Starting phenix.real_space_refine on Tue Aug 26 21:34:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8szj_40918/08_2025/8szj_40918.cif Found real_map, /net/cci-nas-00/data/ceres_data/8szj_40918/08_2025/8szj_40918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8szj_40918/08_2025/8szj_40918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8szj_40918/08_2025/8szj_40918.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8szj_40918/08_2025/8szj_40918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8szj_40918/08_2025/8szj_40918.map" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6660 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 336 5.16 5 C 23064 2.51 5 N 6024 2.21 5 O 6768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36204 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3002 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 17, 'TRANS': 369} Chain: "B" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3002 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 17, 'TRANS': 369} Chain: "C" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3002 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 17, 'TRANS': 369} Chain: "D" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3002 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 17, 'TRANS': 369} Chain: "E" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3002 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 17, 'TRANS': 369} Chain: "G" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3002 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 17, 'TRANS': 369} Chain: "I" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3002 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 17, 'TRANS': 369} Chain: "K" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3002 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 17, 'TRANS': 369} Chain: "F" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3002 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 17, 'TRANS': 369} Chain: "H" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3002 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 17, 'TRANS': 369} Chain: "J" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3002 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 17, 'TRANS': 369} Chain: "L" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3002 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 17, 'TRANS': 369} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {'PO4': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {'PO4': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {'PO4': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {'PO4': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {'PO4': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {'PO4': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "I" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {'PO4': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {'PO4': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {'PO4': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {'PO4': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "J" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {'PO4': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "L" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {'PO4': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Time building chain proxies: 8.35, per 1000 atoms: 0.23 Number of scatterers: 36204 At special positions: 0 Unit cell: (163.75, 161.13, 241.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 336 16.00 P 12 15.00 O 6768 8.00 N 6024 7.00 C 23064 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: 2.03 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.2 microseconds 9240 Ramachandran restraints generated. 4620 Oldfield, 0 Emsley, 4620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8568 Finding SS restraints... Secondary structure from input PDB file: 243 helices and 33 sheets defined 53.8% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 139 through 148 removed outlier: 3.618A pdb=" N LEU A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 163 through 167 removed outlier: 3.893A pdb=" N THR A 166 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 175 through 188 Processing helix chain 'A' and resid 196 through 204 removed outlier: 3.945A pdb=" N VAL A 204 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 223 through 239 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.650A pdb=" N LYS A 255 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE A 256 " --> pdb=" O LEU A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 256' Processing helix chain 'A' and resid 288 through 301 Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 334 through 345 removed outlier: 3.878A pdb=" N ILE A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 366 Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 386 through 398 Processing helix chain 'A' and resid 406 through 419 Processing helix chain 'A' and resid 423 through 430 removed outlier: 3.792A pdb=" N VAL A 429 " --> pdb=" O GLU A 425 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET A 430 " --> pdb=" O SER A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 464 Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 468 through 476 Processing helix chain 'A' and resid 511 through 525 Processing helix chain 'B' and resid 140 through 148 Processing helix chain 'B' and resid 155 through 161 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 175 through 188 removed outlier: 3.784A pdb=" N GLN B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR B 188 " --> pdb=" O LEU B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 204 removed outlier: 3.577A pdb=" N VAL B 204 " --> pdb=" O PHE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 Processing helix chain 'B' and resid 223 through 239 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.526A pdb=" N LYS B 255 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE B 256 " --> pdb=" O LEU B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 256' Processing helix chain 'B' and resid 288 through 301 Processing helix chain 'B' and resid 301 through 306 Processing helix chain 'B' and resid 334 through 345 removed outlier: 3.730A pdb=" N ILE B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 367 removed outlier: 3.554A pdb=" N ASP B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 380 Processing helix chain 'B' and resid 386 through 398 Processing helix chain 'B' and resid 406 through 419 Processing helix chain 'B' and resid 423 through 430 removed outlier: 3.587A pdb=" N VAL B 429 " --> pdb=" O GLU B 425 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 464 Processing helix chain 'B' and resid 465 through 467 No H-bonds generated for 'chain 'B' and resid 465 through 467' Processing helix chain 'B' and resid 468 through 476 Processing helix chain 'B' and resid 511 through 525 Processing helix chain 'C' and resid 140 through 148 Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 175 through 188 removed outlier: 3.701A pdb=" N THR C 188 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 204 removed outlier: 4.043A pdb=" N VAL C 204 " --> pdb=" O PHE C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 223 through 239 Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.656A pdb=" N LYS C 255 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE C 256 " --> pdb=" O LEU C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 252 through 256' Processing helix chain 'C' and resid 288 through 301 Processing helix chain 'C' and resid 301 through 306 Processing helix chain 'C' and resid 334 through 345 removed outlier: 3.850A pdb=" N ILE C 345 " --> pdb=" O VAL C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 366 Processing helix chain 'C' and resid 375 through 380 Processing helix chain 'C' and resid 386 through 398 Processing helix chain 'C' and resid 406 through 419 Processing helix chain 'C' and resid 423 through 430 removed outlier: 3.780A pdb=" N VAL C 429 " --> pdb=" O GLU C 425 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET C 430 " --> pdb=" O SER C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 464 Processing helix chain 'C' and resid 465 through 467 No H-bonds generated for 'chain 'C' and resid 465 through 467' Processing helix chain 'C' and resid 468 through 476 Processing helix chain 'C' and resid 511 through 525 Processing helix chain 'D' and resid 140 through 148 Processing helix chain 'D' and resid 155 through 161 removed outlier: 3.898A pdb=" N PHE D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 175 through 188 removed outlier: 3.594A pdb=" N GLN D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 204 removed outlier: 3.772A pdb=" N VAL D 204 " --> pdb=" O PHE D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 216 removed outlier: 3.533A pdb=" N LEU D 211 " --> pdb=" O ASN D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 239 Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.636A pdb=" N PHE D 256 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 301 Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 334 through 345 removed outlier: 3.772A pdb=" N ILE D 345 " --> pdb=" O VAL D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 367 removed outlier: 3.787A pdb=" N ASP D 356 " --> pdb=" O ALA D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 380 Processing helix chain 'D' and resid 386 through 398 Processing helix chain 'D' and resid 406 through 419 Processing helix chain 'D' and resid 423 through 430 removed outlier: 3.630A pdb=" N VAL D 429 " --> pdb=" O GLU D 425 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET D 430 " --> pdb=" O SER D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 464 Processing helix chain 'D' and resid 465 through 467 No H-bonds generated for 'chain 'D' and resid 465 through 467' Processing helix chain 'D' and resid 468 through 476 Processing helix chain 'D' and resid 511 through 525 Processing helix chain 'E' and resid 140 through 148 Processing helix chain 'E' and resid 155 through 161 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 175 through 188 Processing helix chain 'E' and resid 196 through 204 removed outlier: 4.078A pdb=" N VAL E 204 " --> pdb=" O PHE E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 216 Processing helix chain 'E' and resid 223 through 239 Processing helix chain 'E' and resid 252 through 256 removed outlier: 3.512A pdb=" N LYS E 255 " --> pdb=" O GLN E 252 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE E 256 " --> pdb=" O LEU E 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 252 through 256' Processing helix chain 'E' and resid 288 through 301 Processing helix chain 'E' and resid 301 through 306 Processing helix chain 'E' and resid 334 through 343 Processing helix chain 'E' and resid 350 through 367 Processing helix chain 'E' and resid 375 through 380 Processing helix chain 'E' and resid 386 through 398 Processing helix chain 'E' and resid 406 through 419 Processing helix chain 'E' and resid 423 through 430 removed outlier: 3.708A pdb=" N VAL E 429 " --> pdb=" O GLU E 425 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET E 430 " --> pdb=" O SER E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 464 Processing helix chain 'E' and resid 465 through 467 No H-bonds generated for 'chain 'E' and resid 465 through 467' Processing helix chain 'E' and resid 468 through 476 Processing helix chain 'E' and resid 511 through 525 Processing helix chain 'G' and resid 140 through 148 Processing helix chain 'G' and resid 155 through 161 Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 175 through 188 removed outlier: 3.607A pdb=" N GLN G 187 " --> pdb=" O ARG G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 204 Processing helix chain 'G' and resid 207 through 216 Processing helix chain 'G' and resid 223 through 239 Processing helix chain 'G' and resid 252 through 256 removed outlier: 3.528A pdb=" N LYS G 255 " --> pdb=" O GLN G 252 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE G 256 " --> pdb=" O LEU G 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 252 through 256' Processing helix chain 'G' and resid 288 through 301 Processing helix chain 'G' and resid 301 through 306 Processing helix chain 'G' and resid 334 through 343 Processing helix chain 'G' and resid 350 through 367 removed outlier: 3.613A pdb=" N ASP G 356 " --> pdb=" O ALA G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 375 through 380 Processing helix chain 'G' and resid 386 through 399 Processing helix chain 'G' and resid 406 through 419 Processing helix chain 'G' and resid 423 through 430 removed outlier: 3.634A pdb=" N VAL G 429 " --> pdb=" O GLU G 425 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET G 430 " --> pdb=" O SER G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 449 through 464 Processing helix chain 'G' and resid 465 through 467 No H-bonds generated for 'chain 'G' and resid 465 through 467' Processing helix chain 'G' and resid 468 through 476 Processing helix chain 'G' and resid 511 through 525 Processing helix chain 'I' and resid 140 through 148 Processing helix chain 'I' and resid 155 through 161 removed outlier: 3.739A pdb=" N THR I 161 " --> pdb=" O HIS I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 167 removed outlier: 3.741A pdb=" N THR I 166 " --> pdb=" O LEU I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing helix chain 'I' and resid 175 through 188 removed outlier: 3.762A pdb=" N GLN I 187 " --> pdb=" O ARG I 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 204 removed outlier: 3.868A pdb=" N VAL I 204 " --> pdb=" O PHE I 200 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 216 Processing helix chain 'I' and resid 223 through 239 Processing helix chain 'I' and resid 252 through 256 removed outlier: 3.508A pdb=" N LYS I 255 " --> pdb=" O GLN I 252 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE I 256 " --> pdb=" O LEU I 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 252 through 256' Processing helix chain 'I' and resid 288 through 301 Processing helix chain 'I' and resid 301 through 306 Processing helix chain 'I' and resid 334 through 345 removed outlier: 3.789A pdb=" N ILE I 345 " --> pdb=" O VAL I 341 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 367 Processing helix chain 'I' and resid 375 through 380 Processing helix chain 'I' and resid 386 through 398 Processing helix chain 'I' and resid 406 through 419 Processing helix chain 'I' and resid 423 through 430 removed outlier: 3.875A pdb=" N VAL I 429 " --> pdb=" O GLU I 425 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET I 430 " --> pdb=" O SER I 426 " (cutoff:3.500A) Processing helix chain 'I' and resid 449 through 464 Processing helix chain 'I' and resid 465 through 467 No H-bonds generated for 'chain 'I' and resid 465 through 467' Processing helix chain 'I' and resid 468 through 476 Processing helix chain 'I' and resid 511 through 525 Processing helix chain 'K' and resid 140 through 148 Processing helix chain 'K' and resid 155 through 161 Processing helix chain 'K' and resid 172 through 174 No H-bonds generated for 'chain 'K' and resid 172 through 174' Processing helix chain 'K' and resid 175 through 188 Processing helix chain 'K' and resid 196 through 204 removed outlier: 3.725A pdb=" N PHE K 200 " --> pdb=" O ASP K 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 216 Processing helix chain 'K' and resid 223 through 239 Processing helix chain 'K' and resid 252 through 256 removed outlier: 3.633A pdb=" N PHE K 256 " --> pdb=" O LEU K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 288 through 301 Processing helix chain 'K' and resid 301 through 307 Processing helix chain 'K' and resid 334 through 344 Processing helix chain 'K' and resid 350 through 367 removed outlier: 3.604A pdb=" N ASP K 356 " --> pdb=" O ALA K 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 375 through 380 Processing helix chain 'K' and resid 386 through 399 Processing helix chain 'K' and resid 406 through 419 Processing helix chain 'K' and resid 423 through 430 Processing helix chain 'K' and resid 449 through 464 Processing helix chain 'K' and resid 465 through 467 No H-bonds generated for 'chain 'K' and resid 465 through 467' Processing helix chain 'K' and resid 468 through 476 Processing helix chain 'K' and resid 511 through 525 Processing helix chain 'F' and resid 140 through 148 Processing helix chain 'F' and resid 155 through 160 Processing helix chain 'F' and resid 163 through 167 removed outlier: 3.784A pdb=" N THR F 166 " --> pdb=" O LEU F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 175 through 187 removed outlier: 4.600A pdb=" N GLN F 187 " --> pdb=" O ARG F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 204 removed outlier: 3.538A