Starting phenix.real_space_refine on Wed Jun 25 21:08:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c0b_16357/06_2025/8c0b_16357.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c0b_16357/06_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_16357/06_2025/8c0b_16357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c0b_16357/06_2025/8c0b_16357.map" model { file = "/net/cci-nas-00/data/ceres_data/8c0b_16357/06_2025/8c0b_16357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c0b_16357/06_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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 17.68, per 1000 atoms: 0.59 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: 7.43 Conformation dependent library (CDL) restraints added in 3.4 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: 4.36 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: 12.59 Time building geometry restraints manager: 8.52 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: 1.590 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: 1.390 Check model and map are aligned: 0.240 Set scattering table: 0.310 Process input model: 67.280 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.890 ------------------------------------------------------------------------------- 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 : 3.083 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: 0.4852 time to fit residues: 787.0834 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 : 3.392 ------------------------------------------------------------------------------- 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 = 0.185140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.143981 restraints weight = 55281.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.149494 restraints weight = 30669.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.153168 restraints weight = 19827.408| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.2435 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 10.226 41088 Z= 0.361 Chirality : 0.048 0.169 4672 Planarity : 0.005 0.056 5352 Dihedral : 4.812 48.100 4090 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.57 % Allowed : 11.69 % 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 0.025 0.002 TYR B 224 ARG 0.008 0.001 ARG B 60 Details of bonding type rmsd hydrogen bonds : bond 0.06182 ( 1087) hydrogen bonds : angle 5.46571 ( 2733) covalent geometry : bond 0.00293 (30368) covalent geometry : angle 0.69706 (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 1099 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 1047 time to evaluate : 3.473 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: 0.8133 (mtt-85) cc_final: 0.7904 (mpt-90) REVERT: A 64 GLU cc_start: 0.8343 (tt0) cc_final: 0.8006 (tt0) REVERT: A 72 PHE cc_start: 0.8639 (t80) cc_final: 0.8241 (t80) REVERT: A 78 ASP cc_start: 0.7281 (m-30) cc_final: 0.6745 (m-30) REVERT: A 89 ARG cc_start: 0.8679 (mmm-85) cc_final: 0.8451 (mtp85) REVERT: A 115 LYS cc_start: 0.8087 (mtmm) cc_final: 0.7804 (mtmm) REVERT: A 129 MET cc_start: 0.6927 (mtm) cc_final: 0.6469 (mtm) REVERT: A 135 LYS cc_start: 0.7620 (ttmt) cc_final: 0.7401 (ttmm) REVERT: A 179 THR cc_start: 0.8510 (m) cc_final: 0.8126 (p) REVERT: A 180 GLN cc_start: 0.8550 (mt0) cc_final: 0.8350 (mt0) REVERT: A 185 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8267 (tmmt) REVERT: A 222 ASP cc_start: 0.8157 (m-30) cc_final: 0.7827 (m-30) REVERT: A 253 PHE cc_start: 0.7296 (t80) cc_final: 0.6946 (t80) REVERT: A 259 ASN cc_start: 0.7565 (t0) cc_final: 0.7270 (t0) REVERT: A 280 ILE cc_start: 0.6078 (mt) cc_final: 0.5831 (mm) REVERT: A 341 LYS cc_start: 0.9059 (tttt) cc_final: 0.8778 (ttpp) REVERT: A 386 PHE cc_start: 0.7473 (m-80) cc_final: 0.7236 (m-80) REVERT: A 400 LEU cc_start: 0.8299 (tp) cc_final: 0.8051 (tt) REVERT: A 410 LEU cc_start: 0.8127 (tp) cc_final: 0.7926 (tt) REVERT: A 425 MET cc_start: 0.7516 (ttp) cc_final: 0.7178 (ttp) REVERT: A 426 ASP cc_start: 0.8621 (t0) cc_final: 0.8049 (t0) REVERT: A 491 THR cc_start: 0.8197 (m) cc_final: 0.7914 (t) REVERT: A 501 GLU cc_start: 0.7173 (tt0) cc_final: 0.6766 (tt0) REVERT: B 41 MET cc_start: 0.8526 (mmm) cc_final: 0.8311 (mmm) REVERT: B 50 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7291 (mt-10) REVERT: B 54 ASP cc_start: 0.7831 (t0) cc_final: 0.7591 (t0) REVERT: B 64 GLU cc_start: 0.8472 (tt0) cc_final: 0.7805 (tt0) REVERT: B 72 PHE cc_start: 0.8463 (t80) cc_final: 0.7851 (t80) REVERT: B 89 ARG cc_start: 0.8518 (mmm-85) cc_final: 0.8039 (mmm-85) REVERT: B 94 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7127 (mm-40) REVERT: B 178 ASP cc_start: 0.7322 (p0) cc_final: 0.7104 (p0) REVERT: B 201 TYR cc_start: 0.8024 (m-80) cc_final: 0.7720 (m-80) REVERT: B 224 TYR cc_start: 0.6565 (p90) cc_final: 0.6208 (p90) REVERT: B 232 PHE cc_start: 0.6801 (m-10) cc_final: 0.6446 (m-80) REVERT: B 253 PHE cc_start: 0.7237 (t80) cc_final: 0.6870 (t80) REVERT: B 259 ASN cc_start: 0.7351 (t0) cc_final: 0.7126 (t0) REVERT: B 260 LEU cc_start: 0.8250 (mt) cc_final: 0.7940 (mm) REVERT: B 272 MET cc_start: 0.7536 (tpp) cc_final: 0.7151 (tpp) REVERT: B 281 MET cc_start: 0.6633 (ttm) cc_final: 0.6074 (ttm) REVERT: B 286 LYS cc_start: 0.8070 (mttm) cc_final: 0.7751 (tttm) REVERT: B 304 ARG cc_start: 0.8005 (ttt180) cc_final: 0.7665 (ttt180) REVERT: B 318 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7210 (mt-10) REVERT: B 340 ILE cc_start: 0.9002 (mt) cc_final: 0.8418 (mt) REVERT: B 400 LEU cc_start: 0.8276 (tp) cc_final: 0.8064 (tt) REVERT: B 415 LEU cc_start: 0.8409 (tp) cc_final: 0.8060 (tt) REVERT: B 425 MET cc_start: 0.7248 (ttp) cc_final: 0.6952 (ttp) REVERT: B 426 ASP cc_start: 0.8472 (t0) cc_final: 0.7947 (t0) REVERT: B 441 ASP cc_start: 0.7238 (m-30) cc_final: 0.7025 (m-30) REVERT: B 443 LYS cc_start: 0.7822 (mtpp) cc_final: 0.7596 (mtmm) REVERT: B 447 ASP cc_start: 0.6928 (m-30) cc_final: 0.6700 (m-30) REVERT: B 450 LYS cc_start: 0.8111 (ttpp) cc_final: 0.7812 (ttpp) REVERT: B 491 THR cc_start: 0.8087 (m) cc_final: 0.7774 (t) REVERT: C 41 MET cc_start: 0.8579 (mmm) cc_final: 0.8308 (mmm) REVERT: C 64 GLU cc_start: 0.8051 (tt0) cc_final: 0.7288 (tt0) REVERT: C 72 PHE cc_start: 0.8578 (t80) cc_final: 0.7919 (t80) REVERT: C 89 ARG cc_start: 0.8885 (mmm-85) cc_final: 0.8417 (mmm-85) REVERT: C 102 ASP cc_start: 0.8041 (m-30) cc_final: 0.7617 (p0) REVERT: C 115 LYS cc_start: 0.8386 (ptpt) cc_final: 0.6974 (ptpt) REVERT: C 116 LEU cc_start: 0.7783 (tp) cc_final: 0.7369 (mm) REVERT: C 127 THR cc_start: 0.7321 (p) cc_final: 0.7052 (t) REVERT: C 129 MET cc_start: 0.6839 (mtm) cc_final: 0.6565 (mtm) REVERT: C 135 LYS cc_start: 0.7781 (ttmt) cc_final: 0.7435 (ttmt) REVERT: C 180 GLN cc_start: 0.8491 (mt0) cc_final: 0.8192 (mt0) REVERT: C 181 SER cc_start: 0.8804 (OUTLIER) cc_final: 0.8482 (p) REVERT: C 201 TYR cc_start: 0.7880 (m-80) cc_final: 0.7271 (m-80) REVERT: C 251 TYR cc_start: 0.5611 (m-80) cc_final: 0.5289 (m-80) REVERT: C 253 PHE cc_start: 0.7485 (t80) cc_final: 0.7191 (t80) REVERT: C 259 ASN cc_start: 0.7418 (t0) cc_final: 0.7151 (t0) REVERT: C 282 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6179 (mt-10) REVERT: C 283 LEU cc_start: 0.7616 (mt) cc_final: 0.7241 (mm) REVERT: C 425 MET cc_start: 0.7549 (ttp) cc_final: 0.7325 (ttp) REVERT: C 426 ASP cc_start: 0.8633 (t0) cc_final: 0.8384 (t0) REVERT: C 450 LYS cc_start: 0.8233 (ttpp) cc_final: 0.7980 (ttpp) REVERT: C 479 LYS cc_start: 0.6957 (mttt) cc_final: 0.6643 (mttm) REVERT: C 481 THR cc_start: 0.8002 (m) cc_final: 0.7510 (p) REVERT: C 501 GLU cc_start: 0.7267 (tt0) cc_final: 0.6929 (tt0) REVERT: C 511 ILE cc_start: 0.8418 (mt) cc_final: 0.7976 (tt) REVERT: D 41 MET cc_start: 0.8643 (mmm) cc_final: 0.8442 (mmm) REVERT: D 50 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7388 (mt-10) REVERT: D 64 GLU cc_start: 0.8253 (tt0) cc_final: 0.7381 (tt0) REVERT: D 72 PHE cc_start: 0.8563 (t80) cc_final: 0.7980 (t80) REVERT: D 94 GLN cc_start: 0.7656 (mm-40) cc_final: 0.7094 (mm-40) REVERT: D 121 LEU cc_start: 0.8051 (mt) cc_final: 0.7641 (mt) REVERT: D 147 LEU cc_start: 0.8301 (tp) cc_final: 0.7867 (tp) REVERT: D 170 MET cc_start: 0.7785 (ttt) cc_final: 0.7571 (ptp) REVERT: D 185 LYS cc_start: 0.8518 (ptmt) cc_final: 0.8088 (ptmt) REVERT: D 201 TYR cc_start: 0.8013 (m-80) cc_final: 0.7334 (m-80) REVERT: D 243 LYS cc_start: 0.8841 (mttt) cc_final: 0.8593 (mttt) REVERT: D 260 LEU cc_start: 0.8202 (mt) cc_final: 0.7977 (mm) REVERT: D 270 GLN cc_start: 0.8279 (tp40) cc_final: 0.7995 (tp40) REVERT: D 272 MET cc_start: 0.7579 (tpp) cc_final: 0.7078 (tpp) REVERT: D 304 ARG cc_start: 0.7518 (mtp180) cc_final: 0.6865 (mtt180) REVERT: D 327 TYR cc_start: 0.7546 (m-80) cc_final: 0.7288 (m-80) REVERT: D 387 LYS cc_start: 0.8258 (mttt) cc_final: 0.8044 (mttt) REVERT: D 403 LYS cc_start: 0.7760 (mmtt) cc_final: 0.7228 (tptt) REVERT: D 425 MET cc_start: 0.7507 (ttp) cc_final: 0.7198 (ttp) REVERT: D 443 LYS cc_start: 0.7730 (mtpp) cc_final: 0.7520 (mttm) REVERT: D 481 THR cc_start: 0.8161 (m) cc_final: 0.7721 (p) REVERT: D 491 THR cc_start: 0.8104 (m) cc_final: 0.7680 (t) REVERT: E 41 MET cc_start: 0.8047 (tpp) cc_final: 0.7814 (mmm) REVERT: E 72 PHE cc_start: 0.8621 (t80) cc_final: 0.7823 (t80) REVERT: E 76 LEU cc_start: 0.8431 (mt) cc_final: 0.8135 (mt) REVERT: E 89 ARG cc_start: 0.8599 (mmm-85) cc_final: 0.8186 (mmm-85) REVERT: E 121 LEU cc_start: 0.8219 (mt) cc_final: 0.7682 (mt) REVERT: E 129 MET cc_start: 0.7058 (mtm) cc_final: 0.6402 (mtm) REVERT: E 135 LYS cc_start: 0.7651 (ttmt) cc_final: 0.7387 (tptm) REVERT: E 170 MET cc_start: 0.7612 (ttt) cc_final: 0.7375 (ptp) REVERT: E 180 GLN cc_start: 0.8414 (mt0) cc_final: 0.8072 (mt0) REVERT: E 201 TYR cc_start: 0.7861 (m-80) cc_final: 0.7486 (m-80) REVERT: E 242 ASP cc_start: 0.8649 (m-30) cc_final: 0.8439 (t0) REVERT: E 243 LYS cc_start: 0.8244 (mttt) cc_final: 0.8000 (mttt) REVERT: E 253 PHE cc_start: 0.7277 (t80) cc_final: 0.7052 (t80) REVERT: E 259 ASN cc_start: 0.7523 (t0) cc_final: 0.7235 (t0) REVERT: E 272 MET cc_start: 0.7408 (tpp) cc_final: 0.7159 (tpp) REVERT: E 281 MET cc_start: 0.6736 (ttm) cc_final: 0.6222 (ttm) REVERT: E 282 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6764 (mt-10) REVERT: E 326 LYS cc_start: 0.7726 (ptpt) cc_final: 0.7078 (mptt) REVERT: E 398 ARG cc_start: 0.8513 (tpp-160) cc_final: 0.8160 (tpp-160) REVERT: E 425 MET cc_start: 0.7354 (ttp) cc_final: 0.7112 (ttp) REVERT: E 426 ASP cc_start: 0.8526 (t0) cc_final: 0.8091 (t0) REVERT: E 441 ASP cc_start: 0.7096 (m-30) cc_final: 0.6636 (m-30) REVERT: E 443 LYS cc_start: 0.7734 (mtpp) cc_final: 0.7422 (mttm) REVERT: E 474 ARG cc_start: 0.6889 (ptp-110) cc_final: 0.6671 (ptp-110) REVERT: E 491 THR cc_start: 0.8127 (m) cc_final: 0.7886 (t) REVERT: E 501 GLU cc_start: 0.7077 (tt0) cc_final: 0.6705 (tt0) REVERT: F 72 PHE cc_start: 0.8460 (t80) cc_final: 0.7557 (t80) REVERT: F 87 TRP cc_start: 0.5712 (t-100) cc_final: 0.5250 (t-100) REVERT: F 102 ASP cc_start: 0.7990 (m-30) cc_final: 0.7551 (p0) REVERT: F 170 MET cc_start: 0.7857 (ttt) cc_final: 0.7472 (ptp) REVERT: F 171 ASN cc_start: 0.7661 (m-40) cc_final: 0.7304 (p0) REVERT: F 180 GLN cc_start: 0.8577 (mt0) cc_final: 0.8134 (mt0) REVERT: F 201 TYR cc_start: 0.7958 (m-80) cc_final: 0.7192 (m-80) REVERT: F 232 PHE cc_start: 0.7077 (m-80) cc_final: 0.6847 (m-80) REVERT: F 258 ASP cc_start: 0.5378 (p0) cc_final: 0.4935 (t70) REVERT: F 281 MET cc_start: 0.6713 (ttm) cc_final: 0.6159 (ttm) REVERT: F 304 ARG cc_start: 0.7222 (mtt180) cc_final: 0.6830 (mtp180) REVERT: F 340 ILE cc_start: 0.8912 (mt) cc_final: 0.8671 (mt) REVERT: F 373 TYR cc_start: 0.7897 (m-80) cc_final: 0.7582 (m-80) REVERT: F 387 LYS cc_start: 0.8080 (mttt) cc_final: 0.7842 (mttt) REVERT: F 418 LEU cc_start: 0.8541 (tp) cc_final: 0.8327 (tp) REVERT: F 425 MET cc_start: 0.7428 (ttp) cc_final: 0.7176 (ttp) REVERT: F 426 ASP cc_start: 0.8604 (t0) cc_final: 0.8268 (t0) REVERT: F 441 ASP cc_start: 0.7059 (m-30) cc_final: 0.6526 (m-30) REVERT: F 443 LYS cc_start: 0.7767 (mtpp) cc_final: 0.7563 (mttm) REVERT: F 481 THR cc_start: 0.7965 (m) cc_final: 0.7476 (p) REVERT: F 491 THR cc_start: 0.8046 (m) cc_final: 0.7747 (t) REVERT: F 501 GLU cc_start: 0.7042 (tt0) cc_final: 0.6653 (tt0) REVERT: G 41 MET cc_start: 0.7986 (mmm) cc_final: 0.7699 (mmm) REVERT: G 72 PHE cc_start: 0.8606 (t80) cc_final: 0.7849 (t80) REVERT: G 89 ARG cc_start: 0.8838 (mmm-85) cc_final: 0.8375 (mmm-85) REVERT: G 102 ASP cc_start: 0.8074 (m-30) cc_final: 0.7859 (p0) REVERT: G 129 MET cc_start: 0.6762 (mtm) cc_final: 0.6553 (mtm) REVERT: G 147 LEU cc_start: 0.8517 (tp) cc_final: 0.8252 (tp) REVERT: G 170 MET cc_start: 0.7666 (ttt) cc_final: 0.7418 (ptp) REVERT: G 180 GLN cc_start: 0.8477 (mt0) cc_final: 0.7966 (mt0) REVERT: G 185 LYS cc_start: 0.8640 (ptmt) cc_final: 0.8117 (ptmt) REVERT: G 186 TYR cc_start: 0.7247 (m-80) cc_final: 0.6877 (m-80) REVERT: G 200 ARG cc_start: 0.6889 (mtp-110) cc_final: 0.6339 (ttp80) REVERT: G 242 ASP cc_start: 0.8649 (m-30) cc_final: 0.8317 (t0) REVERT: G 243 LYS cc_start: 0.8841 (mttt) cc_final: 0.8545 (mttt) REVERT: G 259 ASN cc_start: 0.7647 (t0) cc_final: 0.7333 (t0) REVERT: G 304 ARG cc_start: 0.8139 (ttt180) cc_final: 0.7903 (ttt180) REVERT: G 387 LYS cc_start: 0.7989 (mttt) cc_final: 0.7781 (mtmm) REVERT: G 414 ASP cc_start: 0.8042 (p0) cc_final: 0.7788 (t0) REVERT: G 417 ARG cc_start: 0.6331 (mtt-85) cc_final: 0.6086 (mtt-85) REVERT: G 425 MET cc_start: 0.7409 (ttp) cc_final: 0.7096 (ttp) REVERT: G 426 ASP cc_start: 0.8633 (t0) cc_final: 0.8173 (t0) REVERT: G 481 THR cc_start: 0.8161 (m) cc_final: 0.7655 (p) REVERT: G 491 THR cc_start: 0.8018 (m) cc_final: 0.7707 (p) REVERT: G 501 GLU cc_start: 0.7082 (tt0) cc_final: 0.6640 (tt0) REVERT: H 41 MET cc_start: 0.7652 (tpp) cc_final: 0.7328 (tpp) REVERT: H 72 PHE cc_start: 0.8848 (t80) cc_final: 0.8129 (t80) REVERT: H 74 ARG cc_start: 0.8736 (mtm-85) cc_final: 0.8397 (mtm110) REVERT: H 89 ARG cc_start: 0.8697 (mmm-85) cc_final: 0.8202 (mmm-85) REVERT: H 102 ASP cc_start: 0.8172 (m-30) cc_final: 0.7511 (p0) REVERT: H 121 LEU cc_start: 0.8132 (mt) cc_final: 0.7706 (mt) REVERT: H 141 ARG cc_start: 0.7633 (mtp85) cc_final: 0.7275 (ttm-80) REVERT: H 168 VAL cc_start: 0.9003 (t) cc_final: 0.8679 (p) REVERT: H 170 MET cc_start: 0.7952 (ttt) cc_final: 0.7353 (ptp) REVERT: H 171 ASN cc_start: 0.7842 (m-40) cc_final: 0.7305 (p0) REVERT: H 180 GLN cc_start: 0.8489 (mt0) cc_final: 0.8156 (mt0) REVERT: H 185 LYS cc_start: 0.8512 (ptmt) cc_final: 0.8076 (ptmt) REVERT: H 201 TYR cc_start: 0.8076 (m-80) cc_final: 0.7782 (m-80) REVERT: H 232 PHE cc_start: 0.7109 (m-10) cc_final: 0.6866 (m-80) REVERT: H 272 MET cc_start: 0.7520 (tpp) cc_final: 0.7169 (tpp) REVERT: H 281 MET cc_start: 0.6747 (ttm) cc_final: 0.6541 (ttm) REVERT: H 304 ARG cc_start: 0.7992 (mtt180) cc_final: 0.7789 (mtt180) REVERT: H 340 ILE cc_start: 0.9117 (mt) cc_final: 0.8844 (mt) REVERT: H 403 LYS cc_start: 0.7891 (mmtt) cc_final: 0.7575 (mmmt) REVERT: H 425 MET cc_start: 0.7481 (ttp) cc_final: 0.7145 (ttp) REVERT: H 426 ASP cc_start: 0.8302 (t0) cc_final: 0.7957 (t0) REVERT: H 450 LYS cc_start: 0.8156 (ttpp) cc_final: 0.7919 (ttpp) REVERT: H 481 THR cc_start: 0.8300 (m) cc_final: 0.7786 (p) outliers start: 52 outliers final: 22 residues processed: 1071 average time/residue: 0.4742 time to fit residues: 761.4637 Evaluate side-chains 990 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 966 time to evaluate : 3.624 ------------------------------------------------------------------------------- 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 181 SER 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: 0.9980 chunk 254 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 133 optimal weight: 0.4980 chunk 316 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 158 optimal weight: 10.0000 chunk 150 optimal weight: 0.5980 chunk 143 optimal weight: 30.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.185372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.144369 restraints weight = 55025.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.149930 restraints weight = 30309.