 0.7826 (ptp-170) REVERT: D 94 GLN cc_start: 0.7601 (mm-40) cc_final: 0.7001 (mm-40) REVERT: D 148 ASP cc_start: 0.7314 (m-30) cc_final: 0.7023 (m-30) REVERT: D 170 MET cc_start: 0.7837 (ptp) cc_final: 0.7536 (ptp) REVERT: D 179 THR cc_start: 0.8355 (m) cc_final: 0.8062 (p) REVERT: D 180 GLN cc_start: 0.8078 (mt0) cc_final: 0.7655 (mp10) REVERT: D 185 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8092 (ptmt) REVERT: D 201 TYR cc_start: 0.7880 (m-80) cc_final: 0.7295 (m-80) REVERT: D 232 PHE cc_start: 0.7102 (m-10) cc_final: 0.6813 (m-80) REVERT: D 272 MET cc_start: 0.7591 (tpp) cc_final: 0.7055 (tpp) REVERT: D 286 LYS cc_start: 0.8535 (mttm) cc_final: 0.8295 (tttm) REVERT: D 304 ARG cc_start: 0.7621 (mtp180) cc_final: 0.6940 (mtt180) REVERT: D 341 LYS cc_start: 0.9027 (pttp) cc_final: 0.8768 (ptpp) REVERT: D 387 LYS cc_start: 0.8438 (mttt) cc_final: 0.8164 (mttt) REVERT: D 398 ARG cc_start: 0.8378 (tpp-160) cc_final: 0.8005 (tpp-160) REVERT: D 403 LYS cc_start: 0.7876 (mmtt) cc_final: 0.7195 (tptt) REVERT: D 425 MET cc_start: 0.7345 (tpp) cc_final: 0.7019 (tpp) REVERT: D 426 ASP cc_start: 0.8361 (t0) cc_final: 0.8011 (t0) REVERT: D 479 LYS cc_start: 0.7223 (mttt) cc_final: 0.6806 (mttm) REVERT: D 481 THR cc_start: 0.8371 (m) cc_final: 0.8016 (p) REVERT: D 491 THR cc_start: 0.8202 (m) cc_final: 0.7848 (p) REVERT: D 499 VAL cc_start: 0.8523 (t) cc_final: 0.8298 (m) REVERT: E 41 MET cc_start: 0.8339 (mmm) cc_final: 0.8094 (mmm) REVERT: E 50 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7580 (mt-10) REVERT: E 64 GLU cc_start: 0.8646 (tt0) cc_final: 0.7980 (tt0) REVERT: E 72 PHE cc_start: 0.8571 (t80) cc_final: 0.7902 (t80) REVERT: E 89 ARG cc_start: 0.8561 (mmm-85) cc_final: 0.8254 (mmm-85) REVERT: E 129 MET cc_start: 0.6939 (mtm) cc_final: 0.6369 (mtm) REVERT: E 135 LYS cc_start: 0.7776 (ttmt) cc_final: 0.7510 (tptm) REVERT: E 147 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8163 (tp) REVERT: E 168 VAL cc_start: 0.9069 (t) cc_final: 0.8843 (p) REVERT: E 179 THR cc_start: 0.8442 (m) cc_final: 0.8187 (p) REVERT: E 180 GLN cc_start: 0.8411 (mt0) cc_final: 0.7824 (mt0) REVERT: E 201 TYR cc_start: 0.7662 (m-80) cc_final: 0.7379 (m-80) REVERT: E 224 TYR cc_start: 0.6134 (p90) cc_final: 0.5763 (p90) REVERT: E 243 LYS cc_start: 0.8370 (mttt) cc_final: 0.8114 (mttt) REVERT: E 280 ILE cc_start: 0.7278 (mm) cc_final: 0.7041 (mm) REVERT: E 281 MET cc_start: 0.6971 (ttm) cc_final: 0.6733 (ttm) REVERT: E 287 THR cc_start: 0.8184 (t) cc_final: 0.7737 (p) REVERT: E 304 ARG cc_start: 0.8018 (mmt180) cc_final: 0.7777 (tpt-90) REVERT: E 374 GLN cc_start: 0.6476 (mm110) cc_final: 0.5940 (mm-40) REVERT: E 387 LYS cc_start: 0.8410 (mppt) cc_final: 0.8186 (mtmm) REVERT: E 403 LYS cc_start: 0.7520 (mmtt) cc_final: 0.7054 (tptp) REVERT: E 443 LYS cc_start: 0.7602 (mtpp) cc_final: 0.7267 (mttm) REVERT: E 501 GLU cc_start: 0.7081 (tt0) cc_final: 0.6551 (tt0) REVERT: E 503 CYS cc_start: 0.7590 (p) cc_final: 0.7010 (m) REVERT: F 72 PHE cc_start: 0.8532 (t80) cc_final: 0.7607 (t80) REVERT: F 168 VAL cc_start: 0.9105 (t) cc_final: 0.8864 (p) REVERT: F 170 MET cc_start: 0.7766 (ttt) cc_final: 0.7500 (ptp) REVERT: F 171 ASN cc_start: 0.7511 (m-40) cc_final: 0.7243 (p0) REVERT: F 179 THR cc_start: 0.8623 (m) cc_final: 0.8329 (p) REVERT: F 180 GLN cc_start: 0.8519 (mt0) cc_final: 0.8045 (mt0) REVERT: F 181 SER cc_start: 0.9024 (OUTLIER) cc_final: 0.8743 (p) REVERT: F 201 TYR cc_start: 0.7896 (m-80) cc_final: 0.7317 (m-80) REVERT: F 221 GLN cc_start: 0.7804 (tp40) cc_final: 0.7578 (tp40) REVERT: F 243 LYS cc_start: 0.8508 (mttt) cc_final: 0.8232 (mttt) REVERT: F 253 PHE cc_start: 0.7487 (t80) cc_final: 0.7032 (t80) REVERT: F 272 MET cc_start: 0.7187 (tpp) cc_final: 0.6844 (tpp) REVERT: F 281 MET cc_start: 0.6891 (ttm) cc_final: 0.6330 (ttm) REVERT: F 282 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7101 (mt-10) REVERT: F 283 LEU cc_start: 0.8182 (mt) cc_final: 0.7671 (mm) REVERT: F 304 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6984 (mtt90) REVERT: F 415 LEU cc_start: 0.8533 (tp) cc_final: 0.8125 (tt) REVERT: F 425 MET cc_start: 0.7486 (ttp) cc_final: 0.7204 (ttp) REVERT: F 426 ASP cc_start: 0.8403 (t0) cc_final: 0.8039 (t70) REVERT: F 443 LYS cc_start: 0.7845 (mttm) cc_final: 0.7352 (mptp) REVERT: F 503 CYS cc_start: 0.7527 (p) cc_final: 0.6924 (m) REVERT: G 41 MET cc_start: 0.7894 (mmm) cc_final: 0.7661 (mmm) REVERT: G 64 GLU cc_start: 0.8448 (tt0) cc_final: 0.8032 (tt0) REVERT: G 72 PHE cc_start: 0.8717 (t80) cc_final: 0.8009 (t80) REVERT: G 89 ARG cc_start: 0.8781 (mmm-85) cc_final: 0.8372 (mmm-85) REVERT: G 102 ASP cc_start: 0.8063 (m-30) cc_final: 0.7779 (p0) REVERT: G 115 LYS cc_start: 0.7877 (mtmm) cc_final: 0.7382 (ptpp) REVERT: G 129 MET cc_start: 0.7126 (mtm) cc_final: 0.6912 (mtm) REVERT: G 180 GLN cc_start: 0.8516 (mt0) cc_final: 0.8120 (mt0) REVERT: G 243 LYS cc_start: 0.8780 (mttt) cc_final: 0.8451 (tptp) REVERT: G 259 ASN cc_start: 0.7949 (t0) cc_final: 0.6893 (p0) REVERT: G 267 ARG cc_start: 0.8450 (tpp80) cc_final: 0.8075 (tpp80) REVERT: G 282 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6681 (mt-10) REVERT: G 286 LYS cc_start: 0.8372 (mttm) cc_final: 0.7860 (tttm) REVERT: G 304 ARG cc_start: 0.8143 (ttt180) cc_final: 0.7560 (mtt180) REVERT: G 347 