pdb=" N PHE F 200 " --> pdb=" O ASP F 196 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL F 204 " --> pdb=" O PHE F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 216 Processing helix chain 'F' and resid 223 through 239 Processing helix chain 'F' and resid 252 through 256 removed outlier: 3.748A pdb=" N LYS F 255 " --> pdb=" O GLN F 252 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE F 256 " --> pdb=" O LEU F 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 252 through 256' Processing helix chain 'F' and resid 288 through 301 Processing helix chain 'F' and resid 301 through 306 Processing helix chain 'F' and resid 334 through 345 removed outlier: 3.732A pdb=" N ILE F 345 " --> pdb=" O VAL F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 366 Processing helix chain 'F' and resid 375 through 380 Processing helix chain 'F' and resid 386 through 398 Processing helix chain 'F' and resid 406 through 419 Processing helix chain 'F' and resid 423 through 430 removed outlier: 3.826A pdb=" N VAL F 429 " --> pdb=" O GLU F 425 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET F 430 " --> pdb=" O SER F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 464 Processing helix chain 'F' and resid 465 through 467 No H-bonds generated for 'chain 'F' and resid 465 through 467' Processing helix chain 'F' and resid 468 through 476 Processing helix chain 'F' and resid 511 through 525 Processing helix chain 'H' and resid 140 through 148 Processing helix chain 'H' and resid 155 through 161 Processing helix chain 'H' and resid 172 through 174 No H-bonds generated for 'chain 'H' and resid 172 through 174' Processing helix chain 'H' and resid 175 through 188 removed outlier: 3.778A pdb=" N MET H 179 " --> pdb=" O LEU H 175 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLN H 187 " --> pdb=" O ARG H 183 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR H 188 " --> pdb=" O LEU H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 204 removed outlier: 3.925A pdb=" N VAL H 204 " --> pdb=" O PHE H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 216 Processing helix chain 'H' and resid 223 through 239 Processing helix chain 'H' and resid 252 through 256 removed outlier: 3.625A pdb=" N PHE H 256 " --> pdb=" O LEU H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 301 Processing helix chain 'H' and resid 301 through 306 Processing helix chain 'H' and resid 334 through 345 removed outlier: 3.656A pdb=" N ILE H 345 " --> pdb=" O VAL H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 367 Processing helix chain 'H' and resid 375 through 380 Processing helix chain 'H' and resid 386 through 398 Processing helix chain 'H' and resid 406 through 419 Processing helix chain 'H' and resid 423 through 430 Processing helix chain 'H' and resid 449 through 464 Processing helix chain 'H' and resid 465 through 467 No H-bonds generated for 'chain 'H' and resid 465 through 467' Processing helix chain 'H' and resid 468 through 476 Processing helix chain 'H' and resid 511 through 525 Processing helix chain 'J' and resid 140 through 148 Processing helix chain 'J' and resid 155 through 161 removed outlier: 3.700A pdb=" N THR J 161 " --> pdb=" O HIS J 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 163 through 167 removed outlier: 3.757A pdb=" N THR J 166 " --> pdb=" O LEU J 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 174 No H-bonds generated for 'chain 'J' and resid 172 through 174' Processing helix chain 'J' and resid 175 through 188 Processing helix chain 'J' and resid 197 through 204 removed outlier: 3.999A pdb=" N VAL J 204 " --> pdb=" O PHE J 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 207 through 216 Processing helix chain 'J' and resid 223 through 239 Processing helix chain 'J' and resid 252 through 256 removed outlier: 3.741A pdb=" N LYS J 255 " --> pdb=" O GLN J 252 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE J 256 " --> pdb=" O LEU J 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 252 through 256' Processing helix chain 'J' and resid 288 through 301 Processing helix chain 'J' and resid 301 through 306 Processing helix chain 'J' and resid 334 through 345 removed outlier: 3.794A pdb=" N ILE J 345 " --> pdb=" O VAL J 341 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 366 Processing helix chain 'J' and resid 375 through 380 Processing helix chain 'J' and resid 386 through 398 Processing helix chain 'J' and resid 406 through 419 Processing helix chain 'J' and resid 423 through 430 removed outlier: 3.836A pdb=" N VAL J 429 " --> pdb=" O GLU J 425 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET J 430 " --> pdb=" O SER J 426 " (cutoff:3.500A) Processing helix chain 'J' and resid 449 through 464 Processing helix chain 'J' and resid 465 through 467 No H-bonds generated for 'chain 'J' and resid 465 through 467' Processing helix chain 'J' and resid 468 through 476 Processing helix chain 'J' and resid 511 through 525 Processing helix chain 'L' and resid 140 through 148 Processing helix chain 'L' and resid 155 through 161 removed outlier: 3.584A pdb=" N PHE L 159 " --> pdb=" O PRO L 155 " (cutoff:3.500A) Processing helix chain 'L' and resid 175 through 188 Processing helix chain 'L' and resid 196 through 204 removed outlier: 3.621A pdb=" N PHE L 200 " --> pdb=" O ASP L 196 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL L 204 " --> pdb=" O PHE L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 207 through 216 removed outlier: 3.510A pdb=" N ARG L 216 " --> pdb=" O THR L 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 239 Processing helix chain 'L' and resid 252 through 256 removed outlier: 3.614A pdb=" N PHE L 256 " --> pdb=" O LEU L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 288 through 301 Processing helix chain 'L' and resid 301 through 306 Processing helix chain 'L' and resid 334 through 345 removed outlier: 3.641A pdb=" N ILE L 345 " --> pdb=" O VAL L 341 " (cutoff:3.500A) Processing helix chain 'L' and resid 350 through 367 Processing helix chain 'L' and resid 375 through 380 Processing helix chain 'L' and resid 386 through 398 Processing helix chain 'L' and resid 406 through 419 Processing helix chain 'L' and resid 423 through 430 removed outlier: 3.689A pdb=" N VAL L 429 " --> pdb=" O GLU L 425 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET L 430 " --> pdb=" O SER L 426 " (cutoff:3.500A) Processing helix chain 'L' and resid 449 through 464 Processing helix chain 'L' and resid 465 through 467 No H-bonds generated for 'chain 'L' and resid 465 through 467' Processing helix chain 'L' and resid 468 through 476 Processing helix chain 'L' and resid 511 through 525 Processing sheet with id=AA1, first strand: chain 'A' and resid 272 through 276 Processing sheet with id=AA2, first strand: chain 'A' and resid 272 through 276 Processing sheet with id=AA3, first strand: chain 'A' and resid 282 through 283 removed outlier: 3.503A pdb=" N GLU A 421 " --> pdb=" O GLY A 372 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 272 through 276 removed outlier: 3.737A pdb=" N VAL B 263 " --> pdb=" O THR B 275 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 272 through 276 removed outlier: 3.737A pdb=" N VAL B 263 " --> pdb=" O THR B 275 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 282 through 283 Processing sheet with id=AA7, first strand: chain 'C' and resid 272 through 276 Processing sheet with id=AA8, first strand: chain 'C' and resid 272 through 276 Processing sheet with id=AA9, first strand: chain 'C' and resid 282 through 283 removed outlier: 3.519A pdb=" N GLU C 421 " --> pdb=" O GLY C 372 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 272 through 276 removed outlier: 3.509A pdb=" N VAL D 263 " --> pdb=" O THR D 275 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 272 through 276 removed outlier: 3.509A pdb=" N VAL D 263 " --> pdb=" O THR D 275 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 282 through 283 removed outlier: 3.503A pdb=" N GLU D 421 " --> pdb=" O GLY D 372 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 272 through 276 Processing sheet with id=AB5, first strand: chain 'E' and resid 282 through 283 Processing sheet with id=AB6, first strand: chain 'G' and resid 272 through 276 removed outlier: 3.503A pdb=" N VAL G 263 " --> pdb=" O THR G 275 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 272 through 276 removed outlier: 3.503A pdb=" N VAL G 263 " --> pdb=" O THR G 275 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 282 through 283 Processing sheet with id=AB9, first strand: chain 'I' and resid 272 through 276 removed outlier: 4.099A pdb=" N LEU I 490 " --> pdb=" O MET I 498 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 282 through 283 Processing sheet with id=AC2, first strand: chain 'K' and resid 272 through 276 removed outlier: 3.521A pdb=" N VAL K 263 " --> pdb=" O THR K 275 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 272 through 276 removed outlier: 3.521A pdb=" N VAL K 263 " --> pdb=" O THR K 275 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 282 through 283 Processing sheet with id=AC5, first strand: chain 'F' and resid 272 through 276 removed outlier: 3.538A pdb=" N VAL F 263 " --> pdb=" O THR F 275 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 272 through 276 removed outlier: 3.538A pdb=" N VAL F 263 " --> pdb=" O THR F 275 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 282 through 283 Processing sheet with id=AC8, first strand: chain 'H' and resid 272 through 276 removed outlier: 3.571A pdb=" N VAL H 263 " --> pdb=" O THR H 275 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 272 through 276 removed outlier: 3.571A pdb=" N VAL H 263 " --> pdb=" O THR H 275 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 282 through 283 Processing sheet with id=AD2, first strand: chain 'J' and resid 272 through 276 Processing sheet with id=AD3, first strand: chain 'J' and resid 272 through 276 Processing sheet with id=AD4, first strand: chain 'J' and resid 282 through 283 Processing sheet with id=AD5, first strand: chain 'L' and resid 272 through 276 removed outlier: 3.609A pdb=" N VAL L 263 " --> pdb=" O THR L 275 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 282 through 283 1784 hydrogen bonds defined for protein. 5193 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.13 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6012 1.31 - 1.43: 9524 1.43 - 1.56: 20872 1.56 - 1.69: 48 1.69 - 1.81: 516 Bond restraints: 36972 Sorted by residual: bond pdb=" CD GLN L 602 " pdb=" NE2 GLN L 602 " ideal model delta sigma weight residual 1.328 1.453 -0.125 2.10e-02 2.27e+03 3.53e+01 bond pdb=" CD GLN J 602 " pdb=" NE2 GLN J 602 " ideal model delta sigma weight residual 1.328 1.452 -0.124 2.10e-02 2.27e+03 3.50e+01 bond pdb=" CD GLN C 602 " pdb=" NE2 GLN C 602 " ideal model delta sigma weight residual 1.328 1.452 -0.124 2.10e-02 2.27e+03 3.49e+01 bond pdb=" CD GLN H 602 " pdb=" NE2 GLN H 602 " ideal model delta sigma weight residual 1.328 1.452 -0.124 2.10e-02 2.27e+03 3.48e+01 bond pdb=" CD GLN B 602 " pdb=" NE2 GLN B 602 " ideal model delta sigma weight residual 1.328 1.451 -0.123 2.10e-02 2.27e+03 3.46e+01 ... (remaining 36967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 49002 2.05 - 4.10: 729 4.10 - 6.14: 141 6.14 - 8.19: 52 8.19 - 10.24: 8 Bond angle restraints: 49932 Sorted by residual: angle pdb=" C PRO B 222 " pdb=" N ASP B 223 " pdb=" CA ASP B 223 " ideal model delta sigma weight residual 122.82 128.29 -5.47 1.42e+00 4.96e-01 1.48e+01 angle pdb=" C PRO D 222 " pdb=" N ASP D 223 " pdb=" CA ASP D 223 " ideal model delta sigma weight residual 122.82 128.27 -5.45 1.42e+00 4.96e-01 1.47e+01 angle pdb=" C PRO G 222 " pdb=" N ASP G 223 " pdb=" CA ASP G 223 " ideal model delta sigma weight residual 121.54 128.42 -6.88 1.91e+00 2.74e-01 1.30e+01 angle pdb=" C PRO E 222 " pdb=" N ASP E 223 " pdb=" CA ASP E 223 " ideal model delta sigma weight residual 121.54 128.35 -6.81 1.91e+00 2.74e-01 1.27e+01 angle pdb=" N VAL H 193 " pdb=" CA VAL H 193 " pdb=" C VAL H 193 " ideal model delta sigma weight residual 109.34 116.74 -7.40 2.08e+00 2.31e-01 1.27e+01 ... (remaining 49927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 19735 17.62 - 35.23: 2022 35.23 - 52.85: 275 52.85 - 70.46: 62 70.46 - 88.08: 34 Dihedral angle restraints: 22128 sinusoidal: 8796 harmonic: 13332 Sorted by residual: dihedral pdb=" C VAL H 193 " pdb=" N VAL H 193 " pdb=" CA VAL H 193 " pdb=" CB VAL H 193 " ideal model delta harmonic sigma weight residual -122.00 -133.62 11.62 0 2.50e+00 1.60e-01 2.16e+01 dihedral pdb=" C VAL G 193 " pdb=" N VAL G 193 " pdb=" CA VAL G 193 " pdb=" CB VAL G 193 " ideal model delta harmonic sigma weight residual -122.00 -133.18 11.18 0 2.50e+00 1.60e-01 2.00e+01 dihedral pdb=" N VAL H 193 " pdb=" C VAL H 193 " pdb=" CA VAL H 193 " pdb=" CB VAL H 193 " ideal model delta harmonic sigma weight residual 123.40 133.33 -9.93 0 2.50e+00 1.60e-01 1.58e+01 ... (remaining 22125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 4822 0.067 - 0.133: 686 0.133 - 0.200: 23 0.200 - 0.266: 10 0.266 - 0.333: 3 Chirality restraints: 5544 Sorted by residual: chirality pdb=" CA VAL H 193 " pdb=" N VAL H 193 " pdb=" C VAL H 193 " pdb=" CB VAL H 193 " both_signs ideal model delta sigma weight residual False 2.44 2.11 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA VAL G 193 " pdb=" N VAL G 193 " pdb=" C VAL G 193 " pdb=" CB VAL G 193 " both_signs ideal model delta sigma weight residual False 2.44 2.15 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CB VAL F 193 " pdb=" CA VAL F 193 " pdb=" CG1 VAL F 193 " pdb=" CG2 VAL F 193 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 5541 not shown) Planarity restraints: 6408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 172 " -0.039 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO E 173 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO E 173 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 173 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 503 " -0.040 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO F 504 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO F 504 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 504 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO J 503 " 0.039 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO J 504 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO J 504 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO J 504 " 0.033 5.00e-02 4.00e+02 ... (remaining 6405 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 13 2.02 - 2.74: 2364 2.74 - 3.46: 53444 3.46 - 4.18: 84126 4.18 - 4.90: 151597 Nonbonded interactions: 291544 Sorted by model distance: nonbonded pdb=" NH2 ARG C 387 " pdb=" O1 PO4 C 601 " model vdw 1.297 3.120 nonbonded pdb=" NH2 ARG D 387 " pdb=" O4 PO4 D 601 " model vdw 1.297 3.120 nonbonded pdb=" NH2 ARG H 387 " pdb=" O4 PO4 H 601 " model vdw 1.297 3.120 nonbonded pdb=" NH2 ARG I 387 " pdb=" O1 PO4 I 601 " model vdw 1.297 3.120 nonbonded pdb=" NH2 ARG G 387 " pdb=" O4 PO4 G 601 " model vdw 1.297 3.120 ... (remaining 291539 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: 0.01 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' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 28.790 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 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 : 0.004 0.125 36972 Z= 0.182 Angle : 0.661 10.241 49932 Z= 0.358 Chirality : 0.046 0.333 5544 Planarity : 0.005 0.060 6408 Dihedral : 14.366 88.079 13560 Min Nonbonded Distance : 1.297 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.15 % Allowed : 0.45 % Favored : 99.40 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.12), residues: 4620 helix: 0.16 (0.10), residues: 2364 sheet: -0.57 (0.29), residues: 384 loop : -0.62 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 272 TYR 0.019 0.001 TYR H 357 PHE 0.022 0.001 PHE K 227 TRP 0.013 0.001 TRP B 501 HIS 0.006 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00366 (36972) covalent geometry : angle 0.66062 (49932) hydrogen bonds : bond 0.15996 ( 1700) hydrogen bonds : angle 7.15065 ( 5193) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9240 Ramachandran restraints generated. 4620 Oldfield, 0 Emsley, 4620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9240 Ramachandran restraints generated. 