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.153568 restraints weight = 19484.421| |-----------------------------------------------------------------------------| r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30368 Z= 0.122 Angle : 0.646 10.889 41088 Z= 0.329 Chirality : 0.047 0.203 4672 Planarity : 0.005 0.057 5352 Dihedral : 4.361 46.398 4062 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.35 % Allowed : 14.52 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 3720 helix: 0.03 (0.15), residues: 1136 sheet: 0.22 (0.20), residues: 704 loop : 0.32 (0.15), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP E 87 HIS 0.005 0.001 HIS H 514 PHE 0.018 0.001 PHE B 325 TYR 0.025 0.002 TYR C 327 ARG 0.005 0.001 ARG D 338 Details of bonding type rmsd hydrogen bonds : bond 0.05309 ( 1087) hydrogen bonds : angle 5.24062 ( 2733) covalent geometry : bond 0.00252 (30368) covalent geometry : angle 0.64584 (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 1077 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 999 time to evaluate : 3.371 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: A 64 GLU cc_start: 0.8385 (tt0) cc_final: 0.7917 (tt0) REVERT: A 72 PHE cc_start: 0.8606 (t80) cc_final: 0.8186 (t80) REVERT: A 102 ASP cc_start: 0.8147 (m-30) cc_final: 0.7683 (p0) REVERT: A 129 MET cc_start: 0.7019 (mtm) cc_final: 0.6393 (mtm) REVERT: A 180 GLN cc_start: 0.8575 (mt0) cc_final: 0.8300 (mt0) REVERT: A 201 TYR cc_start: 0.7930 (m-80) cc_final: 0.7668 (m-80) REVERT: A 222 ASP cc_start: 0.8220 (m-30) cc_final: 0.7994 (m-30) REVERT: A 224 TYR cc_start: 0.6919 (p90) cc_final: 0.6431 (p90) REVERT: A 253 PHE cc_start: 0.7424 (t80) cc_final: 0.6930 (t80) REVERT: A 254 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.6893 (tp) REVERT: A 259 ASN cc_start: 0.7563 (t0) cc_final: 0.7253 (t0) REVERT: A 270 GLN cc_start: 0.8612 (tp40) cc_final: 0.7968 (tp-100) REVERT: A 280 ILE cc_start: 0.6166 (mt) cc_final: 0.5929 (mm) REVERT: A 304 ARG cc_start: 0.7985 (mtt180) cc_final: 0.7724 (mtp180) REVERT: A 327 TYR cc_start: 0.7251 (m-80) cc_final: 0.7023 (m-80) REVERT: A 341 LYS cc_start: 0.9018 (tttt) cc_final: 0.8487 (ttpp) REVERT: A 400 LEU cc_start: 0.8294 (tp) cc_final: 0.8048 (tt) REVERT: A 425 MET cc_start: 0.7505 (ttp) cc_final: 0.7161 (ttp) REVERT: A 426 ASP cc_start: 0.8209 (t0) cc_final: 0.7703 (t0) REVERT: A 441 ASP cc_start: 0.6572 (p0) cc_final: 0.6362 (p0) REVERT: A 448 PHE cc_start: 0.8093 (t80) cc_final: 0.7348 (t80) REVERT: A 491 THR cc_start: 0.8170 (m) cc_final: 0.7936 (t) REVERT: B 41 MET cc_start: 0.8524 (mmm) cc_final: 0.8237 (mmm) REVERT: B 50 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7119 (mt-10) REVERT: B 64 GLU cc_start: 0.8444 (tt0) cc_final: 0.7812 (tt0) REVERT: B 72 PHE cc_start: 0.8481 (t80) cc_final: 0.7908 (t80) REVERT: B 94 GLN cc_start: 0.7690 (mm-40) cc_final: 0.7175 (mm-40) REVERT: B 180 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7639 (mp10) REVERT: B 181 SER cc_start: 0.8999 (OUTLIER) cc_final: 0.8670 (p) REVERT: B 182 ILE cc_start: 0.9209 (pp) cc_final: 0.8967 (pp) REVERT: B 224 TYR cc_start: 0.5572 (p90) cc_final: 0.5169 (p90) REVERT: B 232 PHE cc_start: 0.6806 (m-10) cc_final: 0.6484 (m-80) REVERT: B 260 LEU cc_start: 0.8261 (mt) cc_final: 0.7973 (mm) REVERT: B 265 ASP cc_start: 0.6595 (t0) cc_final: 0.6365 (t70) REVERT: B 272 MET cc_start: 0.7547 (tpp) cc_final: 0.7227 (tpp) REVERT: B 281 MET cc_start: 0.6667 (ttm) cc_final: 0.6090 (ttm) REVERT: B 282 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6422 (mt-10) REVERT: B 286 LYS cc_start: 0.8205 (mttm) cc_final: 0.7737 (tttm) REVERT: B 318 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7705 (mt-10) REVERT: B 340 ILE cc_start: 0.9057 (mt) cc_final: 0.8417 (mt) REVERT: B 374 GLN cc_start: 0.6700 (mm110) cc_final: 0.6085 (mm-40) REVERT: B 400 LEU cc_start: 0.8207 (tp) cc_final: 0.7980 (tt) REVERT: B 415 LEU cc_start: 0.8421 (tp) cc_final: 0.8177 (tt) REVERT: B 425 MET cc_start: 0.7401 (ttp) cc_final: 0.6993 (ttp) REVERT: B 426 ASP cc_start: 0.8451 (t0) cc_final: 0.7933 (t0) REVERT: B 441 ASP cc_start: 0.7186 (m-30) cc_final: 0.6893 (m-30) REVERT: B 443 LYS cc_start: 0.7847 (mtpp) cc_final: 0.7577 (mtmm) REVERT: B 450 LYS cc_start: 0.8074 (ttpp) cc_final: 0.7868 (ttpp) REVERT: B 481 THR cc_start: 0.8210 (m) cc_final: 0.7722 (p) REVERT: B 491 THR cc_start: 0.8080 (m) cc_final: 0.7749 (t) REVERT: C 41 MET cc_start: 0.8590 (mmm) cc_final: 0.8276 (mmm) REVERT: C 64 GLU cc_start: 0.8313 (tt0) cc_final: 0.7488 (tt0) REVERT: C 72 PHE cc_start: 0.8612 (t80) cc_final: 0.7937 (t80) REVERT: C 89 ARG cc_start: 0.8821 (mmm-85) cc_final: 0.8361 (mmm-85) REVERT: C 94 GLN cc_start: 0.7776 (mm-40) cc_final: 0.7369 (mm-40) REVERT: C 102 ASP cc_start: 0.8043 (m-30) cc_final: 0.7707 (p0) REVERT: C 115 LYS cc_start: 0.8353 (ptpt) cc_final: 0.7910 (mtmm) REVERT: C 116 LEU cc_start: 0.7810 (tp) cc_final: 0.7437 (mm) REVERT: C 119 VAL cc_start: 0.6353 (OUTLIER) cc_final: 0.5981 (m) REVERT: C 127 THR cc_start: 0.7302 (p) cc_final: 0.7033 (t) REVERT: C 135 LYS cc_start: 0.7816 (ttmt) cc_final: 0.7464 (mtpp) REVERT: C 181 SER cc_start: 0.8800 (OUTLIER) cc_final: 0.8517 (p) REVERT: C 184 LYS cc_start: 0.8658 (mttp) cc_final: 0.8439 (mmtm) REVERT: C 185 LYS cc_start: 0.8529 (tmtt) cc_final: 0.8284 (tmtt) REVERT: C 201 TYR cc_start: 0.7914 (m-80) cc_final: 0.7191 (m-80) REVERT: C 224 TYR cc_start: 0.6727 (p90) cc_final: 0.6365 (p90) REVERT: C 232 PHE cc_start: 0.6908 (m-80) cc_final: 0.6678 (m-80) REVERT: C 243 LYS cc_start: 0.8439 (mttt) cc_final: 0.8085 (mttt) REVERT: C 259 ASN cc_start: 0.7485 (t0) cc_final: 0.7211 (t0) REVERT: C 272 MET cc_start: 0.7465 (tpp) cc_final: 0.7037 (tpp) REVERT: C 282 GLU cc_start: 0.6730 (mt-10) cc_final: 0.6098 (mt-10) REVERT: C 283 LEU cc_start: 0.7668 (mt) cc_final: 0.7314 (mm) REVERT: C 425 MET cc_start: 0.7628 (ttp) cc_final: 0.7394 (ttp) REVERT: C 426 ASP cc_start: 0.8567 (t0) cc_final: 0.8074 (t0) REVERT: C 447 ASP cc_start: 0.7253 (p0) cc_final: 0.6989 (p0) REVERT: C 450 LYS cc_start: 0.8251 (ttpp) cc_final: 0.8005 (ttpp) REVERT: C 479 LYS cc_start: 0.6934 (mttt) cc_final: 0.6670 (mttm) REVERT: C 481 THR cc_start: 0.8042 (m) cc_final: 0.7568 (p) REVERT: C 511 ILE cc_start: 0.8429 (mt) cc_final: 0.8035 (tt) REVERT: D 41 MET cc_start: 0.8556 (mmm) cc_final: 0.8281 (mmm) REVERT: D 50 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7301 (mt-10) REVERT: D 64 GLU cc_start: 0.8323 (tt0) cc_final: 0.7485 (tt0) REVERT: D 72 PHE cc_start: 0.8571 (t80) cc_final: 0.7990 (t80) REVERT: D 94 GLN cc_start: 0.7603 (mm-40) cc_final: 0.7056 (mm-40) REVERT: D 121 LEU cc_start: 0.8047 (mt) cc_final: 0.7604 (mt) REVERT: D 147 LEU cc_start: 0.8318 (tp) cc_final: 0.7909 (tp) REVERT: D 185 LYS cc_start: 0.8536 (ptmt) cc_final: 0.8096 (ptmt) REVERT: D 200 ARG cc_start: 0.6611 (mtp-110) cc_final: 0.6376 (ttp-170) REVERT: D 201 TYR cc_start: 0.7967 (m-80) cc_final: 0.7414 (m-80) REVERT: D 224 TYR cc_start: 0.6863 (p90) cc_final: 0.5834 (p90) REVERT: D 241 LEU cc_start: 0.7446 (pt) cc_final: 0.7068 (pp) REVERT: D 243 LYS cc_start: 0.8748 (mttt) cc_final: 0.8508 (mttt) REVERT: D 270 GLN cc_start: 0.8153 (tp40) cc_final: 0.7797 (tp40) REVERT: D 272 MET cc_start: 0.7784 (tpp) cc_final: 0.7210 (tpp) REVERT: D 283 LEU cc_start: 0.7869 (mt) cc_final: 0.7571 (mm) REVERT: D 304 ARG cc_start: 0.7538 (mtp180) cc_final: 0.6845 (mtt180) REVERT: D 374 GLN cc_start: 0.7402 (mt0) cc_final: 0.7085 (pp30) REVERT: D 387 LYS cc_start: 0.8377 (mttt) cc_final: 0.8163 (mttt) REVERT: D 398 ARG cc_start: 0.8194 (tpp-160) cc_final: 0.7629 (tpt170) REVERT: D 403 LYS cc_start: 0.7866 (mmtt) cc_final: 0.7171 (tptt) REVERT: D 425 MET cc_start: 0.7476 (ttp) cc_final: 0.7152 (ttp) REVERT: D 448 PHE cc_start: 0.8293 (t80) cc_final: 0.7354 (t80) REVERT: D 481 THR cc_start: 0.8213 (m) cc_final: 0.7741 (p) REVERT: D 491 THR cc_start: 0.8094 (m) cc_final: 0.7684 (t) REVERT: E 41 MET cc_start: 0.8055 (tpp) cc_final: 0.7804 (mmm) REVERT: E 50 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7612 (mt-10) REVERT: E 72 PHE cc_start: 0.8653 (t80) cc_final: 0.8041 (t80) REVERT: E 89 ARG cc_start: 0.8639 (mmm-85) cc_final: 0.8141 (mmm-85) REVERT: E 121 LEU cc_start: 0.8220 (mt) cc_final: 0.7421 (mt) REVERT: E 129 MET cc_start: 0.7083 (mtm) cc_final: 0.6527 (mtm) REVERT: E 135 LYS cc_start: 0.7703 (ttmt) cc_final: 0.7463 (tptm) REVERT: E 180 GLN cc_start: 0.8507 (mt0) cc_final: 0.7878 (mt0) REVERT: E 201 TYR cc_start: 0.7882 (m-80) cc_final: 0.7529 (m-80) REVERT: E 243 LYS cc_start: 0.8287 (mttt) cc_final: 0.8008 (mttt) REVERT: E 281 MET cc_start: 0.6766 (ttm) cc_final: 0.6152 (ttm) REVERT: E 282 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6581 (mt-10) REVERT: E 304 ARG cc_start: 0.7799 (ttt180) cc_final: 0.7420 (mpt-90) REVERT: E 387 LYS cc_start: 0.8300 (mppt) cc_final: 0.7803 (mtmm) REVERT: E 425 MET cc_start: 0.7348 (ttp) cc_final: 0.7097 (ttp) REVERT: E 426 ASP cc_start: 0.8510 (t0) cc_final: 0.8159 (t0) REVERT: E 441 ASP cc_start: 0.6909 (m-30) cc_final: 0.6673 (m-30) REVERT: E 443 LYS cc_start: 0.7688 (mtpp) cc_final: 0.7465 (mtmm) REVERT: E 474 ARG cc_start: 0.6877 (ptp-110) cc_final: 0.6655 (ptp-110) REVERT: E 481 THR cc_start: 0.8238 (m) cc_final: 0.7732 (p) REVERT: E 491 THR cc_start: 0.8057 (m) cc_final: 0.7807 (t) REVERT: E 501 GLU cc_start: 0.6917 (tt0) cc_final: 0.6642 (tt0) REVERT: F 72 PHE cc_start: 0.8493 (t80) cc_final: 0.7553 (t80) REVERT: F 87 TRP cc_start: 0.5729 (t-100) cc_final: 0.5265 (t-100) REVERT: F 148 ASP cc_start: 0.6852 (m-30) cc_final: 0.6550 (m-30) REVERT: F 168 VAL cc_start: 0.9065 (t) cc_final: 0.8797 (p) REVERT: F 170 MET cc_start: 0.7768 (ttt) cc_final: 0.7341 (ptp) REVERT: F 171 ASN cc_start: 0.7750 (m-40) cc_final: 0.7300 (p0) REVERT: F 180 GLN cc_start: 0.8592 (mt0) cc_final: 0.8205 (mt0) REVERT: F 189 HIS cc_start: 0.7671 (m-70) cc_final: 0.7462 (m-70) REVERT: F 201 TYR cc_start: 0.7929 (m-80) cc_final: 0.7184 (m-80) REVERT: F 232 PHE cc_start: 0.7128 (m-80) cc_final: 0.6814 (m-80) REVERT: F 253 PHE cc_start: 0.7304 (t80) cc_final: 0.6992 (t80) REVERT: F 304 ARG cc_start: 0.7290 (mtt180) cc_final: 0.6747 (mtt90) REVERT: F 340 ILE cc_start: 0.9017 (mt) cc_final: 0.8613 (tt) REVERT: F 387 LYS cc_start: 0.8090 (mttt) cc_final: 0.7867 (mttt) REVERT: F 398 ARG cc_start: 0.8519 (tpp-160) cc_final: 0.8040 (tpt170) REVERT: F 425 MET cc_start: 0.7480 (ttp) cc_final: 0.7238 (ttp) REVERT: F 426 ASP cc_start: 0.8435 (t0) cc_final: 0.7976 (t70) REVERT: F 443 LYS cc_start: 0.7778 (mtpp) cc_final: 0.7470 (mttm) REVERT: F 481 THR cc_start: 0.8028 (m) cc_final: 0.7537 (p) REVERT: F 491 THR cc_start: 0.8087 (m) cc_final: 0.7795 (t) REVERT: F 501 GLU cc_start: 0.6837 (tt0) cc_final: 0.6632 (tt0) REVERT: G 41 MET cc_start: 0.7933 (mmm) cc_final: 0.7631 (mmm) REVERT: G 72 PHE cc_start: 0.8636 (t80) cc_final: 0.7854 (t80) REVERT: G 89 ARG cc_start: 0.8837 (mmm-85) cc_final: 0.8373 (mmm-85) REVERT: G 102 ASP cc_start: 0.8060 (m-30) cc_final: 0.7767 (p0) REVERT: G 129 MET cc_start: 0.6815 (mtm) cc_final: 0.6305 (mtm) REVERT: G 135 LYS cc_start: 0.7836 (ttmm) cc_final: 0.6929 (tptm) REVERT: G 147 LEU cc_start: 0.8467 (tp) cc_final: 0.8225 (tp) REVERT: G 173 PHE cc_start: 0.8130 (p90) cc_final: 0.7392 (p90) REVERT: G 180 GLN cc_start: 0.8515 (mt0) cc_final: 0.8038 (mt0) REVERT: G 185 LYS cc_start: 0.8660 (ptmt) cc_final: 0.8185 (ptmt) REVERT: G 186 TYR cc_start: 0.7278 (m-80) cc_final: 0.6909 (m-80) REVERT: G 232 PHE cc_start: 0.7158 (m-80) cc_final: 0.6706 (m-80) REVERT: G 242 ASP cc_start: 0.8759 (m-30) cc_final: 0.8365 (t0) REVERT: G 243 LYS cc_start: 0.8810 (mttt) cc_final: 0.8503 (mttt) REVERT: G 259 ASN cc_start: 0.7672 (t0) cc_final: 0.7337 (t0) REVERT: G 272 MET cc_start: 0.7700 (tpp) cc_final: 0.7207 (tpp) REVERT: G 282 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6400 (mt-10) REVERT: G 304 ARG cc_start: 0.8145 (ttt180) cc_final: 0.7502 (mtt180) REVERT: G 414 ASP cc_start: 0.7931 (p0) cc_final: 0.7691 (t0) REVERT: G 425 MET cc_start: 0.7507 (ttp) cc_final: 0.7187 (ttp) REVERT: G 426 ASP cc_start: 0.8620 (t0) cc_final: 0.8145 (t0) REVERT: G 443 LYS cc_start: 0.7956 (mtmm) cc_final: 0.7584 (mtmm) REVERT: G 481 THR cc_start: 0.8175 (m) cc_final: 0.7728 (p) REVERT: G 491 THR cc_start: 0.8062 (m) cc_final: 0.7750 (p) REVERT: G 501 GLU cc_start: 0.6926 (tt0) cc_final: 0.6692 (tt0) REVERT: H 41 MET cc_start: 0.7751 (tpp) cc_final: 0.7487 (tpp) REVERT: H 64 GLU cc_start: 0.8587 (tt0) cc_final: 0.7905 (tt0) REVERT: H 72 PHE cc_start: 0.8753 (t80) cc_final: 0.8060 (t80) REVERT: H 74 ARG cc_start: 0.8707 (mtm-85) cc_final: 0.8356 (mtm110) REVERT: H 89 ARG cc_start: 0.8656 (mmm-85) cc_final: 0.8154 (mmm-85) REVERT: H 102 ASP cc_start: 0.8129 (m-30) cc_final: 0.7438 (p0) REVERT: H 121 LEU cc_start: 0.8100 (mt) cc_final: 0.7677 (mt) REVERT: H 129 MET cc_start: 0.7081 (mtm) cc_final: 0.6839 (mtm) REVERT: H 141 ARG cc_start: 0.7587 (mtp85) cc_final: 0.7101 (ttm-80) REVERT: H 168 VAL cc_start: 0.9107 (t) cc_final: 0.8784 (p) REVERT: H 170 MET cc_start: 0.7888 (ttt) cc_final: 0.7321 (ptp) REVERT: H 171 ASN cc_start: 0.7869 (m-40) cc_final: 0.7360 (p0) REVERT: H 180 GLN cc_start: 0.8556 (mt0) cc_final: 0.8117 (mt0) REVERT: H 185 LYS cc_start: 0.8519 (ptmt) cc_final: 0.8060 (ptmt) REVERT: H 201 TYR cc_start: 0.8089 (m-80) cc_final: 0.7526 (m-80) REVERT: H 232 PHE cc_start: 0.7186 (m-10) cc_final: 0.6806 (m-80) REVERT: H 260 LEU cc_start: 0.8326 (mt) cc_final: 0.8096 (mm) REVERT: H 267 ARG cc_start: 0.8633 (tpp80) cc_final: 0.8343 (tpt170) REVERT: H 272 MET cc_start: 0.7361 (tpp) cc_final: 0.7081 (tpp) REVERT: H 304 ARG cc_start: 0.7991 (mtt180) cc_final: 0.7640 (ttt180) REVERT: H 318 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7663 (mt-10) REVERT: H 340 ILE cc_start: 0.9145 (mt) cc_final: 0.8697 (mt) REVERT: H 403 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7596 (mmmt) REVERT: H 425 MET cc_start: 0.7464 (ttp) cc_final: 0.7166 (ttp) REVERT: H 426 ASP cc_start: 0.8221 (t0) cc_final: 0.7801 (t0) REVERT: H 474 ARG cc_start: 0.7412 (ptm-80) cc_final: 0.7069 (ptm-80) REVERT: H 481 THR cc_start: 0.8312 (m) cc_final: 0.7831 (p) outliers start: 78 outliers final: 45 residues processed: 1033 average time/residue: 0.5237 time to fit residues: 810.3216 Evaluate side-chains 1000 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 950 time to evaluate : 3.344 ------------------------------------------------------------------------------- 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 119 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 B residue 99 VAL Chi-restraints excluded: chain B residue 119 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 254 LEU 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 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 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 351 MET Chi-restraints excluded: chain G residue 449 GLN Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 308 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 65 optimal weight: 0.9990 chunk 268 optimal weight: 10.0000 chunk 295 optimal weight: 6.9990 chunk 302 optimal weight: 0.9990 chunk 361 optimal weight: 6.9990 chunk 243 optimal weight: 7.9990 chunk 119 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 chunk 196 optimal weight: 0.6980 chunk 249 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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** ** B 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS C 153 GLN C 180 GLN C 374 GLN ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 514 HIS G 190 ASN H 153 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.182005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.140335 restraints weight = 55167.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.145750 restraints weight = 30554.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.149410 restraints weight = 19742.448| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 30368 Z= 0.184 Angle : 0.664 13.410 41088 Z= 0.341 Chirality : 0.048 0.211 4672 Planarity : 0.005 0.052 5352 Dihedral : 4.585 40.501 4058 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.22 % Allowed : 15.15 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.08 (0.14), residues: 3720 helix: 0.08 (0.16), residues: 1120 sheet: 0.06 (0.19), residues: 744 loop : 0.22 (0.15), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP E 87 HIS 0.006 0.001 HIS D 463 PHE 0.015 0.002 PHE F 442 TYR 0.024 0.002 TYR G 327 ARG 0.007 0.001 ARG A 338 Details of bonding type rmsd hydrogen bonds : bond 0.05328 ( 1087) hydrogen bonds : angle 5.27139 ( 2733) covalent geometry : bond 0.00401 (30368) covalent geometry : angle 0.66441 (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 1110 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 1003 time to evaluate : 3.198 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 64 GLU cc_start: 0.8483 (tt0) cc_final: 0.7966 (tt0) REVERT: A 65 MET cc_start: 0.8333 (mmm) cc_final: 0.7875 (mmm) REVERT: A 72 PHE cc_start: 0.8635 (t80) cc_final: 0.8216 (t80) REVERT: A 102 ASP cc_start: 0.8141 (m-30) cc_final: 0.7802 (p0) REVERT: A 148 ASP cc_start: 0.7312 (m-30) cc_final: 0.6980 (m-30) REVERT: A 185 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.7956 (ptmm) REVERT: A 264 VAL cc_start: 0.6868 (OUTLIER) cc_final: 0.6665 (m) REVERT: A 280 ILE cc_start: 0.6386 (mt) cc_final: 0.6100 (mm) REVERT: A 282 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6671 (mt-10) REVERT: A 300 GLU cc_start: 0.4174 (OUTLIER) cc_final: 0.0121 (mt-10) REVERT: A 327 TYR cc_start: 0.7538 (m-80) cc_final: 0.7313 (m-80) REVERT: A 341 LYS cc_start: 0.9099 (tttt) cc_final: 0.8765 (ttpp) REVERT: A 387 LYS cc_start: 0.8244 (mppt) cc_final: 0.7954 (mtmm) REVERT: A 400 LEU cc_start: 0.8282 (tp) cc_final: 0.8044 (tt) REVERT: A 425 MET cc_start: 0.7495 (ttp) cc_final: 0.7252 (ttp) REVERT: A 481 THR cc_start: 0.8407 (m) cc_final: 0.8005 (p) REVERT: A 482 VAL cc_start: 0.8731 (t) cc_final: 0.8272 (p) REVERT: A 498 SER cc_start: 0.8227 (m) cc_final: 0.7763 (p) REVERT: B 41 MET cc_start: 0.8540 (mmm) cc_final: 0.8230 (mmm) REVERT: B 50 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7125 (mt-10) REVERT: B 64 GLU cc_start: 0.8539 (tt0) cc_final: 0.7849 (tt0) REVERT: B 72 PHE cc_start: 0.8458 (t80) cc_final: 0.7903 (t80) REVERT: B 94 GLN cc_start: 0.7757 (mm-40) cc_final: 0.7220 (mm-40) REVERT: B 168 VAL cc_start: 0.9156 (t) cc_final: 0.8911 (p) REVERT: B 180 GLN cc_start: 0.7911 (mp10) cc_final: 0.7698 (mp10) REVERT: B 181 SER cc_start: 0.9021 (OUTLIER) cc_final: 0.8768 (p) REVERT: B 197 ASN cc_start: 0.7156 (t0) cc_final: 0.6891 (t0) REVERT: B 232 PHE cc_start: 0.6889 (m-10) cc_final: 0.6397 (m-80) REVERT: B 259 ASN cc_start: 0.7394 (t0) cc_final: 0.6452 (p0) REVERT: B 260 LEU cc_start: 0.8308 (mt) cc_final: 0.7902 (mm) REVERT: B 265 ASP cc_start: 0.6648 (t0) cc_final: 0.6391 (t70) REVERT: B 272 MET cc_start: 0.7561 (tpp) cc_final: 0.7249 (tpp) REVERT: B 281 MET cc_start: 0.6674 (ttm) cc_final: 0.6159 (ttm) REVERT: B 282 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6472 (mt-10) REVERT: B 318 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8046 (mt-10) REVERT: B 340 ILE cc_start: 0.9079 (mt) cc_final: 0.8629 (mt) REVERT: B 341 LYS cc_start: 0.9199 (pttm) cc_final: 0.8966 (pmtt) REVERT: B 400 LEU cc_start: 0.8221 (tp) cc_final: 0.8016 (tt) REVERT: B 425 MET cc_start: 0.7447 (ttp) cc_final: 0.7027 (ttp) REVERT: B 426 ASP cc_start: 0.8480 (t0) cc_final: 0.7976 (t0) REVERT: B 443 LYS cc_start: 0.7875 (mtpp) cc_final: 0.7598 (mtmm) REVERT: B 450 LYS cc_start: 0.8297 (ttpp) cc_final: 0.8018 (ttpp) REVERT: B 481 THR cc_start: 0.8295 (m) cc_final: 0.7879 (p) REVERT: B 491 THR cc_start: 0.8134 (m) cc_final: 0.7749 (t) REVERT: B 498 SER cc_start: 0.8272 (m) cc_final: 0.7984 (m) REVERT: C 41 MET cc_start: 0.8597 (mmm) cc_final: 0.8271 (mmm) REVERT: C 64 GLU cc_start: 0.8360 (tt0) cc_final: 0.7450 (tt0) REVERT: C 72 PHE cc_start: 0.8634 (t80) cc_final: 0.7973 (t80) REVERT: C 89 ARG cc_start: 0.8881 (mmm-85) cc_final: 0.8400 (mmm-85) REVERT: C 94 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7467 (mm-40) REVERT: C 115 LYS cc_start: 0.8095 (ptpt) cc_final: 0.7746 (ptpt) REVERT: C 135 LYS cc_start: 0.8075 (ttmt) cc_final: 0.7706 (mtpp) REVERT: C 181 SER cc_start: 0.8863 (OUTLIER) cc_final: 0.8583 (p) REVERT: C 184 LYS cc_start: 0.8703 (mttp) cc_final: 0.8502 (mmtm) REVERT: C 201 TYR cc_start: 0.7993 (m-80) cc_final: 0.7261 (m-80) REVERT: C 221 GLN cc_start: 0.7983 (tp40) cc_final: 0.7704 (tp40) REVERT: C 232 PHE cc_start: 0.7107 (m-80) cc_final: 0.6535 (m-80) REVERT: C 243 LYS cc_start: 0.8592 (mttt) cc_final: 0.8317 (mttt) REVERT: C 272 MET cc_start: 0.7598 (tpp) cc_final: 0.7313 (tpp) REVERT: C 282 GLU cc_start: 0.6809 (mt-10) cc_final: 0.6225 (mt-10) REVERT: C 335 MET cc_start: 0.4391 (mtt) cc_final: 0.3833 (mtt) REVERT: C 357 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7076 (tp30) REVERT: C 425 MET cc_start: 0.7625 (ttp) cc_final: 0.7404 (ttp) REVERT: C 426 ASP cc_start: 0.8546 (t0) cc_final: 0.8167 (t70) REVERT: C 443 LYS cc_start: 0.7847 (mttm) cc_final: 0.7419 (mttp) REVERT: C 447 ASP cc_start: 0.7448 (p0) cc_final: 0.7200 (p0) REVERT: C 450 LYS cc_start: 0.8368 (ttpp) cc_final: 0.8129 (ttpp) REVERT: C 479 LYS cc_start: 0.7030 (mttt) cc_final: 0.6681 (mtmm) REVERT: C 481 THR cc_start: 0.8056 (m) cc_final: 0.7654 (p) REVERT: C 511 ILE cc_start: 0.8460 (mt) cc_final: 0.8091 (tt) REVERT: D 50 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7224 (mt-10) REVERT: D 64 GLU cc_start: 0.8395 (tt0) cc_final: 0.7559 (tt0) REVERT: D 72 PHE cc_start: 0.8566 (t80) cc_final: 0.7983 (t80) REVERT: D 94 GLN cc_start: 0.7690 (mm-40) cc_final: 0.7082 (mm-40) REVERT: D 147 LEU cc_start: 0.8469 (tp) cc_final: 0.8194 (tp) REVERT: D 185 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8134 (ptmt) REVERT: D 201 TYR cc_start: 0.8079 (m-80) cc_final: 0.7455 (m-80) REVERT: D 232 PHE cc_start: 0.7208 (m-80) cc_final: 0.6912 (m-80) REVERT: D 243 LYS cc_start: 0.8785 (mttt) cc_final: 0.8517 (mttt) REVERT: D 270 GLN cc_start: 0.8155 (tp40) cc_final: 0.7782 (tp40) REVERT: D 272 MET cc_start: 0.7784 (tpp) cc_final: 0.7538 (tpp) REVERT: D 304 ARG cc_start: 0.7624 (mtp180) cc_final: 0.6646 (mtp180) REVERT: D 326 LYS cc_start: 0.7856 (ptpt) cc_final: 0.7170 (mmtt) REVERT: D 341 LYS cc_start: 0.9041 (pttp) cc_final: 0.8821 (pmtt) REVERT: D 387 LYS cc_start: 0.8430 (mttt) cc_final: 0.8203 (mttt) REVERT: D 403 LYS cc_start: 0.7999 (mmtt) cc_final: 0.7329 (tptt) REVERT: D 425 MET cc_start: 0.7458 (ttp) cc_final: 0.7186 (ttp) REVERT: D 426 ASP cc_start: 0.8426 (t0) cc_final: 0.8011 (t0) REVERT: D 443 LYS cc_start: 0.7668 (mtpp) cc_final: 0.7321 (mttm) REVERT: D 444 LYS cc_start: 0.6477 (mtpt) cc_final: 0.6037 (mtmm) REVERT: D 447 ASP cc_start: 0.7420 (p0) cc_final: 0.7139 (p0) REVERT: D 448 PHE cc_start: 0.8194 (t80) cc_final: 0.7660 (t80) REVERT: D 474 ARG cc_start: 0.7696 (ptm-80) cc_final: 0.7106 (ptt90) REVERT: D 479 LYS cc_start: 0.7309 (mttt) cc_final: 0.6973 (mttp) REVERT: D 481 THR cc_start: 0.8290 (m) cc_final: 0.7899 (p) REVERT: D 491 THR cc_start: 0.8196 (m) cc_final: 0.7793 (p) REVERT: E 50 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7549 (mt-10) REVERT: E 64 GLU cc_start: 0.8597 (tt0) cc_final: 0.7845 (tt0) REVERT: E 72 PHE cc_start: 0.8657 (t80) cc_final: 0.8063 (t80) REVERT: E 89 ARG cc_start: 0.8646 (mmm-85) cc_final: 0.8282 (mmm-85) REVERT: E 129 MET cc_start: 0.7081 (mtm) cc_final: 0.6515 (mtm) REVERT: E 135 LYS cc_start: 0.7860 (ttmt) cc_final: 0.7622 (tptm) REVERT: E 170 MET cc_start: 0.7655 (ptp) cc_final: 0.7319 (ptt) REVERT: E 180 GLN cc_start: 0.8502 (mt0) cc_final: 0.7968 (mt0) REVERT: E 181 SER cc_start: 0.8860 (OUTLIER) cc_final: 0.8649 (p) REVERT: E 197 ASN cc_start: 0.7054 (t0) cc_final: 0.6839 (t0) REVERT: E 201 TYR cc_start: 0.7986 (m-80) cc_final: 0.7676 (m-80) REVERT: E 228 HIS cc_start: 0.6628 (m170) cc_final: 0.6365 (m-70) REVERT: E 243 LYS cc_start: 0.8358 (mttt) cc_final: 0.8035 (mttt) REVERT: E 281 MET cc_start: 0.6920 (ttm) cc_final: 0.6383 (ttm) REVERT: E 282 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6793 (mt-10) REVERT: E 304 ARG cc_start: 0.7952 (ttt180) cc_final: 0.7508 (mmm-85) REVERT: E 387 LYS cc_start: 0.8409 (mppt) cc_final: 0.7943 (mtmm) REVERT: E 398 ARG cc_start: 0.8474 (tpp-160) cc_final: 0.8206 (tpp-160) REVERT: E 425 MET cc_start: 0.7383 (ttp) cc_final: 0.7166 (ttp) REVERT: E 426 ASP cc_start: 0.8596 (t0) cc_final: 0.8117 (t70) REVERT: E 474 ARG cc_start: 0.7050 (ptp-110) cc_final: 0.6842 (ptp-110) REVERT: E 481 THR cc_start: 0.8337 (m) cc_final: 0.7898 (p) REVERT: E 501 GLU cc_start: 0.7022 (tt0) cc_final: 0.6717 (tt0) REVERT: F 72 PHE cc_start: 0.8523 (t80) cc_final: 0.7616 (t80) REVERT: F 87 TRP cc_start: 0.5764 (t-100) cc_final: 0.5484 (m-90) REVERT: F 89 ARG cc_start: 0.8431 (mmm-85) cc_final: 0.7969 (ttt90) REVERT: F 148 ASP cc_start: 0.6925 (m-30) cc_final: 0.6613 (m-30) REVERT: F 168 VAL cc_start: 0.9073 (t) cc_final: 0.8730 (p) REVERT: F 170 MET cc_start: 0.7824 (ttt) cc_final: 0.7538 (ptp) REVERT: F 171 ASN cc_start: 0.7903 (m-40) cc_final: 0.7607 (p0) REVERT: F 185 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8038 (ptmm) REVERT: F 201 TYR cc_start: 0.8041 (m-80) cc_final: 0.7383 (m-80) REVERT: F 232 PHE cc_start: 0.7202 (m-80) cc_final: 0.6911 (m-80) REVERT: F 243 LYS cc_start: 0.8581 (mttt) cc_final: 0.8333 (mttt) REVERT: F 272 MET cc_start: 0.7184 (tpp) cc_final: 0.6951 (tpp) REVERT: F 281 MET cc_start: 0.6727 (ttm) cc_final: 0.6087 (ttm) REVERT: F 282 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6827 (mt-10) REVERT: F 283 LEU cc_start: 0.8077 (mt) cc_final: 0.7708 (mm) REVERT: F 304 ARG cc_start: 0.7339 (mtt180) cc_final: 0.6910 (mtp85) REVERT: F 326 LYS cc_start: 0.7905 (ptpt) cc_final: 0.7322 (mptt) REVERT: F 340 ILE cc_start: 0.9032 (mt) cc_final: 0.8664 (mt) REVERT: F 341 LYS cc_start: 0.9158 (pttp) cc_final: 0.8946 (pttt) REVERT: F 425 MET cc_start: 0.7404 (ttp) cc_final: 0.7166 (ttp) REVERT: F 426 ASP cc_start: 0.8436 (t0) cc_final: 0.8159 (t70) REVERT: F 443 LYS cc_start: 0.7768 (mtpp) cc_final: 0.7376 (mttm) REVERT: F 444 LYS cc_start: 0.6524 (mtpt) cc_final: 0.6121 (ttmm) REVERT: F 481 THR cc_start: 0.8022 (m) cc_final: 0.7547 (p) REVERT: G 41 MET cc_start: 0.7957 (mmm) cc_final: 0.7743 (mmm) REVERT: G 64 GLU cc_start: 0.8520 (tt0) cc_final: 0.7820 (tt0) REVERT: G 72 PHE cc_start: 0.8658 (t80) cc_final: 0.7863 (t80) REVERT: G 89 ARG cc_start: 0.8830 (mmm-85) cc_final: 0.8400 (mmm-85) REVERT: G 102 ASP cc_start: 0.8091 (m-30) cc_final: 0.7796 (p0) REVERT: G 129 MET cc_start: 0.6938 (mtm) cc_final: 0.6497 (mtm) REVERT: G 135 LYS cc_start: 0.8062 (ttmm) cc_final: 0.7285 (tptm) REVERT: G 147 LEU cc_start: 0.8534 (tp) cc_final: 0.8222 (tp) REVERT: G 170 MET cc_start: 0.7678 (ptp) cc_final: 0.7408 (ptp) REVERT: G 180 GLN cc_start: 0.8533 (mt0) cc_final: 0.8129 (mt0) REVERT: G 185 LYS cc_start: 0.8658 (ptmt) cc_final: 0.8207 (ptmt) REVERT: G 242 ASP cc_start: 0.8783 (m-30) cc_final: 0.8406 (t0) REVERT: G 243 LYS cc_start: 0.8881 (mttt) cc_final: 0.8550 (mttt) REVERT: G 259 ASN cc_start: 0.7949 (t0) cc_final: 0.7675 (t0) REVERT: G 272 MET cc_start: 0.7599 (tpp) cc_final: 0.7132 (tpp) REVERT: G 282 GLU cc_start: 0.6942 (mt-10) cc_final: 0.6560 (mt-10) REVERT: G 304 ARG cc_start: 0.8137 (ttt180) cc_final: 0.7480 (mtt180) REVERT: G 347 ASN cc_start: 0.7077 (t0) cc_final: 0.6870 (t0) REVERT: G 414 ASP cc_start: 0.7927 (p0) cc_final: 0.7539 (t0) REVERT: G 417 ARG cc_start: 0.6279 (mtt-85) cc_final: 0.5752 (mtm-85) REVERT: G 425 MET cc_start: 0.7544 (ttp) cc_final: 0.7275 (ttp) REVERT: G 426 ASP cc_start: 0.8650 (t0) cc_final: 0.8179 (t70) REVERT: G 443 LYS cc_start: 0.8004 (mtmm) cc_final: 0.7360 (mttm) REVERT: G 444 LYS cc_start: 0.6497 (mtpt) cc_final: 0.6027 (ttmm) REVERT: G 481 THR cc_start: 0.8266 (m) cc_final: 0.7795 (p) REVERT: G 501 GLU cc_start: 0.6976 (tt0) cc_final: 0.6768 (tt0) REVERT: H 41 MET cc_start: 0.7817 (tpp) cc_final: 0.7543 (tpp) REVERT: H 64 GLU cc_start: 0.8592 (tt0) cc_final: 0.7872 (tt0) REVERT: H 72 PHE cc_start: 0.8803 (t80) cc_final: 0.8083 (t80) REVERT: H 74 ARG cc_start: 0.8721 (mtm-85) cc_final: 0.8398 (ttm110) REVERT: H 89 ARG cc_start: 0.8671 (mmm-85) cc_final: 0.8233 (mmm-85) REVERT: H 102 ASP cc_start: 0.8112 (m-30) cc_final: 0.7387 (p0) REVERT: H 121 LEU cc_start: 0.8239 (mt) cc_final: 0.7902 (mt) REVERT: H 129 MET cc_start: 0.7248 (mtm) cc_final: 0.6547 (mtm) REVERT: H 141 ARG cc_start: 0.7620 (mtp85) cc_final: 0.7206 (ttm-80) REVERT: H 168 VAL cc_start: 0.9081 (t) cc_final: 0.8708 (p) REVERT: H 170 MET cc_start: 0.7905 (ttt) cc_final: 0.7381 (ptp) REVERT: H 171 ASN cc_start: 0.7952 (m-40) cc_final: 0.7595 (p0) REVERT: H 180 GLN cc_start: 0.8559 (mt0) cc_final: 0.8162 (mt0) REVERT: H 185 LYS cc_start: 0.8504 (ptmt) cc_final: 0.8125 (ptmt) REVERT: H 201 TYR cc_start: 0.8198 (m-80) cc_final: 0.7640 (m-80) REVERT: H 232 PHE cc_start: 0.7229 (m-10) cc_final: 0.6956 (m-80) REVERT: H 260 LEU cc_start: 0.8520 (mt) cc_final: 0.8220 (mm) REVERT: H 265 ASP cc_start: 0.6888 (t0) cc_final: 0.6635 (t70) REVERT: H 267 ARG cc_start: 0.8564 (tpp80) cc_final: 0.7916 (tpt90) REVERT: H 272 MET cc_start: 0.7484 (tpp) cc_final: 0.7190 (tpp) REVERT: H 282 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6553 (mt-10) REVERT: H 304 ARG cc_start: 0.8032 (mtt180) cc_final: 0.7306 (mtt90) REVERT: H 403 LYS cc_start: 0.8076 (mmtt) cc_final: 0.7868 (mmtt) REVERT: H 425 MET cc_start: 0.7482 (ttp) cc_final: 0.7192 (ttp) REVERT: H 426 ASP cc_start: 0.8293 (t0) cc_final: 0.7961 (t0) REVERT: H 443 LYS cc_start: 0.7940 (mtmm) cc_final: 0.7635 (mtmm) REVERT: H 444 LYS cc_start: 0.6726 (mtpt) cc_final: 0.6427 (ttmm) REVERT: H 448 PHE cc_start: 0.8140 (t80) cc_final: 0.7796 (t80) REVERT: H 481 THR cc_start: 0.8373 (m) cc_final: 0.7878 (p) outliers start: 107 outliers final: 70 residues processed: 1050 average time/residue: 0.5228 time to fit residues: 822.3644 Evaluate side-chains 1037 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 959 time to evaluate : 3.325 ------------------------------------------------------------------------------- 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 242 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 351 MET 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 181 SER Chi-restraints excluded: chain B residue 254 LEU 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 280 ILE 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 254 LEU 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 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 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 254 LEU 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 308 ILE Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 423 LEU Chi-restraints excluded: chain H residue 441 ASP 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: 0.9980 chunk 268 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 272 optimal weight: 0.9980 chunk 81 optimal weight: 0.0040 chunk 171 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- 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 ** B 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 514 HIS G 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.181278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.140634 restraints weight = 54342.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.146003 restraints weight = 30030.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.149574 restraints weight = 19295.977| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 30368 Z= 0.120 Angle : 0.640 15.472 41088 Z= 0.321 Chirality : 0.046 0.208 4672 Planarity : 0.005 0.057 5352 Dihedral : 4.367 37.584 4058 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.62 % Allowed : 17.92 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.14), residues: 3720 helix: 0.30 (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 0.037 0.002 TRP D 87 HIS 0.005 0.001 HIS B 514 PHE 0.013 0.001 PHE F 325 TYR 0.028 0.002 TYR B 224 ARG 0.008 0.001 ARG E 457 Details of bonding type rmsd hydrogen bonds : bond 0.04649 ( 1087) hydrogen bonds : angle 5.08692 ( 2733) covalent geometry : bond 0.00252 (30368) covalent geometry : angle 0.63975 (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 1065 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 978 time to evaluate : 3.389 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 64 GLU cc_start: 0.8459 (tt0) cc_final: 0.7925 (tt0) REVERT: A 65 MET cc_start: 0.8351 (mmm) cc_final: 0.7913 (mmm) REVERT: A 72 PHE cc_start: 0.8556 (t80) cc_final: 0.8154 (t80) REVERT: A 102 ASP cc_start: 0.8127 (m-30) cc_final: 0.7779 (p0) REVERT: A 148 ASP cc_start: 0.7185 (m-30) cc_final: 0.6946 (m-30) REVERT: A 180 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7498 (mp10) REVERT: A 185 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8148 (ptmt) REVERT: A 201 TYR cc_start: 0.7861 (m-80) cc_final: 0.7570 (m-80) REVERT: A 253 PHE cc_start: 0.7508 (t80) cc_final: 0.7188 (t80) REVERT: A 280 ILE cc_start: 0.6305 (mt) cc_final: 0.5999 (mm) REVERT: A 282 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6570 (mt-10) REVERT: A 327 TYR cc_start: 0.7508 (m-80) cc_final: 0.7225 (m-80) REVERT: A 341 LYS cc_start: 0.9071 (tttt) cc_final: 0.8744 (ttpp) REVERT: A 387 LYS cc_start: 0.8243 (mppt) cc_final: 0.7983 (mtmm) REVERT: A 400 LEU cc_start: 0.8313 (tp) cc_final: 0.8073 (tt) REVERT: A 420 HIS cc_start: 0.5287 (OUTLIER) cc_final: 0.4961 (m90) REVERT: A 425 MET cc_start: 0.7465 (ttp) cc_final: 0.7157 (ttp) REVERT: A 457 ARG cc_start: 0.8056 (ttm110) cc_final: 0.7587 (mtp-110) REVERT: A 481 THR cc_start: 0.8435 (m) cc_final: 0.8058 (p) REVERT: A 482 VAL cc_start: 0.8768 (t) cc_final: 0.8291 (p) REVERT: A 498 SER cc_start: 0.8276 (m) cc_final: 0.7785 (p) REVERT: B 41 MET cc_start: 0.8623 (mmm) cc_final: 0.8364 (mmm) REVERT: B 50 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7108 (mt-10) REVERT: B 54 ASP cc_start: 0.8037 (t70) cc_final: 0.7815 (t70) REVERT: B 64 GLU cc_start: 0.8582 (tt0) cc_final: 0.7869 (tt0) REVERT: B 72 PHE cc_start: 0.8429 (t80) cc_final: 0.7944 (t80) REVERT: B 74 ARG cc_start: 0.8195 (ttm110) cc_final: 0.7735 (ptp-170) REVERT: B 94 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7208 (mm-40) REVERT: B 141 ARG cc_start: 0.7244 (ttm-80) cc_final: 0.6830 (ttt90) REVERT: B 168 VAL cc_start: 0.9132 (t) cc_final: 0.8888 (p) REVERT: B 179 THR cc_start: 0.8419 (m) cc_final: 0.8199 (p) REVERT: B 181 SER cc_start: 0.8997 (OUTLIER) cc_final: 0.8649 (p) REVERT: B 197 ASN cc_start: 0.7165 (t0) cc_final: 0.6958 (t0) REVERT: B 200 ARG cc_start: 0.6431 (mtp-110) cc_final: 0.6178 (ttp80) REVERT: B 232 PHE cc_start: 0.6819 (m-10) cc_final: 0.6336 (m-80) REVERT: B 260 LEU cc_start: 0.8243 (mt) cc_final: 0.7967 (mm) REVERT: B 265 ASP cc_start: 0.6287 (t0) cc_final: 0.5989 (t70) REVERT: B 267 ARG cc_start: 0.8507 (tpp80) cc_final: 0.7808 (tpt90) REVERT: B 270 GLN cc_start: 0.8639 (tp-100) cc_final: 0.8400 (tp-100) REVERT: B 282 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6496 (mt-10) REVERT: B 318 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7918 (mt-10) REVERT: B 340 ILE cc_start: 0.9059 (mt) cc_final: 0.8618 (mt) REVERT: B 341 LYS cc_start: 0.9179 (pttm) cc_final: 0.8935 (pttt) REVERT: B 398 ARG cc_start: 0.8585 (tpp-160) cc_final: 0.7987 (tpt170) REVERT: B 400 LEU cc_start: 0.8267 (tp) cc_final: 0.8055 (tt) REVERT: B 425 MET cc_start: 0.7403 (ttp) cc_final: 0.7077 (ttp) REVERT: B 426 ASP cc_start: 0.8369 (t0) cc_final: 0.7881 (t0) REVERT: B 443 LYS cc_start: 0.7827 (mtpp) cc_final: 0.7537 (mtmm) REVERT: B 450 LYS cc_start: 0.8184 (ttpp) cc_final: 0.7883 (ttpp) REVERT: B 479 LYS cc_start: 0.7082 (mttt) cc_final: 0.6782 (mtmm) REVERT: B 481 THR cc_start: 0.8299 (m) cc_final: 0.7846 (p) REVERT: B 491 THR cc_start: 0.8129 (m) cc_final: 0.7714 (t) REVERT: B 498 SER cc_start: 0.8200 (m) cc_final: 0.7976 (m) REVERT: C 41 MET cc_start: 0.8531 (mmm) cc_final: 0.8189 (mmm) REVERT: C 64 GLU cc_start: 0.8355 (tt0) cc_final: 0.7464 (tt0) REVERT: C 72 PHE cc_start: 0.8600 (t80) cc_final: 0.8041 (t80) REVERT: C 74 ARG cc_start: 0.8370 (ttm110) cc_final: 0.7830 (ptp-170) REVERT: C 89 ARG cc_start: 0.8801 (mmm-85) cc_final: 0.8382 (mmm-85) REVERT: C 94 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7464 (mm-40) REVERT: C 102 ASP cc_start: 0.8043 (m-30) cc_final: 0.7787 (p0) REVERT: C 115 LYS cc_start: 0.8075 (ptpt) cc_final: 0.7730 (ptpt) REVERT: C 135 LYS cc_start: 0.7991 (ttmt) cc_final: 0.7627 (mtpp) REVERT: C 180 GLN cc_start: 0.8124 (mt0) cc_final: 0.7728 (mp10) REVERT: C 181 SER cc_start: 0.8787 (OUTLIER) cc_final: 0.8497 (p) REVERT: C 184 LYS cc_start: 0.8582 (mttp) cc_final: 0.8287 (mmtm) REVERT: C 200 ARG cc_start: 0.6755 (ttp-110) cc_final: 0.6423 (ttp-170) REVERT: C 201 TYR cc_start: 0.7822 (m-80) cc_final: 0.7083 (m-80) REVERT: C 221 GLN cc_start: 0.7905 (tp40) cc_final: 0.7663 (tp40) REVERT: C 232 PHE cc_start: 0.6996 (m-80) cc_final: 0.6490 (m-80) REVERT: C 243 LYS cc_start: 0.8553 (mttt) cc_final: 0.8275 (mttt) REVERT: C 272 MET cc_start: 0.7559 (tpp) cc_final: 0.7312 (tpp) REVERT: C 282 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6213 (mt-10) REVERT: C 283 LEU cc_start: 0.7699 (mt) cc_final: 0.7354 (mm) REVERT: C 304 ARG cc_start: 0.8148 (mmt180) cc_final: 0.7876 (mmt180) REVERT: C 357 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7107 (tp30) REVERT: C 415 LEU cc_start: 0.8719 (tp) cc_final: 0.8426 (tt) REVERT: C 425 MET cc_start: 0.7627 (ttp) cc_final: 0.7280 (ttp) REVERT: C 426 ASP cc_start: 0.8515 (t0) cc_final: 0.8147 (t70) REVERT: C 443 LYS cc_start: 0.7811 (mttm) cc_final: 0.7412 (mttp) REVERT: C 447 ASP cc_start: 0.7426 (p0) cc_final: 0.7197 (p0) REVERT: C 450 LYS cc_start: 0.8309 (ttpp) cc_final: 0.8084 (ttpp) REVERT: C 479 LYS cc_start: 0.6956 (mttt) cc_final: 0.6662 (mtmm) REVERT: C 481 THR cc_start: 0.7990 (m) cc_final: 0.7608 (p) REVERT: C 498 SER cc_start: 0.8410 (m) cc_final: 0.7985 (p) REVERT: C 511 ILE cc_start: 0.8427 (mt) cc_final: 0.8060 (tt) REVERT: D 50 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7183 (mt-10) REVERT: D 64 GLU cc_start: 0.8414 (tt0) cc_final: 0.7579 (tt0) REVERT: D 65 MET cc_start: 0.8196 (mmm) cc_final: 0.7873 (mmm) REVERT: D 72 PHE cc_start: 0.8551 (t80) cc_final: 0.7975 (t80) REVERT: D 94 GLN cc_start: 0.7641 (mm-40) cc_final: 0.7083 (mm-40) REVERT: D 147 LEU cc_start: 0.8414 (tp) cc_final: 0.8122 (tp) REVERT: D 185 LYS cc_start: 0.8530 (ptmt) cc_final: 0.8050 (ptmt) REVERT: D 201 TYR cc_start: 0.7929 (m-80) cc_final: 0.7315 (m-80) REVERT: D 232 PHE cc_start: 0.7220 (m-80) cc_final: 0.6860 (m-80) REVERT: D 243 LYS cc_start: 0.8741 (mttt) cc_final: 0.8462 (mttt) REVERT: D 267 ARG cc_start: 0.8173 (ttt180) cc_final: 0.7843 (ttt-90) REVERT: D 270 GLN cc_start: 0.8122 (tp40) cc_final: 0.7767 (tp40) REVERT: D 304 ARG cc_start: 0.7575 (mtp180) cc_final: 0.6940 (mtt180) REVERT: D 341 LYS cc_start: 0.9047 (pttp) cc_final: 0.8803 (pmtt) REVERT: D 387 LYS cc_start: 0.8411 (mttt) cc_final: 0.8178 (mttt) REVERT: D 398 ARG cc_start: 0.8256 (tpp-160) cc_final: 0.8031 (tpp-160) REVERT: D 403 LYS cc_start: 0.7953 (mmtt) cc_final: 0.7293 (tptt) REVERT: D 425 MET cc_start: 0.7422 (ttp) cc_final: 0.7172 (ttp) REVERT: D 447 ASP cc_start: 0.7436 (p0) cc_final: 0.7194 (p0) REVERT: D 479 LYS cc_start: 0.7231 (mttt) cc_final: 0.6928 (mttp) REVERT: D 481 THR cc_start: 0.8267 (m) cc_final: 0.7883 (p) REVERT: D 491 THR cc_start: 0.8143 (m) cc_final: 0.7793 (p) REVERT: E 41 MET cc_start: 0.8132 (tpt) cc_final: 0.7745 (mmm) REVERT: E 50 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7538 (mt-10) REVERT: E 64 GLU cc_start: 0.8587 (tt0) cc_final: 0.7853 (tt0) REVERT: E 72 PHE cc_start: 0.8265 (t80) cc_final: 0.7567 (t80) REVERT: E 89 ARG cc_start: 0.8584 (mmm-85) cc_final: 0.8201 (mmm-85) REVERT: E 129 MET cc_start: 0.7038 (mtm) cc_final: 0.6455 (mtm) REVERT: E 135 LYS cc_start: 0.7775 (ttmt) cc_final: 0.7522 (tptm) REVERT: E 180 GLN cc_start: 