ASN cc_start: 0.6817 (t0) cc_final: 0.6397 (t0) REVERT: G 403 LYS cc_start: 0.7752 (mmtt) cc_final: 0.7372 (tptp) REVERT: G 425 MET cc_start: 0.7570 (ttp) cc_final: 0.7299 (ttp) REVERT: G 426 ASP cc_start: 0.8609 (t0) cc_final: 0.8369 (t70) REVERT: G 443 LYS cc_start: 0.7978 (mtmm) cc_final: 0.7747 (mtmm) REVERT: G 466 ILE cc_start: 0.8302 (mt) cc_final: 0.7713 (tt) REVERT: G 479 LYS cc_start: 0.7165 (mttt) cc_final: 0.6836 (mtmm) REVERT: G 481 THR cc_start: 0.8309 (m) cc_final: 0.7776 (p) REVERT: G 492 ILE cc_start: 0.8031 (mt) cc_final: 0.7292 (tt) REVERT: G 501 GLU cc_start: 0.7052 (tt0) cc_final: 0.6447 (tt0) REVERT: G 503 CYS cc_start: 0.7551 (p) cc_final: 0.7061 (m) REVERT: G 511 ILE cc_start: 0.8499 (mt) cc_final: 0.8224 (tt) REVERT: H 41 MET cc_start: 0.7876 (tpp) cc_final: 0.7582 (tpp) REVERT: H 64 GLU cc_start: 0.8638 (tt0) cc_final: 0.7934 (tt0) REVERT: H 72 PHE cc_start: 0.8767 (t80) cc_final: 0.8065 (t80) REVERT: H 74 ARG cc_start: 0.8686 (mtp180) cc_final: 0.8005 (mtm110) REVERT: H 89 ARG cc_start: 0.8743 (mmm-85) cc_final: 0.8491 (mmm160) REVERT: H 102 ASP cc_start: 0.8291 (m-30) cc_final: 0.7575 (p0) REVERT: H 141 ARG cc_start: 0.7666 (mtp85) cc_final: 0.7186 (ttm-80) REVERT: H 168 VAL cc_start: 0.9174 (t) cc_final: 0.8862 (p) REVERT: H 170 MET cc_start: 0.7767 (ttt) cc_final: 0.7194 (ptp) REVERT: H 171 ASN cc_start: 0.7941 (m-40) cc_final: 0.7434 (p0) REVERT: H 180 GLN cc_start: 0.8592 (mt0) cc_final: 0.8180 (mt0) REVERT: H 185 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8091 (ptmt) REVERT: H 201 TYR cc_start: 0.8052 (m-80) cc_final: 0.7454 (m-80) REVERT: H 232 PHE cc_start: 0.7139 (m-10) cc_final: 0.6674 (m-80) REVERT: H 267 ARG cc_start: 0.8474 (tpp80) cc_final: 0.8126 (tpp80) REVERT: H 281 MET cc_start: 0.7114 (ttm) cc_final: 0.6837 (ttm) REVERT: H 282 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6608 (mt-10) REVERT: H 304 ARG cc_start: 0.8056 (mtt180) cc_final: 0.7336 (mtt90) REVERT: H 340 ILE cc_start: 0.9154 (mt) cc_final: 0.8606 (mt) REVERT: H 387 LYS cc_start: 0.8117 (mmtm) cc_final: 0.7914 (mmtm) REVERT: H 398 ARG cc_start: 0.8586 (tpp-160) cc_final: 0.8288 (tpp-160) REVERT: H 443 LYS cc_start: 0.7538 (mtmm) cc_final: 0.7279 (mttp) REVERT: H 481 THR cc_start: 0.8459 (m) cc_final: 0.8011 (p) REVERT: H 482 VAL cc_start: 0.8666 (t) cc_final: 0.8154 (p) outliers start: 91 outliers final: 62 residues processed: 1002 average time/residue: 0.4693 time to fit residues: 699.3947 Evaluate side-chains 1031 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 959 time to evaluate : 3.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 503 CYS Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 185 LYS Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 161 TYR Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 474 ARG Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 513 GLU Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 265 ASP Chi-restraints excluded: chain F residue 304 ARG Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 387 LYS Chi-restraints excluded: chain F residue 474 ARG Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 513 GLU Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 315 HIS Chi-restraints excluded: chain G residue 488 GLU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 185 LYS Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 513 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 52 optimal weight: 10.0000 chunk 211 optimal weight: 2.9990 chunk 356 optimal weight: 10.0000 chunk 235 optimal weight: 70.0000 chunk 84 optimal weight: 0.9980 chunk 236 optimal weight: 9.9990 chunk 349 optimal weight: 7.9990 chunk 95 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 278 optimal weight: 0.0970 chunk 14 optimal weight: 4.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 GLN A 374 GLN ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN ** D 158 ASN ** 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 = 0.4356 r_free = 0.4356 target = 0.177946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.137408 restraints weight = 54175.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.142592 restraints weight = 30044.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.146043 restraints weight = 19412.435| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30368 Z= 0.178 Angle : 0.690 16.947 41088 Z= 0.350 Chirality : 0.048 0.299 4672 Planarity : 0.005 0.072 5352 Dihedral : 4.634 43.727 4058 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.04 % Allowed : 20.57 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3720 helix: 0.13 (0.15), residues: 1152 sheet: -0.66 (0.20), residues: 696 loop : 0.24 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 87 HIS 0.007 0.001 HIS A 271 PHE 0.018 0.002 PHE E 325 TYR 0.035 0.002 TYR A 224 ARG 0.008 0.001 ARG G 74 Details of bonding type rmsd hydrogen bonds : bond 0.04600 ( 1087) hydrogen bonds : angle 5.15059 ( 2733) covalent geometry : bond 0.00389 (30368) covalent geometry : angle 0.69049 (41088) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1084 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 983 time to evaluate : 3.051 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: 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: 