4620 Oldfield, 0 Emsley, 4620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2227 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 2221 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ASP cc_start: 0.8857 (t0) cc_final: 0.8233 (t70) REVERT: A 194 MET cc_start: 0.6290 (tpp) cc_final: 0.5480 (tpp) REVERT: A 213 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8700 (mm-40) REVERT: A 218 LYS cc_start: 0.9479 (mmmt) cc_final: 0.9161 (mmmm) REVERT: A 227 PHE cc_start: 0.9503 (t80) cc_final: 0.9259 (t80) REVERT: A 235 TYR cc_start: 0.9430 (t80) cc_final: 0.9196 (t80) REVERT: A 236 GLU cc_start: 0.9560 (mm-30) cc_final: 0.9237 (mm-30) REVERT: A 261 TRP cc_start: 0.9434 (t-100) cc_final: 0.9064 (t-100) REVERT: A 272 ARG cc_start: 0.8239 (ptm160) cc_final: 0.7899 (ptm160) REVERT: A 277 ASP cc_start: 0.8955 (m-30) cc_final: 0.8234 (p0) REVERT: A 279 LYS cc_start: 0.9678 (mmmt) cc_final: 0.9425 (mmmm) REVERT: A 280 VAL cc_start: 0.9377 (t) cc_final: 0.9090 (p) REVERT: A 285 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7567 (mm-40) REVERT: A 293 TYR cc_start: 0.9097 (t80) cc_final: 0.8484 (t80) REVERT: A 307 ARG cc_start: 0.9215 (mtt180) cc_final: 0.8959 (mtm-85) REVERT: A 320 LYS cc_start: 0.8766 (tppt) cc_final: 0.8328 (tppt) REVERT: A 328 LYS cc_start: 0.8490 (mttt) cc_final: 0.8123 (mtpt) REVERT: A 379 GLN cc_start: 0.9429 (mm110) cc_final: 0.9226 (mm110) REVERT: A 421 GLU cc_start: 0.8214 (pt0) cc_final: 0.7864 (pt0) REVERT: A 445 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8690 (mt-10) REVERT: A 454 ARG cc_start: 0.8713 (ttp80) cc_final: 0.8402 (tpt170) REVERT: A 460 MET cc_start: 0.9131 (mtp) cc_final: 0.8278 (ttm) REVERT: A 498 MET cc_start: 0.8148 (ttm) cc_final: 0.7578 (ttm) REVERT: A 499 MET cc_start: 0.8705 (tpp) cc_final: 0.8172 (tpp) REVERT: B 181 MET cc_start: 0.8022 (tmm) cc_final: 0.7780 (tmm) REVERT: B 196 ASP cc_start: 0.7889 (t70) cc_final: 0.7637 (t70) REVERT: B 213 GLN cc_start: 0.8969 (mm110) cc_final: 0.8755 (mm110) REVERT: B 234 LEU cc_start: 0.9656 (mt) cc_final: 0.9424 (mt) REVERT: B 236 GLU cc_start: 0.9417 (mm-30) cc_final: 0.8814 (mm-30) REVERT: B 241 GLN cc_start: 0.8150 (mp10) cc_final: 0.7529 (mp10) REVERT: B 285 GLN cc_start: 0.8440 (mm-40) cc_final: 0.7776 (mm-40) REVERT: B 293 TYR cc_start: 0.9180 (t80) cc_final: 0.8910 (t80) REVERT: B 323 LEU cc_start: 0.9116 (mt) cc_final: 0.8643 (mp) REVERT: B 344 LEU cc_start: 0.9630 (mt) cc_final: 0.9230 (mt) REVERT: B 375 ASN cc_start: 0.9043 (t0) cc_final: 0.8826 (t0) REVERT: B 379 GLN cc_start: 0.9251 (mm110) cc_final: 0.9046 (mm110) REVERT: B 382 ARG cc_start: 0.9360 (ttp80) cc_final: 0.8962 (ptm160) REVERT: B 386 ASP cc_start: 0.8773 (m-30) cc_final: 0.8534 (m-30) REVERT: B 387 ARG cc_start: 0.8249 (tpt-90) cc_final: 0.7865 (tpt-90) REVERT: B 394 TYR cc_start: 0.9372 (t80) cc_final: 0.9002 (t80) REVERT: B 397 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8752 (tm-30) REVERT: B 421 GLU cc_start: 0.8528 (pt0) cc_final: 0.7953 (pt0) REVERT: B 424 CYS cc_start: 0.9319 (m) cc_final: 0.8770 (m) REVERT: B 426 SER cc_start: 0.9448 (t) cc_final: 0.8993 (p) REVERT: B 436 ASN cc_start: 0.8728 (t0) cc_final: 0.8519 (t0) REVERT: B 454 ARG cc_start: 0.8920 (ttp80) cc_final: 0.8676 (ttp-110) REVERT: B 465 MET cc_start: 0.9567 (mmm) cc_final: 0.9340 (mmm) REVERT: C 172 ASP cc_start: 0.8572 (t0) cc_final: 0.7395 (t70) REVERT: C 179 MET cc_start: 0.7637 (ptp) cc_final: 0.7042 (ptp) REVERT: C 227 PHE cc_start: 0.9597 (t80) cc_final: 0.9311 (t80) REVERT: C 232 ASP cc_start: 0.9518 (t0) cc_final: 0.9280 (m-30) REVERT: C 235 TYR cc_start: 0.9449 (t80) cc_final: 0.9101 (t80) REVERT: C 236 GLU cc_start: 0.9576 (mm-30) cc_final: 0.9181 (mm-30) REVERT: C 260 LEU cc_start: 0.9435 (mt) cc_final: 0.9231 (mt) REVERT: C 272 ARG cc_start: 0.8251 (ptm160) cc_final: 0.7836 (ptm160) REVERT: C 277 ASP cc_start: 0.9034 (m-30) cc_final: 0.8218 (p0) REVERT: C 279 LYS cc_start: 0.9628 (mmmt) cc_final: 0.9400 (mmmm) REVERT: C 285 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8596 (mm-40) REVERT: C 293 TYR cc_start: 0.8995 (t80) cc_final: 0.8441 (t80) REVERT: C 328 LYS cc_start: 0.8590 (mttt) cc_final: 0.8367 (mtpt) REVERT: C 415 PHE cc_start: 0.9359 (m-10) cc_final: 0.9111 (m-80) REVERT: C 421 GLU cc_start: 0.8263 (pt0) cc_final: 0.7972 (pt0) REVERT: C 441 PRO cc_start: 0.9415 (Cg_endo) cc_final: 0.9196 (Cg_exo) REVERT: C 445 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8731 (mt-10) REVERT: C 454 ARG cc_start: 0.8682 (ttp80) cc_final: 0.8401 (tpt170) REVERT: C 465 MET cc_start: 0.9296 (mmm) cc_final: 0.8617 (tpp) REVERT: C 498 MET cc_start: 0.8218 (ttm) cc_final: 0.7815 (ttm) REVERT: C 499 MET cc_start: 0.8269 (tpp) cc_final: 0.7824 (tpp) REVERT: C 506 ASP cc_start: 0.9337 (t0) cc_final: 0.8665 (p0) REVERT: C 510 ASN cc_start: 0.8781 (m-40) cc_final: 0.8365 (m-40) REVERT: D 140 GLU cc_start: 0.8533 (pm20) cc_final: 0.8221 (pp20) REVERT: D 172 ASP cc_start: 0.9022 (t0) cc_final: 0.8743 (t0) REVERT: D 212 THR cc_start: 0.9035 (p) cc_final: 0.8077 (p) REVERT: D 213 GLN cc_start: 0.9253 (mm110) cc_final: 0.9012 (mm110) REVERT: D 235 TYR cc_start: 0.9076 (t80) cc_final: 0.8847 (t80) REVERT: D 236 GLU cc_start: 0.9480 (mm-30) cc_final: 0.9050 (mm-30) REVERT: D 241 GLN cc_start: 0.8172 (mp10) cc_final: 0.7417 (mp10) REVERT: D 245 LYS cc_start: 0.9219 (mmmm) cc_final: 0.9011 (mmmm) REVERT: D 249 TYR cc_start: 0.8352 (p90) cc_final: 0.8143 (p90) REVERT: D 260 LEU cc_start: 0.9611 (tp) cc_final: 0.9191 (tp) REVERT: D 277 ASP cc_start: 0.9079 (m-30) cc_final: 0.8832 (m-30) REVERT: D 279 LYS cc_start: 0.9508 (mmmt) cc_final: 0.9270 (mmmm) REVERT: D 285 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8072 (mm-40) REVERT: D 293 TYR cc_start: 0.9041 (t80) cc_final: 0.8625 (t80) REVERT: D 317 ARG cc_start: 0.8126 (mmt90) cc_final: 0.7875 (mmt90) REVERT: D 318 PHE cc_start: 0.9207 (p90) cc_final: 0.8849 (p90) REVERT: D 323 LEU cc_start: 0.9105 (mt) cc_final: 0.8669 (mp) REVERT: D 344 LEU cc_start: 0.9678 (mt) cc_final: 0.9407 (mt) REVERT: D 350 ASN cc_start: 0.8294 (p0) cc_final: 0.8017 (p0) REVERT: D 369 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8556 (mm-30) REVERT: D 375 ASN cc_start: 0.8999 (t0) cc_final: 0.8773 (t0) REVERT: D 379 GLN cc_start: 0.9233 (mm110) cc_final: 0.8909 (mm110) REVERT: D 382 ARG cc_start: 0.9382 (ttp80) cc_final: 0.8990 (ptm160) REVERT: D 393 TYR cc_start: 0.9483 (m-80) cc_final: 0.9253 (m-10) REVERT: D 394 TYR cc_start: 0.9377 (t80) cc_final: 0.9051 (t80) REVERT: D 397 GLU cc_start: 0.9087 (tm-30) cc_final: 0.8855 (tm-30) REVERT: D 421 GLU cc_start: 0.8352 (pt0) cc_final: 0.7851 (pt0) REVERT: D 423 THR cc_start: 0.9284 (p) cc_final: 0.9032 (t) REVERT: D 430 MET cc_start: 0.9307 (mpp) cc_final: 0.8968 (mmp) REVERT: D 454 ARG cc_start: 0.8959 (ttp80) cc_final: 0.8753 (ttp80) REVERT: D 467 ASP cc_start: 0.8729 (m-30) cc_final: 0.8432 (p0) REVERT: D 499 MET cc_start: 0.7804 (tpp) cc_final: 0.7521 (tpp) REVERT: D 520 ASP cc_start: 0.8784 (m-30) cc_final: 0.8370 (m-30) REVERT: E 172 ASP cc_start: 0.9165 (t0) cc_final: 0.8709 (t0) REVERT: E 213 GLN cc_start: 0.9127 (mm110) cc_final: 0.8758 (mm-40) REVERT: E 235 TYR cc_start: 0.9336 (t80) cc_final: 0.8986 (t80) REVERT: E 252 GLN cc_start: 0.8864 (tp-100) cc_final: 0.8304 (tp-100) REVERT: E 255 LYS cc_start: 0.9557 (mttt) cc_final: 0.9297 (mttm) REVERT: E 261 TRP cc_start: 0.9443 (t-100) cc_final: 0.9082 (t-100) REVERT: E 271 GLN cc_start: 0.8287 (pt0) cc_final: 0.8040 (pt0) REVERT: E 365 MET cc_start: 0.9259 (ttm) cc_final: 0.8995 (tmm) REVERT: E 379 GLN cc_start: 0.8751 (mm110) cc_final: 0.6639 (tt0) REVERT: E 382 ARG cc_start: 0.9396 (ttp80) cc_final: 0.9136 (ptm-80) REVERT: E 386 ASP cc_start: 0.8856 (m-30) cc_final: 0.8636 (m-30) REVERT: E 396 LYS cc_start: 0.9334 (tttt) cc_final: 0.9112 (tttm) REVERT: E 407 MET cc_start: 0.8843 (tmm) cc_final: 0.8535 (tmm) REVERT: E 421 GLU cc_start: 0.8518 (pt0) cc_final: 0.8155 (pt0) REVERT: E 424 CYS cc_start: 0.9185 (m) cc_final: 0.8870 (t) REVERT: E 426 SER cc_start: 0.9530 (t) cc_final: 0.9136 (p) REVERT: E 433 THR cc_start: 0.8295 (m) cc_final: 0.8048 (m) REVERT: E 448 LEU cc_start: 0.9093 (mt) cc_final: 0.8800 (mt) REVERT: E 455 ASN cc_start: 0.8940 (m-40) cc_final: 0.8438 (m-40) REVERT: E 465 MET cc_start: 0.9396 (tpp) cc_final: 0.9072 (mmm) REVERT: E 467 ASP cc_start: 0.9013 (m-30) cc_final: 0.8569 (m-30) REVERT: E 478 LEU cc_start: 0.9627 (mt) cc_final: 0.9413 (mt) REVERT: E 488 ILE cc_start: 0.8648 (mt) cc_final: 0.8217 (mt) REVERT: E 499 MET cc_start: 0.8611 (tpp) cc_final: 0.8313 (tpp) REVERT: E 520 ASP cc_start: 0.8898 (m-30) cc_final: 0.8682 (m-30) REVERT: G 179 MET cc_start: 0.9283 (tpp) cc_final: 0.8719 (tpp) REVERT: G 194 MET cc_start: 0.4939 (tpp) cc_final: 0.4439 (tpp) REVERT: G 232 ASP cc_start: 0.9581 (m-30) cc_final: 0.9069 (m-30) REVERT: G 235 TYR cc_start: 0.9175 (t80) cc_final: 0.8427 (t80) REVERT: G 236 GLU cc_start: 0.9513 (mm-30) cc_final: 0.9041 (mm-30) REVERT: G 264 SER cc_start: 0.8297 (m) cc_final: 0.7204 (p) REVERT: G 271 GLN cc_start: 0.7983 (mt0) cc_final: 0.7724 (mt0) REVERT: G 279 LYS cc_start: 0.9477 (mmmt) cc_final: 0.9166 (mmmt) REVERT: G 285 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8277 (mm-40) REVERT: G 293 TYR cc_start: 0.9185 (t80) cc_final: 0.7490 (t80) REVERT: G 317 ARG cc_start: 0.8424 (mmt90) cc_final: 0.8204 (mmt-90) REVERT: G 320 LYS cc_start: 0.8720 (tppt) cc_final: 0.8107 (tppt) REVERT: G 344 LEU cc_start: 0.9656 (mt) cc_final: 0.9414 (mt) REVERT: G 357 TYR cc_start: 0.8847 (t80) cc_final: 0.8566 (t80) REVERT: G 414 TYR cc_start: 0.9306 (t80) cc_final: 0.8898 (t80) REVERT: G 424 CYS cc_start: 0.9113 (m) cc_final: 0.8358 (t) REVERT: G 426 SER cc_start: 0.9417 (t) cc_final: 0.9141 (p) REVERT: G 436 ASN cc_start: 0.9190 (t0) cc_final: 0.8874 (t0) REVERT: G 451 GLU cc_start: 0.8108 (mp0) cc_final: 0.7857 (mp0) REVERT: G 454 ARG cc_start: 0.8778 (ttp80) cc_final: 0.8420 (ttp-110) REVERT: G 455 ASN cc_start: 0.9183 (m-40) cc_final: 0.8842 (m-40) REVERT: G 499 MET cc_start: 0.8526 (tpp) cc_final: 0.8208 (tpp) REVERT: I 140 GLU cc_start: 0.8834 (pm20) cc_final: 0.8449 (pp20) REVERT: I 166 THR cc_start: 0.9387 (t) cc_final: 0.9048 (t) REVERT: I 172 ASP cc_start: 0.8898 (t0) cc_final: 0.8348 (t0) REVERT: I 194 MET cc_start: 0.7736 (tmm) cc_final: 0.7470 (tmm) REVERT: I 235 TYR cc_start: 0.9201 (t80) cc_final: 0.8995 (t80) REVERT: I 249 TYR cc_start: 0.8772 (p90) cc_final: 0.8061 (p90) REVERT: I 252 GLN cc_start: 0.8854 (tp-100) cc_final: 0.8416 (tp-100) REVERT: I 255 LYS cc_start: 0.9583 (mttt) cc_final: 0.9363 (mttm) REVERT: I 260 LEU cc_start: 0.9556 (mt) cc_final: 0.9272 (mt) REVERT: I 261 TRP cc_start: 0.9360 (t-100) cc_final: 0.8949 (t-100) REVERT: I 277 ASP cc_start: 0.8984 (m-30) cc_final: 0.8460 (p0) REVERT: I 326 ASP cc_start: 0.9471 (m-30) cc_final: 0.9107 (m-30) REVERT: I 375 ASN cc_start: 0.8461 (t0) cc_final: 0.8173 (m-40) REVERT: I 379 GLN cc_start: 0.8974 (mm110) cc_final: 0.6825 (tt0) REVERT: I 382 ARG cc_start: 0.9393 (ttp80) cc_final: 0.9139 (ptm-80) REVERT: I 386 ASP cc_start: 0.8355 (m-30) cc_final: 0.7846 (m-30) REVERT: I 407 MET cc_start: 0.8854 (tmm) cc_final: 0.8333 (tmm) REVERT: I 421 GLU cc_start: 0.8432 (pt0) cc_final: 0.8032 (pt0) REVERT: I 426 SER cc_start: 0.9579 (t) cc_final: 0.9187 (p) REVERT: I 441 PRO cc_start: 0.9360 (Cg_endo) cc_final: 0.9018 (Cg_exo) REVERT: I 455 ASN cc_start: 0.8926 (m-40) cc_final: 0.8409 (m-40) REVERT: I 465 MET cc_start: 0.9433 (mmm) cc_final: 0.8871 (mmm) REVERT: I 467 ASP cc_start: 0.8740 (m-30) cc_final: 0.8109 (p0) REVERT: I 478 LEU cc_start: 0.9595 (mt) cc_final: 0.9391 (mt) REVERT: I 510 ASN cc_start: 0.8698 (m-40) cc_final: 0.7998 (m110) REVERT: I 520 ASP cc_start: 0.8979 (m-30) cc_final: 0.8716 (m-30) REVERT: K 179 MET cc_start: 0.9096 (tpp) cc_final: 0.8466 (tpp) REVERT: K 180 ASP cc_start: 0.9412 (m-30) cc_final: 0.9083 (m-30) REVERT: K 219 PHE cc_start: 0.8048 (m-10) cc_final: 0.7658 (m-10) REVERT: K 223 ASP cc_start: 0.8928 (p0) cc_final: 0.8621 (p0) REVERT: K 232 ASP cc_start: 0.9580 (m-30) cc_final: 0.9248 (m-30) REVERT: K 235 TYR cc_start: 0.9108 (t80) cc_final: 0.8276 (t80) REVERT: K 236 GLU cc_start: 0.9465 (mm-30) cc_final: 0.9084 (mm-30) REVERT: K 249 TYR cc_start: 0.8457 (p90) cc_final: 0.8213 (p90) REVERT: K 264 SER cc_start: 0.8206 (m) cc_final: 0.6982 (p) REVERT: K 271 GLN cc_start: 0.8052 (tt0) cc_final: 0.7806 (tt0) REVERT: K 279 LYS cc_start: 0.9316 (mmmt) cc_final: 0.8877 (mmmt) REVERT: K 293 TYR cc_start: 0.9162 (t80) cc_final: 0.7588 (t80) REVERT: K 344 LEU cc_start: 0.9702 (mt) cc_final: 0.9494 (mt) REVERT: K 382 ARG cc_start: 0.9347 (ttp80) cc_final: 0.9046 (mtp180) REVERT: K 386 ASP cc_start: 0.8909 (m-30) cc_final: 0.8622 (m-30) REVERT: K 407 MET cc_start: 0.8710 (tmm) cc_final: 0.8500 (tmm) REVERT: K 424 CYS cc_start: 0.8809 (m) cc_final: 0.8306 (t) REVERT: K 436 ASN cc_start: 0.9182 (t0) cc_final: 0.8855 (t0) REVERT: K 448 LEU cc_start: 0.9411 (mt) cc_final: 0.9066 (mt) REVERT: K 454 ARG cc_start: 0.8886 (ttp80) cc_final: 0.8459 (ttp-110) REVERT: K 455 ASN cc_start: 0.9093 (m-40) cc_final: 0.8722 (m-40) REVERT: F 140 GLU cc_start: 0.8582 (pm20) cc_final: 0.8292 (pm20) REVERT: F 172 ASP cc_start: 0.8765 (t0) cc_final: 0.8495 (t70) REVERT: F 194 MET cc_start: 0.7195 (tpp) cc_final: 0.6978 (tpp) REVERT: F 196 ASP cc_start: 0.8191 (t70) cc_final: 0.7956 (t70) REVERT: F 212 THR cc_start: 0.9388 (p) cc_final: 0.8970 (t) REVERT: F 213 GLN cc_start: 0.8971 (mm110) cc_final: 0.8587 (mm110) REVERT: F 233 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8539 (mt-10) REVERT: F 235 TYR cc_start: 0.9337 (t80) cc_final: 0.8749 (t80) REVERT: F 239 LYS cc_start: 0.9534 (tttt) cc_final: 0.9227 (mtpp) REVERT: F 245 LYS cc_start: 0.8809 (mtmm) cc_final: 0.8599 (mmmm) REVERT: F 261 TRP cc_start: 0.9250 (t-100) cc_final: 0.8696 (t-100) REVERT: F 279 LYS cc_start: 0.9585 (mmmt) cc_final: 0.9192 (tppt) REVERT: F 285 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8421 (mm-40) REVERT: F 311 LYS cc_start: 0.8502 (ptpp) cc_final: 0.8299 (pttt) REVERT: F 328 LYS cc_start: 0.8416 (mttt) cc_final: 0.8008 (mttm) REVERT: F 371 VAL cc_start: 0.9598 (t) cc_final: 0.9330 (p) REVERT: F 375 ASN cc_start: 0.8918 (t0) cc_final: 0.8700 (t0) REVERT: F 379 GLN cc_start: 0.9243 (mm110) cc_final: 0.8864 (mm110) REVERT: F 397 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8626 (tm-30) REVERT: F 407 MET cc_start: 0.8391 (tmm) cc_final: 0.8153 (tmm) REVERT: F 413 PHE cc_start: 0.8729 (t80) cc_final: 0.8214 (t80) REVERT: F 421 GLU cc_start: 0.8316 (pt0) cc_final: 0.7886 (pt0) REVERT: F 425 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8530 (mt-10) REVERT: F 474 PHE cc_start: 0.9100 (t80) cc_final: 0.8792 (t80) REVERT: F 492 VAL cc_start: 0.9187 (t) cc_final: 0.8658 (m) REVERT: F 499 MET cc_start: 0.8583 (tpp) cc_final: 0.8091 (tpp) REVERT: F 520 ASP cc_start: 0.8848 (m-30) cc_final: 0.8605 (m-30) REVERT: H 215 PHE cc_start: 0.8206 (m-80) cc_final: 0.7769 (m-80) REVERT: H 219 PHE cc_start: 0.8254 (m-10) cc_final: 0.7942 (m-10) REVERT: H 232 ASP cc_start: 0.9570 (m-30) cc_final: 0.8961 (m-30) REVERT: H 235 TYR cc_start: 0.8969 (t80) cc_final: 0.8484 (t80) REVERT: H 236 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8982 (mm-30) REVERT: H 252 GLN cc_start: 0.8562 (tp-100) cc_final: 0.8281 (tp-100) REVERT: H 285 GLN cc_start: 0.8498 (mm-40) cc_final: 0.7754 (mm-40) REVERT: H 293 TYR cc_start: 0.9010 (t80) cc_final: 0.8586 (t80) REVERT: H 308 TYR cc_start: 0.8991 (m-80) cc_final: 0.8575 (m-10) REVERT: H 320 LYS cc_start: 0.8757 (tppt) cc_final: 0.8469 (tppt) REVERT: H 331 ASN cc_start: 0.9243 (p0) cc_final: 0.8506 (p0) REVERT: H 356 ASP cc_start: 0.9330 (t0) cc_final: 0.9121 (t0) REVERT: H 382 ARG cc_start: 0.9367 (ttp80) cc_final: 0.8969 (ptm160) REVERT: H 436 ASN cc_start: 0.8485 (t0) cc_final: 0.8238 (t0) REVERT: H 471 GLN cc_start: 0.9194 (tp-100) cc_final: 0.8931 (tp-100) REVERT: J 172 ASP cc_start: 0.8932 (t0) cc_final: 0.8672 (t0) REVERT: J 179 MET cc_start: 0.8806 (tmm) cc_final: 0.8265 (tmm) REVERT: J 180 ASP cc_start: 0.9308 (p0) cc_final: 0.8833 (p0) REVERT: J 213 GLN cc_start: 0.8884 (mm110) cc_final: 0.8364 (mm-40) REVERT: J 233 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8462 (mt-10) REVERT: J 236 GLU cc_start: 0.9490 (mm-30) cc_final: 0.9282 (mm-30) REVERT: J 239 LYS cc_start: 0.9433 (tttt) cc_final: 0.9055 (mtpp) REVERT: J 245 LYS cc_start: 0.8784 (mtmm) cc_final: 0.8513 (mmmm) REVERT: J 255 LYS cc_start: 0.9367 (mttt) cc_final: 0.9162 (mttp) REVERT: J 261 TRP cc_start: 0.9271 (t-100) cc_final: 0.8977 (t-100) REVERT: J 277 ASP cc_start: 0.9034 (m-30) cc_final: 0.8098 (p0) REVERT: J 279 LYS cc_start: 0.9632 (mmmt) cc_final: 0.9201 (tppt) REVERT: J 320 LYS cc_start: 0.9180 (tppp) cc_final: 0.8809 (tppt) REVERT: J 357 TYR cc_start: 0.8952 (t80) cc_final: 0.8684 (t80) REVERT: J 365 MET cc_start: 0.9348 (ttm) cc_final: 0.8809 (tmm) REVERT: J 368 ASN cc_start: 0.9529 (m110) cc_final: 0.9321 (m110) REVERT: J 371 VAL cc_start: 0.9599 (t) cc_final: 0.9348 (p) REVERT: J 397 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8581 (tm-30) REVERT: J 421 GLU cc_start: 0.8270 (pt0) cc_final: 0.7827 (pt0) REVERT: J 460 MET cc_start: 0.8903 (ptm) cc_final: 0.8505 (ttp) REVERT: J 474 PHE cc_start: 0.9218 (t80) cc_final: 0.8883 (t80) REVERT: L 172 ASP cc_start: 0.8404 (t0) cc_final: 0.8014 (t70) REVERT: L 194 MET cc_start: 0.6895 (tpt) cc_final: 0.5185 (pmm) REVERT: L 197 LYS cc_start: 0.7768 (mttt) cc_final: 0.7461 (mttm) REVERT: L 232 ASP cc_start: 0.9587 (m-30) cc_final: 0.8927 (m-30) REVERT: L 235 TYR cc_start: 0.8991 (t80) cc_final: 0.8437 (t80) REVERT: L 236 GLU cc_start: 0.9251 (mm-30) cc_final: 0.9003 (mm-30) REVERT: L 252 GLN cc_start: 0.8566 (tp-100) cc_final: 0.8241 (tp-100) REVERT: L 260 LEU cc_start: 0.9602 (tp) cc_final: 0.9218 (tp) REVERT: L 277 ASP cc_start: 0.8679 (p0) cc_final: 0.8303 (p0) REVERT: L 285 GLN cc_start: 0.8970 (mm-40) cc_final: 0.8327 (mm-40) REVERT: L 289 LYS cc_start: 0.8874 (mttt) cc_final: 0.8640 (mttp) REVERT: L 308 TYR cc_start: 0.9056 (m-80) cc_final: 0.8650 (m-10) REVERT: L 320 LYS cc_start: 0.8694 (tppt) cc_final: 0.8348 (tppt) REVERT: L 328 LYS cc_start: 0.8785 (mttt) cc_final: 0.8421 (mtpp) REVERT: L 331 ASN cc_start: 0.9209 (p0) cc_final: 0.8558 (p0) REVERT: L 333 MET cc_start: 0.8914 (mmp) cc_final: 0.7850 (mmp) REVERT: L 426 SER cc_start: 0.9251 (t) cc_final: 0.8716 (p) REVERT: L 430 MET cc_start: 0.9131 (mpp) cc_final: 0.8895 (mpp) REVERT: L 436 ASN cc_start: 0.8420 (t0) cc_final: 0.8139 (t0) REVERT: L 474 PHE cc_start: 0.8988 (t80) cc_final: 0.8351 (t80) REVERT: L 513 LYS cc_start: 0.7921 (mttt) cc_final: 0.7681 (mttm) outliers start: 6 outliers final: 3 residues processed: 2227 average time/residue: 0.2052 time to fit residues: 732.3322 Evaluate side-chains 1834 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1831 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain E residue 602 GLN Chi-restraints excluded: chain F residue 602 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 6.