0.8404 (mt0) cc_final: 0.7803 (mt0) REVERT: E 181 SER cc_start: 0.8738 (OUTLIER) cc_final: 0.8515 (p) REVERT: E 197 ASN cc_start: 0.7059 (t0) cc_final: 0.6797 (t0) REVERT: E 201 TYR cc_start: 0.7897 (m-80) cc_final: 0.7565 (m-80) REVERT: E 243 LYS cc_start: 0.8336 (mttt) cc_final: 0.7990 (mttt) REVERT: E 281 MET cc_start: 0.6860 (ttm) cc_final: 0.6053 (ttm) REVERT: E 283 LEU cc_start: 0.8019 (mt) cc_final: 0.7613 (mm) REVERT: E 387 LYS cc_start: 0.8389 (mppt) cc_final: 0.8095 (mtmm) REVERT: E 398 ARG cc_start: 0.8413 (tpp-160) cc_final: 0.8088 (tpp-160) REVERT: E 425 MET cc_start: 0.7387 (ttp) cc_final: 0.7155 (ttp) REVERT: E 481 THR cc_start: 0.8364 (m) cc_final: 0.7871 (p) REVERT: E 501 GLU cc_start: 0.7058 (tt0) cc_final: 0.6736 (tt0) REVERT: F 50 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7411 (mt-10) REVERT: F 72 PHE cc_start: 0.8492 (t80) cc_final: 0.7570 (t80) REVERT: F 87 TRP cc_start: 0.5938 (t-100) cc_final: 0.5736 (m-90) REVERT: F 135 LYS cc_start: 0.8457 (mmmt) cc_final: 0.8174 (tppt) REVERT: F 168 VAL cc_start: 0.9075 (t) cc_final: 0.8786 (p) REVERT: F 170 MET cc_start: 0.7795 (ttt) cc_final: 0.7511 (ptp) REVERT: F 171 ASN cc_start: 0.7802 (m-40) cc_final: 0.7370 (p0) REVERT: F 181 SER cc_start: 0.8977 (OUTLIER) cc_final: 0.8703 (p) REVERT: F 185 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8000 (ptmm) REVERT: F 201 TYR cc_start: 0.8005 (m-80) cc_final: 0.7292 (m-80) REVERT: F 232 PHE cc_start: 0.7107 (m-80) cc_final: 0.6796 (m-80) REVERT: F 243 LYS cc_start: 0.8519 (mttt) cc_final: 0.8256 (mttt) REVERT: F 253 PHE cc_start: 0.7457 (t80) cc_final: 0.7020 (t80) REVERT: F 267 ARG cc_start: 0.8114 (ttt180) cc_final: 0.7677 (mmm-85) REVERT: F 272 MET cc_start: 0.7096 (tpp) cc_final: 0.6715 (tpp) REVERT: F 281 MET cc_start: 0.6622 (ttm) cc_final: 0.6021 (ttm) REVERT: F 282 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6950 (mt-10) REVERT: F 283 LEU cc_start: 0.8026 (mt) cc_final: 0.7755 (mm) REVERT: F 304 ARG cc_start: 0.7329 (mtt180) cc_final: 0.6675 (mtp180) REVERT: F 326 LYS cc_start: 0.7872 (ptpt) cc_final: 0.7225 (mptt) REVERT: F 340 ILE cc_start: 0.9009 (mt) cc_final: 0.8760 (mt) REVERT: F 341 LYS cc_start: 0.9152 (pttp) cc_final: 0.8931 (pttt) REVERT: F 425 MET cc_start: 0.7423 (ttp) cc_final: 0.7145 (ttp) REVERT: F 426 ASP cc_start: 0.8420 (t0) cc_final: 0.8157 (t70) REVERT: F 441 ASP cc_start: 0.7013 (m-30) cc_final: 0.6733 (m-30) REVERT: F 443 LYS cc_start: 0.7729 (mtpp) cc_final: 0.7452 (mttm) REVERT: F 481 THR cc_start: 0.8035 (m) cc_final: 0.7555 (p) REVERT: G 41 MET cc_start: 0.7909 (mmm) cc_final: 0.7680 (mmm) REVERT: G 50 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7422 (mt-10) REVERT: G 64 GLU cc_start: 0.8492 (tt0) cc_final: 0.7421 (tt0) REVERT: G 72 PHE cc_start: 0.8641 (t80) cc_final: 0.7803 (t80) REVERT: G 89 ARG cc_start: 0.8799 (mmm-85) cc_final: 0.8379 (mmm-85) REVERT: G 102 ASP cc_start: 0.8071 (m-30) cc_final: 0.7716 (p0) REVERT: G 129 MET cc_start: 0.6818 (mtm) cc_final: 0.6397 (mtm) REVERT: G 135 LYS cc_start: 0.8029 (ttmm) cc_final: 0.7101 (tptm) REVERT: G 147 LEU cc_start: 0.8484 (tp) cc_final: 0.8183 (tp) REVERT: G 170 MET cc_start: 0.7588 (ptp) cc_final: 0.7201 (ptp) REVERT: G 180 GLN cc_start: 0.8500 (mt0) cc_final: 0.8083 (mt0) REVERT: G 200 ARG cc_start: 0.6781 (mtp-110) cc_final: 0.6407 (ttp-170) REVERT: G 201 TYR cc_start: 0.7874 (m-80) cc_final: 0.7462 (m-80) REVERT: G 243 LYS cc_start: 0.8838 (mttt) cc_final: 0.8512 (mttt) REVERT: G 259 ASN cc_start: 0.7900 (t0) cc_final: 0.6856 (p0) REVERT: G 282 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6550 (mt-10) REVERT: G 304 ARG cc_start: 0.8149 (ttt180) cc_final: 0.7830 (mtp180) REVERT: G 326 LYS cc_start: 0.7808 (ptpt) cc_final: 0.7053 (mptt) REVERT: G 347 ASN cc_start: 0.6913 (t0) cc_final: 0.6664 (t0) REVERT: G 403 LYS cc_start: 0.7900 (mmtt) cc_final: 0.7444 (tppt) REVERT: G 414 ASP cc_start: 0.7829 (p0) cc_final: 0.7554 (t0) REVERT: G 417 ARG cc_start: 0.6237 (mtt-85) cc_final: 0.5722 (mtm-85) REVERT: G 425 MET cc_start: 0.7565 (ttp) cc_final: 0.7281 (ttp) REVERT: G 426 ASP cc_start: 0.8593 (t0) cc_final: 0.8272 (t70) REVERT: G 481 THR cc_start: 0.8302 (m) cc_final: 0.7801 (p) REVERT: G 501 GLU cc_start: 0.7054 (tt0) cc_final: 0.6693 (tt0) REVERT: H 41 MET cc_start: 0.7839 (tpp) cc_final: 0.7563 (tpp) REVERT: H 64 GLU cc_start: 0.8580 (tt0) cc_final: 0.7813 (tt0) REVERT: H 72 PHE cc_start: 0.8775 (t80) cc_final: 0.8052 (t80) REVERT: H 74 ARG cc_start: 0.8673 (mtm-85) cc_final: 0.8343 (ttm110) REVERT: H 89 ARG cc_start: 0.8621 (mmm-85) cc_final: 0.8228 (mmm-85) REVERT: H 102 ASP cc_start: 0.8141 (m-30) cc_final: 0.7478 (p0) REVERT: H 121 LEU cc_start: 0.8267 (mt) cc_final: 0.7979 (mt) REVERT: H 141 ARG cc_start: 0.7571 (mtp85) cc_final: 0.7265 (ttm-80) REVERT: H 168 VAL cc_start: 0.9172 (t) cc_final: 0.8819 (p) REVERT: H 170 MET cc_start: 0.7888 (ttt) cc_final: 0.7443 (ptp) REVERT: H 171 ASN cc_start: 0.7930 (m-40) cc_final: 0.7452 (p0) REVERT: H 180 GLN cc_start: 0.8549 (mt0) cc_final: 0.8136 (mt0) REVERT: H 185 LYS cc_start: 0.8499 (ptmt) cc_final: 0.8083 (ptmt) REVERT: H 201 TYR cc_start: 0.8106 (m-80) cc_final: 0.7503 (m-80) REVERT: H 232 PHE cc_start: 0.7132 (m-10) cc_final: 0.6769 (m-80) REVERT: H 253 PHE cc_start: 0.7372 (t80) cc_final: 0.7090 (t80) REVERT: H 260 LEU cc_start: 0.8535 (mt) cc_final: 0.8200 (mm) REVERT: H 267 ARG cc_start: 0.8576 (tpp80) cc_final: 0.8208 (tpp80) REVERT: H 272 MET cc_start: 0.7408 (tpp) cc_final: 0.7146 (tpp) REVERT: H 282 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6404 (mt-10) REVERT: H 304 ARG cc_start: 0.8055 (mtt180) cc_final: 0.7479 (mtt180) REVERT: H 340 ILE cc_start: 0.9181 (mt) cc_final: 0.8688 (mt) REVERT: H 341 LYS cc_start: 0.9191 (pttp) cc_final: 0.8907 (pmtt) REVERT: H 398 ARG cc_start: 0.8622 (tpp-160) cc_final: 0.8338 (tpp-160) REVERT: H 425 MET cc_start: 0.7420 (ttp) cc_final: 0.7209 (ttp) REVERT: H 438 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7871 (mt) REVERT: H 443 LYS cc_start: 0.7881 (mtmm) cc_final: 0.7677 (mtmm) REVERT: H 481 THR cc_start: 0.8415 (m) cc_final: 0.7925 (p) REVERT: H 482 VAL cc_start: 0.8705 (t) cc_final: 0.8161 (p) outliers start: 87 outliers final: 52 residues processed: 1010 average time/residue: 0.4696 time to fit residues: 704.9824 Evaluate side-chains 1010 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 949 time to evaluate : 3.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 180 GLN 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 300 GLU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 420 HIS Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 99 VAL 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 254 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain C residue 147 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 280 ILE 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 181 SER 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 423 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 488 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 474 ARG Chi-restraints excluded: chain F residue 513 GLU Chi-restraints excluded: chain G residue 76 LEU 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 379 VAL Chi-restraints excluded: chain G residue 449 GLN 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 308 ILE Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 423 LEU Chi-restraints excluded: chain H residue 438 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 18 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 284 optimal weight: 5.9990 chunk 229 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 243 optimal weight: 4.9990 chunk 222 optimal weight: 7.9990 chunk 140 optimal weight: 0.9980 chunk 144 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 HIS A 463 HIS ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 HIS E 463 HIS G 259 ASN ** H 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 315 HIS H 463 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.179111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.137946 restraints weight = 54749.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.143287 restraints weight = 30240.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.146836 restraints weight = 19493.488| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 30368 Z= 0.262 Angle : 0.708 15.569 41088 Z= 0.365 Chirality : 0.049 0.199 4672 Planarity : 0.005 0.054 5352 Dihedral : 4.887 45.785 4058 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.52 % Allowed : 17.71 % Favored : 78.77 % 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: 0.07 (0.16), residues: 1120 sheet: -0.44 (0.22), residues: 592 loop : 0.12 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP D 87 HIS 0.017 0.002 HIS A 420 PHE 0.021 0.002 PHE G 253 TYR 0.029 0.002 TYR D 327 ARG 0.010 0.001 ARG A 89 Details of bonding type rmsd hydrogen bonds : bond 0.05471 ( 1087) hydrogen bonds : angle 5.33284 ( 2733) covalent geometry : bond 0.00567 (30368) covalent geometry : angle 0.70796 (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 1114 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 997 time to evaluate : 3.216 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: A 41 MET cc_start: 0.8678 (mmm) cc_final: 0.8368 (mmm) REVERT: A 64 GLU cc_start: 0.8562 (tt0) cc_final: 0.8069 (tt0) REVERT: A 65 MET cc_start: 0.8352 (mmm) cc_final: 0.7874 (mmm) REVERT: A 72 PHE cc_start: 0.8648 (t80) cc_final: 0.8199 (t80) REVERT: A 102 ASP cc_start: 0.8108 (m-30) cc_final: 0.7815 (p0) REVERT: A 115 LYS cc_start: 0.8139 (pttm) cc_final: 0.7737 (mmmt) REVERT: A 148 ASP cc_start: 0.7331 (m-30) cc_final: 0.7092 (m-30) REVERT: A 179 THR cc_start: 0.8650 (t) cc_final: 0.8221 (p) REVERT: A 185 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8185 (ptmt) REVERT: A 197 ASN cc_start: 0.7108 (t0) cc_final: 0.6852 (t0) REVERT: A 280 ILE cc_start: 0.6736 (mt) cc_final: 0.6421 (mm) REVERT: A 282 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6900 (mt-10) REVERT: A 300 GLU cc_start: 0.4374 (OUTLIER) cc_final: 0.0324 (mt-10) REVERT: A 327 TYR cc_start: 0.7735 (m-80) cc_final: 0.7401 (m-80) REVERT: A 335 MET cc_start: 0.3251 (mtt) cc_final: 0.2438 (mtt) REVERT: A 341 LYS cc_start: 0.9141 (tttt) cc_final: 0.8812 (ttpp) REVERT: A 387 LYS cc_start: 0.8301 (mppt) cc_final: 0.8041 (mtmm) REVERT: A 398 ARG cc_start: 0.8558 (tpp-160) cc_final: 0.7728 (ttp-110) REVERT: A 400 LEU cc_start: 0.8313 (tp) cc_final: 0.8105 (tt) REVERT: A 408 LEU cc_start: 0.7821 (tt) cc_final: 0.7503 (tt) REVERT: A 420 HIS cc_start: 0.5943 (OUTLIER) cc_final: 0.5397 (t70) REVERT: A 425 MET cc_start: 0.7557 (ttp) cc_final: 0.7280 (ttp) REVERT: A 443 LYS cc_start: 0.7976 (mttp) cc_final: 0.7460 (mmtp) REVERT: A 447 ASP cc_start: 0.7650 (p0) cc_final: 0.7437 (p0) REVERT: A 481 THR cc_start: 0.8573 (m) cc_final: 0.8144 (p) REVERT: A 482 VAL cc_start: 0.8779 (t) cc_final: 0.8287 (p) REVERT: B 41 MET cc_start: 0.8692 (mmm) cc_final: 0.8434 (mmm) REVERT: B 50 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7164 (mt-10) REVERT: B 54 ASP cc_start: 0.8130 (t70) cc_final: 0.7906 (t70) REVERT: B 64 GLU cc_start: 0.8639 (tt0) cc_final: 0.7925 (tt0) REVERT: B 72 PHE cc_start: 0.8521 (t80) cc_final: 0.7965 (t80) REVERT: B 89 ARG cc_start: 0.8485 (mmm-85) cc_final: 0.8144 (mmm-85) REVERT: B 94 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7252 (mm-40) REVERT: B 141 ARG cc_start: 0.7390 (ttm-80) cc_final: 0.7047 (ttt-90) REVERT: B 147 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8443 (tp) REVERT: B 168 VAL cc_start: 0.9188 (t) cc_final: 0.8909 (p) REVERT: B 179 THR cc_start: 0.8513 (m) cc_final: 0.8277 (p) REVERT: B 181 SER cc_start: 0.9048 (OUTLIER) cc_final: 0.8753 (p) REVERT: B 200 ARG cc_start: 0.6600 (mtp-110) cc_final: 0.6159 (ttp80) REVERT: B 232 PHE cc_start: 0.6881 (m-10) cc_final: 0.6383 (m-80) REVERT: B 260 LEU cc_start: 0.8299 (mt) cc_final: 0.7991 (mm) REVERT: B 265 ASP cc_start: 0.6459 (t0) cc_final: 0.6230 (t70) REVERT: B 267 ARG cc_start: 0.8489 (tpp80) cc_final: 0.7800 (tpt90) REVERT: B 270 GLN cc_start: 0.8692 (tp-100) cc_final: 0.8482 (tp-100) REVERT: B 280 ILE cc_start: 0.6803 (mm) cc_final: 0.6546 (mm) REVERT: B 304 ARG cc_start: 0.8076 (mmt180) cc_final: 0.7494 (mmm-85) REVERT: B 318 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8006 (mt-10) REVERT: B 340 ILE cc_start: 0.9114 (mt) cc_final: 0.8621 (mt) REVERT: B 341 LYS cc_start: 0.9258 (pttm) cc_final: 0.8987 (pttt) REVERT: B 425 MET cc_start: 0.7418 (ttp) cc_final: 0.7120 (ttp) REVERT: B 426 ASP cc_start: 0.8453 (t0) cc_final: 0.7944 (t0) REVERT: B 443 LYS cc_start: 0.7823 (mtpp) cc_final: 0.7401 (mttm) REVERT: B 479 LYS cc_start: 0.7217 (mttt) cc_final: 0.6885 (mtmm) REVERT: B 481 THR cc_start: 0.8332 (m) cc_final: 0.7909 (p) REVERT: B 491 THR cc_start: 0.8097 (m) cc_final: 0.7706 (t) REVERT: B 498 SER cc_start: 0.8191 (m) cc_final: 0.7961 (m) REVERT: C 41 MET cc_start: 0.8554 (mmm) cc_final: 0.8258 (mmm) REVERT: C 64 GLU cc_start: 0.8414 (tt0) cc_final: 0.7501 (tt0) REVERT: C 72 PHE cc_start: 0.8698 (t80) cc_final: 0.8090 (t80) REVERT: C 89 ARG cc_start: 0.8896 (mmm-85) cc_final: 0.8536 (mmm-85) REVERT: C 135 LYS cc_start: 0.8205 (ttmt) cc_final: 0.7807 (mtpp) REVERT: C 179 THR cc_start: 0.8456 (m) cc_final: 0.8166 (p) REVERT: C 180 GLN cc_start: 0.8209 (mt0) cc_final: 0.7742 (mp10) REVERT: C 181 SER cc_start: 0.8844 (OUTLIER) cc_final: 0.8570 (p) REVERT: C 184 LYS cc_start: 0.8670 (mttp) cc_final: 0.8379 (mmtm) REVERT: C 201 TYR cc_start: 0.7995 (m-80) cc_final: 0.7334 (m-80) REVERT: C 221 GLN cc_start: 0.8021 (tp40) cc_final: 0.7759 (tp40) REVERT: C 232 PHE cc_start: 0.7263 (m-10) cc_final: 0.6762 (m-80) REVERT: C 272 MET cc_start: 0.7657 (tpp) cc_final: 0.7415 (tpp) REVERT: C 282 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6227 (mt-10) REVERT: C 283 LEU cc_start: 0.7841 (mt) cc_final: 0.7463 (mm) REVERT: C 357 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7004 (tp30) REVERT: C 415 LEU cc_start: 0.8756 (tp) cc_final: 0.8469 (tt) REVERT: C 425 MET cc_start: 0.7616 (ttp) cc_final: 0.7268 (ttp) REVERT: C 426 ASP cc_start: 0.8531 (t0) cc_final: 0.8147 (t70) REVERT: C 443 LYS cc_start: 0.7854 (mttm) cc_final: 0.7403 (mttm) REVERT: C 444 LYS cc_start: 0.6676 (mtpt) cc_final: 0.6440 (mtmm) REVERT: C 450 LYS cc_start: 0.8403 (ttpp) cc_final: 0.8166 (ttpp) REVERT: C 479 LYS cc_start: 0.7103 (mttt) cc_final: 0.6698 (mttm) REVERT: C 481 THR cc_start: 0.8040 (m) cc_final: 0.7629 (p) REVERT: C 511 ILE cc_start: 0.8476 (mt) cc_final: 0.8115 (tt) REVERT: D 50 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7251 (mt-10) REVERT: D 64 GLU cc_start: 0.8476 (tt0) cc_final: 0.7701 (tt0) REVERT: D 65 MET cc_start: 0.8190 (mmm) cc_final: 0.7978 (mmm) REVERT: D 72 PHE cc_start: 0.8658 (t80) cc_final: 0.8081 (t80) REVERT: D 94 GLN cc_start: 0.7741 (mm-40) cc_final: 0.7114 (mm-40) REVERT: D 179 THR cc_start: 0.8347 (m) cc_final: 0.8074 (p) REVERT: D 185 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8120 (ptmt) REVERT: D 201 TYR cc_start: 0.8109 (m-80) cc_final: 0.7550 (m-80) REVERT: D 232 PHE cc_start: 0.7369 (m-80) cc_final: 0.7024 (m-80) REVERT: D 243 LYS cc_start: 0.8782 (mttt) cc_final: 0.8501 (mttt) REVERT: D 270 GLN cc_start: 0.8174 (tp40) cc_final: 0.7801 (tp40) REVERT: D 272 MET cc_start: 0.7542 (tpp) cc_final: 0.7119 (tpp) REVERT: D 304 ARG cc_start: 0.7696 (mtp180) cc_final: 0.7348 (mtt180) REVERT: D 387 LYS cc_start: 0.8457 (mttt) cc_final: 0.8206 (mttt) REVERT: D 398 ARG cc_start: 0.8362 (tpp-160) cc_final: 0.8124 (tpp-160) REVERT: D 403 LYS cc_start: 0.7853 (mmtt) cc_final: 0.7242 (tptt) REVERT: D 426 ASP cc_start: 0.8384 (t0) cc_final: 0.8002 (t0) REVERT: D 448 PHE cc_start: 0.8343 (t80) cc_final: 0.7809 (t80) REVERT: D 479 LYS cc_start: 0.7355 (mttt) cc_final: 0.6907 (mtmm) REVERT: D 481 THR cc_start: 0.8335 (m) cc_final: 0.7931 (p) REVERT: D 499 VAL cc_start: 0.8417 (t) cc_final: 0.8053 (p) REVERT: E 64 GLU cc_start: 0.8625 (tt0) cc_final: 0.7915 (tt0) REVERT: E 72 PHE cc_start: 0.8456 (t80) cc_final: 0.7850 (t80) REVERT: E 89 ARG cc_start: 0.8633 (mmm-85) cc_final: 0.8314 (mmm-85) REVERT: E 129 MET cc_start: 0.7014 (mtm) cc_final: 0.6476 (mtm) REVERT: E 135 LYS cc_start: 0.7978 (ttmt) cc_final: 0.7711 (tptm) REVERT: E 147 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8312 (tp) REVERT: E 168 VAL cc_start: 0.9075 (t) cc_final: 0.8746 (p) REVERT: E 180 GLN cc_start: 0.8493 (mt0) cc_final: 0.7938 (mt0) REVERT: E 201 TYR cc_start: 0.7961 (m-80) cc_final: 0.7578 (m-80) REVERT: E 224 TYR cc_start: 0.6984 (p90) cc_final: 0.6556 (p90) REVERT: E 243 LYS cc_start: 0.8394 (mttt) cc_final: 0.8048 (mttt) REVERT: E 280 ILE cc_start: 0.7422 (mm) cc_final: 0.7120 (mm) REVERT: E 281 MET cc_start: 0.7110 (ttm) cc_final: 0.6261 (ttm) REVERT: E 283 LEU cc_start: 0.8117 (mt) cc_final: 0.7696 (mm) REVERT: E 304 ARG cc_start: 0.8098 (ttt180) cc_final: 0.7896 (ttt180) REVERT: E 387 LYS cc_start: 0.8397 (mppt) cc_final: 0.7931 (mtmm) REVERT: E 415 LEU cc_start: 0.8483 (tp) cc_final: 0.8281 (tt) REVERT: E 425 MET cc_start: 0.7445 (ttp) cc_final: 0.7063 (ttp) REVERT: E 426 ASP cc_start: 0.8418 (t0) cc_final: 0.8030 (t70) REVERT: E 444 LYS cc_start: 0.6645 (OUTLIER) cc_final: 0.6302 (ttmm) REVERT: E 481 THR cc_start: 0.8425 (m) cc_final: 0.7873 (p) REVERT: E 501 GLU cc_start: 0.7199 (tt0) cc_final: 0.6601 (tt0) REVERT: E 503 CYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7059 (m) REVERT: F 72 PHE cc_start: 0.8556 (t80) cc_final: 0.7688 (t80) REVERT: F 87 TRP cc_start: 0.6185 (t-100) cc_final: 0.5955 (m-90) REVERT: F 141 ARG cc_start: 0.7622 (ttm-80) cc_final: 0.7285 (ptm160) REVERT: F 168 VAL cc_start: 0.9101 (t) cc_final: 0.8823 (p) REVERT: F 171 ASN cc_start: 0.7921 (m-40) cc_final: 0.7519 (p0) REVERT: F 179 THR cc_start: 0.8709 (m) cc_final: 0.8439 (p) REVERT: F 180 GLN cc_start: 0.8627 (mt0) cc_final: 0.8254 (mt0) REVERT: F 181 SER cc_start: 0.9082 (OUTLIER) cc_final: 0.7989 (p) REVERT: F 184 LYS cc_start: 0.8636 (mttp) cc_final: 0.8359 (mttp) REVERT: F 185 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7961 (ptmm) REVERT: F 201 TYR cc_start: 0.8070 (m-80) cc_final: 0.7249 (m-80) REVERT: F 224 TYR cc_start: 0.6801 (p90) cc_final: 0.6186 (p90) REVERT: F 232 PHE cc_start: 0.7292 (m-80) cc_final: 0.6967 (m-80) REVERT: F 243 LYS cc_start: 0.8600 (mttt) cc_final: 0.8319 (mttt) REVERT: F 267 ARG cc_start: 0.8179 (ttt180) cc_final: 0.7914 (mmm-85) REVERT: F 272 MET cc_start: 0.7296 (tpp) cc_final: 0.6947 (tpp) REVERT: F 281 MET cc_start: 0.6863 (ttm) cc_final: 0.6497 (ttm) REVERT: F 282 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7109 (mt-10) REVERT: F 304 ARG cc_start: 0.7571 (mtt180) cc_final: 0.6976 (mtt90) REVERT: F 340 ILE cc_start: 0.9032 (mt) cc_final: 0.8711 (mt) REVERT: F 398 ARG cc_start: 0.8636 (tpp-160) cc_final: 0.8394 (tpp-160) REVERT: F 406 SER cc_start: 0.8933 (m) cc_final: 0.8707 (p) REVERT: F 425 MET cc_start: 0.7491 (ttp) cc_final: 0.7238 (ttp) REVERT: F 426 ASP cc_start: 0.8439 (t0) cc_final: 0.8189 (t70) REVERT: F 438 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7537 (mp) REVERT: F 443 LYS cc_start: 0.7811 (mtpp) cc_final: 0.7367 (mttm) REVERT: F 444 LYS cc_start: 0.6729 (mtpt) cc_final: 0.6329 (ttmm) REVERT: G 41 MET cc_start: 0.7974 (mmm) cc_final: 0.7740 (mmm) REVERT: G 64 GLU cc_start: 0.8541 (tt0) cc_final: 0.7999 (tt0) REVERT: G 72 PHE cc_start: 0.8738 (t80) cc_final: 0.7914 (t80) REVERT: G 102 ASP cc_start: 0.8174 (m-30) cc_final: 0.7804 (p0) REVERT: G 135 LYS cc_start: 0.8196 (ttmm) cc_final: 0.7665 (tptm) REVERT: G 170 MET cc_start: 0.7448 (ptp) cc_final: 0.7111 (ptp) REVERT: G 180 GLN cc_start: 0.8606 (mt0) cc_final: 0.8150 (mt0) REVERT: G 185 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8241 (ptmt) REVERT: G 200 ARG cc_start: 0.6942 (mtp-110) cc_final: 0.6632 (ttp-170) REVERT: G 232 PHE cc_start: 0.7125 (m-80) cc_final: 0.6739 (m-80) REVERT: G 243 LYS cc_start: 0.8880 (mttt) cc_final: 0.8559 (mttt) REVERT: G 258 ASP cc_start: 0.5810 (p0) cc_final: 0.5227 (p0) REVERT: G 259 ASN cc_start: 0.8022 (t0) cc_final: 0.7078 (p0) REVERT: G 267 ARG cc_start: 0.8507 (tpp80) cc_final: 0.8114 (tpp80) REVERT: G 272 MET cc_start: 0.7778 (tpp) cc_final: 0.7339 (tpp) REVERT: G 282 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6712 (mt-10) REVERT: G 286 LYS cc_start: 0.8280 (mttm) cc_final: 0.7779 (tttm) REVERT: G 326 LYS cc_start: 0.8012 (ptpt) cc_final: 0.7310 (mptt) REVERT: G 347 ASN cc_start: 0.7123 (t0) cc_final: 0.6853 (t0) REVERT: G 414 ASP cc_start: 0.7875 (p0) cc_final: 0.7660 (t0) REVERT: G 417 ARG cc_start: 0.6288 (mtt-85) cc_final: 0.5784 (mtm-85) REVERT: G 425 MET cc_start: 0.7553 (ttp) cc_final: 0.7295 (ttp) REVERT: G 426 ASP cc_start: 0.8634 (t0) cc_final: 0.8353 (t70) REVERT: G 443 LYS cc_start: 0.7963 (mttm) cc_final: 0.7518 (mttm) REVERT: G 444 LYS cc_start: 0.6744 (mtpt) cc_final: 0.6448 (ttmm) REVERT: G 481 THR cc_start: 0.8342 (m) cc_final: 0.7807 (p) REVERT: G 482 VAL cc_start: 0.8742 (t) cc_final: 0.8244 (p) REVERT: G 501 GLU cc_start: 0.7137 (tt0) cc_final: 0.6467 (tt0) REVERT: G 503 CYS cc_start: 0.7647 (OUTLIER) cc_final: 0.6981 (m) REVERT: H 41 MET cc_start: 0.7900 (tpp) cc_final: 0.7608 (tpp) REVERT: H 64 GLU cc_start: 0.8605 (tt0) cc_final: 0.8011 (tt0) REVERT: H 72 PHE cc_start: 0.8835 (t80) cc_final: 0.8124 (t80) REVERT: H 74 ARG cc_start: 0.8735 (mtm-85) cc_final: 0.8464 (ttm110) REVERT: H 89 ARG cc_start: 0.8718 (mmm-85) cc_final: 0.8413 (mmm-85) REVERT: H 102 ASP cc_start: 0.8269 (m-30) cc_final: 0.7570 (p0) REVERT: H 121 LEU cc_start: 0.8323 (mt) cc_final: 0.7701 (mt) REVERT: H 141 ARG cc_start: 0.7739 (mtp85) cc_final: 0.7261 (ttm-80) REVERT: H 168 VAL cc_start: 0.9168 (t) cc_final: 0.8775 (p) REVERT: H 170 MET cc_start: 0.7893 (ttt) cc_final: 0.7316 (ptp) REVERT: H 171 ASN cc_start: 0.8020 (m-40) cc_final: 0.7700 (p0) REVERT: H 180 GLN cc_start: 0.8623 (mt0) cc_final: 0.8217 (mt0) REVERT: H 185 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8102 (ptmt) REVERT: H 201 TYR cc_start: 0.8233 (m-80) cc_final: 0.7900 (m-80) REVERT: H 232 PHE cc_start: 0.7302 (m-10) cc_final: 0.6788 (m-80) REVERT: H 260 LEU cc_start: 0.8617 (mt) cc_final: 0.8388 (mm) REVERT: H 267 ARG cc_start: 0.8546 (tpp80) cc_final: 0.8100 (tpp80) REVERT: H 272 MET cc_start: 0.7575 (tpp) cc_final: 0.7337 (tpp) REVERT: H 280 ILE cc_start: 0.6727 (mm) cc_final: 0.6481 (mm) REVERT: H 282 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6591 (mt-10) REVERT: H 304 ARG cc_start: 0.8028 (mtt180) cc_final: 0.7403 (mtt180) REVERT: H 340 ILE cc_start: 0.9164 (mt) cc_final: 0.8602 (mt) REVERT: H 403 LYS cc_start: 0.7941 (mmtt) cc_final: 0.7263 (tptp) REVERT: H 438 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7918 (mt) REVERT: H 443 LYS cc_start: 0.7882 (mtmm) cc_final: 0.7642 (mtmm) REVERT: H 448 PHE cc_start: 0.8256 (t80) cc_final: 0.7948 (t80) REVERT: H 481 THR cc_start: 0.8456 (m) cc_final: 0.7919 (p) outliers start: 117 outliers final: 77 residues processed: 1043 average time/residue: 0.5220 time to fit residues: 816.7929 Evaluate side-chains 1062 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 968 time to evaluate : 3.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP 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 300 GLU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 420 HIS 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 147 LEU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 181 SER 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 147 LEU 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 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 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 241 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 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 251 TYR Chi-restraints excluded: chain E residue 254 LEU 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 444 LYS 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 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 379 VAL 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 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 488 GLU Chi-restraints excluded: chain G residue 503 CYS 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 308 ILE Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 423 LEU Chi-restraints excluded: chain H residue 438 LEU Chi-restraints excluded: chain H residue 488 GLU Chi-restraints excluded: chain H residue 503 CYS Chi-restraints excluded: chain H residue 504 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 266 optimal weight: 0.5980 chunk 308 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 193 optimal weight: 0.5980 chunk 142 optimal weight: 20.0000 chunk 352 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 275 optimal weight: 0.9980 chunk 297 optimal weight: 8.9990 chunk 192 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 HIS A 374 GLN A 463 HIS B 374 GLN B 463 HIS C 270 GLN ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 GLN E 463 HIS F 374 GLN G 259 ASN H 463 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.184228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.143034 restraints weight = 53713.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.148328 restraints weight = 29401.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.151817 restraints weight = 18884.207| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30368 Z= 0.125 Angle : 0.661 16.247 41088 Z= 0.334 Chirality : 0.047 0.198 4672 Planarity : 0.005 0.065 5352 Dihedral : 4.550 41.860 4058 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.04 % Allowed : 19.88 % Favored : 77.08 % 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: 0.12 (0.14), residues: 3720 helix: 0.21 (0.16), residues: 1136 sheet: -0.12 (0.20), residues: 704 loop : 0.26 (0.15), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP G 87 HIS 0.021 0.001 HIS A 420 PHE 0.018 0.001 PHE B 325 TYR 0.030 0.002 TYR B 224 ARG 0.009 0.001 ARG A 89 Details of bonding type rmsd hydrogen bonds : bond 0.04499 ( 1087) hydrogen bonds : angle 5.16489 ( 2733) covalent geometry : bond 0.00272 (30368) covalent geometry : angle 0.66117 (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 1064 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 963 time to evaluate : 3.155 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: A 41 MET cc_start: 0.8667 (mmm) cc_final: 0.8444 (mmm) REVERT: A 64 GLU cc_start: 0.8540 (tt0) cc_final: 0.8075 (tt0) REVERT: A 65 MET cc_start: 0.8369 (mmm) cc_final: 0.7970 (mmm) REVERT: A 72 PHE cc_start: 0.8650 (t80) cc_final: 0.8203 (t80) REVERT: A 179 THR cc_start: 0.8484 (t) cc_final: 0.8202 (p) REVERT: A 185 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8156 (ptmt) REVERT: A 197 ASN cc_start: 0.7135 (t0) cc_final: 0.6919 (t0) REVERT: A 270 GLN cc_start: 0.8524 (tp-100) cc_final: 0.8171 (tp-100) REVERT: A 271 HIS cc_start: 0.7440 (t70) cc_final: 0.6949 (t70) REVERT: A 280 ILE cc_start: 0.6626 (mt) cc_final: 0.6345 (mm) REVERT: A 282 GLU cc_start: 0.7560 (mt-10) cc_final: 0.6951 (mt-10) REVERT: A 287 THR cc_start: 0.8263 (t) cc_final: 0.7847 (p) REVERT: A 300 GLU cc_start: 0.4007 (OUTLIER) cc_final: 0.3409 (mp0) REVERT: A 304 ARG cc_start: 0.8046 (ttt180) cc_final: 0.7704 (mtt90) REVERT: A 335 MET cc_start: 0.3224 (mtt) cc_final: 0.2446 (mtt) REVERT: A 341 LYS cc_start: 0.9076 (tttt) cc_final: 0.8708 (ttpp) REVERT: A 387 LYS cc_start: 0.8299 (mppt) cc_final: 0.7976 (ptpp) REVERT: A 420 HIS cc_start: 0.5789 (OUTLIER) cc_final: 0.5469 (t70) REVERT: A 425 MET cc_start: 0.7563 (ttp) cc_final: 0.7287 (ttp) REVERT: A 443 LYS cc_start: 0.7872 (mttp) cc_final: 0.7445 (mptt) REVERT: A 482 VAL cc_start: 0.8721 (t) cc_final: 0.8264 (p) REVERT: B 41 MET cc_start: 0.8705 (mmm) cc_final: 0.8223 (mmm) REVERT: B 45 LEU cc_start: 0.9160 (mt) cc_final: 0.8877 (mt) REVERT: B 64 GLU cc_start: 0.8708 (tt0) cc_final: 0.8169 (tt0) REVERT: B 65 MET cc_start: 0.8082 (mmm) cc_final: 0.7793 (mmm) REVERT: B 72 PHE cc_start: 0.8445 (t80) cc_final: 0.7970 (t80) REVERT: B 74 ARG cc_start: 0.8150 (ttm110) cc_final: 0.7734 (ptp-170) REVERT: B 94 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7134 (mm-40) REVERT: B 141 ARG cc_start: 0.7380 (ttm-80) cc_final: 0.7133 (ttt-90) REVERT: B 147 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8311 (tp) REVERT: B 148 ASP cc_start: 0.7507 (m-30) cc_final: 0.7206 (m-30) REVERT: B 168 VAL cc_start: 0.9138 (t) cc_final: 0.8894 (p) REVERT: B 179 THR cc_start: 0.8449 (m) cc_final: 0.8172 (p) REVERT: B 181 SER cc_start: 0.8958 (OUTLIER) cc_final: 0.8680 (p) REVERT: B 232 PHE cc_start: 0.6762 (m-10) cc_final: 0.6305 (m-80) REVERT: B 243 LYS cc_start: 0.8400 (mttt) cc_final: 0.8136 (mttt) REVERT: B 253 PHE cc_start: 0.7290 (t80) cc_final: 0.6945 (t80) REVERT: B 260 LEU cc_start: 0.8311 (mt) cc_final: 0.7969 (mm) REVERT: B 265 ASP cc_start: 0.6411 (t0) cc_final: 0.6171 (t70) REVERT: B 282 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6524 (mt-10) REVERT: B 304 ARG cc_start: 0.7952 (mmt180) cc_final: 0.7695 (mmt180) REVERT: B 318 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8009 (mt-10) REVERT: B 340 ILE cc_start: 0.9061 (mt) cc_final: 0.8644 (mt) REVERT: B 341 LYS cc_start: 0.9238 (pttm) cc_final: 0.8962 (pttt) REVERT: B 398 ARG cc_start: 0.8559 (tpp-160) cc_final: 0.8220 (tpp-160) REVERT: B 425 MET cc_start: 0.7439 (ttp) cc_final: 0.7152 (ttp) REVERT: B 426 ASP cc_start: 0.8390 (t0) cc_final: 0.7966 (t0) REVERT: B 443 LYS cc_start: 0.7707 (mtpp) cc_final: 0.7444 (mttm) REVERT: B 448 PHE cc_start: 0.8098 (t80) cc_final: 0.7873 (t80) REVERT: B 450 LYS cc_start: 0.8286 (ttpp) cc_final: 0.7936 (ttpp) REVERT: B 479 LYS cc_start: 0.7160 (mttt) cc_final: 0.6854 (mtmm) REVERT: B 481 THR cc_start: 0.8295 (m) cc_final: 0.7891 (p) REVERT: B 491 THR cc_start: 0.8043 (m) cc_final: 0.7689 (t) REVERT: C 41 MET cc_start: 0.8507 (mmm) cc_final: 0.8164 (mmm) REVERT: C 54 ASP cc_start: 0.7736 (t70) cc_final: 0.7507 (t0) REVERT: C 64 GLU cc_start: 0.8449 (tt0) cc_final: 0.7552 (tt0) REVERT: C 72 PHE cc_start: 0.8621 (t80) cc_final: 0.8060 (t80) REVERT: C 74 ARG cc_start: 0.8415 (ttm110) cc_final: 0.7854 (ptp-170) REVERT: C 94 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7413 (mm-40) REVERT: C 115 LYS cc_start: 0.8066 (mtmm) cc_final: 0.7375 (mmmt) REVERT: C 135 LYS cc_start: 0.8060 (ttmt) cc_final: 0.7704 (ttmt) REVERT: C 179 THR cc_start: 0.8349 (m) cc_final: 0.7972 (p) REVERT: C 180 GLN cc_start: 0.8147 (mt0) cc_final: 0.7666 (mp10) REVERT: C 184 LYS cc_start: 0.8580 (mttp) cc_final: 0.8300 (mmtm) REVERT: C 200 ARG cc_start: 0.6644 (ttp-170) cc_final: 0.6437 (ttp-170) REVERT: C 201 TYR cc_start: 0.7896 (m-80) cc_final: 0.7195 (m-80) REVERT: C 221 GLN cc_start: 0.7962 (tp40) cc_final: 0.7749 (tp40) REVERT: C 232 PHE cc_start: 0.7169 (m-10) cc_final: 0.6740 (m-80) REVERT: C 267 ARG cc_start: 0.8420 (tpt-90) cc_final: 0.7633 (tpt-90) REVERT: C 282 GLU cc_start: 0.6827 (mt-10) cc_final: 0.6096 (mt-10) REVERT: C 283 LEU cc_start: 0.7661 (mt) cc_final: 0.7291 (mm) REVERT: C 357 GLU cc_start: 0.7551 (mm-30) cc_final: 0.6874 (tp30) REVERT: C 415 LEU cc_start: 0.8698 (tp) cc_final: 0.8448 (tt) REVERT: C 425 MET cc_start: 0.7674 (ttp) cc_final: 0.7279 (ttp) REVERT: C 426 ASP cc_start: 0.8483 (t0) cc_final: 0.8125 (t70) REVERT: C 443 LYS cc_start: 0.7847 (mttm) cc_final: 0.7578 (mttm) REVERT: C 450 LYS cc_start: 0.8336 (ttpp) cc_final: 0.8119 (ttpp) REVERT: C 479 LYS cc_start: 0.7039 (mttt) cc_final: 0.6555 (mttm) REVERT: C 481 THR cc_start: 0.8004 (m) cc_final: 0.7648 (p) REVERT: C 499 VAL cc_start: 0.8525 (t) cc_final: 0.8213 (m) REVERT: C 511 ILE cc_start: 0.8405 (mt) cc_final: 0.8080 (tt) REVERT: D 50 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7185 (mt-10) REVERT: D 64 GLU cc_start: 0.8471 (tt0) cc_final: 0.7730 (tt0) REVERT: D 72 PHE cc_start: 0.8654 (t80) cc_final: 0.8040 (t80) REVERT: D 94 GLN cc_start: 0.7613 (mm-40) cc_final: 0.7002 (mm-40) REVERT: D 148 ASP cc_start: 0.7328 (m-30) cc_final: 0.7027 (m-30) REVERT: D 179 THR cc_start: 0.8296 (m) cc_final: 0.7987 (p) REVERT: D 185 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8159 (ptmt) REVERT: D 200 ARG cc_start: 0.6567 (mtp-110) cc_final: 0.6136 (ttp-110) REVERT: D 201 TYR cc_start: 0.7996 (m-80) cc_final: 0.7349 (m-80) REVERT: D 232 PHE cc_start: 0.7277 (m-80) cc_final: 0.6968 (m-80) REVERT: D 243 LYS cc_start: 0.8746 (mttt) cc_final: 0.8461 (mttt) REVERT: D 272 MET cc_start: 0.7461 (tpp) cc_final: 0.7053 (tpp) REVERT: D 304 ARG cc_start: 0.7664 (mtp180) cc_final: 0.7312 (mtt180) REVERT: D 341 LYS cc_start: 0.8995 (pttp) cc_final: 0.8747 (ptpp) REVERT: D 387 LYS cc_start: 0.8436 (mttt) cc_final: 0.8179 (mttt) REVERT: D 398 ARG cc_start: 0.8261 (tpp-160) cc_final: 0.8001 (tpp-160) REVERT: D 403 LYS cc_start: 0.7842 (mmtt) cc_final: 0.7089 (tptp) REVERT: D 438 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7463 (mm) REVERT: D 443 LYS cc_start: 0.7593 (mtpp) cc_final: 0.7225 (mttm) REVERT: D 479 LYS cc_start: 0.7241 (mttt) cc_final: 0.6843 (mtmm) REVERT: D 481 THR cc_start: 0.8289 (m) cc_final: 0.7948 (p) REVERT: D 491 THR cc_start: 0.8237 (m) cc_final: 0.7885 (p) REVERT: D 499 VAL cc_start: 0.8447 (t) cc_final: 0.8095 (p) REVERT: E 50 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7630 (mt-10) REVERT: E 64 GLU cc_start: 0.8626 (tt0) cc_final: 0.7919 (tt0) REVERT: E 72 PHE cc_start: 0.8613 (t80) cc_final: 0.7936 (t80) REVERT: E 89 ARG cc_start: 0.8602 (mmm-85) cc_final: 0.8294 (mmm-85) REVERT: E 129 MET cc_start: 0.6998 (mtm) cc_final: 0.6440 (mtm) REVERT: E 135 LYS cc_start: 0.7920 (ttmt) cc_final: 0.7629 (tptm) REVERT: E 147 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8140 (tp) REVERT: E 168 VAL cc_start: 0.9063 (t) cc_final: 0.8797 (p) REVERT: E 180 GLN cc_start: 0.8428 (mt0) cc_final: 0.7780 (mt0) REVERT: E 201 TYR cc_start: 0.7805 (m-80) cc_final: 0.7470 (m-80) REVERT: E 243 LYS cc_start: 0.8429 (mttt) cc_final: 0.8163 (mttt) REVERT: E 267 ARG cc_start: 0.8517 (tpt-90) cc_final: 0.8136 (tpp80) REVERT: E 280 ILE cc_start: 0.7230 (mm) cc_final: 0.7021 (mm) REVERT: E 281 MET cc_start: 0.6922 (ttm) cc_final: 0.6641 (ttm) REVERT: E 304 ARG cc_start: 0.8077 (ttt180) cc_final: 0.7807 (ttt180) REVERT: E 374 GLN cc_start: 0.6509 (mm110) cc_final: 0.5974 (mm-40) REVERT: E 387 LYS cc_start: 0.8395 (mppt) cc_final: 0.8164 (mtmm) REVERT: E 398 ARG cc_start: 0.8425 (tpp-160) cc_final: 0.8088 (tpp-160) REVERT: E 415 LEU cc_start: 0.8512 (tp) cc_final: 0.8223 (tt) REVERT: E 425 MET cc_start: 0.7496 (ttp) cc_final: 0.7071 (ttp) REVERT: E 438 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7330 (mt) REVERT: E 443 LYS cc_start: 0.7553 (mtpp) cc_final: 0.7244 (mttm) REVERT: E 481 THR cc_start: 0.8378 (m) cc_final: 0.7826 (p) REVERT: E 501 GLU cc_start: 0.7141 (tt0) cc_final: 0.6576 (tt0) REVERT: E 503 CYS cc_start: 0.7563 (p) cc_final: 0.7003 (m) REVERT: F 72 PHE cc_start: 0.8504 (t80) cc_final: 0.7675 (t80) REVERT: F 135 LYS cc_start: 0.8557 (tptm) cc_final: 0.8345 (tppt) REVERT: F 168 VAL cc_start: 0.9113 (t) cc_final: 0.8830 (p) REVERT: F 170 MET cc_start: 0.7762 (ttt) cc_final: 0.7482 (ptp) REVERT: F 171 ASN cc_start: 0.7536 (m-40) cc_final: 0.7269 (p0) REVERT: F 179 THR cc_start: 0.8646 (m) cc_final: 0.8345 (p) REVERT: F 181 SER cc_start: 0.9019 (OUTLIER) cc_final: 0.7837 (p) REVERT: F 184 LYS cc_start: 0.8564 (mttp) cc_final: 0.8252 (mttp) REVERT: F 185 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7988 (ptmm) REVERT: F 201 TYR cc_start: 0.7866 (m-80) cc_final: 0.7048 (m-80) REVERT: F 232 PHE cc_start: 0.7187 (m-80) cc_final: 0.6901 (m-80) REVERT: F 243 LYS cc_start: 0.8524 (mttt) cc_final: 0.8236 (mttt) REVERT: F 253 PHE cc_start: 0.7493 (t80) cc_final: 0.7067 (t80) REVERT: F 272 MET cc_start: 0.7206 (tpp) cc_final: 0.6852 (tpp) REVERT: F 281 MET cc_start: 0.6778 (ttm) cc_final: 0.6427 (ttm) REVERT: F 282 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7078 (mt-10) REVERT: F 304 ARG cc_start: 0.7447 (mtt180) cc_final: 0.6740 (mtp180) REVERT: F 340 ILE cc_start: 0.9021 (mt) cc_final: 0.8762 (mt) REVERT: F 341 LYS cc_start: 0.9170 (pttt) cc_final: 0.8906 (pmtt) REVERT: F 425 MET cc_start: 0.7565 (ttp) cc_final: 0.7264 (ttp) REVERT: F 426 ASP cc_start: 0.8392 (t0) cc_final: 0.8137 (t70) REVERT: F 441 ASP cc_start: 0.7042 (m-30) cc_final: 0.6774 (m-30) REVERT: F 443 LYS cc_start: 0.7760 (mtpp) cc_final: 0.7420 (mttm) REVERT: G 41 MET cc_start: 0.7884 (mmm) cc_final: 0.7651 (mmm) REVERT: G 64 GLU cc_start: 0.8543 (tt0) cc_final: 0.8074 (tt0) REVERT: G 72 PHE cc_start: 0.8664 (t80) cc_final: 0.7815 (t80) REVERT: G 89 ARG cc_start: 0.8800 (mmm-85) cc_final: 0.8385 (mmm-85) REVERT: G 102 ASP cc_start: 0.8138 (m-30) cc_final: 0.7775 (p0) REVERT: G 103 ASP cc_start: 0.7475 (p0) cc_final: 0.7105 (p0) REVERT: G 129 MET cc_start: 0.7026 (mtm) cc_final: 0.6229 (mtm) REVERT: G 170 MET cc_start: 0.7448 (ptp) cc_final: 0.7033 (ptp) REVERT: G 179 THR cc_start: 0.8386 (m) cc_final: 0.8118 (p) REVERT: G 180 GLN cc_start: 0.8531 (mt0) cc_final: 0.8033 (mt0) REVERT: G 185 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8166 (ptmt) REVERT: G 200 ARG cc_start: 0.6688 (mtp-110) cc_final: 0.6235 (ttp80) REVERT: G 243 LYS cc_start: 0.8846 (mttt) cc_final: 0.8502 (mttt) REVERT: G 259 ASN cc_start: 0.7819 (t0) cc_final: 0.7539 (t0) REVERT: G 267 ARG cc_start: 0.8498 (tpp80) cc_final: 0.8121 (tpp80) REVERT: G 