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 41 MET cc_start: 0.8647 (mmm) cc_final: 0.8430 (mmm) REVERT: A 60 ARG cc_start: 0.8425 (tpt170) cc_final: 0.7144 (tpt170) REVERT: A 64 GLU cc_start: 0.8663 (tt0) cc_final: 0.8443 (mt-10) REVERT: A 72 PHE cc_start: 0.8581 (t80) cc_final: 0.8110 (t80) REVERT: A 89 ARG cc_start: 0.8715 (mtp85) cc_final: 0.8469 (mmm-85) REVERT: A 99 VAL cc_start: 0.8261 (OUTLIER) cc_final: 0.8052 (m) REVERT: A 102 ASP cc_start: 0.8170 (m-30) cc_final: 0.7848 (p0) REVERT: A 144 MET cc_start: 0.6886 (tmm) cc_final: 0.6641 (tmm) REVERT: A 170 MET cc_start: 0.7336 (ptp) cc_final: 0.6983 (ptp) REVERT: A 180 GLN cc_start: 0.7876 (mt0) cc_final: 0.7486 (mp10) REVERT: A 185 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8231 (ptmt) REVERT: A 197 ASN cc_start: 0.7122 (t0) cc_final: 0.6897 (t0) REVERT: A 201 TYR cc_start: 0.7969 (m-80) cc_final: 0.7680 (m-80) REVERT: A 259 ASN cc_start: 0.7289 (t0) cc_final: 0.6757 (p0) REVERT: A 260 LEU cc_start: 0.8585 (tp) cc_final: 0.8317 (tp) REVERT: A 271 HIS cc_start: 0.7436 (t70) cc_final: 0.7058 (t70) REVERT: A 280 ILE cc_start: 0.6889 (mt) cc_final: 0.6575 (mm) REVERT: A 282 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7115 (mt-10) REVERT: A 335 MET cc_start: 0.3380 (mtt) cc_final: 0.2757 (mtt) REVERT: A 341 LYS cc_start: 0.9046 (tttt) cc_final: 0.8693 (ttpp) REVERT: A 386 PHE cc_start: 0.7550 (m-80) cc_final: 0.7177 (m-80) REVERT: A 387 LYS cc_start: 0.8292 (mppt) cc_final: 0.8053 (mtmm) REVERT: A 425 MET cc_start: 0.7479 (ttp) cc_final: 0.7245 (ttp) REVERT: A 426 ASP cc_start: 0.8273 (t0) cc_final: 0.7825 (t0) REVERT: A 479 LYS cc_start: 0.7343 (mttt) cc_final: 0.6959 (mttm) REVERT: A 481 THR cc_start: 0.8606 (m) cc_final: 0.8204 (p) REVERT: B 41 MET cc_start: 0.8686 (mmm) cc_final: 0.8437 (mmm) REVERT: B 64 GLU cc_start: 0.8763 (tt0) cc_final: 0.8216 (tt0) REVERT: B 72 PHE cc_start: 0.8437 (t80) cc_final: 0.7933 (t80) REVERT: B 89 ARG cc_start: 0.8531 (mmm-85) cc_final: 0.8137 (mmm-85) REVERT: B 94 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7177 (mm-40) REVERT: B 147 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8425 (tp) REVERT: B 168 VAL cc_start: 0.9146 (t) cc_final: 0.8912 (p) REVERT: B 201 TYR cc_start: 0.7833 (m-80) cc_final: 0.7370 (t80) REVERT: B 232 PHE cc_start: 0.6817 (m-10) cc_final: 0.6327 (m-80) REVERT: B 243 LYS cc_start: 0.8432 (mttt) cc_final: 0.8130 (mttt) REVERT: B 267 ARG cc_start: 0.8531 (tpt-90) cc_final: 0.8020 (tpp80) REVERT: B 281 MET cc_start: 0.7099 (ttm) cc_final: 0.6826 (ttm) REVERT: B 282 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6743 (mt-10) REVERT: B 318 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8072 (mt-10) REVERT: B 340 ILE cc_start: 0.9091 (mt) cc_final: 0.8639 (mt) REVERT: B 374 GLN cc_start: 0.5815 (OUTLIER) cc_final: 0.5515 (mm-40) REVERT: B 398 ARG cc_start: 0.8590 (tpp-160) cc_final: 0.8285 (tpp-160) REVERT: B 415 LEU cc_start: 0.8524 (tp) cc_final: 0.8223 (tt) REVERT: B 425 MET cc_start: 0.7532 (ttp) cc_final: 0.7110 (ttp) REVERT: B 426 ASP cc_start: 0.8485 (t0) cc_final: 0.8025 (t0) REVERT: B 443 LYS cc_start: 0.7810 (mtpp) cc_final: 0.7316 (mttm) REVERT: B 448 PHE cc_start: 0.8232 (t80) cc_final: 0.8015 (t80) REVERT: B 479 LYS cc_start: 0.7233 (mttt) cc_final: 0.6866 (mtmm) REVERT: B 481 THR cc_start: 0.8424 (m) cc_final: 0.8005 (p) REVERT: B 491 THR cc_start: 0.8081 (m) cc_final: 0.7833 (t) REVERT: B 499 VAL cc_start: 0.8526 (t) cc_final: 0.8239 (m) REVERT: B 503 CYS cc_start: 0.7621 (p) cc_final: 0.7140 (m) REVERT: C 41 MET cc_start: 0.8505 (mmm) cc_final: 0.8228 (mmm) REVERT: C 54 ASP cc_start: 0.7754 (t70) cc_final: 0.7500 (t0) REVERT: C 64 GLU cc_start: 0.8530 (tt0) cc_final: 0.7968 (tt0) REVERT: C 72 PHE cc_start: 0.8649 (t80) cc_final: 0.8056 (t80) REVERT: C 94 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7365 (mm-40) REVERT: C 135 LYS cc_start: 0.8107 (ttmt) cc_final: 0.7789 (ttmt) REVERT: C 179 THR cc_start: 0.8348 (m) cc_final: 0.8020 (p) REVERT: C 181 SER cc_start: 0.8648 (OUTLIER) cc_final: 0.8345 (p) REVERT: C 221 GLN cc_start: 0.7984 (tp40) cc_final: 0.7738 (tp40) REVERT: C 232 PHE cc_start: 0.7208 (m-10) cc_final: 0.6827 (m-80) REVERT: C 282 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6210 (mt-10) REVERT: C 283 LEU cc_start: 0.7705 (mt) cc_final: 0.7330 (mm) REVERT: C 426 ASP cc_start: 0.8458 (t0) cc_final: 0.8148 (t70) REVERT: C 443 LYS cc_start: 0.7763 (mttm) cc_final: 0.7496 (mttm) REVERT: C 448 PHE cc_start: 0.8160 (t80) cc_final: 0.7579 (t80) REVERT: C 450 LYS cc_start: 0.8346 (ttpp) cc_final: 0.8080 (ttpp) REVERT: C 479 LYS cc_start: 0.7048 (mttt) cc_final: 0.6718 (mttm) REVERT: C 481 THR cc_start: 0.8099 (m) cc_final: 0.7665 (p) REVERT: C 503 CYS cc_start: 0.7466 (p) cc_final: 0.7060 (m) REVERT: C 511 ILE cc_start: 0.8470 (mt) cc_final: 0.8128 (tt) REVERT: D 64 GLU cc_start: 0.8566 (tt0) cc_final: 0.7847 (tt0) REVERT: D 72 PHE cc_start: 0.8608 (t80) cc_final: 0.8025 (t80) REVERT: D 94 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7044 (mm-40) REVERT: D 141 ARG cc_start: 0.7829 (ptm160) cc_final: 0.7351 (ttm-80) REVERT: D 148 ASP cc_start: 0.7363 (m-30) cc_final: 0.7062 (m-30) REVERT: D 170 MET cc_start: 0.7779 (ptp) cc_final: 0.7524 (ptp) REVERT: D 179 THR