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 ASN A 475 HIS B 298 ASN B 351 ASN ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 HIS C 213 GLN C 351 ASN ** C 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 HIS ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 ASN ** D 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN D 475 HIS E 319 ASN E 510 ASN E 516 HIS E 519 HIS G 207 ASN ** G 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 351 ASN G 360 GLN G 416 GLN ** I 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 271 GLN K 298 ASN K 351 ASN K 360 GLN ** K 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN ** F 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 360 GLN F 455 ASN F 475 HIS F 519 HIS H 213 GLN H 455 ASN ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 241 GLN J 252 GLN ** J 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 335 ASN J 360 GLN ** J 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 455 ASN J 475 HIS J 519 HIS L 455 ASN ** L 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.153668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111832 restraints weight = 66602.099| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 4.09 r_work: 0.3178 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 36972 Z= 0.167 Angle : 0.629 9.223 49932 Z= 0.331 Chirality : 0.044 0.205 5544 Planarity : 0.005 0.054 6408 Dihedral : 5.011 56.243 4929 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.61 % Favored : 94.37 % Rotamer: Outliers : 2.49 % Allowed : 17.76 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.13), residues: 4620 helix: 0.98 (0.11), residues: 2400 sheet: -0.52 (0.29), residues: 384 loop : -0.50 (0.15), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 387 TYR 0.022 0.002 TYR C 235 PHE 0.031 0.001 PHE C 322 TRP 0.017 0.002 TRP K 261 HIS 0.005 0.001 HIS K 516 Details of bonding type rmsd covalent geometry : bond 0.00379 (36972) covalent geometry : angle 0.62868 (49932) hydrogen bonds : bond 0.03686 ( 1700) hydrogen bonds : angle 5.04149 ( 5193) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9240 Ramachandran restraints generated. 4620 Oldfield, 0 Emsley, 4620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9240 Ramachandran restraints generated. 4620 Oldfield, 0 Emsley, 4620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1989 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 1889 time to evaluate : 1.500 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: A 164 LYS cc_start: 0.9165 (mtmt) cc_final: 0.8929 (mtmm) REVERT: A 177 GLU cc_start: 0.8877 (pp20) cc_final: 0.8603 (pm20) REVERT: A 194 MET cc_start: 0.6685 (tpp) cc_final: 0.5834 (tpp) REVERT: A 207 ASN cc_start: 0.8993 (m-40) cc_final: 0.8357 (m-40) REVERT: A 213 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8608 (mm-40) REVERT: A 216 ARG cc_start: 0.8818 (mtp180) cc_final: 0.8479 (mtp180) REVERT: A 218 LYS cc_start: 0.9489 (mmmt) cc_final: 0.9283 (mmmm) REVERT: A 236 GLU cc_start: 0.9650 (mm-30) cc_final: 0.9327 (mm-30) REVERT: A 261 TRP cc_start: 0.9546 (t-100) cc_final: 0.9226 (t-100) REVERT: A 277 ASP cc_start: 0.9151 (m-30) cc_final: 0.8793 (p0) REVERT: A 293 TYR cc_start: 0.9365 (t80) cc_final: 0.8762 (t80) REVERT: A 306 HIS cc_start: 0.9032 (m-70) cc_final: 0.8721 (m-70) REVERT: A 320 LYS cc_start: 0.9293 (tppt) cc_final: 0.8922 (tppt) REVERT: A 347 GLN cc_start: 0.8730 (mp10) cc_final: 0.8451 (mp10) REVERT: A 357 TYR cc_start: 0.9352 (t80) cc_final: 0.9108 (t80) REVERT: A 365 MET cc_start: 0.9450 (ttm) cc_final: 0.8948 (tmm) REVERT: A 370 TYR cc_start: 0.9396 (t80) cc_final: 0.8903 (t80) REVERT: A 421 GLU cc_start: 0.8892 (pt0) cc_final: 0.8539 (pt0) REVERT: A 426 SER cc_start: 0.9653 (t) cc_final: 0.9429 (p) REVERT: A 445 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8986 (mt-10) REVERT: A 454 ARG cc_start: 0.9043 (ttp80) cc_final: 0.8691 (tpt170) REVERT: A 498 MET cc_start: 0.8779 (ttm) cc_final: 0.8341 (ttm) REVERT: A 499 MET cc_start: 0.9127 (tpp) cc_final: 0.8681 (tpp) REVERT: B 196 ASP cc_start: 0.7762 (t70) cc_final: 0.7239 (t70) REVERT: B 218 LYS cc_start: 0.9472 (mmmm) cc_final: 0.9045 (mtpp) REVERT: B 224 PHE cc_start: 0.9469 (t80) cc_final: 0.9234 (t80) REVERT: B 234 LEU cc_start: 0.9706 (mt) cc_final: 0.9415 (mt) REVERT: B 235 TYR cc_start: 0.9407 (t80) cc_final: 0.8556 (t80) REVERT: B 236 GLU cc_start: 0.9533 (mm-30) cc_final: 0.9075 (mm-30) REVERT: B 252 GLN cc_start: 0.8590 (tp-100) cc_final: 0.8068 (tp-100) REVERT: B 263 VAL cc_start: 0.9503 (t) cc_final: 0.9230 (p) REVERT: B 282 PHE cc_start: 0.8779 (p90) cc_final: 0.8555 (p90) REVERT: B 285 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8247 (mm-40) REVERT: B 293 TYR cc_start: 0.9383 (t80) cc_final: 0.9061 (t80) REVERT: B 318 PHE cc_start: 0.9155 (p90) cc_final: 0.8889 (p90) REVERT: B 331 ASN cc_start: 0.9285 (p0) cc_final: 0.8608 (p0) REVERT: B 375 ASN cc_start: 0.9308 (t0) cc_final: 0.9016 (t0) REVERT: B 379 GLN cc_start: 0.9322 (mm110) cc_final: 0.9058 (mm110) REVERT: B 394 TYR cc_start: 0.9697 (t80) cc_final: 0.9391 (t80) REVERT: B 407 MET cc_start: 0.8821 (tmm) cc_final: 0.8301 (tmm) REVERT: B 421 GLU cc_start: 0.8965 (pt0) cc_final: 0.8509 (pt0) REVERT: B 426 SER cc_start: 0.9464 (t) cc_final: 0.9158 (p) REVERT: B 436 ASN cc_start: 0.8972 (t0) cc_final: 0.8720 (t0) REVERT: B 454 ARG cc_start: 0.9122 (ttp80) cc_final: 0.8891 (ttp80) REVERT: B 467 ASP cc_start: 0.9259 (OUTLIER) cc_final: 0.8940 (p0) REVERT: C 164 LYS cc_start: 0.9264 (mtmt) cc_final: 0.8989 (mtpp) REVERT: C 172 ASP cc_start: 0.8570 (t0) cc_final: 0.7478 (t70) REVERT: C 179 MET cc_start: 0.7725 (ptp) cc_final: 0.7086 (ptp) REVERT: C 235 TYR cc_start: 0.9618 (t80) cc_final: 0.9376 (t80) REVERT: C 277 ASP cc_start: 0.9200 (m-30) cc_final: 0.8690 (p0) REVERT: C 293 TYR cc_start: 0.9318 (t80) cc_final: 0.8695 (t80) REVERT: C 316 LEU cc_start: 0.9470 (mt) cc_final: 0.9231 (mt) REVERT: C 365 MET cc_start: 0.9465 (ttm) cc_final: 0.9000 (tmm) REVERT: C 375 ASN cc_start: 0.9126 (t0) cc_final: 0.8918 (t0) REVERT: C 379 GLN cc_start: 0.9569 (mm110) cc_final: 0.9299 (mm110) REVERT: C 407 MET cc_start: 0.8967 (tmm) cc_final: 0.8757 (tmm) REVERT: C 421 GLU cc_start: 0.8819 (pt0) cc_final: 0.8564 (pt0) REVERT: C 426 SER cc_start: 0.9692 (t) cc_final: 0.9486 (p) REVERT: C 445 GLU cc_start: 0.9329 (mt-10) cc_final: 0.9091 (mt-10) REVERT: C 498 MET cc_start: 0.8851 (ttm) cc_final: 0.8489 (ttm) REVERT: C 499 MET cc_start: 0.9003 (tpp) cc_final: 0.8555 (tpp) REVERT: D 140 GLU cc_start: 0.8620 (pm20) cc_final: 0.8264 (pp20) REVERT: D 196 ASP cc_start: 0.7499 (t0) cc_final: 0.7109 (t0) REVERT: D 212 THR cc_start: 0.9091 (p) cc_final: 0.8229 (p) REVERT: D 213 GLN cc_start: 0.9154 (mm110) cc_final: 0.8899 (mm-40) REVERT: D 224 PHE cc_start: 0.9447 (t80) cc_final: 0.9241 (t80) REVERT: D 232 ASP cc_start: 0.9714 (m-30) cc_final: 0.9224 (m-30) REVERT: D 235 TYR cc_start: 0.9410 (t80) cc_final: 0.9199 (t80) REVERT: D 236 GLU cc_start: 0.9586 (mm-30) cc_final: 0.9209 (mm-30) REVERT: D 241 GLN cc_start: 0.8380 (mp10) cc_final: 0.7909 (mp10) REVERT: D 249 TYR cc_start: 0.8557 (p90) cc_final: 0.8171 (p90) REVERT: D 260 LEU cc_start: 0.9548 (tp) cc_final: 0.9100 (tp) REVERT: D 263 VAL cc_start: 0.9575 (t) cc_final: 0.9276 (p) REVERT: D 277 ASP cc_start: 0.9308 (m-30) cc_final: 0.9103 (m-30) REVERT: D 285 GLN cc_start: 0.9026 (mm-40) cc_final: 0.8444 (mm-40) REVERT: D 293 TYR cc_start: 0.9316 (t80) cc_final: 0.8882 (t80) REVERT: D 303 GLU cc_start: 0.9318 (tm-30) cc_final: 0.9117 (tm-30) REVERT: D 306 HIS cc_start: 0.8911 (m-70) cc_final: 0.8704 (m90) REVERT: D 318 PHE cc_start: 0.9270 (p90) cc_final: 0.9046 (p90) REVERT: D 344 LEU cc_start: 0.9607 (mt) cc_final: 0.9333 (mt) REVERT: D 394 TYR cc_start: 0.9684 (t80) cc_final: 0.9389 (t80) REVERT: D 397 GLU cc_start: 0.9412 (tm-30) cc_final: 0.9129 (tm-30) REVERT: D 414 TYR cc_start: 0.9426 (t80) cc_final: 0.8941 (t80) REVERT: D 421 GLU cc_start: 0.8815 (pt0) cc_final: 0.8280 (pt0) REVERT: D 454 ARG cc_start: 0.9122 (ttp80) cc_final: 0.8833 (ttp80) REVERT: D 499 MET cc_start: 0.8588 (tpp) cc_final: 0.8387 (tpp) REVERT: D 506 ASP cc_start: 0.9562 (t0) cc_final: 0.9336 (t0) REVERT: E 172 ASP cc_start: 0.8721 (t0) cc_final: 0.8199 (t0) REVERT: E 179 MET cc_start: 0.8909 (tpp) cc_final: 0.8616 (tpp) REVERT: E 181 MET cc_start: 0.7305 (tmm) cc_final: 0.7039 (tmm) REVERT: E 183 ARG cc_start: 0.8921 (mmm-85) cc_final: 0.8583 (ttp-110) REVERT: E 213 GLN cc_start: 0.9189 (mm110) cc_final: 0.8902 (mm110) REVERT: E 233 GLU cc_start: 0.9466 (tp30) cc_final: 0.9230 (tp30) REVERT: E 271 GLN cc_start: 0.8430 (pt0) cc_final: 0.7900 (pt0) REVERT: E 272 ARG cc_start: 0.8681 (mtp180) cc_final: 0.8345 (mtp180) REVERT: E 279 LYS cc_start: 0.9535 (mmmt) cc_final: 0.9232 (mmmm) REVERT: E 323 LEU cc_start: 0.9409 (mp) cc_final: 0.9032 (mp) REVERT: E 331 ASN cc_start: 0.9190 (p0) cc_final: 0.8541 (p0) REVERT: E 365 MET cc_start: 0.9411 (ttm) cc_final: 0.9174 (ttm) REVERT: E 379 GLN cc_start: 0.8819 (mm110) cc_final: 0.6913 (tt0) REVERT: E 396 LYS cc_start: 0.9445 (tttt) cc_final: 0.9160 (tttm) REVERT: E 407 MET cc_start: 0.8925 (tmm) cc_final: 0.8528 (tmm) REVERT: E 421 GLU cc_start: 0.8824 (pt0) cc_final: 0.8498 (pt0) REVERT: E 424 CYS cc_start: 0.9374 (m) cc_final: 0.9083 (t) REVERT: E 426 SER cc_start: 0.9591 (t) cc_final: 0.9313 (p) REVERT: E 430 MET cc_start: 0.8928 (mmt) cc_final: 0.8610 (mmp) REVERT: E 446 ARG cc_start: 0.9260 (tpp80) cc_final: 0.8973 (tpp80) REVERT: E 455 ASN cc_start: 0.9140 (m-40) cc_final: 0.8635 (m-40) REVERT: E 465 MET cc_start: 0.9585 (tpp) cc_final: 0.9310 (mmm) REVERT: E 499 MET cc_start: 0.8729 (tpp) cc_final: 0.8403 (tpp) REVERT: G 179 MET cc_start: 0.9214 (tpp) cc_final: 0.8930 (tpp) REVERT: G 181 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8393 (mtm) REVERT: G 194 MET cc_start: 0.4747 (tpp) cc_final: 0.4166 (tpp) REVERT: G 227 PHE cc_start: 0.9635 (t80) cc_final: 0.9389 (t80) REVERT: G 232 ASP cc_start: 0.9741 (m-30) cc_final: 0.9225 (m-30) REVERT: G 235 TYR cc_start: 0.9394 (t80) cc_final: 0.9130 (t80) REVERT: G 236 GLU cc_start: 0.9622 (mm-30) cc_final: 0.9164 (mm-30) REVERT: G 240 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.8947 (mtmm) REVERT: G 261 TRP cc_start: 0.8902 (t-100) cc_final: 0.8602 (t-100) REVERT: G 271 GLN cc_start: 0.8741 (mt0) cc_final: 0.8515 (mt0) REVERT: G 277 ASP cc_start: 0.9338 (m-30) cc_final: 0.8974 (p0) REVERT: G 285 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8225 (mm-40) REVERT: G 293 TYR cc_start: 0.9346 (t80) cc_final: 0.7475 (t80) REVERT: G 300 LEU cc_start: 0.9577 (mm) cc_final: 0.9317 (mt) REVERT: G 303 GLU cc_start: 0.9273 (tm-30) cc_final: 0.9048 (tm-30) REVERT: G 317 ARG cc_start: 0.8659 (mmt90) cc_final: 0.8356 (mmt-90) REVERT: G 318 PHE cc_start: 0.9341 (p90) cc_final: 0.9081 (p90) REVERT: G 361 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.8592 (t80) REVERT: G 382 ARG cc_start: 0.9622 (ttp80) cc_final: 0.9293 (mtp180) REVERT: G 421 GLU cc_start: 0.8662 (pt0) cc_final: 0.8438 (pt0) REVERT: G 424 CYS cc_start: 0.9207 (m) cc_final: 0.8872 (m) REVERT: G 426 SER cc_start: 0.9414 (t) cc_final: 0.9183 (p) REVERT: G 436 ASN cc_start: 0.9281 (t0) cc_final: 0.8915 (t0) REVERT: G 445 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8546 (mm-30) REVERT: G 451 GLU cc_start: 0.8739 (mp0) cc_final: 0.8419 (mp0) REVERT: G 454 ARG cc_start: 0.9020 (ttp80) cc_final: 0.8629 (ttp-110) REVERT: G 455 ASN cc_start: 0.9301 (m-40) cc_final: 0.8782 (m-40) REVERT: G 499 MET cc_start: 0.9010 (tpp) cc_final: 0.8667 (tpp) REVERT: G 516 HIS cc_start: 0.8223 (t-90) cc_final: 0.7534 (t-90) REVERT: I 140 GLU cc_start: 0.8589 (pm20) cc_final: 0.8220 (pp20) REVERT: I 166 THR cc_start: 0.9631 (t) cc_final: 0.9232 (t) REVERT: I 172 ASP cc_start: 0.8633 (t0) cc_final: 0.8127 (t0) REVERT: I 194 MET cc_start: 0.7768 (tmm) cc_final: 0.7356 (tmm) REVERT: I 235 TYR cc_start: 0.9003 (t80) cc_final: 0.8572 (t80) REVERT: I 261 TRP cc_start: 0.9402 (t-100) cc_final: 0.8704 (t-100) REVERT: I 271 GLN cc_start: 0.7990 (mt0) cc_final: 0.7758 (mm-40) REVERT: I 277 ASP cc_start: 0.9040 (m-30) cc_final: 0.8818 (p0) REVERT: I 279 LYS cc_start: 0.9557 (mmmt) cc_final: 0.9256 (mmmm) REVERT: I 331 ASN cc_start: 0.9129 (p0) cc_final: 0.8442 (p0) REVERT: I 347 GLN cc_start: 0.8650 (mt0) cc_final: 0.8441 (mp10) REVERT: I 375 ASN cc_start: 0.8560 (t0) cc_final: 0.8169 (m-40) REVERT: I 379 GLN cc_start: 0.8763 (mm110) cc_final: 0.6863 (tt0) REVERT: I 386 ASP cc_start: 0.8520 (m-30) cc_final: 0.8015 (m-30) REVERT: I 407 MET cc_start: 0.8872 (tmm) cc_final: 0.8470 (tmm) REVERT: I 421 GLU cc_start: 0.8842 (pt0) cc_final: 0.8451 (pt0) REVERT: I 426 SER cc_start: 0.9677 (t) cc_final: 0.9239 (p) REVERT: I 455 ASN cc_start: 0.9079 (m-40) cc_final: 0.8658 (m-40) REVERT: I 465 MET cc_start: 0.9588 (mmm) cc_final: 0.9218 (tpp) REVERT: I 467 ASP cc_start: 0.8911 (m-30) cc_final: 0.8613 (p0) REVERT: I 494 ASN cc_start: 0.9520 (m110) cc_final: 0.9163 (m-40) REVERT: I 498 MET cc_start: 0.9287 (mtp) cc_final: 0.9042 (mtp) REVERT: I 499 MET cc_start: 0.8815 (tpp) cc_final: 0.8478 (tpp) REVERT: I 520 ASP cc_start: 0.9058 (m-30) cc_final: 0.8832 (m-30) REVERT: K 218 LYS cc_start: 0.9566 (mmmm) cc_final: 0.9054 (mmmm) REVERT: K 219 PHE cc_start: 0.8360 (m-10) cc_final: 0.7945 (m-10) REVERT: K 232 ASP cc_start: 0.9723 (m-30) cc_final: 0.9392 (m-30) REVERT: K 235 TYR cc_start: 0.9352 (t80) cc_final: 0.8953 (t80) REVERT: K 236 GLU cc_start: 0.9590 (mm-30) cc_final: 0.9158 (mm-30) REVERT: K 240 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8935 (mtmm) REVERT: K 260 LEU cc_start: 0.9455 (tp) cc_final: 0.9209 (tt) REVERT: K 285 GLN cc_start: 0.9040 (mm-40) cc_final: 0.8435 (mm-40) REVERT: K 293 TYR cc_start: 0.9314 (t80) cc_final: 0.7680 (t80) REVERT: K 361 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.8530 (t80) REVERT: K 382 ARG cc_start: 0.9617 (ttp80) cc_final: 0.9336 (mtp180) REVERT: K 407 MET cc_start: 0.8746 (tmm) cc_final: 0.8456 (tmm) REVERT: K 424 CYS cc_start: 0.9055 (m) cc_final: 0.8753 (m) REVERT: K 436 ASN cc_start: 0.9291 (t0) cc_final: 0.8958 (t0) REVERT: K 451 GLU cc_start: 0.8523 (mp0) cc_final: 0.8154 (mp0) REVERT: K 454 ARG cc_start: 0.9059 (ttp80) cc_final: 0.8665 (ttp-110) REVERT: K 455 ASN cc_start: 0.9238 (m-40) cc_final: 0.8825 (m-40) REVERT: K 467 ASP cc_start: 0.9543 (p0) cc_final: 0.9183 (p0) REVERT: K 499 MET cc_start: 0.8858 (tpp) cc_final: 0.8429 (tpp) REVERT: K 501 TRP cc_start: 0.8821 (t-100) cc_final: 0.8141 (t-100) REVERT: K 508 MET cc_start: 0.8848 (mmm) cc_final: 0.8471 (mmm) REVERT: K 516 HIS cc_start: 0.8331 (t-90) cc_final: 0.7742 (t-90) REVERT: F 140 GLU cc_start: 0.8713 (pm20) cc_final: 0.8508 (pm20) REVERT: F 164 LYS cc_start: 0.9328 (mtmt) cc_final: 0.9025 (mtmm) REVERT: F 172 ASP cc_start: 0.8799 (t0) cc_final: 0.8339 (t70) REVERT: F 179 MET cc_start: 0.8809 (tpp) cc_final: 0.8316 (tpt) REVERT: F 194 MET cc_start: 0.7345 (tpp) cc_final: 0.7136 (tpp) REVERT: F 196 ASP cc_start: 0.8369 (t70) cc_final: 0.8098 (t70) REVERT: F 212 THR cc_start: 0.9434 (p) cc_final: 0.9072 (t) REVERT: F 213 GLN cc_start: 0.8818 (mm110) cc_final: 0.8395 (mm110) REVERT: F 233 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8895 (mt-10) REVERT: F 236 GLU cc_start: 0.9547 (mm-30) cc_final: 0.9097 (mm-30) REVERT: F 252 GLN