272 MET cc_start: 0.7612 (tpp) cc_final: 0.7206 (tpp) REVERT: G 282 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6618 (mt-10) REVERT: G 286 LYS cc_start: 0.8240 (mttm) cc_final: 0.7788 (tttm) REVERT: G 347 ASN cc_start: 0.7024 (t0) cc_final: 0.6734 (t0) REVERT: G 403 LYS cc_start: 0.7598 (mmtt) cc_final: 0.6842 (tptp) REVERT: G 414 ASP cc_start: 0.7820 (p0) cc_final: 0.7540 (t0) REVERT: G 417 ARG cc_start: 0.6237 (mtt-85) cc_final: 0.5743 (mtm-85) REVERT: G 425 MET cc_start: 0.7592 (ttp) cc_final: 0.7293 (ttp) REVERT: G 426 ASP cc_start: 0.8567 (t0) cc_final: 0.8318 (t70) REVERT: G 481 THR cc_start: 0.8309 (m) cc_final: 0.7735 (p) REVERT: G 501 GLU cc_start: 0.7158 (tt0) cc_final: 0.6517 (tt0) REVERT: G 503 CYS cc_start: 0.7465 (p) cc_final: 0.6903 (m) REVERT: H 41 MET cc_start: 0.7863 (tpp) cc_final: 0.7582 (tpp) REVERT: H 64 GLU cc_start: 0.8612 (tt0) cc_final: 0.8035 (tt0) REVERT: H 65 MET cc_start: 0.8319 (mmm) cc_final: 0.8097 (mmm) REVERT: H 72 PHE cc_start: 0.8760 (t80) cc_final: 0.8052 (t80) REVERT: H 74 ARG cc_start: 0.8677 (mtm-85) cc_final: 0.8354 (ttm110) REVERT: H 89 ARG cc_start: 0.8713 (mmm-85) cc_final: 0.8353 (mmm-85) REVERT: H 102 ASP cc_start: 0.8297 (m-30) cc_final: 0.7622 (p0) REVERT: H 121 LEU cc_start: 0.8265 (mt) cc_final: 0.7773 (mt) REVERT: H 141 ARG cc_start: 0.7654 (mtp85) cc_final: 0.7243 (ttm-80) REVERT: H 168 VAL cc_start: 0.9187 (t) cc_final: 0.8837 (p) REVERT: H 170 MET cc_start: 0.7858 (ttt) cc_final: 0.7328 (ptp) REVERT: H 171 ASN cc_start: 0.7934 (m-40) cc_final: 0.7415 (p0) REVERT: H 180 GLN cc_start: 0.8596 (mt0) cc_final: 0.8105 (mt0) REVERT: H 185 LYS cc_start: 0.8512 (ptmt) cc_final: 0.8095 (ptmt) REVERT: H 201 TYR cc_start: 0.8088 (m-80) cc_final: 0.7822 (m-80) REVERT: H 232 PHE cc_start: 0.7200 (m-10) cc_final: 0.6741 (m-80) REVERT: H 253 PHE cc_start: 0.7434 (t80) cc_final: 0.7128 (t80) REVERT: H 267 ARG cc_start: 0.8506 (tpp80) cc_final: 0.8074 (tpp80) REVERT: H 272 MET cc_start: 0.7540 (tpp) cc_final: 0.7277 (tpp) REVERT: H 282 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6575 (mt-10) REVERT: H 304 ARG cc_start: 0.8044 (mtt180) cc_final: 0.7373 (mtt180) REVERT: H 340 ILE cc_start: 0.9170 (mt) cc_final: 0.8654 (mt) REVERT: H 341 LYS cc_start: 0.9236 (pttp) cc_final: 0.9006 (pttm) REVERT: H 403 LYS cc_start: 0.7769 (mmtt) cc_final: 0.7172 (tptt) REVERT: H 438 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7745 (mt) REVERT: H 443 LYS cc_start: 0.7762 (mtmm) cc_final: 0.7523 (mttp) REVERT: H 481 THR cc_start: 0.8459 (m) cc_final: 0.7947 (p) REVERT: H 482 VAL cc_start: 0.8656 (t) cc_final: 0.8113 (p) outliers start: 101 outliers final: 66 residues processed: 999 average time/residue: 0.4840 time to fit residues: 720.8607 Evaluate side-chains 1038 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 959 time to evaluate : 3.576 ------------------------------------------------------------------------------- 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 241 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 300 GLU 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 420 HIS 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 147 LEU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 181 SER 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 147 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 265 ASP 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 149 LEU 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 241 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 438 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 351 MET Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 474 ARG Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 504 VAL 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 379 VAL 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 504 VAL Chi-restraints excluded: chain F residue 513 GLU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 185 LYS Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 284 THR Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 449 GLN Chi-restraints excluded: chain G residue 474 ARG Chi-restraints excluded: chain G residue 488 GLU 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 333 ILE Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 423 LEU Chi-restraints excluded: chain H residue 438 LEU 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: 5.9990 chunk 172 optimal weight: 8.9990 chunk 209 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 123 optimal weight: 0.0980 chunk 63 optimal weight: 20.0000 chunk 346 optimal weight: 0.0670 chunk 375 optimal weight: 0.9980 chunk 306 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 261 optimal weight: 0.9980 overall best weight: 1.2320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN B 374 GLN C 374 GLN ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.183674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.142587 restraints weight = 54225.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.147893 restraints weight = 29934.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.151277 restraints weight = 19257.541| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 30368 Z= 0.138 Angle : 0.668 15.777 41088 Z= 0.337 Chirality : 0.047 0.236 4672 Planarity : 0.005 0.079 5352 Dihedral : 4.535 41.215 4058 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.98 % Allowed : 20.36 % Favored : 76.66 % 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: 0.07 (0.14), residues: 3720 helix: 0.22 (0.16), residues: 1144 sheet: -0.25 (0.20), residues: 720 loop : 0.24 (0.15), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 87 HIS 0.010 0.001 HIS A 420 PHE 0.021 0.001 PHE F 325 TYR 0.034 0.002 TYR A 327 ARG 0.008 0.001 ARG D 74 Details of bonding type rmsd hydrogen bonds : bond 0.04431 ( 1087) hydrogen bonds : angle 5.14739 ( 2733) covalent geometry : bond 0.00305 (30368) covalent geometry : angle 0.66838 (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 1071 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 972 time to evaluate : 3.186 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: A 60 ARG cc_start: 0.8366 (tpt170) cc_final: 0.7217 (tpt90) REVERT: A 72 PHE cc_start: 0.8681 (t80) cc_final: 0.8203 (t80) REVERT: A 89 ARG cc_start: 0.8721 (mmm-85) cc_final: 0.8255 (mtp85) REVERT: A 168 VAL cc_start: 0.9099 (t) cc_final: 0.8868 (p) REVERT: A 179 THR cc_start: 0.8444 (t) cc_final: 0.8224 (p) REVERT: A 185 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.7903 (ptmm) REVERT: A 197 ASN cc_start: 0.7149 (t0) cc_final: 0.6908 (t0) REVERT: A 228 HIS cc_start: 0.6333 (m90) cc_final: 0.5877 (t-170) REVERT: A 271 HIS cc_start: 0.7377 (t70) cc_final: 0.6898 (t70) REVERT: A 280 ILE cc_start: 0.6720 (mt) cc_final: 0.6420 (mm) REVERT: A 282 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7073 (mt-10) REVERT: A 287 THR cc_start: 0.8263 (t) cc_final: 0.7822 (p) REVERT: A 300 GLU cc_start: 0.4143 (OUTLIER) cc_final: -0.0150 (mt-10) REVERT: A 327 TYR cc_start: 0.7491 (m-80) cc_final: 0.7179 (m-80) REVERT: A 335 MET cc_start: 0.3260 (mtt) cc_final: 0.2560 (mtt) REVERT: A 341 LYS cc_start: 0.9096 (tttt) cc_final: 0.8721 (ttpp) REVERT: A 387 LYS cc_start: 0.8362 (mppt) cc_final: 0.8040 (mtmm) REVERT: A 403 LYS cc_start: 0.7412 (mmtm) cc_final: 0.7024 (tptp) REVERT: A 420 HIS cc_start: 0.5512 (OUTLIER) cc_final: 0.4934 (m-70) REVERT: A 425 MET cc_start: 0.7571 (ttp) cc_final: 0.7306 (ttp) REVERT: A 443 LYS cc_start: 0.7883 (mttp) cc_final: 0.7500 (mmtm) REVERT: A 479 LYS cc_start: 0.7297 (mttt) cc_final: 0.7013 (mttp) REVERT: A 482 VAL cc_start: 0.8744 (t) cc_final: 0.8306 (p) REVERT: B 41 MET cc_start: 0.8707 (mmm) cc_final: 0.8210 (mmm) REVERT: B 45 LEU cc_start: 0.9210 (mt) cc_final: 0.8929 (mt) REVERT: B 64 GLU cc_start: 0.8669 (tt0) cc_final: 0.8174 (tt0) REVERT: B 65 MET cc_start: 0.7970 (mmm) cc_final: 0.7744 (mmm) REVERT: B 72 PHE cc_start: 0.8494 (t80) cc_final: 0.8034 (t80) REVERT: B 74 ARG cc_start: 0.8130 (ttm110) cc_final: 0.7750 (ptp-170) REVERT: B 94 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7143 (mm-40) REVERT: B 141 ARG cc_start: 0.7405 (ttm-80) cc_final: 0.7175 (ttt-90) REVERT: B 147 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8372 (tp) REVERT: B 168 VAL cc_start: 0.9140 (t) cc_final: 0.8886 (p) REVERT: B 179 THR cc_start: 0.8431 (m) cc_final: 0.8164 (p) REVERT: B 181 SER cc_start: 0.8861 (OUTLIER) cc_final: 0.8577 (p) REVERT: B 232 PHE cc_start: 0.6795 (m-10) cc_final: 0.6337 (m-80) REVERT: B 243 LYS cc_start: 0.8406 (mttt) cc_final: 0.8126 (mttt) REVERT: B 265 ASP cc_start: 0.6531 (t0) cc_final: 0.6279 (t70) REVERT: B 280 ILE cc_start: 0.7084 (mm) cc_final: 0.6824 (mm) REVERT: B 281 MET cc_start: 0.6966 (ttm) cc_final: 0.6687 (ttm) REVERT: B 282 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6615 (mt-10) REVERT: B 304 ARG cc_start: 0.7940 (mmt180) cc_final: 0.7615 (mmt180) REVERT: B 318 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8029 (mt-10) REVERT: B 340 ILE cc_start: 0.9063 (mt) cc_final: 0.8648 (mt) REVERT: B 398 ARG cc_start: 0.8581 (tpp-160) cc_final: 0.8229 (tpp-160) REVERT: B 425 MET cc_start: 0.7447 (ttp) cc_final: 0.7181 (ttp) REVERT: B 426 ASP cc_start: 0.8396 (t0) cc_final: 0.7960 (t0) REVERT: B 448 PHE cc_start: 0.8111 (t80) cc_final: 0.7896 (t80) REVERT: B 450 LYS cc_start: 0.8286 (ttpp) cc_final: 0.7916 (ttpp) REVERT: B 479 LYS cc_start: 0.7171 (mttt) cc_final: 0.6855 (mtmm) REVERT: B 481 THR cc_start: 0.8345 (m) cc_final: 0.7915 (p) REVERT: B 491 THR cc_start: 0.8048 (m) cc_final: 0.7771 (t) REVERT: B 503 CYS cc_start: 0.7629 (p) cc_final: 0.7148 (m) REVERT: C 41 MET cc_start: 0.8493 (mmm) cc_final: 0.8217 (mmm) REVERT: C 54 ASP cc_start: 0.7747 (t70) cc_final: 0.7514 (t0) REVERT: C 64 GLU cc_start: 0.8508 (tt0) cc_final: 0.7938 (tt0) REVERT: C 72 PHE cc_start: 0.8658 (t80) cc_final: 0.8082 (t80) REVERT: C 74 ARG cc_start: 0.8402 (ttm110) cc_final: 0.7862 (ptp-170) REVERT: C 135 LYS cc_start: 0.8079 (ttmt) cc_final: 0.7614 (mtpp) REVERT: C 170 MET cc_start: 0.7666 (ptp) cc_final: 0.7444 (pmm) REVERT: C 179 THR cc_start: 0.8371 (m) cc_final: 0.8077 (p) REVERT: C 181 SER cc_start: 0.8766 (OUTLIER) cc_final: 0.8468 (p) REVERT: C 184 LYS cc_start: 0.8578 (mttp) cc_final: 0.8259 (mmtm) REVERT: C 221 GLN cc_start: 0.7992 (tp40) cc_final: 0.7767 (tp40) REVERT: C 232 PHE cc_start: 0.7191 (m-10) cc_final: 0.6858 (m-80) REVERT: C 267 ARG cc_start: 0.8421 (tpt-90) cc_final: 0.7795 (tpt-90) REVERT: C 282 GLU cc_start: 0.6837 (mt-10) cc_final: 0.6165 (mt-10) REVERT: C 283 LEU cc_start: 0.7496 (mt) cc_final: 0.7119 (mm) REVERT: C 304 ARG cc_start: 0.8068 (mmt180) cc_final: 0.7864 (mmt180) REVERT: C 357 GLU cc_start: 0.7523 (mm-30) cc_final: 0.6848 (tp30) REVERT: C 415 LEU cc_start: 0.8793 (tp) cc_final: 0.8527 (tt) REVERT: C 425 MET cc_start: 0.7669 (ttp) cc_final: 0.7317 (ttp) REVERT: C 426 ASP cc_start: 0.8482 (t0) cc_final: 0.8127 (t70) REVERT: C 443 LYS cc_start: 0.7852 (mttm) cc_final: 0.7566 (mttm) REVERT: C 450 LYS cc_start: 0.8350 (ttpp) cc_final: 0.8111 (ttpp) REVERT: C 479 LYS cc_start: 0.7048 (mttt) cc_final: 0.6567 (mttm) REVERT: C 481 THR cc_start: 0.8016 (m) cc_final: 0.7625 (p) REVERT: C 499 VAL cc_start: 0.8519 (t) cc_final: 0.8238 (m) REVERT: C 503 CYS cc_start: 0.7417 (p) cc_final: 0.7012 (m) REVERT: C 511 ILE cc_start: 0.8404 (mt) cc_final: 0.8116 (tt) REVERT: D 64 GLU cc_start: 0.8524 (tt0) cc_final: 0.7787 (tt0) REVERT: D 72 PHE cc_start: 0.8660 (t80) cc_final: 0.8114 (t80) REVERT: D 74 ARG cc_start: 0.8369 (ttm110) cc_final: 0.7886 (ptp-170) REVERT: D 94 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7028 (mm-40) REVERT: D 148 ASP cc_start: 0.7337 (m-30) cc_final: 0.7053 (m-30) REVERT: D 179 THR cc_start: 0.8335 (m) cc_final: 0.8094 (p) REVERT: D 185 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8138 (ptmt) REVERT: D 201 TYR cc_start: 0.7966 (m-80) cc_final: 0.7353 (m-80) REVERT: D 232 PHE cc_start: 0.7127 (m-10) cc_final: 0.6832 (m-80) REVERT: D 243 LYS cc_start: 0.8748 (mttt) cc_final: 0.8455 (mttt) REVERT: D 272 MET cc_start: 0.7528 (tpp) cc_final: 0.7139 (tpp) REVERT: D 286 LYS cc_start: 0.8529 (mttm) cc_final: 0.8291 (tttm) REVERT: D 304 ARG cc_start: 0.7697 (mtp180) cc_final: 0.7358 (mtt180) REVERT: D 387 LYS cc_start: 0.8442 (mttt) cc_final: 0.8176 (mttt) REVERT: D 398 ARG cc_start: 0.8249 (tpp-160) cc_final: 0.8017 (tpp-160) REVERT: D 403 LYS cc_start: 0.7830 (mmtt) cc_final: 0.7177 (tptt) REVERT: D 415 LEU cc_start: 0.8615 (tp) cc_final: 0.7914 (tp) REVERT: D 425 MET cc_start: 0.7344 (tpp) cc_final: 0.6802 (tpp) REVERT: D 426 ASP cc_start: 0.8345 (t0) cc_final: 0.7964 (t0) REVERT: D 438 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7573 (mt) REVERT: D 479 LYS cc_start: 0.7261 (mttt) cc_final: 0.6930 (mttm) REVERT: D 481 THR cc_start: 0.8310 (m) cc_final: 0.7956 (p) REVERT: D 491 THR cc_start: 0.8267 (m) cc_final: 0.7907 (p) REVERT: D 499 VAL cc_start: 0.8475 (t) cc_final: 0.8153 (p) REVERT: E 64 GLU cc_start: 0.8661 (tt0) cc_final: 0.8026 (tt0) REVERT: E 72 PHE cc_start: 0.8643 (t80) cc_final: 0.7945 (t80) REVERT: E 89 ARG cc_start: 0.8599 (mmm-85) cc_final: 0.8294 (mmm-85) REVERT: E 129 MET cc_start: 0.6950 (mtm) cc_final: 0.6417 (mtm) REVERT: E 135 LYS cc_start: 0.7952 (ttmt) cc_final: 0.7667 (tptm) REVERT: E 147 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8183 (tp) REVERT: E 168 VAL cc_start: 0.9036 (t) cc_final: 0.8718 (p) REVERT: E 180 GLN cc_start: 0.8516 (mt0) cc_final: 0.7846 (mt0) REVERT: E 201 TYR cc_start: 0.7870 (m-80) cc_final: 0.7548 (m-80) REVERT: E 243 LYS cc_start: 0.8422 (mttt) cc_final: 0.8145 (mttt) REVERT: E 267 ARG cc_start: 0.8428 (tpt-90) cc_final: 0.8079 (tpp80) REVERT: E 281 MET cc_start: 0.7021 (ttm) cc_final: 0.6742 (ttm) REVERT: E 304 ARG cc_start: 0.8093 (ttt180) cc_final: 0.7439 (mmm-85) REVERT: E 374 GLN cc_start: 0.6514 (mm110) cc_final: 0.5806 (mm-40) REVERT: E 387 LYS cc_start: 0.8418 (mppt) cc_final: 0.8182 (mtmm) REVERT: E 398 ARG cc_start: 0.8436 (tpp-160) cc_final: 0.8101 (tpp-160) REVERT: E 412 LYS cc_start: 0.7474 (mttt) cc_final: 0.7030 (mttp) REVERT: E 415 LEU cc_start: 0.8530 (tp) cc_final: 0.8244 (tt) REVERT: E 425 MET cc_start: 0.7535 (ttp) cc_final: 0.7059 (ttp) REVERT: E 438 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7313 (mt) REVERT: E 481 THR cc_start: 0.8383 (m) cc_final: 0.7815 (p) REVERT: E 501 GLU cc_start: 0.7132 (tt0) cc_final: 0.6560 (tt0) REVERT: E 503 CYS cc_start: 0.7557 (p) cc_final: 0.7013 (m) REVERT: E 511 ILE cc_start: 0.8524 (mt) cc_final: 0.8192 (tt) REVERT: F 72 PHE cc_start: 0.8503 (t80) cc_final: 0.7670 (t80) REVERT: F 135 LYS cc_start: 0.8473 (tptm) cc_final: 0.8264 (tppt) REVERT: F 168 VAL cc_start: 0.9126 (t) cc_final: 0.8840 (p) REVERT: F 170 MET cc_start: 0.7808 (ttt) cc_final: 0.7515 (ptp) REVERT: F 171 ASN cc_start: 0.7550 (m-40) cc_final: 0.7259 (p0) REVERT: F 179 THR cc_start: 0.8678 (m) cc_final: 0.8356 (p) REVERT: F 180 GLN cc_start: 0.8554 (mt0) cc_final: 0.8089 (mt0) REVERT: F 181 SER cc_start: 0.9052 (OUTLIER) cc_final: 0.8770 (p) REVERT: F 185 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7951 (ptmm) REVERT: F 201 TYR cc_start: 0.7886 (m-80) cc_final: 0.7288 (m-80) REVERT: F 221 GLN cc_start: 0.7876 (tp40) cc_final: 0.7621 (tp40) REVERT: F 243 LYS cc_start: 0.8591 (mttt) cc_final: 0.8309 (mttt) REVERT: F 253 PHE cc_start: 0.7551 (t80) cc_final: 0.7038 (t80) REVERT: F 272 MET cc_start: 0.7269 (tpp) cc_final: 0.6918 (tpp) REVERT: F 281 MET cc_start: 0.6917 (ttm) cc_final: 0.6505 (ttm) REVERT: F 304 ARG cc_start: 0.7335 (mtt180) cc_final: 0.6695 (mtt180) REVERT: F 425 MET cc_start: 0.7615 (ttp) cc_final: 0.7320 (ttp) REVERT: F 426 ASP cc_start: 0.8400 (t0) cc_final: 0.8144 (t70) REVERT: F 443 LYS cc_start: 0.7797 (mtpp) cc_final: 0.7462 (mttm) REVERT: F 503 CYS cc_start: 0.7518 (p) cc_final: 0.6886 (m) REVERT: G 41 MET cc_start: 0.7880 (mmm) cc_final: 0.7639 (mmm) REVERT: G 64 GLU cc_start: 0.8488 (tt0) cc_final: 0.8067 (tt0) REVERT: G 72 PHE cc_start: 0.8712 (t80) cc_final: 0.7870 (t80) REVERT: G 89 ARG cc_start: 0.8831 (mmm-85) cc_final: 0.8415 (mmm-85) REVERT: G 102 ASP cc_start: 0.8121 (m-30) cc_final: 0.7790 (p0) REVERT: G 103 ASP cc_start: 0.7433 (p0) cc_final: 0.7067 (p0) REVERT: G 170 MET cc_start: 0.7433 (ptp) cc_final: 0.7042 (ptp) REVERT: G 180 GLN cc_start: 0.8557 (mt0) cc_final: 0.8167 (mt0) REVERT: G 185 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8131 (ptmt) REVERT: G 186 TYR cc_start: 0.7234 (m-80) cc_final: 0.6966 (m-80) REVERT: G 243 LYS cc_start: 0.8850 (mttt) cc_final: 0.8496 (mttt) REVERT: G 259 ASN cc_start: 0.7907 (t0) cc_final: 0.6836 (p0) REVERT: G 267 ARG cc_start: 0.8471 (tpp80) cc_final: 0.8077 (tpp80) REVERT: G 272 MET cc_start: 0.7578 (tpp) cc_final: 0.7106 (tpp) REVERT: G 282 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6677 (mt-10) REVERT: G 286 LYS cc_start: 0.8303 (mttm) cc_final: 0.7808 (tttm) REVERT: G 347 ASN cc_start: 0.7191 (t0) cc_final: 0.6874 (t0) REVERT: G 403 LYS cc_start: 0.7643 (mmtt) cc_final: 0.7134 (tptt) REVERT: G 414 ASP cc_start: 0.7829 (p0) cc_final: 0.7588 (t0) REVERT: G 417 ARG cc_start: 0.6213 (mtt-85) cc_final: 0.5728 (mtm-85) REVERT: G 425 MET cc_start: 0.7564 (ttp) cc_final: 0.7279 (ttp) REVERT: G 426 ASP cc_start: 0.8571 (t0) cc_final: 0.8347 (t70) REVERT: G 443 LYS cc_start: 0.7899 (mttp) cc_final: 0.7501 (mttp) REVERT: G 481 THR cc_start: 0.8265 (m) cc_final: 0.7706 (p) REVERT: G 501 GLU cc_start: 0.7162 (tt0) cc_final: 0.6504 (tt0) REVERT: G 503 CYS cc_start: 0.7538 (p) cc_final: 0.7000 (m) REVERT: H 41 MET cc_start: 0.7864 (tpp) cc_final: 0.7580 (tpp) REVERT: H 64 GLU cc_start: 0.8632 (tt0) cc_final: 0.7935 (tt0) REVERT: H 72 PHE cc_start: 0.8775 (t80) cc_final: 0.8063 (t80) REVERT: H 74 ARG cc_start: 0.8679 (mtm-85) cc_final: 0.8363 (ttm110) REVERT: H 89 ARG cc_start: 0.8759 (mmm-85) cc_final: 0.8491 (mmm160) REVERT: H 102 ASP cc_start: 0.8288 (m-30) cc_final: 0.7568 (p0) REVERT: H 121 LEU cc_start: 0.8256 (mt) cc_final: 0.7769 (mt) REVERT: H 141 ARG cc_start: 0.7678 (mtp85) cc_final: 0.7273 (ttm-80) REVERT: H 168 VAL cc_start: 0.9187 (t) cc_final: 0.8835 (p) REVERT: H 170 MET cc_start: 0.7792 (ttt) cc_final: 0.7296 (ptp) REVERT: H 171 ASN cc_start: 0.7912 (m-40) cc_final: 0.7414 (p0) REVERT: H 180 GLN cc_start: 0.8646 (mt0) cc_final: 0.8233 (mt0) REVERT: H 201 TYR cc_start: 0.8123 (m-80) cc_final: 0.7519 (m-80) REVERT: H 232 PHE cc_start: 0.7202 (m-10) cc_final: 0.6747 (m-80) REVERT: H 253 PHE cc_start: 0.7508 (t80) cc_final: 0.7139 (t80) REVERT: H 260 LEU cc_start: 0.8634 (mt) cc_final: 0.8153 (tt) REVERT: H 267 ARG cc_start: 0.8468 (tpp80) cc_final: 0.8073 (tpp80) REVERT: H 272 MET cc_start: 0.7557 (tpp) cc_final: 0.7308 (tpp) REVERT: H 282 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6640 (mt-10) REVERT: H 304 ARG cc_start: 0.8052 (mtt180) cc_final: 0.7386 (mtt180) REVERT: H 318 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8091 (mt-10) REVERT: H 340 ILE cc_start: 0.9156 (mt) cc_final: 0.8639 (mt) REVERT: H 341 LYS cc_start: 0.9274 (pttp) cc_final: 0.8935 (pmtt) REVERT: H 403 LYS cc_start: 0.7811 (mmtt) cc_final: 0.7138 (tptt) REVERT: H 443 LYS cc_start: 0.7767 (mtmm) cc_final: 0.7532 (mttp) REVERT: H 474 ARG cc_start: 0.7685 (ptm-80) cc_final: 0.7228 (ptm-80) REVERT: H 481 THR cc_start: 0.8448 (m) cc_final: 0.7961 (p) REVERT: H 482 VAL cc_start: 0.8626 (t) cc_final: 0.8070 (p) outliers start: 99 outliers final: 64 residues processed: 1008 average time/residue: 0.4942 time to fit residues: 740.6705 Evaluate side-chains 1050 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 973 time to evaluate : 3.220 ------------------------------------------------------------------------------- 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 265 ASP Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 420 HIS Chi-restraints excluded: chain A residue 488 GLU 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 147 LEU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 308 ILE 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 147 LEU 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 161 TYR Chi-restraints excluded: chain D residue 168 VAL 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 284 THR Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain D residue 438 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 438 LEU Chi-restraints excluded: chain E residue 474 ARG Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 504 VAL 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 379 VAL 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 504 VAL Chi-restraints excluded: chain F residue 513 GLU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 185 LYS Chi-restraints excluded: chain G residue 254 LEU 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 488 GLU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 52 optimal weight: 0.0970 chunk 211 optimal weight: 0.8980 chunk 356 optimal weight: 10.0000 chunk 235 optimal weight: 70.0000 chunk 84 optimal weight: 2.9990 chunk 236 optimal weight: 7.9990 chunk 349 optimal weight: 1.9990 chunk 95 optimal weight: 20.0000 chunk 40 optimal weight: 0.0050 chunk 278 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 HIS ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN C 315 HIS C 374 GLN ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.183938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.142994 restraints weight = 53542.