cc_start: 0.8413 (m) cc_final: 0.8117 (p) REVERT: D 185 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8078 (ptmt) REVERT: D 200 ARG cc_start: 0.6642 (mtp-110) cc_final: 0.6080 (mtp180) REVERT: D 201 TYR cc_start: 0.8005 (m-80) cc_final: 0.7468 (m-80) REVERT: D 232 PHE cc_start: 0.7185 (m-10) cc_final: 0.6891 (m-80) REVERT: D 272 MET cc_start: 0.7587 (tpp) cc_final: 0.7105 (tpp) REVERT: D 286 LYS cc_start: 0.8559 (mttm) cc_final: 0.8265 (tttm) REVERT: D 318 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7940 (mt-10) REVERT: D 341 LYS cc_start: 0.9053 (pttp) cc_final: 0.8806 (pmtt) REVERT: D 387 LYS cc_start: 0.8455 (mttt) cc_final: 0.8183 (mttt) REVERT: D 398 ARG cc_start: 0.8404 (tpp-160) cc_final: 0.8051 (tpp-160) REVERT: D 403 LYS cc_start: 0.7869 (mmtt) cc_final: 0.7141 (tptt) REVERT: D 415 LEU cc_start: 0.8578 (tp) cc_final: 0.8086 (tp) REVERT: D 425 MET cc_start: 0.7291 (tpp) cc_final: 0.6887 (tpp) REVERT: D 479 LYS cc_start: 0.7250 (mttt) cc_final: 0.6854 (mttm) REVERT: D 481 THR cc_start: 0.8371 (m) cc_final: 0.8034 (p) REVERT: D 491 THR cc_start: 0.8303 (m) cc_final: 0.7910 (p) REVERT: D 499 VAL cc_start: 0.8465 (t) cc_final: 0.8198 (m) REVERT: E 41 MET cc_start: 0.8324 (mmm) cc_final: 0.8094 (mmm) REVERT: E 50 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7584 (mt-10) REVERT: E 54 ASP cc_start: 0.7956 (t70) cc_final: 0.7689 (t0) REVERT: E 64 GLU cc_start: 0.8664 (tt0) cc_final: 0.8014 (tt0) REVERT: E 72 PHE cc_start: 0.8575 (t80) cc_final: 0.7921 (t80) REVERT: E 129 MET cc_start: 0.6984 (mtm) cc_final: 0.6225 (mtm) REVERT: E 135 LYS cc_start: 0.7999 (ttmt) cc_final: 0.7728 (tptm) REVERT: E 147 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8229 (tp) REVERT: E 168 VAL cc_start: 0.9090 (t) cc_final: 0.8800 (p) REVERT: E 179 THR cc_start: 0.8530 (m) cc_final: 0.8213 (p) REVERT: E 180 GLN cc_start: 0.8411 (mt0) cc_final: 0.7777 (mt0) REVERT: E 201 TYR cc_start: 0.7790 (m-80) cc_final: 0.7471 (m-80) REVERT: E 243 LYS cc_start: 0.8439 (mttt) cc_final: 0.8173 (mttt) REVERT: E 287 THR cc_start: 0.8253 (t) cc_final: 0.7897 (p) REVERT: E 304 ARG cc_start: 0.8067 (mmt180) cc_final: 0.7677 (mmt180) REVERT: E 387 LYS cc_start: 0.8448 (mppt) cc_final: 0.8234 (mtmm) REVERT: E 403 LYS cc_start: 0.7624 (mmtt) cc_final: 0.7067 (tptp) REVERT: E 412 LYS cc_start: 0.7536 (mttt) cc_final: 0.7246 (mttp) REVERT: E 441 ASP cc_start: 0.6967 (m-30) cc_final: 0.6649 (m-30) REVERT: E 443 LYS cc_start: 0.7614 (mtpp) cc_final: 0.7314 (mttm) REVERT: E 474 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6861 (ptp-110) REVERT: E 501 GLU cc_start: 0.7157 (tt0) cc_final: 0.6616 (tt0) REVERT: E 503 CYS cc_start: 0.7601 (p) cc_final: 0.7032 (m) REVERT: F 72 PHE cc_start: 0.8534 (t80) cc_final: 0.7605 (t80) REVERT: F 168 VAL cc_start: 0.9119 (t) cc_final: 0.8787 (p) REVERT: F 171 ASN cc_start: 0.7680 (m-40) cc_final: 0.7385 (p0) REVERT: F 179 THR cc_start: 0.8651 (m) cc_final: 0.8390 (p) REVERT: F 180 GLN cc_start: 0.8528 (mt0) cc_final: 0.8080 (mt0) REVERT: F 181 SER cc_start: 0.9024 (OUTLIER) cc_final: 0.8796 (p) REVERT: F 185 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7941 (ptmm) REVERT: F 196 PHE cc_start: 0.7053 (p90) cc_final: 0.6517 (p90) REVERT: F 201 TYR cc_start: 0.8051 (m-80) cc_final: 0.7428 (m-80) REVERT: F 221 GLN cc_start: 0.7836 (tp40) cc_final: 0.7583 (tp40) REVERT: F 243 LYS cc_start: 0.8562 (mttt) cc_final: 0.8278 (mttt) REVERT: F 253 PHE cc_start: 0.7557 (t80) cc_final: 0.7048 (t80) REVERT: F 272 MET cc_start: 0.7242 (tpp) cc_final: 0.6890 (tpp) REVERT: F 281 MET cc_start: 0.7017 (ttm) cc_final: 0.6604 (ttm) REVERT: F 282 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7235 (mt-10) REVERT: F 304 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.6864 (mtp85) REVERT: F 425 MET cc_start: 0.7473 (ttp) cc_final: 0.7173 (ttp) REVERT: F 426 ASP cc_start: 0.8436 (t0) cc_final: 0.8218 (t70) REVERT: F 443 LYS cc_start: 0.7879 (mttm) cc_final: 0.7421 (mmtm) REVERT: F 503 CYS cc_start: 0.7654 (p) cc_final: 0.7037 (m) REVERT: G 41 MET cc_start: 0.7884 (mmm) cc_final: 0.7646 (mmm) REVERT: G 64 GLU cc_start: 0.8492 (tt0) cc_final: 0.8149 (tt0) REVERT: G 72 PHE cc_start: 0.8699 (t80) cc_final: 0.8018 (t80) REVERT: G 89 ARG cc_start: 0.8764 (mmm-85) cc_final: 0.8483 (mmm-85) REVERT: G 102 ASP cc_start: 0.8088 (m-30) cc_final: 0.7812 (p0) REVERT: G 115 LYS cc_start: 0.7995 (mtmm) cc_final: 0.7515 (ptpp) REVERT: G 129 MET cc_start: 0.7178 (mtm) cc_final: 0.6956 (mtm) REVERT: G 144 MET cc_start: 0.6562 (ttt) cc_final: 0.5456 (ttp) REVERT: G 179 THR cc_start: 0.8398 (m) cc_final: 0.8167 (p) REVERT: G 180 GLN cc_start: 0.8555 (mt0) cc_final: 0.8095 (mt0) REVERT: G 185 LYS cc_start: 0.8641 (tmmt) cc_final: 0.8439 (ptmm) REVERT: G 243 LYS cc_start: 0.8820 (mttt) cc_final: 0.8481 (tptp) REVERT: G 259 ASN cc_start: 0.7995 (t0) cc_final: 0.7038 (p0) REVERT: G 267 ARG cc_start: 0.8479 (tpp80) cc_final: 0.8043 (tpp80) REVERT: G 272 MET cc_start: 0.7731 (tpp) cc_final: 0.7312 (tpp) REVERT: G 282 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6684 (mt-10) REVERT: G 286 LYS cc_start: 0.8387 (mttm) cc_final: 0.7876 (tttm) REVERT: G 304 ARG cc_start: 0.8202 (ttt180) cc_final: 0.7861 (mtp180) REVERT: G 318 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8171 (mt-10) REVERT: G 326 LYS cc_start: 0.7939 (ptpt) cc_final: 0.7372 (mttp) REVERT: G 347 ASN cc_start: 0.6755 (t0) cc_final: 0.6345 (t0) REVERT: G 403 LYS cc_start: 0.7747 (mmtt) cc_final: 0.7439 (tptp) REVERT: G 425 MET cc_start: 0.7537 (ttp) cc_final: 0.7304 (ttp) REVERT: G 443 LYS cc_start: 0.8009 (mtmm) cc_final: 0.7605 (mttm) REVERT: G 444 LYS cc_start: 0.6690 (mtpt) cc_final: 0.6241 (ttmm) REVERT: G 479 LYS cc_start: 0.7211 (mttt) cc_final: 0.6883 (mtmm) REVERT: G 481 THR cc_start: 0.8316 (m) cc_final: 0.7781 (p) REVERT: G 482 VAL cc_start: 0.8715 (t) cc_final: 0.8240 (p) REVERT: G 501 GLU cc_start: 0.7124 (tt0) cc_final: 0.6609 (tt0) REVERT: G 503 CYS cc_start: 0.7668 (p) cc_final: 0.7008 (m) REVERT: G 511 ILE cc_start: 0.8534 (mt) cc_final: 0.8279 (tt) REVERT: H 41 MET cc_start: 0.7870 (tpp) cc_final: 0.7582 (tpp) REVERT: H 64 GLU cc_start: 0.8630 (tt0) cc_final: 0.7932 (tt0) REVERT: H 72 PHE cc_start: 0.8832 (t80) cc_final: 0.8129 (t80) REVERT: H 74 ARG cc_start: 0.8708 (mtp180) cc_final: 0.8044 (mtm110) REVERT: H 89 ARG cc_start: 0.8712 (mmm-85) cc_final: 0.8369 (mmm-85) REVERT: H 102 ASP cc_start: 0.8315 (m-30) cc_final: 0.7594 (p0) REVERT: H 141 ARG cc_start: 0.7743 (mtp85) cc_final: 0.7292 (ttm-80) REVERT: H 168 VAL cc_start: 0.9220 (t) cc_final: 0.8828 (p) REVERT: H 171 ASN cc_start: 0.7951 (m-40) cc_final: 0.7445 (p0) REVERT: H 180 GLN cc_start: 0.8620 (mt0) cc_final: 0.8225 (mt0) REVERT: H 185 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8016 (ptmt) REVERT: H 201 TYR cc_start: 0.8189 (m-80) cc_final: 0.7598 (m-80) REVERT: H 232 PHE cc_start: 0.7190 (m-10) cc_final: 0.6692 (m-80) REVERT: H 267 ARG cc_start: 0.8449 (tpp80) cc_final: 0.8072 (tpp80) REVERT: H 281 MET cc_start: 0.7216 (ttm) cc_final: 0.6900 (ttm) REVERT: H 282 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6805 (mt-10) REVERT: H 304 ARG cc_start: 0.8046 (mtt180) cc_final: 0.7371 (mtt180) REVERT: H 341 LYS cc_start: 0.9278 (pttp) cc_final: 0.9059 (pttm) REVERT: H 387 LYS cc_start: 0.8213 (mmtm) cc_final: 0.7977 (mmtm) REVERT: H 398 ARG cc_start: 0.8622 (tpp-160) cc_final: 0.8319 (tpp-160) REVERT: H 403 LYS cc_start: 0.8171 (mmtt) cc_final: 0.7501 (tptt) REVERT: H 443 LYS cc_start: 0.7596 (mtmm) cc_final: 0.7325 (mttp) REVERT: H 481 THR cc_start: 0.8461 (m) cc_final: 0.8007 (p) REVERT: H 511 ILE cc_start: 0.8596 (mt) cc_final: 0.8220 (tt) outliers start: 101 outliers final: 70 residues processed: 1014 average time/residue: 0.4702 time to fit residues: 708.8821 Evaluate side-chains 1062 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 980 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 503 CYS Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 474 ARG Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 185 LYS Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 161 TYR Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 474 ARG Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 513 GLU Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 265 ASP Chi-restraints excluded: chain F residue 304 ARG Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 387 LYS Chi-restraints excluded: chain F residue 474 ARG Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 513 GLU Chi-restraints excluded: chain G residue 87 TRP Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 315 HIS Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 474 ARG Chi-restraints excluded: chain G residue 488 GLU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 185 LYS Chi-restraints excluded: chain H residue 307 GLU Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain H residue 333 ILE Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 423 LEU Chi-restraints excluded: chain H residue 504 VAL Chi-restraints excluded: chain H residue 513 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 283 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 352 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 188 optimal weight: 40.0000 chunk 230 optimal weight: 4.9990 chunk 160 optimal weight: 7.9990 chunk 243 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 GLN B 198 GLN ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.178714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.138666 restraints weight = 54642.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.143853 restraints weight = 30171.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.147202 restraints weight = 19479.299| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 30368 Z= 0.151 Angle : 0.698 16.599 41088 Z= 0.354 Chirality : 0.048 0.304 4672 Planarity : 0.005 0.067 5352 Dihedral : 4.622 43.713 4058 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.65 % Allowed : 21.33 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3720 helix: 0.12 (0.16), residues: 1152 sheet: -0.77 (0.20), residues: 712 loop : 0.24 (0.15), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 87 HIS 0.008 0.001 HIS A 271 PHE 0.018 0.002 PHE E 325 TYR 0.036 0.002 TYR E 224 ARG 0.013 0.001 ARG G 247 Details of bonding type rmsd hydrogen bonds : bond 0.04444 ( 1087) hydrogen bonds : angle 5.15519 ( 2733) covalent geometry : bond 0.00334 (30368) covalent geometry : angle 0.69775 (41088) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1064 