cc_start: 0.9169 (tp40) cc_final: 0.8752 (tp-100) REVERT: F 261 TRP cc_start: 0.9267 (t-100) cc_final: 0.8999 (t-100) REVERT: F 279 LYS cc_start: 0.9649 (mmmt) cc_final: 0.9407 (tppt) REVERT: F 285 GLN cc_start: 0.9144 (mm-40) cc_final: 0.8727 (mm-40) REVERT: F 347 GLN cc_start: 0.8517 (mp10) cc_final: 0.8104 (mp10) REVERT: F 379 GLN cc_start: 0.9545 (mm110) cc_final: 0.9314 (mm110) REVERT: F 397 GLU cc_start: 0.9192 (tm-30) cc_final: 0.8973 (tm-30) REVERT: F 413 PHE cc_start: 0.8968 (t80) cc_final: 0.8466 (t80) REVERT: F 421 GLU cc_start: 0.8890 (pt0) cc_final: 0.8361 (pt0) REVERT: F 454 ARG cc_start: 0.9382 (ttp-110) cc_final: 0.9139 (ttp-110) REVERT: F 496 MET cc_start: 0.8742 (ppp) cc_final: 0.8068 (ppp) REVERT: F 498 MET cc_start: 0.8863 (mtp) cc_final: 0.8648 (mtp) REVERT: F 499 MET cc_start: 0.8955 (tpp) cc_final: 0.8487 (tpp) REVERT: H 172 ASP cc_start: 0.8220 (t0) cc_final: 0.8020 (t70) REVERT: H 178 CYS cc_start: 0.8581 (m) cc_final: 0.8379 (t) REVERT: H 181 MET cc_start: 0.8065 (mtt) cc_final: 0.7502 (tmm) REVERT: H 194 MET cc_start: 0.7285 (tpp) cc_final: 0.6880 (tpt) REVERT: H 215 PHE cc_start: 0.8279 (m-80) cc_final: 0.7967 (m-80) REVERT: H 219 PHE cc_start: 0.8365 (m-10) cc_final: 0.7910 (m-10) REVERT: H 232 ASP cc_start: 0.9654 (m-30) cc_final: 0.9163 (m-30) REVERT: H 236 GLU cc_start: 0.9447 (mm-30) cc_final: 0.9148 (mm-30) REVERT: H 285 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8378 (mm-40) REVERT: H 293 TYR cc_start: 0.8893 (t80) cc_final: 0.8598 (t80) REVERT: H 295 ILE cc_start: 0.8976 (mm) cc_final: 0.8770 (mm) REVERT: H 308 TYR cc_start: 0.9058 (m-80) cc_final: 0.8600 (m-10) REVERT: H 320 LYS cc_start: 0.9155 (tppt) cc_final: 0.8779 (tppt) REVERT: H 328 LYS cc_start: 0.8640 (mtpp) cc_final: 0.8221 (mtpt) REVERT: H 346 LYS cc_start: 0.8061 (mtpp) cc_final: 0.7819 (ttmm) REVERT: H 347 GLN cc_start: 0.8842 (pm20) cc_final: 0.7820 (mp10) REVERT: H 378 PHE cc_start: 0.9213 (t80) cc_final: 0.8757 (t80) REVERT: H 382 ARG cc_start: 0.9374 (ttp80) cc_final: 0.8839 (ptm160) REVERT: H 397 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8833 (tm-30) REVERT: H 436 ASN cc_start: 0.8442 (t0) cc_final: 0.8200 (t0) REVERT: H 446 ARG cc_start: 0.9105 (tmm-80) cc_final: 0.8613 (tpp80) REVERT: H 455 ASN cc_start: 0.8864 (m-40) cc_final: 0.8657 (m-40) REVERT: H 460 MET cc_start: 0.8465 (ttm) cc_final: 0.8211 (ttm) REVERT: H 465 MET cc_start: 0.9421 (mmm) cc_final: 0.9183 (mmm) REVERT: H 499 MET cc_start: 0.8759 (tpp) cc_final: 0.7403 (tpp) REVERT: H 508 MET cc_start: 0.9065 (mmm) cc_final: 0.8836 (mmm) REVERT: J 172 ASP cc_start: 0.8689 (t0) cc_final: 0.8298 (t70) REVERT: J 179 MET cc_start: 0.8919 (tmm) cc_final: 0.8548 (tmm) REVERT: J 180 ASP cc_start: 0.9299 (p0) cc_final: 0.8823 (p0) REVERT: J 196 ASP cc_start: 0.8239 (t70) cc_final: 0.7855 (p0) REVERT: J 213 GLN cc_start: 0.8662 (mm110) cc_final: 0.8443 (mm110) REVERT: J 215 PHE cc_start: 0.8754 (m-80) cc_final: 0.8472 (m-80) REVERT: J 233 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8922 (mt-10) REVERT: J 236 GLU cc_start: 0.9713 (mm-30) cc_final: 0.9369 (mm-30) REVERT: J 245 LYS cc_start: 0.8918 (mtmm) cc_final: 0.8654 (mmmm) REVERT: J 249 TYR cc_start: 0.8787 (p90) cc_final: 0.8454 (p90) REVERT: J 252 GLN cc_start: 0.8818 (tp40) cc_final: 0.8587 (tp-100) REVERT: J 303 GLU cc_start: 0.9144 (tm-30) cc_final: 0.8943 (tm-30) REVERT: J 320 LYS cc_start: 0.9187 (tppp) cc_final: 0.8893 (tppt) REVERT: J 413 PHE cc_start: 0.9042 (t80) cc_final: 0.8458 (t80) REVERT: J 421 GLU cc_start: 0.8880 (pt0) cc_final: 0.8381 (pt0) REVERT: J 499 MET cc_start: 0.9138 (tpt) cc_final: 0.8489 (tpt) REVERT: J 508 MET cc_start: 0.9280 (ttp) cc_final: 0.9070 (ttp) REVERT: L 172 ASP cc_start: 0.7818 (t0) cc_final: 0.7461 (t70) REVERT: L 194 MET cc_start: 0.7329 (tpt) cc_final: 0.5040 (pmm) REVERT: L 223 ASP cc_start: 0.8881 (p0) cc_final: 0.8657 (p0) REVERT: L 233 GLU cc_start: 0.9581 (mm-30) cc_final: 0.8830 (tp30) REVERT: L 236 GLU cc_start: 0.9415 (mm-30) cc_final: 0.9039 (tm-30) REVERT: L 260 LEU cc_start: 0.9337 (tp) cc_final: 0.9025 (tp) REVERT: L 285 GLN cc_start: 0.8968 (mm-40) cc_final: 0.8530 (mm-40) REVERT: L 320 LYS cc_start: 0.9117 (tppt) cc_final: 0.8752 (tppt) REVERT: L 331 ASN cc_start: 0.8927 (p0) cc_final: 0.8284 (p0) REVERT: L 333 MET cc_start: 0.8879 (mmp) cc_final: 0.7657 (mmp) REVERT: L 347 GLN cc_start: 0.8888 (pm20) cc_final: 0.7846 (mp10) REVERT: L 353 GLU cc_start: 0.9415 (mt-10) cc_final: 0.9193 (mt-10) REVERT: L 378 PHE cc_start: 0.9191 (t80) cc_final: 0.8946 (t80) REVERT: L 426 SER cc_start: 0.9101 (t) cc_final: 0.8500 (p) REVERT: L 430 MET cc_start: 0.9124 (mpp) cc_final: 0.8814 (mpp) REVERT: L 455 ASN cc_start: 0.8895 (m-40) cc_final: 0.8598 (m-40) REVERT: L 465 MET cc_start: 0.9496 (mmm) cc_final: 0.9265 (mmm) REVERT: L 471 GLN cc_start: 0.9282 (tp-100) cc_final: 0.9056 (tp-100) REVERT: L 602 GLN cc_start: 0.6051 (OUTLIER) cc_final: 0.5449 (pt0) outliers start: 100 outliers final: 68 residues processed: 1930 average time/residue: 0.1981 time to fit residues: 625.4541 Evaluate side-chains 1858 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 1783 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 510 ASN Chi-restraints excluded: chain E residue 312 GLU Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain G residue 181 MET Chi-restraints excluded: chain G residue 240 LYS Chi-restraints excluded: chain G residue 266 CYS Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain G residue 361 PHE Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 469 SER Chi-restraints excluded: chain G residue 511 SER Chi-restraints excluded: chain G residue 523 SER Chi-restraints excluded: chain I residue 266 CYS Chi-restraints excluded: chain I residue 312 GLU Chi-restraints excluded: chain I residue 442 ILE Chi-restraints excluded: chain I residue 469 SER Chi-restraints excluded: chain I residue 484 VAL Chi-restraints excluded: chain K residue 240 LYS Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain K residue 360 GLN Chi-restraints excluded: chain K residue 361 PHE Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 511 SER Chi-restraints excluded: chain K residue 523 SER Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 407 MET Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 458 SER Chi-restraints excluded: chain H residue 510 ASN Chi-restraints excluded: chain H residue 512 VAL Chi-restraints excluded: chain J residue 231 ILE Chi-restraints excluded: chain J residue 386 ASP Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain L residue 231 ILE Chi-restraints excluded: chain L residue 362 LEU Chi-restraints excluded: chain L residue 458 SER Chi-restraints excluded: chain L residue 467 ASP Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain D residue 602 GLN Chi-restraints excluded: chain E residue 602 GLN Chi-restraints excluded: chain F residue 602 GLN Chi-restraints excluded: chain L residue 602 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 368 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 330 optimal weight: 6.9990 chunk 284 optimal weight: 0.9990 chunk 390 optimal weight: 0.9990 chunk 422 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 357 optimal weight: 0.9990 chunk 428 optimal weight: 9.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN A 368 ASN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN C 207 ASN C 213 GLN ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 GLN E 252 GLN ** E 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 GLN G 298 ASN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 516 HIS K 271 GLN K 298 ASN ** K 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 360 GLN F 519 HIS ** H 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 471 GLN ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 241 GLN ** J 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 360 GLN J 519 HIS L 213 GLN ** L 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 475 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.150710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.108723 restraints weight = 66878.716| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 4.05 r_work: 0.3129 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 36972 Z= 0.194 Angle : 0.632 9.161 49932 Z= 0.333 Chirality : 0.044 0.203 5544 Planarity : 0.005 0.051 6408 Dihedral : 5.068 56.005 4929 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.95 % Favored : 94.00 % Rotamer: Outliers : 4.40 % Allowed : 21.52 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.13), residues: 4620 helix: 1.22 (0.11), residues: 2328 sheet: -0.61 (0.30), residues: 360 loop : -0.51 (0.15), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 217 TYR 0.024 0.002 TYR C 235 PHE 0.024 0.001 PHE I 361 TRP 0.012 0.002 TRP A 261 HIS 0.006 0.001 HIS J 157 Details of bonding type rmsd covalent geometry : bond 0.00440 (36972) covalent geometry : angle 0.63236 (49932) hydrogen bonds : bond 0.03581 ( 1700) hydrogen bonds : angle 4.94600 ( 5193) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9240 Ramachandran restraints generated. 4620 Oldfield, 0 Emsley, 4620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9240 Ramachandran restraints generated. 4620 Oldfield, 0 Emsley, 4620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2008 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 1831 time to evaluate : 1.074 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 164 LYS cc_start: 0.9182 (mtmt) cc_final: 0.8914 (mtmm) REVERT: A 194 MET cc_start: 0.6865 (tpp) cc_final: 0.6000 (tpp) REVERT: A 207 ASN cc_start: 0.8932 (m-40) cc_final: 0.8298 (m-40) REVERT: A 213 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8472 (mm-40) REVERT: A 218 LYS cc_start: 0.9484 (mmmt) cc_final: 0.9124 (mmmm) REVERT: A 236 GLU cc_start: 0.9660 (mm-30) cc_final: 0.9366 (mm-30) REVERT: A 277 ASP cc_start: 0.9085 (m-30) cc_final: 0.8760 (p0) REVERT: A 293 TYR cc_start: 0.9429 (t80) cc_final: 0.8769 (t80) REVERT: A 306 HIS cc_start: 0.9047 (m-70) cc_final: 0.8762 (m-70) REVERT: A 347 GLN cc_start: 0.8855 (mp10) cc_final: 0.8600 (mp10) REVERT: A 357 TYR cc_start: 0.9449 (t80) cc_final: 0.9152 (t80) REVERT: A 360 GLN cc_start: 0.9430 (tm130) cc_final: 0.9109 (tm-30) REVERT: A 365 MET cc_start: 0.9410 (ttm) cc_final: 0.8857 (tmm) REVERT: A 375 ASN cc_start: 0.9177 (t0) cc_final: 0.8972 (t0) REVERT: A 403 GLU cc_start: 0.8885 (pm20) cc_final: 0.8676 (pm20) REVERT: A 415 PHE cc_start: 0.9424 (m-80) cc_final: 0.9117 (m-80) REVERT: A 421 GLU cc_start: 0.8849 (pt0) cc_final: 0.8416 (pt0) REVERT: A 445 GLU cc_start: 0.9359 (mt-10) cc_final: 0.9017 (mt-10) REVERT: A 454 ARG cc_start: 0.9089 (ttp80) cc_final: 0.8723 (tpt170) REVERT: A 498 MET cc_start: 0.8961 (ttm) cc_final: 0.8665 (ttm) REVERT: A 499 MET cc_start: 0.8992 (tpp) cc_final: 0.8549 (tpp) REVERT: B 196 ASP cc_start: 0.7450 (t70) cc_final: 0.7181 (t70) REVERT: B 218 LYS cc_start: 0.9462 (mmmm) cc_final: 0.8795 (mtmm) REVERT: B 224 PHE cc_start: 0.9481 (t80) cc_final: 0.9225 (t80) REVERT: B 234 LEU cc_start: 0.9671 (mt) cc_final: 0.9449 (mt) REVERT: B 235 TYR cc_start: 0.9399 (t80) cc_final: 0.8374 (t80) REVERT: B 236 GLU cc_start: 0.9522 (mm-30) cc_final: 0.9047 (mm-30) REVERT: B 263 VAL cc_start: 0.9450 (t) cc_final: 0.9210 (p) REVERT: B 282 PHE cc_start: 0.9009 (p90) cc_final: 0.8710 (p90) REVERT: B 285 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8287 (mm-40) REVERT: B 293 TYR cc_start: 0.9402 (t80) cc_final: 0.9140 (t80) REVERT: B 297 VAL cc_start: 0.9754 (t) cc_final: 0.9445 (m) REVERT: B 318 PHE cc_start: 0.9247 (p90) cc_final: 0.9022 (p90) REVERT: B 331 ASN cc_start: 0.9255 (p0) cc_final: 0.8917 (p0) REVERT: B 375 ASN cc_start: 0.9391 (t0) cc_final: 0.9035 (t0) REVERT: B 379 GLN cc_start: 0.9398 (mm110) cc_final: 0.9016 (mm-40) REVERT: B 394 TYR cc_start: 0.9630 (t80) cc_final: 0.9260 (t80) REVERT: B 396 LYS cc_start: 0.9303 (tttp) cc_final: 0.8992 (tttt) REVERT: B 407 MET cc_start: 0.8913 (tmm) cc_final: 0.8408 (tmm) REVERT: B 421 GLU cc_start: 0.8909 (pt0) cc_final: 0.8503 (pt0) REVERT: B 426 SER cc_start: 0.9498 (t) cc_final: 0.9265 (p) REVERT: B 436 ASN cc_start: 0.9044 (t0) cc_final: 0.8812 (t0) REVERT: B 454 ARG cc_start: 0.9173 (ttp80) cc_final: 0.8855 (ttp80) REVERT: B 467 ASP cc_start: 0.9372 (OUTLIER) cc_final: 0.9129 (p0) REVERT: B 499 MET cc_start: 0.8833 (tpp) cc_final: 0.8495 (tpp) REVERT: C 164 LYS cc_start: 0.9271 (mtmt) cc_final: 0.9031 (mtpp) REVERT: C 172 ASP cc_start: 0.8817 (t0) cc_final: 0.7688 (t70) REVERT: C 179 MET cc_start: 0.7756 (ptp) cc_final: 0.7158 (ptp) REVERT: C 227 PHE cc_start: 0.9584 (t80) cc_final: 0.9333 (t80) REVERT: C 260 LEU cc_start: 0.9439 (mt) cc_final: 0.9100 (mt) REVERT: C 277 ASP cc_start: 0.9060 (m-30) cc_final: 0.8379 (p0) REVERT: C 293 TYR cc_start: 0.9371 (t80) cc_final: 0.8820 (t80) REVERT: C 365 MET cc_start: 0.9487 (ttm) cc_final: 0.9001 (tmm) REVERT: C 379 GLN cc_start: 0.9576 (mm110) cc_final: 0.9343 (mm110) REVERT: C 407 MET cc_start: 0.9037 (tmm) cc_final: 0.8723 (tmm) REVERT: C 415 PHE cc_start: 0.9531 (m-10) cc_final: 0.9232 (m-80) REVERT: C 421 GLU cc_start: 0.8765 (pt0) cc_final: 0.8507 (pt0) REVERT: C 445 GLU cc_start: 0.9367 (mt-10) cc_final: 0.9059 (mt-10) REVERT: C 454 ARG cc_start: 0.9464 (ttp-110) cc_final: 0.8568 (tpt170) REVERT: C 498 MET cc_start: 0.8947 (ttm) cc_final: 0.8689 (ttm) REVERT: C 499 MET cc_start: 0.8922 (tpp) cc_final: 0.8479 (tpp) REVERT: D 140 GLU cc_start: 0.8649 (pm20) cc_final: 0.8270 (pp20) REVERT: D 212 THR cc_start: 0.9114 (p) cc_final: 0.8265 (p) REVERT: D 213 GLN cc_start: 0.9362 (mm110) cc_final: 0.9096 (mm-40) REVERT: D 224 PHE cc_start: 0.9487 (t80) cc_final: 0.9272 (t80) REVERT: D 232 ASP cc_start: 0.9775 (m-30) cc_final: 0.9284 (m-30) REVERT: D 236 GLU cc_start: 0.9582 (mm-30) cc_final: 0.9210 (mm-30) REVERT: D 249 TYR cc_start: 0.8646 (p90) cc_final: 0.8325 (p90) REVERT: D 263 VAL cc_start: 0.9547 (t) cc_final: 0.9283 (p) REVERT: D 285 GLN cc_start: 0.9072 (mm-40) cc_final: 0.8396 (mm-40) REVERT: D 293 TYR cc_start: 0.9366 (t80) cc_final: 0.9090 (t80) REVERT: D 303 GLU cc_start: 0.9378 (tm-30) cc_final: 0.9152 (tm-30) REVERT: D 304 TYR cc_start: 0.9401 (t80) cc_final: 0.8880 (t80) REVERT: D 318 PHE cc_start: 0.9295 (p90) cc_final: 0.9088 (p90) REVERT: D 331 ASN cc_start: 0.9275 (p0) cc_final: 0.8748 (p0) REVERT: D 394 TYR cc_start: 0.9726 (t80) cc_final: 0.9416 (t80) REVERT: D 397 GLU cc_start: 0.9468 (tm-30) cc_final: 0.9101 (tm-30) REVERT: D 407 MET cc_start: 0.8874 (tmm) cc_final: 0.8516 (tmm) REVERT: D 421 GLU cc_start: 0.8845 (pt0) cc_final: 0.8357 (pt0) REVERT: D 436 ASN cc_start: 0.8923 (t0) cc_final: 0.8518 (t0) REVERT: D 454 ARG cc_start: 0.9152 (ttp80) cc_final: 0.8853 (ttp80) REVERT: D 471 GLN cc_start: 0.9606 (mm110) cc_final: 0.9185 (tp40) REVERT: D 520 ASP cc_start: 0.8973 (m-30) cc_final: 0.8492 (m-30) REVERT: E 172 ASP cc_start: 0.8764 (t0) cc_final: 0.8344 (t0) REVERT: E 181 MET cc_start: 0.7306 (tmm) cc_final: 0.7070 (tmm) REVERT: E 213 GLN cc_start: 0.9157 (mm110) cc_final: 0.8893 (mm-40) REVERT: E 233 GLU cc_start: 0.9476 (tp30) cc_final: 0.9189 (tp30) REVERT: E 271 GLN cc_start: 0.8613 (pt0) cc_final: 0.8041 (pt0) REVERT: E 272 ARG cc_start: 0.8821 (mtp180) cc_final: 0.8602 (mtp180) REVERT: E 279 LYS cc_start: 0.9532 (mmmt) cc_final: 0.9268 (mmmm) REVERT: E 323 LEU cc_start: 0.9469 (mp) cc_final: 0.9225 (mp) REVERT: E 331 ASN cc_start: 0.9167 (p0) cc_final: 0.8587 (p0) REVERT: E 365 MET cc_start: 0.9363 (ttm) cc_final: 0.9080 (ttm) REVERT: E 379 GLN cc_start: 0.8885 (mm110) cc_final: 0.6948 (tt0) REVERT: E 407 MET cc_start: 0.9026 (tmm) cc_final: 0.8746 (tmm) REVERT: E 421 GLU cc_start: 0.8846 (pt0) cc_final: 0.8543 (pt0) REVERT: E 424 CYS cc_start: 0.9420 (m) cc_final: 0.9023 (t) REVERT: E 426 SER cc_start: 0.9583 (t) cc_final: 0.9331 (p) REVERT: E 430 MET cc_start: 0.8912 (mmt) cc_final: 0.8637 (mmp) REVERT: E 455 ASN cc_start: 0.9116 (m-40) cc_final: 0.8777 (m-40) REVERT: E 467 ASP cc_start: 0.9208 (m-30) cc_final: 0.8862 (m-30) REVERT: G 179 MET cc_start: 0.9318 (tpp) cc_final: 0.8735 (tpp) REVERT: G 181 MET cc_start: 0.8786 (tpp) cc_final: 0.8542 (mtm) REVERT: G 183 ARG cc_start: 0.9309 (mmm160) cc_final: 0.8779 (mmm160) REVERT: G 194 MET cc_start: 0.4872 (tpp) cc_final: 0.4223 (tpp) REVERT: G 218 LYS cc_start: 0.9674 (mmmm) cc_final: 0.9142 (mtmm) REVERT: G 227 PHE cc_start: 0.9641 (t80) cc_final: 0.9402 (t80) REVERT: G 232 ASP cc_start: 0.9767 (m-30) cc_final: 0.9196 (m-30) REVERT: G 235 TYR cc_start: 0.9317 (t80) cc_final: 0.8875 (t80) REVERT: G 236 GLU cc_start: 0.9621 (mm-30) cc_final: 0.9180 (mm-30) REVERT: G 240 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8898 (mtmm) REVERT: G 293 TYR cc_start: 0.9339 (t80) cc_final: 0.7456 (t80) REVERT: G 300 LEU cc_start: 0.9584 (mm) cc_final: 0.9275 (mt) REVERT: G 303 GLU cc_start: 0.9381 (tm-30) cc_final: 0.9134 (tm-30) REVERT: G 312 