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.148161 restraints weight = 29708.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.151585 restraints weight = 19189.124| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 30368 Z= 0.136 Angle : 0.680 15.660 41088 Z= 0.344 Chirality : 0.048 0.246 4672 Planarity : 0.005 0.071 5352 Dihedral : 4.541 40.364 4058 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.71 % Allowed : 20.87 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3720 helix: 0.14 (0.15), residues: 1152 sheet: -0.20 (0.21), residues: 720 loop : 0.23 (0.15), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 87 HIS 0.007 0.001 HIS B 514 PHE 0.018 0.001 PHE E 325 TYR 0.035 0.002 TYR A 224 ARG 0.010 0.001 ARG E 457 Details of bonding type rmsd hydrogen bonds : bond 0.04359 ( 1087) hydrogen bonds : angle 5.14809 ( 2733) covalent geometry : bond 0.00300 (30368) covalent geometry : angle 0.68036 (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 1064 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 974 time to evaluate : 3.098 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: A 41 MET cc_start: 0.8501 (mmm) cc_final: 0.8092 (mmm) REVERT: A 72 PHE cc_start: 0.8547 (t80) cc_final: 0.8093 (t80) REVERT: A 135 LYS cc_start: 0.8361 (tptp) cc_final: 0.8104 (tppt) REVERT: A 168 VAL cc_start: 0.9120 (t) cc_final: 0.8885 (p) REVERT: A 185 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8154 (ptmt) REVERT: A 197 ASN cc_start: 0.7135 (t0) cc_final: 0.6862 (t0) REVERT: A 201 TYR cc_start: 0.7888 (m-80) cc_final: 0.7595 (m-80) REVERT: A 228 HIS cc_start: 0.6420 (m90) cc_final: 0.5940 (t70) REVERT: A 271 HIS cc_start: 0.7426 (t70) cc_final: 0.6976 (t70) REVERT: A 280 ILE cc_start: 0.6743 (mt) cc_final: 0.6449 (mm) REVERT: A 282 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7122 (mt-10) REVERT: A 300 GLU cc_start: 0.4148 (OUTLIER) cc_final: 0.3553 (mp0) REVERT: A 327 TYR cc_start: 0.7531 (m-80) cc_final: 0.7128 (m-80) REVERT: A 335 MET cc_start: 0.3278 (mtt) cc_final: 0.2522 (mtt) REVERT: A 341 LYS cc_start: 0.9085 (tttt) cc_final: 0.8726 (ttpp) REVERT: A 387 LYS cc_start: 0.8352 (mppt) cc_final: 0.7993 (ptpp) REVERT: A 403 LYS cc_start: 0.7445 (mmtm) cc_final: 0.7102 (tptt) REVERT: A 420 HIS cc_start: 0.5960 (OUTLIER) cc_final: 0.5321 (m90) REVERT: A 425 MET cc_start: 0.7533 (ttp) cc_final: 0.7283 (ttp) REVERT: A 443 LYS cc_start: 0.7878 (mttp) cc_final: 0.7488 (mptt) REVERT: A 479 LYS cc_start: 0.7310 (mttt) cc_final: 0.6872 (mttm) REVERT: A 481 THR cc_start: 0.8527 (m) cc_final: 0.8120 (p) REVERT: A 482 VAL cc_start: 0.8728 (t) cc_final: 0.8250 (p) REVERT: A 499 VAL cc_start: 0.8486 (t) cc_final: 0.8247 (m) REVERT: B 41 MET cc_start: 0.8699 (mmm) cc_final: 0.8199 (mmm) REVERT: B 45 LEU cc_start: 0.9211 (mt) cc_final: 0.8946 (mt) REVERT: B 64 GLU cc_start: 0.8636 (tt0) cc_final: 0.8159 (tt0) REVERT: B 65 MET cc_start: 0.7845 (mmm) cc_final: 0.7618 (mmm) REVERT: B 72 PHE cc_start: 0.8514 (t80) cc_final: 0.8057 (t80) REVERT: B 74 ARG cc_start: 0.8119 (ttm110) cc_final: 0.7753 (ptp-170) REVERT: B 94 GLN cc_start: 0.7657 (mm-40) cc_final: 0.7128 (mm-40) REVERT: B 141 ARG cc_start: 0.7439 (ttm-80) cc_final: 0.7205 (ttt-90) REVERT: B 147 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8348 (tp) REVERT: B 168 VAL cc_start: 0.9133 (t) cc_final: 0.8882 (p) REVERT: B 179 THR cc_start: 0.8443 (m) cc_final: 0.8161 (p) REVERT: B 201 TYR cc_start: 0.7710 (m-80) cc_final: 0.7222 (t80) REVERT: B 232 PHE cc_start: 0.6781 (m-10) cc_final: 0.6334 (m-80) REVERT: B 243 LYS cc_start: 0.8390 (mttt) cc_final: 0.8098 (mttt) REVERT: B 265 ASP cc_start: 0.6607 (t0) cc_final: 0.6355 (t70) REVERT: B 282 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6635 (mt-10) REVERT: B 304 ARG cc_start: 0.7931 (mmt180) cc_final: 0.7376 (mmm-85) REVERT: B 318 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8057 (mt-10) REVERT: B 340 ILE cc_start: 0.9067 (mt) cc_final: 0.8646 (mt) REVERT: B 341 LYS cc_start: 0.9193 (pttt) cc_final: 0.8909 (ptpp) REVERT: B 374 GLN cc_start: 0.6297 (OUTLIER) cc_final: 0.4818 (mm110) REVERT: B 398 ARG cc_start: 0.8575 (tpp-160) cc_final: 0.8234 (tpp-160) REVERT: B 425 MET cc_start: 0.7422 (ttp) cc_final: 0.7126 (ttp) REVERT: B 426 ASP cc_start: 0.8402 (t0) cc_final: 0.7968 (t0) REVERT: B 450 LYS cc_start: 0.8277 (ttpp) cc_final: 0.8038 (ttpp) REVERT: B 479 LYS cc_start: 0.7147 (mttt) cc_final: 0.6855 (mtmm) REVERT: B 481 THR cc_start: 0.8360 (m) cc_final: 0.7920 (p) REVERT: B 491 THR cc_start: 0.8088 (m) cc_final: 0.7820 (t) REVERT: B 503 CYS cc_start: 0.7614 (p) cc_final: 0.7149 (m) REVERT: C 41 MET cc_start: 0.8506 (mmm) cc_final: 0.8223 (mmm) REVERT: C 54 ASP cc_start: 0.7743 (t70) cc_final: 0.7502 (t0) REVERT: C 64 GLU cc_start: 0.8492 (tt0) cc_final: 0.7900 (tt0) REVERT: C 72 PHE cc_start: 0.8636 (t80) cc_final: 0.8079 (t80) REVERT: C 74 ARG cc_start: 0.8392 (ttm110) cc_final: 0.7835 (ptp-170) REVERT: C 115 LYS cc_start: 0.8154 (mtmm) cc_final: 0.7449 (mmmt) REVERT: C 135 LYS cc_start: 0.8044 (ttmt) cc_final: 0.7578 (mtpp) REVERT: C 170 MET cc_start: 0.7623 (ptp) cc_final: 0.7185 (pmm) REVERT: C 179 THR cc_start: 0.8348 (m) cc_final: 0.8002 (p) REVERT: C 181 SER cc_start: 0.8742 (OUTLIER) cc_final: 0.8423 (p) REVERT: C 184 LYS cc_start: 0.8552 (mttp) cc_final: 0.8256 (mmtm) REVERT: C 200 ARG cc_start: 0.6815 (ttp-110) cc_final: 0.6439 (ttp-170) REVERT: C 232 PHE cc_start: 0.7195 (m-10) cc_final: 0.6864 (m-80) REVERT: C 282 GLU cc_start: 0.6935 (mt-10) cc_final: 0.6288 (mt-10) REVERT: C 283 LEU cc_start: 0.7668 (mt) cc_final: 0.7278 (mm) REVERT: C 357 GLU cc_start: 0.7471 (mm-30) cc_final: 0.6790 (tp30) REVERT: C 415 LEU cc_start: 0.8784 (tp) cc_final: 0.8492 (tt) REVERT: C 425 MET cc_start: 0.7641 (ttp) cc_final: 0.7293 (ttp) REVERT: C 426 ASP cc_start: 0.8486 (t0) cc_final: 0.8149 (t70) REVERT: C 443 LYS cc_start: 0.7863 (mttm) cc_final: 0.7567 (mttm) REVERT: C 450 LYS cc_start: 0.8347 (ttpp) cc_final: 0.8096 (ttpp) REVERT: C 479 LYS cc_start: 0.7055 (mttt) cc_final: 0.6565 (mttm) REVERT: C 481 THR cc_start: 0.8029 (m) cc_final: 0.7627 (p) REVERT: C 499 VAL cc_start: 0.8502 (t) cc_final: 0.8238 (m) REVERT: C 503 CYS cc_start: 0.7400 (p) cc_final: 0.7011 (m) REVERT: C 511 ILE cc_start: 0.8411 (mt) cc_final: 0.8181 (tt) REVERT: D 64 GLU cc_start: 0.8548 (tt0) cc_final: 0.7784 (tt0) REVERT: D 72 PHE cc_start: 0.8640 (t80) cc_final: 0.8107 (t80) REVERT: D 74 ARG cc_start: 0.8353 (ttm110) cc_final: 0.7869 (ptp-170) REVERT: D 94 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7022 (mm-40) REVERT: D 185 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8124 (ptmt) REVERT: D 201 TYR cc_start: 0.7971 (m-80) cc_final: 0.7371 (m-80) REVERT: D 232 PHE cc_start: 0.7135 (m-10) cc_final: 0.6855 (m-80) REVERT: D 243 LYS cc_start: 0.8665 (mttt) cc_final: 0.8391 (mttt) REVERT: D 272 MET cc_start: 0.7476 (tpp) cc_final: 0.7153 (tpp) REVERT: D 286 LYS cc_start: 0.8542 (mttm) cc_final: 0.8278 (tttm) REVERT: D 304 ARG cc_start: 0.7675 (mtp180) cc_final: 0.7293 (mtt180) REVERT: D 387 LYS cc_start: 0.8437 (mttt) cc_final: 0.8168 (mttt) REVERT: D 403 LYS cc_start: 0.7825 (mmtt) cc_final: 0.7151 (tptt) REVERT: D 415 LEU cc_start: 0.8617 (tp) cc_final: 0.7910 (tp) REVERT: D 425 MET cc_start: 0.7353 (tpp) cc_final: 0.6852 (tpp) REVERT: D 426 ASP cc_start: 0.8353 (t0) cc_final: 0.7975 (t0) REVERT: D 438 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7590 (mt) REVERT: D 479 LYS cc_start: 0.7263 (mttt) cc_final: 0.6937 (mttm) REVERT: D 481 THR cc_start: 0.8322 (m) cc_final: 0.7963 (p) REVERT: D 491 THR cc_start: 0.8286 (m) cc_final: 0.7930 (t) REVERT: D 499 VAL cc_start: 0.8483 (t) cc_final: 0.8159 (p) REVERT: E 64 GLU cc_start: 0.8641 (tt0) cc_final: 0.8028 (tt0) REVERT: E 72 PHE cc_start: 0.8615 (t80) cc_final: 0.7911 (t80) REVERT: E 89 ARG cc_start: 0.8580 (mmm-85) cc_final: 0.8321 (mmp80) REVERT: E 129 MET cc_start: 0.6976 (mtm) cc_final: 0.6355 (mtm) REVERT: E 135 LYS cc_start: 0.7953 (ttmt) cc_final: 0.7671 (tptm) REVERT: E 147 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8175 (tp) REVERT: E 168 VAL cc_start: 0.9016 (t) cc_final: 0.8686 (p) REVERT: E 180 GLN cc_start: 0.8455 (mt0) cc_final: 0.7876 (mt0) REVERT: E 201 TYR cc_start: 0.7868 (m-80) cc_final: 0.7628 (m-80) REVERT: E 243 LYS cc_start: 0.8409 (mttt) cc_final: 0.8136 (mttt) REVERT: E 267 ARG cc_start: 0.8391 (tpt-90) cc_final: 0.8069 (tpp80) REVERT: E 281 MET cc_start: 0.6958 (ttm) cc_final: 0.6734 (ttm) REVERT: E 283 LEU cc_start: 0.8067 (mt) cc_final: 0.7864 (mm) REVERT: E 304 ARG cc_start: 0.8094 (ttt180) cc_final: 0.7439 (mmm-85) REVERT: E 387 LYS cc_start: 0.8443 (mppt) cc_final: 0.8216 (mtmm) REVERT: E 398 ARG cc_start: 0.8420 (tpp-160) cc_final: 0.8079 (tpp-160) REVERT: E 415 LEU cc_start: 0.8538 (tp) cc_final: 0.8192 (tt) REVERT: E 419 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7863 (tm-30) REVERT: E 425 MET cc_start: 0.7526 (ttp) cc_final: 0.7027 (ttp) REVERT: E 438 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7750 (mm) REVERT: E 444 LYS cc_start: 0.6426 (OUTLIER) cc_final: 0.6086 (ttmm) REVERT: E 481 THR cc_start: 0.8188 (m) cc_final: 0.7678 (p) REVERT: E 501 GLU cc_start: 0.7127 (tt0) cc_final: 0.6564 (tt0) REVERT: E 503 CYS cc_start: 0.7551 (p) cc_final: 0.6997 (m) REVERT: E 511 ILE cc_start: 0.8520 (mt) cc_final: 0.8206 (tt) REVERT: F 72 PHE cc_start: 0.8541 (t80) cc_final: 0.7726 (t80) REVERT: F 121 LEU cc_start: 0.8094 (mt) cc_final: 0.7549 (mt) REVERT: F 168 VAL cc_start: 0.9130 (t) cc_final: 0.8852 (p) REVERT: F 170 MET cc_start: 0.7773 (ttt) cc_final: 0.7561 (ptp) REVERT: F 171 ASN cc_start: 0.7498 (m-40) cc_final: 0.7269 (p0) REVERT: F 179 THR cc_start: 0.8650 (m) cc_final: 0.8344 (p) REVERT: F 180 GLN cc_start: 0.8547 (mt0) cc_final: 0.8083 (mt0) REVERT: F 181 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8760 (p) REVERT: F 185 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7935 (ptmm) REVERT: F 196 PHE cc_start: 0.6982 (p90) cc_final: 0.6494 (p90) REVERT: F 201 TYR cc_start: 0.7937 (m-80) cc_final: 0.7317 (m-80) REVERT: F 221 GLN cc_start: 0.7834 (tp40) cc_final: 0.7592 (tp40) REVERT: F 243 LYS cc_start: 0.8557 (mttt) cc_final: 0.8289 (mttt) REVERT: F 253 PHE cc_start: 0.7506 (t80) cc_final: 0.7017 (t80) REVERT: F 267 ARG cc_start: 0.8156 (ttt180) cc_final: 0.7700 (tpt-90) REVERT: F 272 MET cc_start: 0.7259 (tpp) cc_final: 0.6878 (tpp) REVERT: F 281 MET cc_start: 0.6903 (ttm) cc_final: 0.6522 (ttm) REVERT: F 304 ARG cc_start: 0.7449 (mtt180) cc_final: 0.6986 (mtt90) REVERT: F 425 MET cc_start: 0.7595 (ttp) cc_final: 0.7290 (ttp) REVERT: F 426 ASP cc_start: 0.8401 (t0) cc_final: 0.8154 (t70) REVERT: F 443 LYS cc_start: 0.7804 (mtpp) cc_final: 0.7455 (mttm) REVERT: F 503 CYS cc_start: 0.7606 (p) cc_final: 0.6995 (m) REVERT: G 41 MET cc_start: 0.7896 (mmm) cc_final: 0.7659 (mmm) REVERT: G 64 GLU cc_start: 0.8500 (tt0) cc_final: 0.8116 (tt0) REVERT: G 72 PHE cc_start: 0.8733 (t80) cc_final: 0.7912 (t80) REVERT: G 89 ARG cc_start: 0.8793 (mmm-85) cc_final: 0.8418 (mmm-85) REVERT: G 102 ASP cc_start: 0.8087 (m-30) cc_final: 0.7783 (p0) REVERT: G 103 ASP cc_start: 0.7398 (p0) cc_final: 0.7064 (p0) REVERT: G 170 MET cc_start: 0.7435 (ptp) cc_final: 0.7028 (ptp) REVERT: G 180 GLN cc_start: 0.8543 (mt0) cc_final: 0.8141 (mt0) REVERT: G 185 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8161 (ptmt) REVERT: G 186 TYR cc_start: 0.7250 (m-80) cc_final: 0.6971 (m-80) REVERT: G 243 LYS cc_start: 0.8846 (mttt) cc_final: 0.8545 (mttt) REVERT: G 267 ARG cc_start: 0.8442 (tpp80) cc_final: 0.8036 (tpp80) REVERT: G 272 MET cc_start: 0.7555 (tpp) cc_final: 0.7073 (tpp) REVERT: G 282 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6707 (mt-10) REVERT: G 286 LYS cc_start: 0.8291 (mttm) cc_final: 0.7811 (tttm) REVERT: G 347 ASN cc_start: 0.7191 (t0) cc_final: 0.6884 (t0) REVERT: G 403 LYS cc_start: 0.7454 (mmtt) cc_final: 0.7122 (tptt) REVERT: G 414 ASP cc_start: 0.7839 (p0) cc_final: 0.7552 (t0) REVERT: G 417 ARG cc_start: 0.6191 (mtt-85) cc_final: 0.5797 (mtm-85) REVERT: G 425 MET cc_start: 0.7552 (ttp) cc_final: 0.7276 (ttp) REVERT: G 426 ASP cc_start: 0.8559 (t0) cc_final: 0.8346 (t70) REVERT: G 481 THR cc_start: 0.8280 (m) cc_final: 0.7722 (p) REVERT: G 501 GLU cc_start: 0.7153 (tt0) cc_final: 0.6514 (tt0) REVERT: G 503 CYS cc_start: 0.7441 (p) cc_final: 0.6892 (m) REVERT: H 41 MET cc_start: 0.7858 (tpp) cc_final: 0.7575 (tpp) REVERT: H 64 GLU cc_start: 0.8640 (tt0) cc_final: 0.7944 (tt0) REVERT: H 72 PHE cc_start: 0.8785 (t80) cc_final: 0.8068 (t80) REVERT: H 74 ARG cc_start: 0.8681 (mtm-85) cc_final: 0.8362 (ttm110) REVERT: H 89 ARG cc_start: 0.8759 (mmm-85) cc_final: 0.8400 (mmm-85) REVERT: H 102 ASP cc_start: 0.8278 (m-30) cc_final: 0.7592 (p0) REVERT: H 129 MET cc_start: 0.7478 (mtm) cc_final: 0.7272 (mtm) REVERT: H 135 LYS cc_start: 0.8638 (tptp) cc_final: 0.8385 (tppt) REVERT: H 141 ARG cc_start: 0.7706 (mtp85) cc_final: 0.7304 (ttm-80) REVERT: H 168 VAL cc_start: 0.9196 (t) cc_final: 0.8819 (p) REVERT: H 170 MET cc_start: 0.7807 (ttt) cc_final: 0.7337 (ptp) REVERT: H 171 ASN cc_start: 0.7910 (m-40) cc_final: 0.7436 (p0) REVERT: H 180 GLN cc_start: 0.8597 (mt0) cc_final: 0.8133 (mt0) REVERT: H 181 SER cc_start: 0.8777 (OUTLIER) cc_final: 0.8490 (p) REVERT: H 185 LYS cc_start: 0.8519 (ptmt) cc_final: 0.8074 (ptmt) REVERT: H 201 TYR cc_start: 0.8123 (m-80) cc_final: 0.7510 (m-80) REVERT: H 232 PHE cc_start: 0.7193 (m-10) cc_final: 0.6736 (m-80) REVERT: H 260 LEU cc_start: 0.8626 (mt) cc_final: 0.8144 (tt) REVERT: H 267 ARG cc_start: 0.8411 (tpp80) cc_final: 0.8057 (tpp80) REVERT: H 272 MET cc_start: 0.7523 (tpp) cc_final: 0.7288 (tpp) REVERT: H 282 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6693 (mt-10) REVERT: H 304 ARG cc_start: 0.8048 (mtt180) cc_final: 0.7368 (mtt180) REVERT: H 318 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8090 (mt-10) REVERT: H 340 ILE cc_start: 0.9147 (mt) cc_final: 0.8625 (mt) REVERT: H 341 LYS cc_start: 0.9294 (pttp) cc_final: 0.8947 (pmtt) REVERT: H 398 ARG cc_start: 0.8592 (tpp-160) cc_final: 0.8243 (tpp-160) REVERT: H 403 LYS cc_start: 0.7762 (mmtt) cc_final: 0.7035 (tptt) REVERT: H 449 GLN cc_start: 0.7977 (tt0) cc_final: 0.7771 (tt0) REVERT: H 452 ILE cc_start: 0.8533 (mt) cc_final: 0.8252 (tp) REVERT: H 474 ARG cc_start: 0.7676 (ptm-80) cc_final: 0.7216 (ptm-80) REVERT: H 481 THR cc_start: 0.8440 (m) cc_final: 0.7958 (p) REVERT: H 482 VAL cc_start: 0.8629 (t) cc_final: 0.8078 (p) REVERT: H 511 ILE cc_start: 0.8558 (mt) cc_final: 0.8238 (tt) outliers start: 90 outliers final: 63 residues processed: 1007 average time/residue: 0.4875 time to fit residues: 734.2875 Evaluate side-chains 1047 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 969 time to evaluate : 3.934 ------------------------------------------------------------------------------- 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 265 ASP Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 420 HIS Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 119 VAL 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 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 C residue 147 LEU 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 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 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 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 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 379 VAL Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 444 LYS Chi-restraints excluded: chain E residue 474 ARG Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 504 VAL 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 379 VAL 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 504 VAL Chi-restraints excluded: chain F residue 513 GLU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 185 LYS Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 284 THR 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 400 LEU Chi-restraints excluded: chain G residue 488 GLU 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 281 MET 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 513 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 283 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 352 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 188 optimal weight: 40.0000 chunk 230 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 chunk 243 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN C 221 GLN C 374 GLN ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 GLN E 374 GLN ** G 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.183393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.142177 restraints weight = 54163.