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 976 time to evaluate : 3.502 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: 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: 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: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8580 (mmm) cc_final: 0.8357 (mmm) REVERT: A 72 PHE cc_start: 0.8574 (t80) cc_final: 0.8106 (t80) REVERT: A 89 ARG cc_start: 0.8755 (mtp85) cc_final: 0.8493 (mmm-85) REVERT: A 102 ASP cc_start: 0.8191 (m-30) cc_final: 0.7874 (p0) REVERT: A 144 MET cc_start: 0.6854 (tmm) cc_final: 0.6606 (tmm) REVERT: A 170 MET cc_start: 0.7294 (ptp) cc_final: 0.6947 (ptp) REVERT: A 180 GLN cc_start: 0.7772 (mt0) cc_final: 0.7455 (mp10) REVERT: A 185 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8120 (ptmt) REVERT: A 197 ASN cc_start: 0.7113 (t0) cc_final: 0.6850 (t0) REVERT: A 201 TYR cc_start: 0.7942 (m-80) cc_final: 0.7651 (m-80) REVERT: A 260 LEU cc_start: 0.8493 (tp) cc_final: 0.8265 (tp) REVERT: A 271 HIS cc_start: 0.7474 (t70) cc_final: 0.7073 (t70) REVERT: A 280 ILE cc_start: 0.6880 (mt) cc_final: 0.6549 (mm) REVERT: A 282 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7080 (mt-10) REVERT: A 335 MET cc_start: 0.3395 (mtt) cc_final: 0.2801 (mtt) REVERT: A 341 LYS cc_start: 0.9014 (tttt) cc_final: 0.8665 (ttpp) REVERT: A 374 GLN cc_start: 0.6072 (OUTLIER) cc_final: 0.4756 (mm110) REVERT: A 386 PHE cc_start: 0.7552 (m-80) cc_final: 0.7183 (m-80) REVERT: A 387 LYS cc_start: 0.8313 (mppt) cc_final: 0.8072 (mtmm) REVERT: A 425 MET cc_start: 0.7523 (ttp) cc_final: 0.7266 (ttp) REVERT: A 426 ASP cc_start: 0.8273 (t0) cc_final: 0.7824 (t0) REVERT: A 479 LYS cc_start: 0.7356 (mttt) cc_final: 0.6965 (mttm) REVERT: A 481 THR cc_start: 0.8612 (m) cc_final: 0.8195 (p) REVERT: B 41 MET cc_start: 0.8669 (mmm) cc_final: 0.8066 (mmm) REVERT: B 45 LEU cc_start: 0.9207 (mt) cc_final: 0.8978 (mt) REVERT: B 64 GLU cc_start: 0.8747 (tt0) cc_final: 0.8187 (tt0) REVERT: B 72 PHE cc_start: 0.8428 (t80) cc_final: 0.7954 (t80) REVERT: B 74 ARG cc_start: 0.7992 (ttm110) cc_final: 0.7604 (ptp-170) REVERT: B 89 ARG cc_start: 0.8538 (mmm-85) cc_final: 0.8154 (mmm-85) REVERT: B 94 GLN cc_start: 0.7673 (mm-40) cc_final: 0.7145 (mm-40) REVERT: B 147 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8395 (tp) REVERT: B 168 VAL cc_start: 0.9138 (t) cc_final: 0.8899 (p) REVERT: B 201 TYR cc_start: 0.7869 (m-80) cc_final: 0.7366 (t80) REVERT: B 232 PHE cc_start: 0.6752 (m-10) cc_final: 0.6327 (m-80) REVERT: B 243 LYS cc_start: 0.8394 (mttt) cc_final: 0.8092 (mttt) REVERT: B 281 MET cc_start: 0.7138 (ttm) cc_final: 0.6859 (ttm) REVERT: B 282 GLU cc_start: 0.7473 (mt-10) cc_final: 0.6758 (mt-10) REVERT: B 283 LEU cc_start: 0.7974 (mt) cc_final: 0.7763 (tt) REVERT: B 304 ARG cc_start: 0.8044 (ttt180) cc_final: 0.7553 (ttt180) REVERT: B 318 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8059 (mt-10) REVERT: B 340 ILE cc_start: 0.9077 (mt) cc_final: 0.8647 (mt) REVERT: B 415 LEU cc_start: 0.8517 (tp) cc_final: 0.8196 (tt) REVERT: B 425 MET cc_start: 0.7512 (ttp) cc_final: 0.7094 (ttp) REVERT: B 426 ASP cc_start: 0.8472 (t0) cc_final: 0.8017 (t0) REVERT: B 479 LYS cc_start: 0.7231 (mttt) cc_final: 0.6879 (mtmm) REVERT: B 481 THR cc_start: 0.8428 (m) cc_final: 0.7994 (p) REVERT: B 491 THR cc_start: 0.8079 (m) cc_final: 0.7824 (t) REVERT: B 499 VAL cc_start: 0.8515 (t) cc_final: 0.8272 (m) REVERT: B 503 CYS cc_start: 0.7606 (p) cc_final: 0.7126 (m) REVERT: C 41 MET cc_start: 0.8477 (mmm) cc_final: 0.8221 (mmm) REVERT: C 64 GLU cc_start: 0.8509 (tt0) cc_final: 0.7958 (tt0) REVERT: C 72 PHE cc_start: 0.8652 (t80) cc_final: 0.8117 (t80) REVERT: C 74 ARG cc_start: 0.8337 (ttm110) cc_final: 0.7814 (ptp-170) REVERT: C 135 LYS cc_start: 0.8101 (ttmt) cc_final: 0.7761 (ttmt) REVERT: C 170 MET cc_start: 0.7674 (ptp) cc_final: 0.7419 (pmm) REVERT: C 221 GLN cc_start: 0.8033 (tp40) cc_final: 0.7759 (tp40) REVERT: C 232 PHE cc_start: 0.7078 (m-10) cc_final: 0.6769 (m-80) REVERT: C 282 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6308 (mt-10) REVERT: C 283 LEU cc_start: 0.7676 (mt) cc_final: 0.7298 (mm) REVERT: C 304 ARG cc_start: 0.8176 (mmt180) cc_final: 0.7941 (mmt180) REVERT: C 426 ASP cc_start: 0.8414 (t0) cc_final: 0.8130 (t70) REVERT: C 479 LYS cc_start: 0.7009 (mttt) cc_final: 0.6710 (mttm) REVERT: C 481 THR cc_start: 0.8091 (m) cc_final: 0.7648 (p) REVERT: C 503 CYS cc_start: 0.7481 (p) cc_final: 0.7061 (m) REVERT: C 511 ILE cc_start: 0.8477 (mt) cc_final: 0.8133 (tt) REVERT: D 64 GLU cc_start: 0.8541 (tt0) cc_final: 0.7799 (tt0) REVERT: D 72 PHE cc_start: 0.8608 (t80) cc_final: 0.8067 (t80) REVERT: D 74 ARG cc_start: 0.8333 (ttm110) cc_final: 0.7852 (ptp-170) REVERT: D 94 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7033 (mm-40) REVERT: D 141 ARG cc_start: 0.7743 (ptm160) cc_final: 0.7324 (ttm-80) REVERT: D 170 MET cc_start: 0.7833 (ptp) cc_final: 0.7620 (ptp) REVERT: D 179 THR cc_start: 0.8349 (m) cc_final: 0.8070 (p) REVERT: D 185 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8086 (ptmt) REVERT: D 200 ARG cc_start: 0.6505 (mtp-110) cc_final: 0.5967 (mtp180) REVERT: D 201 TYR cc_start: 0.7976 (m-80) cc_final: 0.7441 (m-80) REVERT: D 232 PHE cc_start: 0.7107 (m-10) cc_final: 0.6875 (m-80) REVERT: D 272 MET cc_start: 0.7563 (tpp) cc_final: 0.7099 (tpp) REVERT: D 286 LYS cc_start: 0.8566 (mttm) cc_final: 0.8261 (tttm) REVERT: D 318 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7957 (mt-10) REVERT: D 341 LYS cc_start: 0.9046 (pttp) cc_final: 0.8808 (pmtt) REVERT: D 387 LYS cc_start: 0.8449 (mttt) cc_final: 0.8181 (mttt) REVERT: D 398 ARG cc_start: 0.8392 (tpp-160) cc_final: 0.8105 (tpp-160) REVERT: D 403 LYS cc_start: 0.7874 (mmtt) cc_final: 0.7133 (tptt) REVERT: D 415 LEU cc_start: 0.8627 (tp) cc_final: 0.8031 (tp) REVERT: D 425 MET cc_start: 0.7322 (tpp) cc_final: 0.6909 (tpp) REVERT: D 479 LYS cc_start: 0.7261 (mttt) cc_final: 0.6855 (mttm) REVERT: D 481 THR cc_start: 0.8386 (m) cc_final: 0.8039 (p) REVERT: D 491 THR cc_start: 0.8295 (m) cc_final: 0.7955 (t) REVERT: D 499 VAL cc_start: 0.8474 (t) cc_final: 0.8209 (m) REVERT: E 41 MET cc_start: 0.8316 (mmm) cc_final: 0.8082 (mmm) REVERT: E 50 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7588 (mt-10) REVERT: E 64 GLU cc_start: 0.8643 (tt0) cc_final: 0.7988 (tt0) REVERT: E 72 PHE cc_start: 0.8551 (t80) cc_final: 0.7900 (t80) REVERT: E 102 ASP cc_start: 0.8098 (m-30) cc_final: 0.7870 (p0) REVERT: E 129 MET cc_start: 0.6967 (mtm) cc_final: 0.6164 (mtm) REVERT: E 135 LYS cc_start: 0.7951 (ttmt) cc_final: 0.7698 (tptm) REVERT: E 147 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8118 (tp) REVERT: E 168 VAL cc_start: 0.9076 (t) cc_final: 0.8807 (p) REVERT: E 179 THR cc_start: 0.8453 (m) cc_final: 0.8191 (p) REVERT: E 180 GLN cc_start: 0.8430 (mt0) cc_final: 0.7769 (mt0) REVERT: E 201 TYR cc_start: 0.7803 (m-80) cc_final: 0.7429 (m-80) REVERT: E 243 LYS cc_start: 0.8424 (mttt) cc_final: 0.8153 (mttt) REVERT: E 267 ARG cc_start: 0.8497 (tpp80) cc_final: 0.8273 (tpp80) REVERT: E 304 ARG cc_start: 0.8049 (mmt180) cc_final: 0.7166 (mmm-85) REVERT: E 387 LYS cc_start: 0.8444 (mppt) cc_final: 0.8225 (mtmm) REVERT: E 403 LYS cc_start: 0.7573 (mmtt) cc_final: 0.7063 (tptp) REVERT: E 412 LYS cc_start: 0.7517 (mttt) cc_final: 0.7208 (mttp) REVERT: E 426 ASP cc_start: 0.8057 (t0) cc_final: 0.7686 (t70) REVERT: E 437 LYS cc_start: 0.7751 (mmtt) cc_final: 0.7181 (mppt) REVERT: E 474 ARG cc_start: 0.7084 (OUTLIER) cc_final: 0.6853 (ptp-110) REVERT: E 501 GLU cc_start: 0.7158 (tt0) cc_final: 0.6617 (tt0) REVERT: E 503 CYS cc_start: 0.7621 (p) cc_final: 0.7023 (m) REVERT: F 72 PHE cc_start: 0.8542 (t80) cc_final: 0.7590 (t80) REVERT: F 168 VAL cc_start: 0.9101 (t) cc_final: 0.8795 (p) REVERT: F 171 ASN cc_start: 0.7635 (m-40) cc_final: 0.7309 (p0) REVERT: F 179 THR cc_start: 0.8653 (m) cc_final: 0.8375 (p) REVERT: F 180 GLN cc_start: 0.8559 (mt0) cc_final: 0.8166 (mt0) REVERT: F 181 SER cc_start: 0.9009 (OUTLIER) cc_final: 0.8735 (p) REVERT: F 185 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7919 (ptmm) REVERT: F 196 PHE cc_start: 0.6968 (p90) cc_final: 0.6439 (p90) REVERT: F 201 TYR cc_start: 0.8033 (m-80) cc_final: 0.7417 (m-80) REVERT: F 221 GLN cc_start: 0.7832 (tp40) cc_final: 0.7596 (tp40) REVERT: F 243 LYS cc_start: 0.8560 (mttt) cc_final: 0.8274 (mttt) REVERT: F 253 PHE cc_start: 0.7545 (t80) cc_final: 0.7048 (t80) REVERT: F 267 ARG cc_start: 0.8279 (ttt180) cc_final: 0.7741 (mmm-85) REVERT: F 272 MET cc_start: 0.7330 (tpp) cc_final: 0.6997 (tpp) REVERT: F 281 MET cc_start: 0.7074 (ttm) cc_final: 0.6597 (ttm) REVERT: F 282 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7226 (mt-10) REVERT: F 283 LEU cc_start: 0.8228 (mt) cc_final: 0.7668 (mt) REVERT: F 286 LYS cc_start: 0.8293 (mttm) cc_final: 0.7754 (mttm) REVERT: F 304 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6927 (mtt-85) REVERT: F 425 MET cc_start: 0.7472 (ttp) cc_final: 0.7163 (ttp) REVERT: F 443 LYS cc_start: 0.7863 (mttm) cc_final: 0.7368 (mptp) REVERT: F 503 CYS cc_start: 0.7643 (p) cc_final: 0.7025 (m) REVERT: G 41 MET cc_start: 0.7897 (mmm) cc_final: 0.7672 (mmm) REVERT: G 64 GLU cc_start: 0.8568 (tt0) cc_final: 0.8243 (tt0) REVERT: G 72 PHE cc_start: 0.8692 (t80) cc_final: 0.8015 (t80) REVERT: G 89 ARG cc_start: 0.8832 (mmm-85) cc_final: 0.8488 (mmm-85) REVERT: G 102 ASP cc_start: 0.8074 (m-30) cc_final: 0.7785 (p0) REVERT: G 115 LYS cc_start: 0.8092 (mtmm) cc_final: 0.7815 (ptpp) REVERT: G 179 THR cc_start: 0.8368 (m) cc_final: 0.8125 (p) REVERT: G 180 GLN cc_start: 0.8497 (mt0) cc_final: 0.8060 (mt0) REVERT: G 185 LYS cc_start: 0.8654 (tmmt) cc_final: 0.8430 (ptmm) REVERT: G 200 ARG cc_start: 0.6732 (mtp-110) cc_final: 0.6315 (ttp80) REVERT: G 243 LYS cc_start: 0.8807 (mttt) cc_final: 0.8474 (tptp) REVERT: G 259 ASN cc_start: 0.7962 (t0) cc_final: 0.6999 (p0) REVERT: G 267 ARG cc_start: 0.8436 (tpp80) cc_final: 0.7980 (tpp80) REVERT: G 272 MET cc_start: 0.7652 (tpp) cc_final: 0.7255 (tpp) REVERT: G 282 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6704 (mt-10) REVERT: G 286 LYS cc_start: 0.8394 (mttm) cc_final: 0.7859 (tttm) REVERT: G 304 ARG cc_start: 0.8226 (ttt180) cc_final: 0.7892 (mtp180) REVERT: G 318 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8171 (mt-10) REVERT: G 326 LYS cc_start: 0.7869 (ptpt) cc_final: 0.7267 (mttp) REVERT: G 347 ASN cc_start: 0.6730 (t0) cc_final: 0.6314 (t0) REVERT: G 403 LYS cc_start: 0.7714 (mmtt) cc_final: 0.7407 (tptp) REVERT: G 425 MET cc_start: 0.7542 (ttp) cc_final: 