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8268 (mt-10) REVERT: G 361 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8540 (t80) REVERT: G 382 ARG cc_start: 0.9630 (ttp80) cc_final: 0.9276 (mtp180) REVERT: G 421 GLU cc_start: 0.8838 (pt0) cc_final: 0.8578 (pt0) REVERT: G 424 CYS cc_start: 0.9254 (m) cc_final: 0.8953 (m) REVERT: G 436 ASN cc_start: 0.9312 (t0) cc_final: 0.8945 (t0) REVERT: G 445 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8544 (mm-30) REVERT: G 446 ARG cc_start: 0.8318 (ttp80) cc_final: 0.6999 (ttp80) REVERT: G 451 GLU cc_start: 0.8799 (mp0) cc_final: 0.8433 (mp0) REVERT: G 454 ARG cc_start: 0.9126 (ttp80) cc_final: 0.8669 (ttp-110) REVERT: G 455 ASN cc_start: 0.9317 (m-40) cc_final: 0.8920 (m-40) REVERT: G 499 MET cc_start: 0.9019 (tpp) cc_final: 0.8711 (tpp) REVERT: G 516 HIS cc_start: 0.8484 (t-90) cc_final: 0.7801 (t-90) REVERT: I 140 GLU cc_start: 0.8600 (pm20) cc_final: 0.8184 (pp20) REVERT: I 166 THR cc_start: 0.9645 (t) cc_final: 0.9364 (t) REVERT: I 172 ASP cc_start: 0.8714 (t0) cc_final: 0.8239 (t0) REVERT: I 183 ARG cc_start: 0.9025 (mtp85) cc_final: 0.8326 (ptp-110) REVERT: I 194 MET cc_start: 0.7941 (tmm) cc_final: 0.7593 (tmm) REVERT: I 213 GLN cc_start: 0.9157 (mm-40) cc_final: 0.8624 (tp-100) REVERT: I 218 LYS cc_start: 0.9193 (mmmm) cc_final: 0.8817 (mtmm) REVERT: I 235 TYR cc_start: 0.9004 (t80) cc_final: 0.8590 (t80) REVERT: I 252 GLN cc_start: 0.8997 (tp40) cc_final: 0.8714 (tp40) REVERT: I 261 TRP cc_start: 0.9341 (t-100) cc_final: 0.8766 (t-100) REVERT: I 271 GLN cc_start: 0.8143 (mt0) cc_final: 0.7938 (mt0) REVERT: I 277 ASP cc_start: 0.9065 (m-30) cc_final: 0.8834 (p0) REVERT: I 279 LYS cc_start: 0.9553 (mmmt) cc_final: 0.9270 (mmmm) REVERT: I 331 ASN cc_start: 0.9189 (p0) cc_final: 0.8504 (p0) REVERT: I 347 GLN cc_start: 0.8729 (mt0) cc_final: 0.8456 (mp10) REVERT: I 375 ASN cc_start: 0.8354 (t0) cc_final: 0.7949 (m-40) REVERT: I 407 MET cc_start: 0.8914 (tmm) cc_final: 0.8580 (tmm) REVERT: I 421 GLU cc_start: 0.8844 (pt0) cc_final: 0.8475 (pt0) REVERT: I 426 SER cc_start: 0.9618 (t) cc_final: 0.9266 (p) REVERT: I 455 ASN cc_start: 0.9072 (m-40) cc_final: 0.8605 (m-40) REVERT: I 467 ASP cc_start: 0.8998 (m-30) cc_final: 0.8625 (p0) REVERT: I 494 ASN cc_start: 0.9463 (m110) cc_final: 0.9141 (m-40) REVERT: I 499 MET cc_start: 0.8779 (tpp) cc_final: 0.8556 (tpp) REVERT: I 520 ASP cc_start: 0.9069 (m-30) cc_final: 0.8817 (m-30) REVERT: K 179 MET cc_start: 0.9244 (tpp) cc_final: 0.8687 (tpp) REVERT: K 218 LYS cc_start: 0.9484 (mmmm) cc_final: 0.9230 (mtpp) REVERT: K 219 PHE cc_start: 0.8353 (m-10) cc_final: 0.8152 (m-10) REVERT: K 232 ASP cc_start: 0.9740 (m-30) cc_final: 0.9395 (m-30) REVERT: K 235 TYR cc_start: 0.9159 (t80) cc_final: 0.8569 (t80) REVERT: K 236 GLU cc_start: 0.9601 (mm-30) cc_final: 0.9190 (mm-30) REVERT: K 240 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8921 (mtmm) REVERT: K 252 GLN cc_start: 0.8573 (tp40) cc_final: 0.8139 (tp-100) REVERT: K 260 LEU cc_start: 0.9440 (tp) cc_final: 0.9156 (tt) REVERT: K 293 TYR cc_start: 0.9323 (t80) cc_final: 0.7620 (t80) REVERT: K 318 PHE cc_start: 0.9296 (p90) cc_final: 0.9086 (p90) REVERT: K 331 ASN cc_start: 0.9278 (p0) cc_final: 0.8966 (p0) REVERT: K 361 PHE cc_start: 0.9146 (OUTLIER) cc_final: 0.8578 (t80) REVERT: K 382 ARG cc_start: 0.9606 (ttp80) cc_final: 0.9259 (mtp180) REVERT: K 407 MET cc_start: 0.8766 (tmm) cc_final: 0.8411 (tmm) REVERT: K 421 GLU cc_start: 0.8837 (pt0) cc_final: 0.8618 (pt0) REVERT: K 424 CYS cc_start: 0.9021 (m) cc_final: 0.8641 (m) REVERT: K 436 ASN cc_start: 0.9323 (t0) cc_final: 0.8972 (t0) REVERT: K 446 ARG cc_start: 0.8466 (ttp80) cc_final: 0.7073 (ttp80) REVERT: K 451 GLU cc_start: 0.8552 (mp0) cc_final: 0.8213 (mp0) REVERT: K 454 ARG cc_start: 0.9135 (ttp80) cc_final: 0.8771 (ttp-110) REVERT: K 455 ASN cc_start: 0.9267 (m-40) cc_final: 0.8833 (m-40) REVERT: K 467 ASP cc_start: 0.9552 (p0) cc_final: 0.9147 (p0) REVERT: K 508 MET cc_start: 0.8989 (mmm) cc_final: 0.8712 (mmm) REVERT: K 516 HIS cc_start: 0.8348 (t-90) cc_final: 0.7780 (t-90) REVERT: F 140 GLU cc_start: 0.8750 (pm20) cc_final: 0.8548 (pm20) REVERT: F 164 LYS cc_start: 0.9339 (mtmt) cc_final: 0.9041 (mtmm) REVERT: F 172 ASP cc_start: 0.8773 (t0) cc_final: 0.8450 (t0) REVERT: F 179 MET cc_start: 0.8828 (tpp) cc_final: 0.8392 (tpt) REVERT: F 194 MET cc_start: 0.7501 (tpp) cc_final: 0.7295 (tpp) REVERT: F 196 ASP cc_start: 0.8307 (t70) cc_final: 0.8036 (t70) REVERT: F 212 THR cc_start: 0.9403 (p) cc_final: 0.8562 (t) REVERT: F 213 GLN cc_start: 0.8805 (mm110) cc_final: 0.8027 (mm110) REVERT: F 216 ARG cc_start: 0.8444 (mtp180) cc_final: 0.7472 (mtp180) REVERT: F 233 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8834 (mt-10) REVERT: F 236 GLU cc_start: 0.9600 (mm-30) cc_final: 0.8968 (mm-30) REVERT: F 252 GLN cc_start: 0.9249 (tp40) cc_final: 0.8920 (tp40) REVERT: F 285 GLN cc_start: 0.9224 (mm-40) cc_final: 0.8826 (mm-40) REVERT: F 397 GLU cc_start: 0.9258 (tm-30) cc_final: 0.9021 (tm-30) REVERT: F 407 MET cc_start: 0.8819 (tmm) cc_final: 0.8607 (tmm) REVERT: F 413 PHE cc_start: 0.9002 (t80) cc_final: 0.8500 (t80) REVERT: F 421 GLU cc_start: 0.8908 (pt0) cc_final: 0.8378 (pt0) REVERT: F 425 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8896 (mt-10) REVERT: F 454 ARG cc_start: 0.9409 (ttp-110) cc_final: 0.9153 (ttp-110) REVERT: F 499 MET cc_start: 0.8901 (tpp) cc_final: 0.8491 (tpp) REVERT: H 172 ASP cc_start: 0.8294 (t0) cc_final: 0.8079 (t0) REVERT: H 177 GLU cc_start: 0.8019 (tt0) cc_final: 0.7693 (tt0) REVERT: H 194 MET cc_start: 0.7327 (tpp) cc_final: 0.6895 (tpt) REVERT: H 215 PHE cc_start: 0.8411 (m-80) cc_final: 0.8008 (m-80) REVERT: H 232 ASP cc_start: 0.9657 (m-30) cc_final: 0.9089 (m-30) REVERT: H 236 GLU cc_start: 0.9463 (mm-30) cc_final: 0.9102 (mm-30) REVERT: H 252 GLN cc_start: 0.8501 (tp-100) cc_final: 0.8255 (tp-100) REVERT: H 285 GLN cc_start: 0.8915 (mm-40) cc_final: 0.8415 (mm-40) REVERT: H 289 LYS cc_start: 0.8819 (mtmm) cc_final: 0.8574 (mtmp) REVERT: H 293 TYR cc_start: 0.8943 (t80) cc_final: 0.8675 (t80) REVERT: H 308 TYR cc_start: 0.9066 (m-80) cc_final: 0.8582 (m-10) REVERT: H 320 LYS cc_start: 0.9216 (tppt) cc_final: 0.8805 (tppt) REVERT: H 328 LYS cc_start: 0.8647 (mtpp) cc_final: 0.8353 (mtpt) REVERT: H 331 ASN cc_start: 0.8981 (p0) cc_final: 0.8338 (p0) REVERT: H 346 LYS cc_start: 0.8352 (mtpp) cc_final: 0.7967 (mtpp) REVERT: H 347 GLN cc_start: 0.8848 (pm20) cc_final: 0.7855 (mp10) REVERT: H 397 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8652 (tm-30) REVERT: H 436 ASN cc_start: 0.8449 (t0) cc_final: 0.8177 (t0) REVERT: H 446 ARG cc_start: 0.9265 (tmm-80) cc_final: 0.8674 (tpp80) REVERT: H 465 MET cc_start: 0.9466 (mmm) cc_final: 0.9186 (mmm) REVERT: J 172 ASP cc_start: 0.8883 (t0) cc_final: 0.8424 (t70) REVERT: J 179 MET cc_start: 0.8757 (tmm) cc_final: 0.8500 (tmm) REVERT: J 180 ASP cc_start: 0.9302 (p0) cc_final: 0.8923 (p0) REVERT: J 196 ASP cc_start: 0.7873 (t70) cc_final: 0.7468 (p0) REVERT: J 213 GLN cc_start: 0.8694 (mm110) cc_final: 0.7961 (mm110) REVERT: J 215 PHE cc_start: 0.8867 (m-80) cc_final: 0.8540 (m-80) REVERT: J 216 ARG cc_start: 0.8670 (mtp180) cc_final: 0.8233 (mtp180) REVERT: J 232 ASP cc_start: 0.9660 (m-30) cc_final: 0.9424 (m-30) REVERT: J 233 GLU cc_start: 0.9151 (mt-10) cc_final: 0.8874 (mt-10) REVERT: J 235 TYR cc_start: 0.9356 (t80) cc_final: 0.9064 (t80) REVERT: J 245 LYS cc_start: 0.8895 (mtmm) cc_final: 0.8671 (mmmm) REVERT: J 252 GLN cc_start: 0.8995 (tp40) cc_final: 0.8390 (tp-100) REVERT: J 293 TYR cc_start: 0.9206 (t80) cc_final: 0.8971 (t80) REVERT: J 303 GLU cc_start: 0.9188 (tm-30) cc_final: 0.8955 (tm-30) REVERT: J 320 LYS cc_start: 0.9209 (tppp) cc_final: 0.8927 (tppt) REVERT: J 347 GLN cc_start: 0.8516 (mp10) cc_final: 0.8147 (mp10) REVERT: J 407 MET cc_start: 0.8779 (tmm) cc_final: 0.8474 (tmm) REVERT: J 421 GLU cc_start: 0.8909 (pt0) cc_final: 0.8331 (pt0) REVERT: J 425 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8564 (mt-10) REVERT: J 496 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8069 (ppp) REVERT: J 499 MET cc_start: 0.9096 (tpt) cc_final: 0.8451 (tpt) REVERT: L 144 PHE cc_start: 0.8426 (t80) cc_final: 0.8054 (t80) REVERT: L 172 ASP cc_start: 0.7996 (t0) cc_final: 0.7584 (t70) REVERT: L 194 MET cc_start: 0.7170 (tpt) cc_final: 0.4997 (pmm) REVERT: L 233 GLU cc_start: 0.9580 (mm-30) cc_final: 0.8922 (tp30) REVERT: L 235 TYR cc_start: 0.9008 (t80) cc_final: 0.8750 (t80) REVERT: L 236 GLU cc_start: 0.9408 (mm-30) cc_final: 0.9048 (tm-30) REVERT: L 285 GLN cc_start: 0.8993 (mm-40) cc_final: 0.8634 (mm-40) REVERT: L 317 ARG cc_start: 0.8491 (mmt-90) cc_final: 0.8000 (mmt-90) REVERT: L 320 LYS cc_start: 0.9181 (tppt) cc_final: 0.8770 (tppt) REVERT: L 331 ASN cc_start: 0.8897 (p0) cc_final: 0.8440 (p0) REVERT: L 333 MET cc_start: 0.9009 (mmp) cc_final: 0.8568 (mmp) REVERT: L 353 GLU cc_start: 0.9434 (mt-10) cc_final: 0.9225 (mt-10) REVERT: L 361 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8615 (t80) REVERT: L 381 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8722 (tm-30) REVERT: L 387 ARG cc_start: 0.9123 (mmm-85) cc_final: 0.8873 (mmm-85) REVERT: L 426 SER cc_start: 0.9076 (t) cc_final: 0.8369 (p) REVERT: L 430 MET cc_start: 0.9217 (mpp) cc_final: 0.8794 (mpp) REVERT: L 446 ARG cc_start: 0.9156 (tmm-80) cc_final: 0.8630 (tpp80) REVERT: L 499 MET cc_start: 0.8748 (tpp) cc_final: 0.7489 (tpp) outliers start: 177 outliers final: 128 residues processed: 1882 average time/residue: 0.1997 time to fit residues: 613.0661 Evaluate side-chains 1913 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 1777 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 513 LYS Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 510 ASN Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 283 CYS Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 510 ASN Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 498 MET Chi-restraints excluded: chain D residue 510 ASN Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain E residue 312 GLU Chi-restraints excluded: chain E residue 343 SER Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 496 MET Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 240 LYS Chi-restraints excluded: chain G residue 266 CYS Chi-restraints excluded: chain G residue 312 GLU Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 343 SER Chi-restraints excluded: chain G residue 361 PHE Chi-restraints excluded: chain G residue 380 SER Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 469 SER Chi-restraints excluded: chain G residue 505 LEU Chi-restraints excluded: chain G residue 523 SER Chi-restraints excluded: chain I residue 266 CYS Chi-restraints excluded: chain I residue 283 CYS Chi-restraints excluded: chain I residue 289 LYS Chi-restraints excluded: chain I residue 312 GLU Chi-restraints excluded: chain I residue 419 SER Chi-restraints excluded: chain I residue 428 SER Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 442 ILE Chi-restraints excluded: chain I residue 469 SER Chi-restraints excluded: chain I residue 484 VAL Chi-restraints excluded: chain I residue 506 ASP Chi-restraints excluded: chain I residue 510 ASN Chi-restraints excluded: chain K residue 231 ILE Chi-restraints excluded: chain K residue 240 LYS Chi-restraints excluded: chain K residue 283 CYS Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain K residue 325 GLU Chi-restraints excluded: chain K residue 361 PHE Chi-restraints excluded: chain K residue 399 LYS Chi-restraints excluded: chain K residue 423 THR Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 505 LEU Chi-restraints excluded: chain K residue 523 SER Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 325 GLU Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain F residue 506 ASP Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 266 CYS Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain H residue 327 ASP Chi-restraints excluded: chain H residue 360 GLN Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 407 MET Chi-restraints excluded: chain H residue 408 VAL Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 458 SER Chi-restraints excluded: chain H residue 510 ASN Chi-restraints excluded: chain H residue 512 VAL Chi-restraints excluded: chain J residue 231 ILE Chi-restraints excluded: chain J residue 325 GLU Chi-restraints excluded: chain J residue 380 SER Chi-restraints excluded: chain J residue 429 VAL Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 496 MET Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain L residue 231 ILE Chi-restraints excluded: chain L residue 343 SER Chi-restraints excluded: chain L residue 360 GLN Chi-restraints excluded: chain L residue 361 PHE Chi-restraints excluded: chain L residue 362 LEU Chi-restraints excluded: chain L residue 408 VAL Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 458 SER Chi-restraints excluded: chain L residue 507 LYS Chi-restraints excluded: chain L residue 510 ASN Chi-restraints excluded: chain L residue 520 ASP Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain D residue 602 GLN Chi-restraints excluded: chain E residue 602 GLN Chi-restraints excluded: chain F residue 602 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 323 optimal weight: 10.0000 chunk 315 optimal weight: 0.0050 chunk 274 optimal weight: 0.9990 chunk 156 optimal weight: 20.0000 chunk 27 optimal weight: 0.9990 chunk 364 optimal weight: 0.9990 chunk 305 optimal weight: 0.0870 chunk 147 optimal weight: 0.0670 chunk 219 optimal weight: 4.9990 chunk 416 optimal weight: 2.9990 chunk 361 optimal weight: 1.9990 overall best weight: 0.4314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN C 351 ASN C 375 ASN C 379 GLN ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 ASN ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 ASN E 510 ASN ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 375 ASN ** K 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 298 ASN F 360 GLN F 519 HIS H 471 GLN ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 241 GLN J 360 GLN J 375 ASN J 519 HIS ** L 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.155445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.115480 restraints weight = 65795.078| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.96 r_work: 0.3244 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36972 Z= 0.115 Angle : 0.612 9.787 49932 Z= 0.314 Chirality : 0.043 0.213 5544 Planarity : 0.004 0.047 6408 Dihedral : 4.892 53.938 4929 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.06 % Favored : 93.90 % Rotamer: Outliers : 3.51 % Allowed : 24.73 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.13), residues: 4620 helix: 1.21 (0.11), residues: 2388 sheet: -0.39 (0.30), residues: 360 loop : -0.24 (0.16), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 446 TYR 0.026 0.001 TYR F 293 PHE 0.029 0.001 PHE G 144 TRP 0.009 0.001 TRP J 261 HIS 0.006 0.001 HIS J 157 Details of bonding type rmsd covalent geometry : bond 0.00259 (36972) covalent geometry : angle 0.61169 (49932) hydrogen bonds : bond 0.02909 ( 1700) hydrogen bonds : angle 4.74041 ( 5193) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9240 Ramachandran restraints generated. 4620 Oldfield, 0 Emsley, 4620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9240 Ramachandran restraints generated. 