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.147473 restraints weight = 29730.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.150934 restraints weight = 19077.567| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 30368 Z= 0.147 Angle : 0.695 15.774 41088 Z= 0.354 Chirality : 0.048 0.269 4672 Planarity : 0.005 0.065 5352 Dihedral : 4.581 40.659 4058 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.77 % Allowed : 21.05 % Favored : 76.17 % 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: 0.09 (0.14), residues: 3720 helix: 0.16 (0.16), residues: 1152 sheet: -0.06 (0.20), residues: 784 loop : 0.25 (0.16), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 87 HIS 0.019 0.001 HIS A 420 PHE 0.047 0.002 PHE G 253 TYR 0.031 0.002 TYR E 224 ARG 0.009 0.001 ARG G 60 Details of bonding type rmsd hydrogen bonds : bond 0.04389 ( 1087) hydrogen bonds : angle 5.15718 ( 2733) covalent geometry : bond 0.00327 (30368) covalent geometry : angle 0.69490 (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 1065 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 973 time to evaluate : 3.297 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: A 41 MET cc_start: 0.8527 (mmm) cc_final: 0.8108 (mmm) REVERT: A 57 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7634 (mm-30) REVERT: A 72 PHE cc_start: 0.8577 (t80) cc_final: 0.8120 (t80) REVERT: A 89 ARG cc_start: 0.8694 (mmm-85) cc_final: 0.8359 (mtp85) REVERT: A 115 LYS cc_start: 0.8029 (ptpp) cc_final: 0.7503 (mmmt) REVERT: A 135 LYS cc_start: 0.8453 (tptp) cc_final: 0.8138 (tppt) REVERT: A 168 VAL cc_start: 0.9102 (t) cc_final: 0.8862 (p) REVERT: A 185 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8129 (ptmt) REVERT: A 197 ASN cc_start: 0.7131 (t0) cc_final: 0.6857 (t0) REVERT: A 201 TYR cc_start: 0.7913 (m-80) cc_final: 0.7604 (m-80) REVERT: A 228 HIS cc_start: 0.6478 (m90) cc_final: 0.6016 (t70) REVERT: A 260 LEU cc_start: 0.8521 (tp) cc_final: 0.8216 (tp) REVERT: A 280 ILE cc_start: 0.6836 (mt) cc_final: 0.6489 (mm) REVERT: A 282 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7159 (mt-10) REVERT: A 300 GLU cc_start: 0.4187 (OUTLIER) cc_final: 0.0347 (mt-10) REVERT: A 327 TYR cc_start: 0.7545 (m-80) cc_final: 0.7145 (m-80) REVERT: A 335 MET cc_start: 0.3283 (mtt) cc_final: 0.2589 (mtt) REVERT: A 341 LYS cc_start: 0.9090 (tttt) cc_final: 0.8732 (ttpp) REVERT: A 387 LYS cc_start: 0.8355 (mppt) cc_final: 0.8064 (mtmm) REVERT: A 415 LEU cc_start: 0.8660 (tp) cc_final: 0.8383 (tt) REVERT: A 420 HIS cc_start: 0.5948 (OUTLIER) cc_final: 0.5053 (m-70) REVERT: A 425 MET cc_start: 0.7513 (ttp) cc_final: 0.7156 (ttp) REVERT: A 443 LYS cc_start: 0.7888 (mttp) cc_final: 0.7496 (mptt) REVERT: A 479 LYS cc_start: 0.7320 (mttt) cc_final: 0.6885 (mttm) REVERT: A 481 THR cc_start: 0.8548 (m) cc_final: 0.8140 (p) REVERT: A 482 VAL cc_start: 0.8731 (t) cc_final: 0.8256 (p) REVERT: A 499 VAL cc_start: 0.8489 (t) cc_final: 0.8255 (m) REVERT: B 41 MET cc_start: 0.8674 (mmm) cc_final: 0.8185 (mmm) REVERT: B 45 LEU cc_start: 0.9207 (mt) cc_final: 0.8956 (mt) REVERT: B 64 GLU cc_start: 0.8596 (tt0) cc_final: 0.8155 (tt0) REVERT: B 65 MET cc_start: 0.7815 (mmm) cc_final: 0.7578 (mmm) REVERT: B 72 PHE cc_start: 0.8508 (t80) cc_final: 0.8047 (t80) REVERT: B 74 ARG cc_start: 0.8077 (ttm110) cc_final: 0.7739 (ptp-170) REVERT: B 94 GLN cc_start: 0.7653 (mm-40) cc_final: 0.7139 (mm-40) REVERT: B 141 ARG cc_start: 0.7457 (ttm-80) cc_final: 0.7238 (ttt-90) REVERT: B 168 VAL cc_start: 0.9132 (t) cc_final: 0.8883 (p) REVERT: B 179 THR cc_start: 0.8391 (m) cc_final: 0.8138 (p) REVERT: B 201 TYR cc_start: 0.7703 (m-80) cc_final: 0.7217 (t80) REVERT: B 232 PHE cc_start: 0.6788 (m-10) cc_final: 0.6339 (m-80) REVERT: B 243 LYS cc_start: 0.8386 (mttt) cc_final: 0.8096 (mttt) REVERT: B 260 LEU cc_start: 0.8498 (mt) cc_final: 0.7980 (tt) REVERT: B 265 ASP cc_start: 0.6713 (t0) cc_final: 0.6451 (t70) REVERT: B 281 MET cc_start: 0.6982 (OUTLIER) cc_final: 0.6691 (ttm) REVERT: B 282 GLU cc_start: 0.7445 (mt-10) cc_final: 0.6676 (mt-10) REVERT: B 304 ARG cc_start: 0.7937 (mmt180) cc_final: 0.7383 (mmm-85) REVERT: B 318 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8061 (mt-10) REVERT: B 340 ILE cc_start: 0.9067 (mt) cc_final: 0.8645 (mt) REVERT: B 374 GLN cc_start: 0.5895 (OUTLIER) cc_final: 0.4959 (mm110) REVERT: B 425 MET cc_start: 0.7393 (ttp) cc_final: 0.7070 (ttp) REVERT: B 426 ASP cc_start: 0.8379 (t0) cc_final: 0.7945 (t0) REVERT: B 450 LYS cc_start: 0.8332 (ttpp) cc_final: 0.8087 (ttpp) REVERT: B 479 LYS cc_start: 0.7175 (mttt) cc_final: 0.6897 (mtmm) REVERT: B 481 THR cc_start: 0.8188 (m) cc_final: 0.7764 (p) REVERT: B 491 THR cc_start: 0.8102 (m) cc_final: 0.7845 (t) REVERT: B 503 CYS cc_start: 0.7614 (p) cc_final: 0.7157 (m) REVERT: C 41 MET cc_start: 0.8463 (mmm) cc_final: 0.8209 (mmm) REVERT: C 64 GLU cc_start: 0.8483 (tt0) cc_final: 0.7919 (tt0) REVERT: C 72 PHE cc_start: 0.8680 (t80) cc_final: 0.8132 (t80) REVERT: C 74 ARG cc_start: 0.8381 (ttm110) cc_final: 0.7817 (ptp-170) REVERT: C 135 LYS cc_start: 0.8086 (ttmt) cc_final: 0.7626 (mtpp) REVERT: C 170 MET cc_start: 0.7424 (ptp) cc_final: 0.7168 (pmm) REVERT: C 181 SER cc_start: 0.8764 (OUTLIER) cc_final: 0.8433 (p) REVERT: C 184 LYS cc_start: 0.8515 (mttp) cc_final: 0.8215 (mmtm) REVERT: C 200 ARG cc_start: 0.6861 (ttp-110) cc_final: 0.6572 (ttp-170) REVERT: C 232 PHE cc_start: 0.7238 (m-10) cc_final: 0.6930 (m-80) REVERT: C 282 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6291 (mt-10) REVERT: C 283 LEU cc_start: 0.7672 (mt) cc_final: 0.7286 (mm) REVERT: C 304 ARG cc_start: 0.8101 (mmt180) cc_final: 0.7411 (mpt-90) REVERT: C 374 GLN cc_start: 0.6140 (OUTLIER) cc_final: 0.4746 (mm110) REVERT: C 415 LEU cc_start: 0.8786 (tp) cc_final: 0.8448 (tt) REVERT: C 425 MET cc_start: 0.7655 (ttp) cc_final: 0.7304 (ttp) REVERT: C 426 ASP cc_start: 0.8491 (t0) cc_final: 0.8161 (t70) REVERT: C 443 LYS cc_start: 0.7862 (mttm) cc_final: 0.7555 (mttm) REVERT: C 448 PHE cc_start: 0.8070 (t80) cc_final: 0.7461 (t80) REVERT: C 450 LYS cc_start: 0.8352 (ttpp) cc_final: 0.8095 (ttpp) REVERT: C 479 LYS cc_start: 0.7049 (mttt) cc_final: 0.6697 (mttm) REVERT: C 481 THR cc_start: 0.8043 (m) cc_final: 0.7630 (p) REVERT: C 499 VAL cc_start: 0.8503 (t) cc_final: 0.8270 (m) REVERT: C 503 CYS cc_start: 0.7410 (p) cc_final: 0.7019 (m) REVERT: C 511 ILE cc_start: 0.8425 (mt) cc_final: 0.8199 (tt) REVERT: D 64 GLU cc_start: 0.8521 (tt0) cc_final: 0.7709 (tt0) REVERT: D 72 PHE cc_start: 0.8647 (t80) cc_final: 0.8107 (t80) REVERT: D 74 ARG cc_start: 0.8330 (ttm110) cc_final: 0.7843 (ptp-170) REVERT: D 94 GLN cc_start: 0.7612 (mm-40) cc_final: 0.7033 (mm-40) REVERT: D 170 MET cc_start: 0.7762 (ptp) cc_final: 0.7555 (pmm) REVERT: D 185 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8159 (ptmt) REVERT: D 201 TYR cc_start: 0.7968 (m-80) cc_final: 0.7370 (m-80) REVERT: D 232 PHE cc_start: 0.7230 (m-10) cc_final: 0.6992 (m-80) REVERT: D 243 LYS cc_start: 0.8590 (mttt) cc_final: 0.8359 (mttt) REVERT: D 260 LEU cc_start: 0.8619 (mt) cc_final: 0.8248 (tt) REVERT: D 272 MET cc_start: 0.7484 (tpp) cc_final: 0.7181 (tpp) REVERT: D 286 LYS cc_start: 0.8558 (mttm) cc_final: 0.8270 (tttm) REVERT: D 387 LYS cc_start: 0.8439 (mttt) cc_final: 0.8178 (mttt) REVERT: D 398 ARG cc_start: 0.8277 (tpp-160) cc_final: 0.7568 (tpt170) REVERT: D 403 LYS cc_start: 0.7831 (mmtt) cc_final: 0.7130 (tptt) REVERT: D 415 LEU cc_start: 0.8630 (tp) cc_final: 0.7906 (tp) REVERT: D 425 MET cc_start: 0.7350 (tpp) cc_final: 0.6835 (tpp) REVERT: D 426 ASP cc_start: 0.8367 (t0) cc_final: 0.8017 (t0) REVERT: D 438 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7618 (mt) REVERT: D 479 LYS cc_start: 0.7277 (mttt) cc_final: 0.6925 (mttm) REVERT: D 481 THR cc_start: 0.8314 (m) cc_final: 0.7941 (p) REVERT: D 491 THR cc_start: 0.8304 (m) cc_final: 0.7950 (t) REVERT: D 499 VAL cc_start: 0.8456 (t) cc_final: 0.8166 (p) REVERT: E 64 GLU cc_start: 0.8704 (tt0) cc_final: 0.8043 (tt0) REVERT: E 72 PHE cc_start: 0.8621 (t80) cc_final: 0.7944 (t80) REVERT: E 89 ARG cc_start: 0.8572 (mmm-85) cc_final: 0.8325 (mmp80) REVERT: E 129 MET cc_start: 0.6968 (mtm) cc_final: 0.6350 (mtm) REVERT: E 135 LYS cc_start: 0.7967 (ttmt) cc_final: 0.7691 (tptm) REVERT: E 147 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8143 (tp) REVERT: E 168 VAL cc_start: 0.8986 (t) cc_final: 0.8672 (p) REVERT: E 180 GLN cc_start: 0.8489 (mt0) cc_final: 0.7861 (mt0) REVERT: E 201 TYR cc_start: 0.7883 (m-80) cc_final: 0.7264 (m-80) REVERT: E 243 LYS cc_start: 0.8422 (mttt) cc_final: 0.8148 (mttt) REVERT: E 267 ARG cc_start: 0.8361 (tpt-90) cc_final: 0.8053 (tpp80) REVERT: E 281 MET cc_start: 0.6988 (ttm) cc_final: 0.6700 (ttm) REVERT: E 387 LYS cc_start: 0.8436 (mppt) cc_final: 0.8229 (mtmm) REVERT: E 398 ARG cc_start: 0.8412 (tpp-160) cc_final: 0.8073 (tpp-160) REVERT: E 415 LEU cc_start: 0.8538 (tp) cc_final: 0.8092 (tt) REVERT: E 419 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7891 (tm-30) REVERT: E 425 MET cc_start: 0.7491 (ttp) cc_final: 0.7017 (ttp) REVERT: E 438 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7744 (mm) REVERT: E 444 LYS cc_start: 0.6477 (OUTLIER) cc_final: 0.6127 (ttmm) REVERT: E 481 THR cc_start: 0.8194 (m) cc_final: 0.7681 (p) REVERT: E 501 GLU cc_start: 0.7151 (tt0) cc_final: 0.6578 (tt0) REVERT: E 503 CYS cc_start: 0.7556 (p) cc_final: 0.6988 (m) REVERT: F 72 PHE cc_start: 0.8552 (t80) cc_final: 0.7735 (t80) REVERT: F 121 LEU cc_start: 0.8105 (mt) cc_final: 0.7502 (mt) REVERT: F 168 VAL cc_start: 0.9122 (t) cc_final: 0.8850 (p) REVERT: F 170 MET cc_start: 0.7786 (ttt) cc_final: 0.7547 (ptp) REVERT: F 171 ASN cc_start: 0.7515 (m-40) cc_final: 0.7277 (p0) REVERT: F 179 THR cc_start: 0.8642 (m) cc_final: 0.8337 (p) REVERT: F 180 GLN cc_start: 0.8534 (mt0) cc_final: 0.8073 (mt0) REVERT: F 181 SER cc_start: 0.9053 (OUTLIER) cc_final: 0.8769 (p) REVERT: F 185 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7910 (ptmm) REVERT: F 196 PHE cc_start: 0.6963 (p90) cc_final: 0.6484 (p90) REVERT: F 201 TYR cc_start: 0.7985 (m-80) cc_final: 0.7363 (m-80) REVERT: F 243 LYS cc_start: 0.8551 (mttt) cc_final: 0.8261 (mttt) REVERT: F 253 PHE cc_start: 0.7494 (t80) cc_final: 0.7006 (t80) REVERT: F 267 ARG cc_start: 0.8180 (ttt180) cc_final: 0.7719 (tpt-90) REVERT: F 272 MET cc_start: 0.7269 (tpp) cc_final: 0.6889 (tpp) REVERT: F 281 MET cc_start: 0.6917 (ttm) cc_final: 0.6505 (ttm) REVERT: F 304 ARG cc_start: 0.7463 (mtt180) cc_final: 0.6941 (mtt90) REVERT: F 425 MET cc_start: 0.7590 (ttp) cc_final: 0.7280 (ttp) REVERT: F 426 ASP cc_start: 0.8408 (t0) cc_final: 0.8169 (t70) REVERT: F 443 LYS cc_start: 0.7828 (mtpp) cc_final: 0.7474 (mttm) REVERT: F 503 CYS cc_start: 0.7605 (p) cc_final: 0.7011 (m) REVERT: G 41 MET cc_start: 0.7895 (mmm) cc_final: 0.7651 (mmm) REVERT: G 64 GLU cc_start: 0.8600 (tt0) cc_final: 0.8226 (tt0) REVERT: G 72 PHE cc_start: 0.8727 (t80) cc_final: 0.7895 (t80) REVERT: G 89 ARG cc_start: 0.8787 (mmm-85) cc_final: 0.8425 (mmm-85) REVERT: G 102 ASP cc_start: 0.8091 (m-30) cc_final: 0.7804 (p0) REVERT: G 129 MET cc_start: 0.6943 (mtm) cc_final: 0.6575 (mmm) REVERT: G 170 MET cc_start: 0.7357 (ptp) cc_final: 0.6969 (ptp) REVERT: G 180 GLN cc_start: 0.8511 (mt0) cc_final: 0.8131 (mt0) REVERT: G 185 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8096 (ptmt) REVERT: G 186 TYR cc_start: 0.7191 (m-80) cc_final: 0.6923 (m-80) REVERT: G 243 LYS cc_start: 0.8844 (mttt) cc_final: 0.8541 (mttt) REVERT: G 259 ASN cc_start: 0.7599 (t0) cc_final: 0.7107 (p0) REVERT: G 267 ARG cc_start: 0.8398 (tpp80) cc_final: 0.7984 (tpp80) REVERT: G 272 MET cc_start: 0.7551 (tpp) cc_final: 0.7118 (tpp) REVERT: G 282 GLU cc_start: 0.7369 (mt-10) cc_final: 0.6753 (mt-10) REVERT: G 286 LYS cc_start: 0.8313 (mttm) cc_final: 0.7853 (tttm) REVERT: G 318 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8154 (mt-10) REVERT: G 326 LYS cc_start: 0.7824 (ptpt) cc_final: 0.7156 (mptt) REVERT: G 347 ASN cc_start: 0.7189 (t0) cc_final: 0.6920 (t0) REVERT: G 403 LYS cc_start: 0.7511 (mmtt) cc_final: 0.7012 (tptt) REVERT: G 414 ASP cc_start: 0.7813 (p0) cc_final: 0.7560 (t0) REVERT: G 417 ARG cc_start: 0.6196 (mtt-85) cc_final: 0.5811 (mtm-85) REVERT: G 425 MET cc_start: 0.7540 (ttp) cc_final: 0.7251 (ttp) REVERT: G 426 ASP cc_start: 0.8569 (t0) cc_final: 0.8364 (t70) REVERT: G 443 LYS cc_start: 0.7907 (mttp) cc_final: 0.7520 (mmtm) REVERT: G 481 THR cc_start: 0.8289 (m) cc_final: 0.7737 (p) REVERT: G 482 VAL cc_start: 0.8733 (t) cc_final: 0.8264 (p) REVERT: G 501 GLU cc_start: 0.7174 (tt0) cc_final: 0.6649 (tt0) REVERT: G 503 CYS cc_start: 0.7520 (p) cc_final: 0.6981 (m) REVERT: H 41 MET cc_start: 0.7855 (tpp) cc_final: 0.7576 (tpp) REVERT: H 64 GLU cc_start: 0.8623 (tt0) cc_final: 0.7947 (tt0) REVERT: H 72 PHE cc_start: 0.8791 (t80) cc_final: 0.8073 (t80) REVERT: H 74 ARG cc_start: 0.8683 (mtm-85) cc_final: 0.8361 (ttm110) REVERT: H 89 ARG cc_start: 0.8726 (mmm-85) cc_final: 0.8390 (mmm-85) REVERT: H 102 ASP cc_start: 0.8261 (m-30) cc_final: 0.7601 (p0) REVERT: H 129 MET cc_start: 0.7468 (mtm) cc_final: 0.7111 (mtm) REVERT: H 141 ARG cc_start: 0.7724 (mtp85) cc_final: 0.7290 (ttm-80) REVERT: H 168 VAL cc_start: 0.9189 (t) cc_final: 0.8832 (p) REVERT: H 171 ASN cc_start: 0.7872 (m-40) cc_final: 0.7407 (p0) REVERT: H 180 GLN cc_start: 0.8616 (mt0) cc_final: 0.8206 (mt0) REVERT: H 182 ILE cc_start: 0.9025 (pp) cc_final: 0.8780 (pp) REVERT: H 185 LYS cc_start: 0.8487 (ptmt) cc_final: 0.8130 (ptmt) REVERT: H 201 TYR cc_start: 0.8103 (m-80) cc_final: 0.7544 (m-80) REVERT: H 232 PHE cc_start: 0.7216 (m-10) cc_final: 0.6745 (m-80) REVERT: H 260 LEU cc_start: 0.8602 (mt) cc_final: 0.8111 (tt) REVERT: H 267 ARG cc_start: 0.8389 (tpp80) cc_final: 0.8013 (tpp80) REVERT: H 272 MET cc_start: 0.7536 (tpp) cc_final: 0.7301 (tpp) REVERT: H 282 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6842 (mt-10) REVERT: H 304 ARG cc_start: 0.8060 (mtt180) cc_final: 0.7377 (mtt180) REVERT: H 318 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8092 (mt-10) REVERT: H 398 ARG cc_start: 0.8598 (tpp-160) cc_final: 0.8241 (tpp-160) REVERT: H 403 LYS cc_start: 0.7737 (mmtt) cc_final: 0.7067 (tptt) REVERT: H 452 ILE cc_start: 0.8548 (mt) cc_final: 0.8262 (tp) REVERT: H 474 ARG cc_start: 0.7706 (ptm-80) cc_final: 0.7242 (ptm-80) REVERT: H 481 THR cc_start: 0.8453 (m) cc_final: 0.7963 (p) REVERT: H 482 VAL cc_start: 0.8637 (t) cc_final: 0.8090 (p) REVERT: H 511 ILE cc_start: 0.8568 (mt) cc_final: 0.8251 (tt) outliers start: 92 outliers final: 70 residues processed: 1010 average time/residue: 0.5982 time to fit residues: 909.1769 Evaluate side-chains 1055 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 970 time to evaluate : 3.504 ------------------------------------------------------------------------------- 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 265 ASP Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 420 HIS Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 513 GLU 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 180 GLN Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 281 MET 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 147 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 374 GLN 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 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 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 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 379 VAL Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 444 LYS Chi-restraints excluded: chain E residue 474 ARG Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 504 VAL 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 379 VAL 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 504 VAL Chi-restraints excluded: chain F residue 513 GLU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 185 LYS Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 284 THR 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 400 LEU Chi-restraints excluded: chain G residue 488 GLU 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 281 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 158 optimal weight: 0.0870 chunk 36 optimal weight: 2.9990 chunk 139 optimal weight: 0.0040 chunk 30 optimal weight: 0.7980 chunk 312 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 358 optimal weight: 4.9990 chunk 198 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 201 optimal weight: 0.3980 overall best weight: 0.4572 ------------------------------------------------------------------------------- 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** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 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 = 0.4390 r_free = 0.4390 target = 0.183082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.141630 restraints weight = 54006.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.147051 restraints weight = 29415.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.150592 restraints weight = 18738.326| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.255 30368 Z= 0.226 Angle : 0.851 59.196 41088 Z= 0.463 Chirality : 0.048 0.527 4672 Planarity : 0.006 0.160 5352 Dihedral : 4.576 40.629 4058 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.53 % Allowed : 21.60 % Favored : 75.87 % Cbeta Deviations : 0.06 % 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: 0.10 (0.14), residues: 3720 helix: 0.17 (0.16), residues: 1152 sheet: -0.12 (0.20), residues: 744 loop : 0.28 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.004 TRP G 334 HIS 0.016 0.001 HIS A 420 PHE 0.044 0.002 PHE G 253 TYR 0.030 0.002 TYR E 224 ARG 0.039 0.001 ARG G 247 Details of bonding type rmsd hydrogen bonds : bond 0.04369 ( 1087) hydrogen bonds : angle 5.15152 ( 2733) covalent geometry : bond 0.00480 (30368) covalent geometry : angle 0.85073 (41088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14834.62 seconds wall clock time: 260 minutes 21.67 seconds (15621.67 seconds total)