0.7302 (ttp) REVERT: G 443 LYS cc_start: 0.8019 (mtmm) cc_final: 0.7655 (mttp) REVERT: G 444 LYS cc_start: 0.6632 (mtpt) cc_final: 0.6162 (ttmm) REVERT: G 479 LYS cc_start: 0.7217 (mttt) cc_final: 0.6891 (mtmm) REVERT: G 481 THR cc_start: 0.8357 (m) cc_final: 0.7826 (p) REVERT: G 482 VAL cc_start: 0.8748 (t) cc_final: 0.8264 (p) REVERT: G 501 GLU cc_start: 0.7088 (tt0) cc_final: 0.6492 (tt0) REVERT: G 503 CYS cc_start: 0.7542 (p) cc_final: 0.6996 (m) REVERT: G 511 ILE cc_start: 0.8507 (mt) cc_final: 0.8238 (tt) REVERT: H 41 MET cc_start: 0.7861 (tpp) cc_final: 0.7582 (tpp) REVERT: H 64 GLU cc_start: 0.8689 (tt0) cc_final: 0.8026 (tt0) REVERT: H 72 PHE cc_start: 0.8827 (t80) cc_final: 0.8092 (t80) REVERT: H 89 ARG cc_start: 0.8716 (mmm-85) cc_final: 0.8405 (mmm-85) REVERT: H 102 ASP cc_start: 0.8299 (m-30) cc_final: 0.7598 (p0) REVERT: H 141 ARG cc_start: 0.7741 (mtp85) cc_final: 0.7313 (ttm-80) REVERT: H 168 VAL cc_start: 0.9206 (t) cc_final: 0.8888 (p) REVERT: H 171 ASN cc_start: 0.7902 (m-40) cc_final: 0.7428 (p0) REVERT: H 180 GLN cc_start: 0.8636 (mt0) cc_final: 0.8127 (mt0) REVERT: H 185 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8212 (ptmt) REVERT: H 201 TYR cc_start: 0.8135 (m-80) cc_final: 0.7556 (m-80) REVERT: H 232 PHE cc_start: 0.7160 (m-10) cc_final: 0.6705 (m-80) REVERT: H 267 ARG cc_start: 0.8429 (tpp80) cc_final: 0.8049 (tpp80) REVERT: H 281 MET cc_start: 0.7213 (ttm) cc_final: 0.6904 (ttm) REVERT: H 282 GLU cc_start: 0.7520 (mt-10) cc_final: 0.6821 (mt-10) REVERT: H 304 ARG cc_start: 0.8038 (mtt180) cc_final: 0.7361 (mtt180) REVERT: H 341 LYS cc_start: 0.9285 (pttp) cc_final: 0.9079 (pttm) REVERT: H 387 LYS cc_start: 0.8152 (mmtm) cc_final: 0.7925 (mmtm) REVERT: H 398 ARG cc_start: 0.8601 (tpp-160) cc_final: 0.8359 (tpp-160) REVERT: H 403 LYS cc_start: 0.8153 (mmtt) cc_final: 0.7494 (tptt) REVERT: H 443 LYS cc_start: 0.7615 (mtmm) cc_final: 0.7350 (mttp) REVERT: H 481 THR cc_start: 0.8465 (m) cc_final: 0.8006 (p) REVERT: H 482 VAL cc_start: 0.8651 (t) cc_final: 0.8136 (p) REVERT: H 511 ILE cc_start: 0.8590 (mt) cc_final: 0.8228 (tt) outliers start: 88 outliers final: 70 residues processed: 1002 average time/residue: 0.4866 time to fit residues: 725.9209 Evaluate side-chains 1043 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 963 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 503 CYS Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 87 TRP Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 185 LYS Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 503 CYS Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 161 TYR Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 474 ARG Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 513 GLU Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 265 ASP Chi-restraints excluded: chain F residue 304 ARG Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 387 LYS Chi-restraints excluded: chain F residue 474 ARG Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 513 GLU Chi-restraints excluded: chain G residue 87 TRP Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 315 HIS Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 474 ARG Chi-restraints excluded: chain G residue 488 GLU Chi-restraints excluded: chain G residue 504 VAL Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 185 LYS Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 307 GLU Chi-restraints excluded: chain H residue 333 ILE Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 423 LEU Chi-restraints excluded: chain H residue 488 GLU Chi-restraints excluded: chain H residue 504 VAL Chi-restraints excluded: chain H residue 513 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 158 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 139 optimal weight: 0.0030 chunk 30 optimal weight: 2.9990 chunk 312 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 358 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 overall best weight: 1.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 GLN ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.178469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.138531 restraints weight = 54308.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.143665 restraints weight = 30105.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.147082 restraints weight = 19439.194| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.262 30368 Z= 0.203 Angle : 0.802 59.160 41088 Z= 0.427 Chirality : 0.049 0.392 4672 Planarity : 0.005 0.066 5352 Dihedral : 4.613 43.719 4058 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.65 % Allowed : 21.63 % Favored : 75.72 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3720 helix: 0.12 (0.15), residues: 1152 sheet: -0.76 (0.20), residues: 712 loop : 0.23 (0.15), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 87 HIS 0.007 0.001 HIS A 271 PHE 0.015 0.001 PHE C 232 TYR 0.032 0.002 TYR E 224 ARG 0.027 0.001 ARG G 247 Details of bonding type rmsd hydrogen bonds : bond 0.04465 ( 1087) hydrogen bonds : angle 5.14853 ( 2733) covalent geometry : bond 0.00451 (30368) covalent geometry : angle 0.80178 (41088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13731.22 seconds wall clock time: 238 minutes 43.33 seconds (14323.33 seconds total)