4620 Oldfield, 0 Emsley, 4620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1996 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 1855 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 LYS cc_start: 0.9207 (mtmt) cc_final: 0.8946 (mtmm) REVERT: A 194 MET cc_start: 0.6765 (tpp) cc_final: 0.5811 (tpp) REVERT: A 213 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8582 (mm-40) REVERT: A 227 PHE cc_start: 0.9499 (t80) cc_final: 0.9242 (t80) REVERT: A 236 GLU cc_start: 0.9661 (mm-30) cc_final: 0.9333 (mm-30) REVERT: A 252 GLN cc_start: 0.8772 (tp40) cc_final: 0.8531 (tp-100) REVERT: A 261 TRP cc_start: 0.9467 (t-100) cc_final: 0.9158 (t-100) REVERT: A 277 ASP cc_start: 0.9080 (m-30) cc_final: 0.8820 (p0) REVERT: A 289 LYS cc_start: 0.9169 (mttp) cc_final: 0.8920 (mttp) REVERT: A 293 TYR cc_start: 0.9400 (t80) cc_final: 0.8818 (t80) REVERT: A 306 HIS cc_start: 0.8967 (m-70) cc_final: 0.8628 (m-70) REVERT: A 347 GLN cc_start: 0.8836 (mp10) cc_final: 0.8512 (mp10) REVERT: A 357 TYR cc_start: 0.9358 (t80) cc_final: 0.8878 (t80) REVERT: A 360 GLN cc_start: 0.9397 (tm130) cc_final: 0.8999 (tm-30) REVERT: A 387 ARG cc_start: 0.9267 (tpp80) cc_final: 0.8998 (tpp80) REVERT: A 403 GLU cc_start: 0.8838 (pm20) cc_final: 0.8636 (pm20) REVERT: A 407 MET cc_start: 0.8882 (tmm) cc_final: 0.8586 (tmm) REVERT: A 415 PHE cc_start: 0.9423 (m-80) cc_final: 0.9156 (m-80) REVERT: A 421 GLU cc_start: 0.8784 (pt0) cc_final: 0.8397 (pt0) REVERT: A 445 GLU cc_start: 0.9316 (mt-10) cc_final: 0.9025 (mt-10) REVERT: A 454 ARG cc_start: 0.9016 (ttp80) cc_final: 0.8699 (tpt170) REVERT: A 498 MET cc_start: 0.8806 (ttm) cc_final: 0.8552 (ttm) REVERT: A 499 MET cc_start: 0.9129 (tpp) cc_final: 0.8750 (tpp) REVERT: B 196 ASP cc_start: 0.7382 (t70) cc_final: 0.7119 (t70) REVERT: B 218 LYS cc_start: 0.9488 (mmmm) cc_final: 0.8698 (mmmm) REVERT: B 224 PHE cc_start: 0.9331 (t80) cc_final: 0.9124 (t80) REVERT: B 234 LEU cc_start: 0.9705 (mt) cc_final: 0.9476 (mt) REVERT: B 235 TYR cc_start: 0.9374 (t80) cc_final: 0.8363 (t80) REVERT: B 236 GLU cc_start: 0.9533 (mm-30) cc_final: 0.9036 (mm-30) REVERT: B 252 GLN cc_start: 0.8344 (tp40) cc_final: 0.7302 (tp-100) REVERT: B 282 PHE cc_start: 0.8922 (p90) cc_final: 0.8678 (p90) REVERT: B 285 GLN cc_start: 0.9051 (mm-40) cc_final: 0.8329 (mm-40) REVERT: B 293 TYR cc_start: 0.9360 (t80) cc_final: 0.9068 (t80) REVERT: B 297 VAL cc_start: 0.9688 (t) cc_final: 0.9409 (m) REVERT: B 318 PHE cc_start: 0.9160 (p90) cc_final: 0.8735 (p90) REVERT: B 331 ASN cc_start: 0.9205 (p0) cc_final: 0.8919 (p0) REVERT: B 375 ASN cc_start: 0.9178 (t0) cc_final: 0.8944 (t0) REVERT: B 394 TYR cc_start: 0.9545 (t80) cc_final: 0.9215 (t80) REVERT: B 396 LYS cc_start: 0.9163 (tttp) cc_final: 0.8961 (tttp) REVERT: B 407 MET cc_start: 0.8879 (tmm) cc_final: 0.8366 (tmm) REVERT: B 414 TYR cc_start: 0.9511 (t80) cc_final: 0.8905 (t80) REVERT: B 421 GLU cc_start: 0.8949 (pt0) cc_final: 0.8534 (pt0) REVERT: B 426 SER cc_start: 0.9454 (t) cc_final: 0.9249 (p) REVERT: B 436 ASN cc_start: 0.8962 (t0) cc_final: 0.8716 (t0) REVERT: B 454 ARG cc_start: 0.9163 (ttp80) cc_final: 0.8893 (ttp80) REVERT: B 467 ASP cc_start: 0.9343 (OUTLIER) cc_final: 0.9118 (p0) REVERT: C 164 LYS cc_start: 0.9290 (mtmt) cc_final: 0.9051 (mtpp) REVERT: C 172 ASP cc_start: 0.8824 (t0) cc_final: 0.7859 (t70) REVERT: C 175 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8466 (pp) REVERT: C 179 MET cc_start: 0.7735 (ptp) cc_final: 0.7015 (ptp) REVERT: C 213 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8540 (tp40) REVERT: C 227 PHE cc_start: 0.9575 (t80) cc_final: 0.9319 (t80) REVERT: C 277 ASP cc_start: 0.9034 (m-30) cc_final: 0.8680 (p0) REVERT: C 347 GLN cc_start: 0.8693 (mp10) cc_final: 0.8369 (mp10) REVERT: C 365 MET cc_start: 0.9476 (ttm) cc_final: 0.8976 (tmm) REVERT: C 387 ARG cc_start: 0.9209 (tpp80) cc_final: 0.8939 (tpp80) REVERT: C 407 MET cc_start: 0.8912 (tmm) cc_final: 0.8658 (tmm) REVERT: C 415 PHE cc_start: 0.9476 (m-10) cc_final: 0.9210 (m-80) REVERT: C 421 GLU cc_start: 0.8751 (pt0) cc_final: 0.8491 (pt0) REVERT: C 445 GLU cc_start: 0.9282 (mt-10) cc_final: 0.9004 (mt-10) REVERT: C 467 ASP cc_start: 0.9370 (p0) cc_final: 0.8624 (p0) REVERT: C 498 MET cc_start: 0.8844 (ttm) cc_final: 0.8623 (ttm) REVERT: C 499 MET cc_start: 0.9055 (tpp) cc_final: 0.8694 (tpp) REVERT: C 508 MET cc_start: 0.9264 (mtt) cc_final: 0.8786 (mtt) REVERT: D 140 GLU cc_start: 0.8677 (pm20) cc_final: 0.8338 (pp20) REVERT: D 196 ASP cc_start: 0.7072 (t0) cc_final: 0.6822 (t0) REVERT: D 212 THR cc_start: 0.9104 (p) cc_final: 0.8283 (p) REVERT: D 213 GLN cc_start: 0.9200 (mm110) cc_final: 0.8966 (mm-40) REVERT: D 225 MET cc_start: 0.9432 (mmp) cc_final: 0.9227 (mmp) REVERT: D 232 ASP cc_start: 0.9784 (m-30) cc_final: 0.9466 (m-30) REVERT: D 236 GLU cc_start: 0.9561 (mm-30) cc_final: 0.9167 (mm-30) REVERT: D 246 VAL cc_start: 0.8597 (OUTLIER) cc_final: 0.7946 (t) REVERT: D 249 TYR cc_start: 0.8522 (p90) cc_final: 0.8106 (p90) REVERT: D 260 LEU cc_start: 0.9467 (tp) cc_final: 0.8939 (tp) REVERT: D 277 ASP cc_start: 0.9278 (m-30) cc_final: 0.8915 (p0) REVERT: D 293 TYR cc_start: 0.9307 (t80) cc_final: 0.9020 (t80) REVERT: D 303 GLU cc_start: 0.9383 (tm-30) cc_final: 0.9161 (tm-30) REVERT: D 318 PHE cc_start: 0.9166 (p90) cc_final: 0.8849 (p90) REVERT: D 360 GLN cc_start: 0.9102 (tm-30) cc_final: 0.8860 (tm-30) REVERT: D 373 PHE cc_start: 0.8880 (t80) cc_final: 0.8416 (t80) REVERT: D 379 GLN cc_start: 0.9594 (mm-40) cc_final: 0.9321 (mm110) REVERT: D 394 TYR cc_start: 0.9641 (t80) cc_final: 0.9255 (t80) REVERT: D 397 GLU cc_start: 0.9485 (tm-30) cc_final: 0.9114 (tm-30) REVERT: D 407 MET cc_start: 0.8808 (tmm) cc_final: 0.8405 (tmm) REVERT: D 414 TYR cc_start: 0.9452 (t80) cc_final: 0.8821 (t80) REVERT: D 421 GLU cc_start: 0.8865 (pt0) cc_final: 0.8391 (pt0) REVERT: D 436 ASN cc_start: 0.8925 (t0) cc_final: 0.8596 (t0) REVERT: D 454 ARG cc_start: 0.9188 (ttp80) cc_final: 0.8871 (ttp80) REVERT: D 520 ASP cc_start: 0.8924 (m-30) cc_final: 0.8437 (m-30) REVERT: E 172 ASP cc_start: 0.8854 (t0) cc_final: 0.8424 (t0) REVERT: E 194 MET cc_start: 0.8283 (tpp) cc_final: 0.7965 (tpt) REVERT: E 213 GLN cc_start: 0.9165 (mm110) cc_final: 0.8894 (mm-40) REVERT: E 279 LYS cc_start: 0.9527 (mmmt) cc_final: 0.9304 (mmmm) REVERT: E 318 PHE cc_start: 0.9124 (p90) cc_final: 0.8882 (p90) REVERT: E 323 LEU cc_start: 0.9548 (mp) cc_final: 0.9326 (mp) REVERT: E 331 ASN cc_start: 0.9044 (p0) cc_final: 0.8308 (p0) REVERT: E 365 MET cc_start: 0.9296 (ttm) cc_final: 0.9046 (ttm) REVERT: E 379 GLN cc_start: 0.8878 (mm110) cc_final: 0.6854 (tt0) REVERT: E 387 ARG cc_start: 0.9049 (mmm-85) cc_final: 0.8781 (tpp80) REVERT: E 407 MET cc_start: 0.8822 (tmm) cc_final: 0.8517 (tmm) REVERT: E 421 GLU cc_start: 0.8833 (pt0) cc_final: 0.8535 (pt0) REVERT: E 424 CYS cc_start: 0.9429 (m) cc_final: 0.8851 (t) REVERT: E 426 SER cc_start: 0.9510 (t) cc_final: 0.9270 (p) REVERT: E 430 MET cc_start: 0.8805 (mmt) cc_final: 0.8562 (mmp) REVERT: E 455 ASN cc_start: 0.9084 (m-40) cc_final: 0.8697 (m-40) REVERT: E 467 ASP cc_start: 0.9147 (m-30) cc_final: 0.8782 (m-30) REVERT: G 179 MET cc_start: 0.9304 (tpp) cc_final: 0.8748 (tpp) REVERT: G 181 MET cc_start: 0.9011 (tpp) cc_final: 0.8716 (mtm) REVERT: G 183 ARG cc_start: 0.9249 (mmm160) cc_final: 0.8673 (mmm160) REVERT: G 194 MET cc_start: 0.4926 (tpp) cc_final: 0.4177 (tpp) REVERT: G 218 LYS cc_start: 0.9675 (mmmm) cc_final: 0.9282 (mtmm) REVERT: G 223 ASP cc_start: 0.8888 (p0) cc_final: 0.8610 (p0) REVERT: G 227 PHE cc_start: 0.9634 (t80) cc_final: 0.9377 (t80) REVERT: G 232 ASP cc_start: 0.9768 (m-30) cc_final: 0.9213 (m-30) REVERT: G 235 TYR cc_start: 0.9283 (t80) cc_final: 0.8830 (t80) REVERT: G 236 GLU cc_start: 0.9637 (mm-30) cc_final: 0.9199 (mm-30) REVERT: G 240 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8998 (mtmm) REVERT: G 252 GLN cc_start: 0.8664 (tp-100) cc_final: 0.8255 (tp40) REVERT: G 260 LEU cc_start: 0.9396 (tp) cc_final: 0.9130 (tt) REVERT: G 293 TYR cc_start: 0.9260 (t80) cc_final: 0.7429 (t80) REVERT: G 300 LEU cc_start: 0.9548 (mm) cc_final: 0.9259 (mt) REVERT: G 312 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8277 (mt-10) REVERT: G 328 LYS cc_start: 0.9026 (mtpt) cc_final: 0.8697 (mtpp) REVERT: G 333 MET cc_start: 0.9150 (mmp) cc_final: 0.8720 (mmp) REVERT: G 361 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8592 (t80) REVERT: G 382 ARG cc_start: 0.9600 (ttp80) cc_final: 0.9317 (mtp180) REVERT: G 421 GLU cc_start: 0.8857 (pt0) cc_final: 0.8605 (pt0) REVERT: G 424 CYS cc_start: 0.9194 (m) cc_final: 0.8890 (m) REVERT: G 436 ASN cc_start: 0.9396 (t0) cc_final: 0.9038 (t0) REVERT: G 445 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8493 (mm-30) REVERT: G 446 ARG cc_start: 0.8334 (ttp80) cc_final: 0.7038 (ttp80) REVERT: G 451 GLU cc_start: 0.8790 (mp0) cc_final: 0.8384 (mp0) REVERT: G 454 ARG cc_start: 0.9143 (ttp80) cc_final: 0.8707 (ttp-110) REVERT: G 455 ASN cc_start: 0.9324 (m-40) cc_final: 0.8788 (m110) REVERT: G 516 HIS cc_start: 0.8352 (t-90) cc_final: 0.7666 (t-90) REVERT: G 517 PHE cc_start: 0.9412 (t80) cc_final: 0.9195 (t80) REVERT: I 140 GLU cc_start: 0.8591 (pm20) cc_final: 0.8370 (pp20) REVERT: I 172 ASP cc_start: 0.8797 (t0) cc_final: 0.8306 (t0) REVERT: I 183 ARG cc_start: 0.9043 (mtp85) cc_final: 0.8266 (ptp-110) REVERT: I 194 MET cc_start: 0.7934 (tmm) cc_final: 0.7605 (tmm) REVERT: I 213 GLN cc_start: 0.9122 (mm-40) cc_final: 0.8669 (tp40) REVERT: I 218 LYS cc_start: 0.9214 (mmmm) cc_final: 0.8821 (mtmm) REVERT: I 235 TYR cc_start: 0.8965 (t80) cc_final: 0.8645 (t80) REVERT: I 236 GLU cc_start: 0.9570 (mm-30) cc_final: 0.9121 (mm-30) REVERT: I 249 TYR cc_start: 0.9045 (p90) cc_final: 0.8738 (p90) REVERT: I 261 TRP cc_start: 0.9306 (t-100) cc_final: 0.8874 (t-100) REVERT: I 277 ASP cc_start: 0.8996 (m-30) cc_final: 0.8642 (p0) REVERT: I 279 LYS cc_start: 0.9523 (mmmt) cc_final: 0.9245 (mmmm) REVERT: I 331 ASN cc_start: 0.9107 (p0) cc_final: 0.8415 (p0) REVERT: I 347 GLN cc_start: 0.8579 (mt0) cc_final: 0.8077 (mp10) REVERT: I 407 MET cc_start: 0.8863 (tmm) cc_final: 0.8515 (tmm) REVERT: I 421 GLU cc_start: 0.8846 (pt0) cc_final: 0.8483 (pt0) REVERT: I 426 SER cc_start: 0.9579 (t) cc_final: 0.9230 (p) REVERT: I 455 ASN cc_start: 0.8991 (m-40) cc_final: 0.8657 (m-40) REVERT: I 465 MET cc_start: 0.9572 (mmm) cc_final: 0.9346 (mmm) REVERT: I 467 ASP cc_start: 0.9014 (m-30) cc_final: 0.8656 (p0) REVERT: I 520 ASP cc_start: 0.9034 (m-30) cc_final: 0.8811 (m-30) REVERT: K 179 MET cc_start: 0.9194 (tpp) cc_final: 0.8639 (tpp) REVERT: K 232 ASP cc_start: 0.9739 (m-30) cc_final: 0.9415 (m-30) REVERT: K 235 TYR cc_start: 0.9170 (t80) cc_final: 0.8571 (t80) REVERT: K 236 GLU cc_start: 0.9591 (mm-30) cc_final: 0.9135 (mm-30) REVERT: K 240 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.8922 (mtmm) REVERT: K 277 ASP cc_start: 0.9315 (m-30) cc_final: 0.8882 (p0) REVERT: K 293 TYR cc_start: 0.9272 (t80) cc_final: 0.7572 (t80) REVERT: K 312 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8388 (mt-10) REVERT: K 318 PHE cc_start: 0.9247 (p90) cc_final: 0.8918 (p90) REVERT: K 333 MET cc_start: 0.9142 (mmp) cc_final: 0.8758 (mmp) REVERT: K 361 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8622 (t80) REVERT: K 382 ARG cc_start: 0.9590 (ttp80) cc_final: 0.9380 (mtp180) REVERT: K 388 ASN cc_start: 0.9176 (m-40) cc_final: 0.8974 (m-40) REVERT: K 407 MET cc_start: 0.8593 (tmm) cc_final: 0.8289 (tmm) REVERT: K 421 GLU cc_start: 0.8858 (pt0) cc_final: 0.8646 (pt0) REVERT: K 424 CYS cc_start: 0.8899 (m) cc_final: 0.8516 (t) REVERT: K 436 ASN cc_start: 0.9359 (t0) cc_final: 0.8990 (t0) REVERT: K 446 ARG cc_start: 0.8482 (ttp80) cc_final: 0.7083 (ttp80) REVERT: K 451 GLU cc_start: 0.8476 (mp0) cc_final: 0.8122 (mp0) REVERT: K 454 ARG cc_start: 0.9067 (ttp80) cc_final: 0.8743 (ttp-110) REVERT: K 455 ASN cc_start: 0.9273 (m-40) cc_final: 0.8726 (m-40) REVERT: K 467 ASP cc_start: 0.9455 (p0) cc_final: 0.8959 (p0) REVERT: K 499 MET cc_start: 0.8863 (tpp) cc_final: 0.8603 (tpp) REVERT: K 508 MET cc_start: 0.8927 (mmm) cc_final: 0.8664 (mmm) REVERT: K 516 HIS cc_start: 0.8311 (t-90) cc_final: 0.7932 (t70) REVERT: F 140 GLU cc_start: 0.8741 (pm20) cc_final: 0.8511 (pm20) REVERT: F 164 LYS cc_start: 0.9357 (mtmt) cc_final: 0.9059 (mtmm) REVERT: F 172 ASP cc_start: 0.8770 (t0) cc_final: 0.8340 (t70) REVERT: F 179 MET cc_start: 0.8667 (tpp) cc_final: 0.8450 (tpp) REVERT: F 196 ASP cc_start: 0.8211 (t70) cc_final: 0.7913 (t70) REVERT: F 212 THR cc_start: 0.9421 (p) cc_final: 0.8558 (t) REVERT: F 213 GLN cc_start: 0.8923 (mm110) cc_final: 0.8069 (mm110) REVERT: F 216 ARG cc_start: 0.8477 (mtp180) cc_final: 0.7451 (mtp180) REVERT: F 233 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8837 (mt-10) REVERT: F 236 GLU cc_start: 0.9564 (mm-30) cc_final: 0.9062 (mm-30) REVERT: F 252 GLN cc_start: 0.9054 (tp40) cc_final: 0.8779 (tp40) REVERT: F 285 GLN cc_start: 0.9159 (mm-40) cc_final: 0.8854 (mm-40) REVERT: F 347 GLN cc_start: 0.8531 (mp10) cc_final: 0.8216 (mp10) REVERT: F 365 MET cc_start: 0.9462 (ttm) cc_final: 0.9009 (tmm) REVERT: F 382 ARG cc_start: 0.9511 (ttp80) cc_final: 0.9154 (mtp-110) REVERT: F 397 GLU cc_start: 0.9252 (tm-30) cc_final: 0.9028 (tm-30) REVERT: F 421 GLU cc_start: 0.8878 (pt0) cc_final: 0.8313 (pt0) REVERT: F 454 ARG cc_start: 0.9431 (ttp-110) cc_final: 0.9197 (ttp-110) REVERT: F 496 MET cc_start: 0.8499 (ppp) cc_final: 0.7786 (ppp) REVERT: F 498 MET cc_start: 0.9155 (mtp) cc_final: 0.8716 (mtp) REVERT: F 499 MET cc_start: 0.8847 (tpp) cc_final: 0.8594 (tpp) REVERT: H 172 ASP cc_start: 0.8220 (t0) cc_final: 0.7965 (t0) REVERT: H 194 MET cc_start: 0.7414 (tpp) cc_final: 0.7004 (tpt) REVERT: H 215 PHE cc_start: 0.8338 (m-80) cc_final: 0.8015 (m-80) REVERT: H 232 ASP cc_start: 0.9659 (m-30) cc_final: 0.9087 (m-30) REVERT: H 236 GLU cc_start: 0.9433 (mm-30) cc_final: 0.9064 (mm-30) REVERT: H 252 GLN cc_start: 0.8668 (tp-100) cc_final: 0.7920 (tp-100) REVERT: H 255 LYS cc_start: 0.9531 (mtmm) cc_final: 0.8939 (mttt) REVERT: H 285 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8455 (mm-40) REVERT: H 293 TYR cc_start: 0.8913 (t80) cc_final: 0.8681 (t80) REVERT: H 299 ASP cc_start: 0.8094 (m-30) cc_final: 0.7646 (m-30) REVERT: H 308 TYR cc_start: 0.9028 (m-80) cc_final: 0.8477 (m-10) REVERT: H 320 LYS cc_start: 0.9207 (tppt) cc_final: 0.8794 (tppt) REVERT: H 328 LYS cc_start: 0.8645 (mtpp) cc_final: 0.8347 (mtpt) REVERT: H 331 ASN cc_start: 0.8913 (p0) cc_final: 0.8358 (p0) REVERT: H 378 PHE cc_start: 0.9099 (t80) cc_final: 0.8886 (t80) REVERT: H 396 LYS cc_start: 0.8723 (tttt) cc_final: 0.8523 (tttm) REVERT: H 397 GLU cc_start: 0.9078 (tm-30) cc_final: 0.8650 (tm-30) REVERT: H 440 CYS cc_start: 0.8560 (t) cc_final: 0.8105 (t) REVERT: H 446 ARG cc_start: 0.9237 (tmm-80) cc_final: 0.8685 (tpp80) REVERT: H 465 MET cc_start: 0.9488 (mmm) cc_final: 0.9101 (mmm) REVERT: H 471 GLN cc_start: 0.9248 (tp-100) cc_final: 0.8986 (mm110) REVERT: J 172 ASP cc_start: 0.8893 (t0) cc_final: 0.8491 (t70) REVERT: J 180 ASP cc_start: 0.9302 (p0) cc_final: 0.8921 (p0) REVERT: J 196 ASP cc_start: 0.8038 (t70) cc_final: 0.7770 (p0) REVERT: J 213 GLN cc_start: 0.8867 (mm110) cc_final: 0.8386 (mm-40) REVERT: J 215 PHE cc_start: 0.8760 (m-80) cc_final: 0.8360 (m-80) REVERT: J 216 ARG cc_start: 0.8706 (mtp180) cc_final: 0.8475 (mtp180) REVERT: J 232 ASP cc_start: 0.9670 (m-30) cc_final: 0.9252 (m-30) REVERT: J 233 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8851 (mt-10) REVERT: J 236 GLU cc_start: 0.9609 (mm-30) cc_final: 0.9253 (mm-30) REVERT: J 245 LYS cc_start: 0.8883 (mtmm) cc_final: 0.8626 (mmmm) REVERT: J 303 GLU cc_start: 0.9224 (tm-30) cc_final: 0.9005 (tm-30) REVERT: J 320 LYS cc_start: 0.9156 (tppp) cc_final: 0.8824 (tppt) REVERT: J 347 GLN cc_start: 0.8628 (mp10) cc_final: 0.8128 (mp10) REVERT: J 397 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8745 (tt0) REVERT: J 407 MET cc_start: 0.8667 (tmm) cc_final: 0.8383 (tmm) REVERT: J 421 GLU cc_start: 0.8903 (pt0) cc_final: 0.8303 (pt0) REVERT: J 496 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8038 (ppp) REVERT: J 499 MET cc_start: 0.9079 (tpt) cc_final: 0.8549 (tpt) REVERT: L 172 ASP cc_start: 0.7846 (t0) cc_final: 0.7484 (t70) REVERT: L 194 MET cc_start: 0.7050 (tpt) cc_final: 0.4958 (pmm) REVERT: L 213 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8482 (mm-40) REVERT: L 235 TYR cc_start: 0.8961 (t80) cc_final: 0.8611 (t80) REVERT: L 236 GLU cc_start: 0.9389 (mm-30) cc_final: 0.9007 (mm-30) REVERT: L 252 GLN cc_start: 0.8837 (tp40) cc_final: 0.8159 (tp-100) REVERT: L 255 LYS cc_start: 0.9515 (mtmm) cc_final: 0.9027 (mttt) REVERT: L 271 GLN cc_start: 0.7115 (tt0) cc_final: 0.6739 (tt0) REVERT: L 285 GLN cc_start: 0.9082 (mm-40) cc_final: 0.8841 (mm-40) REVERT: L 320 LYS cc_start: 0.9228 (tppt) cc_final: 0.8805 (tppt) REVERT: L 331 ASN cc_start: 0.8877 (p0) cc_final: 0.8448 (p0) REVERT: L 347 GLN cc_start: 0.8668 (mp10) cc_final: 0.8215 (pm20) REVERT: L 353 GLU cc_start: 0.9413 (mt-10) cc_final: 0.9154 (mt-10) REVERT: L 378 PHE cc_start: 0.9121 (t80) cc_final: 0.8875 (t80) REVERT: L 381 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8723 (tm-30) REVERT: L 387 ARG cc_start: 0.9161 (mmm-85) cc_final: 0.8919 (mmm-85) REVERT: L 423 THR cc_start: 0.8859 (p) cc_final: 0.8591 (t) REVERT: L 426 SER cc_start: 0.9069 (t) cc_final: 0.8574 (p) REVERT: L 430 MET cc_start: 0.9170 (mpp) cc_final: 0.8745 (mpp) REVERT: L 446 ARG cc_start: 0.9134 (tmm-80) cc_final: 0.8621 (tpp80) REVERT: L 447 VAL cc_start: 0.9360 (t) cc_final: 0.9104 (m) REVERT: L 465 MET cc_start: 0.9424 (mmm) cc_final: 0.9160 (mmm) REVERT: D 602 GLN cc_start: 0.6713 (OUTLIER) cc_final: 0.4786 (pp30) outliers start: 141 outliers final: 93 residues processed: 1897 average time/residue: 0.1968 time to fit residues: 610.1329 Evaluate side-chains 1879 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 1774 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 510 ASN Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 187 GLN Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain C residue 283 CYS Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 510 ASN Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 498 MET Chi-restraints excluded: chain D residue 510 ASN Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 496 MET Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain G residue 240 LYS Chi-restraints excluded: chain G residue 312 GLU Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 361 PHE Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain G residue 380 SER Chi-restraints excluded: chain G residue 469 SER Chi-restraints excluded: chain G residue 498 MET Chi-restraints excluded: chain G residue 505 LEU Chi-restraints excluded: chain G residue 522 VAL Chi-restraints excluded: chain I residue 408 VAL Chi-restraints excluded: chain I residue 423 THR Chi-restraints excluded: chain I residue 484 VAL Chi-restraints excluded: chain K residue 240 LYS Chi-restraints excluded: chain K residue 283 CYS Chi-restraints excluded: chain K residue 312 GLU Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain K residue 325 GLU Chi-restraints excluded: chain K residue 361 PHE Chi-restraints excluded: chain K residue 381 GLU Chi-restraints excluded: chain K residue 400 CYS Chi-restraints excluded: chain K residue 403 GLU Chi-restraints excluded: chain K residue 419 SER Chi-restraints excluded: chain K residue 423 THR Chi-restraints excluded: chain K residue 505 LEU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain H residue 325 GLU Chi-restraints excluded: chain H residue 360 GLN Chi-restraints excluded: chain H residue 407 MET Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 458 SER Chi-restraints excluded: chain H residue 496 MET Chi-restraints excluded: chain H residue 510 ASN Chi-restraints excluded: chain J residue 381 GLU Chi-restraints excluded: chain J residue 429 VAL Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 496 MET Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain L residue 360 GLN Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 451 GLU Chi-restraints excluded: chain L residue 458 SER Chi-restraints excluded: chain L residue 467 ASP Chi-restraints excluded: chain L residue 510 ASN Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain D residue 602 GLN Chi-restraints excluded: chain E residue 602 GLN Chi-restraints excluded: chain F residue 602 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 119 optimal weight: 20.0000 chunk 307 optimal weight: 6.9990 chunk 428 optimal weight: 0.0170 chunk 232 optimal weight: 3.9990 chunk 266 optimal weight: 20.0000 chunk 293 optimal weight: 0.9980 chunk 438 optimal weight: 1.9990 chunk 235 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 229 optimal weight: 0.9990 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN C 455 ASN ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 ASN ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN E 351 ASN G 298 ASN I 271 GLN K 271 GLN K 375 ASN K 388 ASN F 360 GLN F 510 ASN F 519 HIS ** H 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 241 GLN J 360 GLN J 519 HIS ** L 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.153770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.114966 restraints weight = 65248.085| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.88 r_work: 0.3181 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 36972 Z= 0.179 Angle : 0.652 10.288 49932 Z= 0.336 Chirality : 0.045 0.241 5544 Planarity : 0.005 0.048 6408 Dihedral : 4.933 52.040 4929 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.95 % Favored : 93.96 % Rotamer: Outliers : 4.70 % Allowed : 25.45 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.13), residues: 4620 helix: 1.19 (0.11), residues: 2388 sheet: -0.45 (0.30), residues: 360 loop : -0.23 (0.16), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 217 TYR 0.026 0.002 TYR J 293 PHE 0.022 0.001 PHE E 322 TRP 0.018 0.002 TRP G 501 HIS 0.007 0.001 HIS J 157 Details of bonding type rmsd covalent geometry : bond 0.00412 (36972) covalent geometry : angle 0.65157 (49932) hydrogen bonds : bond 0.03273 ( 1700) hydrogen bonds : angle 4.84219 ( 5193) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9240 Ramachandran restraints generated. 4620 Oldfield, 0 Emsley, 4620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9240 Ramachandran restraints generated. 4620 Oldfield, 0 Emsley, 4620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1984 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 1795 time to evaluate : 1.041 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 164 LYS cc_start: 0.9261 (mtmt) cc_final: 0.8979 (mtmm) REVERT: A 194 MET cc_start: 0.6790 (tpp) cc_final: 0.5714 (tpp) REVERT: A 213 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8632 (mm-40) REVERT: A 236 GLU cc_start: 0.9686 (mm-30) cc_final: 0.9386 (mm-30) REVERT: A 252 GLN cc_start: 0.8994 (tp40) cc_final: 0.8717 (tp-100) REVERT: A 277 ASP cc_start: 0.9120 (m-30) cc_final: 0.8834 (p0) REVERT: A 293 TYR cc_start: 0.9450 (t80) cc_final: 0.8871 (t80) REVERT: A 306 HIS cc_start: 0.9043 (m-70) cc_final: 0.8787 (m-70) REVERT: A 347 GLN cc_start: 0.8938 (mp10) cc_final: 0.8614 (mp10) REVERT: A 357 TYR cc_start: 0.9406 (t80) cc_final: 0.9131 (t80) REVERT: A 360 GLN cc_start: 0.9431 (tm130) cc_final: 0.9058 (tm-30) REVERT: A 361 PHE cc_start: 0.9263 (OUTLIER) cc_final: 0.8400 (t80) REVERT: A 387 ARG cc_start: 0.9308 (tpp80) cc_final: 0.8973 (tpp80) REVERT: A 415 PHE cc_start: 0.9474 (m-80) cc_final: 0.9094 (m-80) REVERT: A 421 GLU cc_start: 0.8818 (pt0) cc_final: 0.8433 (pt0) REVERT: A 434 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8909 (pp) REVERT: A 445 GLU cc_start: 0.9361 (mt-10) cc_final: 0.9023 (mt-10) REVERT: A 454 ARG cc_start: 0.9080 (ttp80) cc_final: 0.8724 (tpt170) REVERT: A 498 MET cc_start: 0.8917 (ttm) cc_final: 0.8624 (ttm) REVERT: A 499 MET cc_start: 0.9145 (tpp) cc_final: 0.8741 (tpp) REVERT: B 196 ASP cc_start: 0.7407 (t70) cc_final: 0.7150 (t70) REVERT: B 234 LEU cc_start: 0.9683 (mt) cc_final: 0.9454 (mt) REVERT: B 235 TYR cc_start: 0.9409 (t80) cc_final: 0.8236 (t80) REVERT: B 236 GLU cc_start: 0.9542 (mm-30) cc_final: 0.9072 (mm-30) REVERT: B 252 GLN cc_start: 0.8646 (tp40) cc_final: 0.7696 (tp-100) REVERT: B 263 VAL cc_start: 0.9460 (t) cc_final: 0.9195 (p) REVERT: B 282 PHE cc_start: 0.9043 (p90) cc_final: 0.8585 (p90) REVERT: B 285 GLN cc_start: 0.9094 (mm-40) cc_final: 0.8353 (mm-40) REVERT: B 293 TYR cc_start: 0.9372 (t80) cc_final: 0.9168 (t80) REVERT: B 318 PHE cc_start: 0.9200 (p90) cc_final: 0.8992 (p90) REVERT: B 331 ASN cc_start: 0.9269 (p0) cc_final: 0.9043 (p0) REVERT: B 396 LYS cc_start: 0.9247 (tttp) cc_final: 0.8962 (tttp) REVERT: B 407 MET cc_start: 0.8859 (tmm) cc_final: 0.8469 (tmm) REVERT: B 421 GLU cc_start: 0.8899 (pt0) cc_final: 0.8498 (pt0) REVERT: B 426 SER cc_start: 0.9520 (t) cc_final: 0.9307 (p) REVERT: B 436 ASN cc_start: 0.9013 (t0) cc_final: 0.8779 (t0) REVERT: B 454 ARG cc_start: 0.9189 (ttp80) cc_final: 0.8898 (ttp80) REVERT: B 467 ASP cc_start: 0.9384 (OUTLIER) cc_final: 0.9174 (p0) REVERT: C 164 LYS cc_start: 0.9304 (mtmt) cc_final: 0.9072 (mtpp) REVERT: C 172 ASP cc_start: 0.8760 (t0) cc_final: 0.7801 (t70) REVERT: C 175 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8491 (pp) REVERT: C 179 MET cc_start: 0.7754 (ptp) cc_final: 0.7139 (ptp) REVERT: C 227 PHE cc_start: 0.9620 (t80) cc_final: 0.9358 (t80) REVERT: C 246 VAL cc_start: 0.8519 (OUTLIER) cc_final: 0.8011 (t) REVERT: C 277 ASP cc_start: 0.9038 (m-30) cc_final: 0.8630 (p0) REVERT: C 293 TYR cc_start: 0.9405 (t80) cc_final: 0.8848 (t80) REVERT: C 347 GLN cc_start: 0.8847 (mp10) cc_final: 0.8442 (mp10) REVERT: C 375 ASN cc_start: 0.9157 (t0) cc_final: 0.8709 (t0) REVERT: C 387 ARG cc_start: 0.9257 (tpp80) cc_final: 0.8981 (tpp80) REVERT: C 397 GLU cc_start: 0.9220 (tm-30) cc_final: 0.8939 (tm-30) REVERT: C 415 PHE cc_start: 0.9548 (m-10) cc_final: 0.9239 (m-80) REVERT: C 421 GLU cc_start: 0.8729 (pt0) cc_final: 0.8422 (pt0) REVERT: C 445 GLU cc_start: 0.9343 (mt-10) cc_final: 0.9073 (mt-10) REVERT: C 455 ASN cc_start: 0.9278 (m-40) cc_final: 0.9008 (m-40) REVERT: C 467 ASP cc_start: 0.9536 (p0) cc_final: 0.9050 (p0) REVERT: C 498 MET cc_start: 0.8936 (ttm) cc_final: 0.8718 (ttm) REVERT: C 499 MET cc_start: 0.8931 (tpp) cc_final: 0.8505 (tpp) REVERT: C 508 MET cc_start: 0.9356 (mtt) cc_final: 0.9010 (mtt) REVERT: D 140 GLU cc_start: 0.8697 (pm20) cc_final: 0.8347 (pp20) REVERT: D 196 ASP cc_start: 0.7223 (t0) cc_final: 0.6946 (t0) REVERT: D 212 THR cc_start: 0.9069 (p) cc_final: 0.8273 (p) REVERT: D 213 GLN cc_start: 0.9322 (mm110) cc_final: 0.9039 (mm-40) REVERT: D 232 ASP cc_start: 0.9793 (m-30) cc_final: 0.9264 (m-30) REVERT: D 236 GLU cc_start: 0.9569 (mm-30) cc_final: 0.9184 (mm-30) REVERT: D 249 TYR cc_start: 0.8619 (p90) cc_final: 0.8181 (p90) REVERT: D 260 LEU cc_start: 0.9453 (tp) cc_final: 0.9063 (tp) REVERT: D 263 VAL cc_start: 0.9552 (t) cc_final: 0.9293 (p) REVERT: D 285 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8403 (mm-40) REVERT: D 293 TYR cc_start: 0.9364 (t80) cc_final: 0.9096 (t80) REVERT: D 303 GLU cc_start: 0.9463 (tm-30) cc_final: 0.9239 (tm-30) REVERT: D 318 PHE cc_start: 0.9273 (p90) cc_final: 0.8995 (p90) REVERT: D 394 TYR cc_start: 0.9705 (t80) cc_final: 0.9363 (t80) REVERT: D 397 GLU cc_start: 0.9541 (tm-30) cc_final: 0.9194 (tm-30) REVERT: D 407 MET cc_start: 0.8862 (tmm) cc_final: 0.8427 (tmm) REVERT: D 414 TYR cc_start: 0.9498 (t80) cc_final: 0.8867 (t80) REVERT: D 421 GLU cc_start: 0.8895 (pt0) cc_final: 0.8423 (pt0) REVERT: D 454 ARG cc_start: 0.9159 (ttp80) cc_final: 0.8841 (ttp80) REVERT: D 471 GLN cc_start: 0.9563 (mm110) cc_final: 0.9343 (tp40) REVERT: D 511 SER cc_start: 0.9153 (t) cc_final: 0.8945 (t) REVERT: D 520 ASP cc_start: 0.8945 (m-30) cc_final: 0.8474 (m-30) REVERT: E 172 ASP cc_start: 0.8780 (t0) cc_final: 0.8461 (t0) REVERT: E 183 ARG cc_start: 0.8822 (mmm-85) cc_final: 0.8478 (ttp-110) REVERT: E 213 GLN cc_start: 0.9164 (mm110) cc_final: 0.8881 (mm110) REVERT: E 233 GLU cc_start: 0.9443 (tp30) cc_final: 0.9117 (tp30) REVERT: E 271 GLN cc_start: 0.8626 (pt0) cc_final: 0.7975 (pt0) REVERT: E 279 LYS cc_start: 0.9520 (mmmt) cc_final: 0.9282 (mmmm) REVERT: E 323 LEU cc_start: 0.9582 (mp) cc_final: 0.9368 (mp) REVERT: E 331 ASN cc_start: 0.9117 (p0) cc_final: 0.8331 (p0) REVERT: E 365 MET cc_start: 0.9280 (ttm) cc_final: 0.8913 (ttm) REVERT: E 407 MET cc_start: 0.8928 (tmm) cc_final: 0.8573 (tmm) REVERT: E 421 GLU cc_start: 0.8814 (pt0) cc_final: 0.8535 (pt0) REVERT: E 424 CYS cc_start: 0.9454 (m) cc_final: 0.8884 (t) REVERT: E 426 SER cc_start: 0.9552 (t) cc_final: 0.9317 (p) REVERT: E 430 MET cc_start: 0.8946 (mmt) cc_final: 0.8676 (mmp) REVERT: E 455 ASN cc_start: 0.9144 (m-40) cc_final: 0.8740 (m-40) REVERT: E 467 ASP cc_start: 0.9175 (m-30) cc_final: 0.8827 (m-30) REVERT: G 179 MET cc_start: 0.9354 (tpp) cc_final: 0.8711 (ptt) REVERT: G 181 MET cc_start: 0.9057 (tpp) cc_final: 0.8816 (mtm) REVERT: G 183 ARG cc_start: 0.9254 (mmm160) cc_final: 0.8871 (mmm160) REVERT: G 194 MET cc_start: 0.5227 (tpp) cc_final: 0.4879 (tpp) REVERT: G 227 PHE cc_start: 0.9638 (t80) cc_final: 0.9380 (t80) REVERT: G 232 ASP cc_start: 0.9785 (m-30) cc_final: 0.9191 (m-30) REVERT: G 235 TYR cc_start: 0.9243 (t80) cc_final: 0.8759 (t80) REVERT: G 236 GLU cc_start: 0.9635 (mm-30) cc_final: 0.9209 (mm-30) REVERT: G 240 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.8944 (mtmm) REVERT: G 260 LEU cc_start: 0.9456 (tp) cc_final: 0.9180 (tt) REVERT: G 293 TYR cc_start: 0.9314 (t80) cc_final: 0.7500 (t80) REVERT: G 300 LEU cc_start: 0.9556 (mm) cc_final: 0.9257 (mt) REVERT: G 312 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8298 (mt-10) REVERT: G 361 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8619 (t80) REVERT: G 370 TYR cc_start: 0.9093 (t80) cc_final: 0.8872 (t80) REVERT: G 382 ARG cc_start: 0.9637 (ttp80) cc_final: 0.9344 (mtp180) REVERT: G 421 GLU cc_start: 0.8868 (pt0) cc_final: 0.8576 (pt0) REVERT: G 424 CYS cc_start: 0.9247 (m) cc_final: 0.8952 (m) REVERT: G 436 ASN cc_start: 0.9358 (t0) cc_final: 0.8997 (t0) REVERT: G 446 ARG cc_start: 0.8387 (ttp80) cc_final: 0.7153 (ttp80) REVERT: G 451 GLU cc_start: 0.8835 (mp0) cc_final: 0.8368 (mp0) REVERT: G 454 ARG cc_start: 0.9189 (ttp80) cc_final: 0.8680 (ttp-110) REVERT: G 455 ASN cc_start: 0.9323 (m-40) cc_final: 0.8853 (m-40) REVERT: G 499 MET cc_start: 0.9027 (tpp) cc_final: 0.8722 (tpp) REVERT: G 516 HIS cc_start: 0.8405 (t-90) cc_final: 0.7741 (t-90) REVERT: I 140 GLU cc_start: 0.8606 (pm20) cc_final: 0.8367 (pp20) REVERT: I 172 ASP cc_start: 0.8840 (t0) cc_final: 0.8370 (t0) REVERT: I 183 ARG cc_start: 0.9026 (mtp85) cc_final: 0.8291 (ptp-110) REVERT: I 218 LYS cc_start: 0.9269 (mmmm) cc_final: 0.8990 (mtpp) REVERT: I 235 TYR cc_start: 0.8992 (t80) cc_final: 0.8701 (t80) REVERT: I 236 GLU cc_start: 0.9581 (mm-30) cc_final: 0.9142 (mm-30) REVERT: I 261 TRP cc_start: 0.9303 (t-100) cc_final: 0.8863 (t-100) REVERT: I 279 LYS cc_start: 0.9546 (mmmt) cc_final: 0.9297 (mmmm) REVERT: I 331 ASN cc_start: 0.9144 (p0) cc_final: 0.8463 (p0) REVERT: I 347 GLN cc_start: 0.8700 (mt0) cc_final: 0.8177 (mp10) REVERT: I 379 GLN cc_start: 0.8843 (mm110) cc_final: 0.6889 (tt0) REVERT: I 407 MET cc_start: 0.8949 (tmm) cc_final: 0.8573 (tmm) REVERT: I 421 GLU cc_start: 0.8845 (pt0) cc_final: 0.8513 (pt0) REVERT: I 426 SER cc_start: 0.9597 (t) cc_final: 0.9293 (p) REVERT: I 455 ASN cc_start: 0.9091 (m-40) cc_final: 0.8714 (m-40) REVERT: I 494 ASN cc_start: 0.9412 (m-40) cc_final: 0.9091 (m-40) REVERT: I 520 ASP cc_start: 0.9069 (m-30) cc_final: 0.8829 (m-30) REVERT: K 179 MET cc_start: 0.9194 (tpp) cc_final: 0.8749 (tpp) REVERT: K 218 LYS cc_start: 0.9535 (mmmm) cc_final: 0.9221 (mtpp) REVERT: K 232 ASP cc_start: 0.9763 (m-30) cc_final: 0.9404 (m-30) REVERT: K 235 TYR cc_start: 0.9172 (t80) cc_final: 0.8607 (t80) REVERT: K 236 GLU cc_start: 0.9596 (mm-30) cc_final: 0.9160 (mm-30) REVERT: K 240 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.8945 (mtmm) REVERT: K 252 GLN cc_start: 0.8511 (tp40) cc_final: 0.8300 (tp-100) REVERT: K 260 LEU cc_start: 0.9410 (tp) cc_final: 0.9145 (tt) REVERT: K 293 TYR cc_start: 0.9297 (t80) cc_final: 0.7585 (t80) REVERT: K 318 PHE cc_start: 0.9281 (p90) cc_final: 0.9045 (p90) REVERT: K 331 ASN cc_start: 0.9248 (p0) cc_final: 0.8821 (p0) REVERT: K 344 LEU cc_start: 0.9596 (mt) cc_final: 0.9378 (mp) REVERT: K 361 PHE cc_start: 0.9024 (OUTLIER) cc_final: 0.8633 (t80) REVERT: K 370 TYR cc_start: 0.9184 (t80) cc_final: 0.8930 (t80) REVERT: K 382 ARG cc_start: 0.9603 (ttp80) cc_final: 0.9247 (mtp180) REVERT: K 388 ASN cc_start: 0.9214 (m110) cc_final: 0.8996 (m110) REVERT: K 407 MET cc_start: 0.8658 (tmm) cc_final: 0.8349 (tmm) REVERT: K 416 GLN cc_start: 0.9419 (mt0) cc_final: 0.9002 (mt0) REVERT: K 421 GLU cc_start: 0.8840 (pt0) cc_final: 0.8573 (pt0) REVERT: K 424 CYS cc_start: 0.8925 (m) cc_final: 0.8407 (m) REVERT: K 430 MET cc_start: 0.9349 (OUTLIER) cc_final: 0.8758 (mpp) REVERT: K 436 ASN cc_start: 0.9312 (t0) cc_final: 0.8948 (t0) REVERT: K 446 ARG cc_start: 0.8465 (ttp80) cc_final: 0.7323 (ttp80) REVERT: K 451 GLU cc_start: 0.8503 (mp0) cc_final: 0.7893 (mp0) REVERT: K 455 ASN cc_start: 0.9290 (m-40) cc_final: 0.8822 (m-40) REVERT: K 467 ASP cc_start: 0.9459 (p0) cc_final: 0.8827 (p0) REVERT: K 508 MET cc_start: 0.8946 (mmm) cc_final: 0.8645 (mmm) REVERT: K 516 HIS cc_start: 0.8347 (t-90) cc_final: 0.7776 (t-90) REVERT: K 520 ASP cc_start: 0.9022 (m-30) cc_final: 0.8564 (m-30) REVERT: F 140 GLU cc_start: 0.8781 (pm20) cc_final: 0.8525 (pm20) REVERT: F 172 ASP cc_start: 0.8712 (t0) cc_final: 0.8407 (t0) REVERT: F 196 ASP cc_start: 0.7991 (t70) cc_final: 0.7603 (t70) REVERT: F 212 THR cc_start: 0.9374 (p) cc_final: 0.8350 (t) REVERT: F 213 GLN cc_start: 0.8909 (mm110) cc_final: 0.8082 (mm-40) REVERT: F 216 ARG cc_start: 0.8446 (mtp180) cc_final: 0.7449 (mtp180) REVERT: F 233 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8865 (mt-10) REVERT: F 236 GLU cc_start: 0.9572 (mm-30) cc_final: 0.8994 (mm-30) REVERT: F 279 LYS cc_start: 0.9638 (mmmt) cc_final: 0.9274 (mmmt) REVERT: F 285 GLN cc_start: 0.9263 (mm-40) cc_final: 0.8999 (mm-40) REVERT: F 299 ASP cc_start: 0.8935 (m-30) cc_final: 0.8715 (m-30) REVERT: F 379 GLN cc_start: 0.9586 (mm110) cc_final: 0.9297 (mm110) REVERT: F 382 ARG cc_start: 0.9496 (ttp80) cc_final: 0.9158 (mtp-110) REVERT: F 397 GLU cc_start: 0.9279 (tm-30) cc_final: 0.9051 (tm-30) REVERT: F 421 GLU cc_start: 0.8897 (pt0) cc_final: 0.8311 (pt0) REVERT: F 425 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8715 (mt-10) REVERT: F 454 ARG cc_start: 0.9405 (ttp-110) cc_final: 0.9169 (ttp-110) REVERT: F 499 MET cc_start: 0.8811 (tpp) cc_final: 0.8542 (tpp) REVERT: H 172 ASP cc_start: 0.8146 (t0) cc_final: 0.7870 (t0) REVERT: H 194 MET cc_start: 0.7331 (tpp) cc_final: 0.6949 (tpt) REVERT: H 215 PHE cc_start: 0.8271 (m-80) cc_final: 0.8041 (m-80) REVERT: H 218 LYS cc_start: 0.9323 (tptt) cc_final: 0.9094 (mtmm) REVERT: H 232 ASP cc_start: 0.9653 (m-30) cc_final: 0.9090 (m-30) REVERT: H 236 GLU cc_start: 0.9433 (mm-30) cc_final: 0.9062 (mm-30) REVERT: H 252 GLN cc_start: 0.8645 (tp-100) cc_final: 0.7947 (tp-100) REVERT: H 255 LYS cc_start: 0.9443 (mtmm) cc_final: 0.8743 (mttt) REVERT: H 299 ASP cc_start: 0.8132 (m-30) cc_final: 0.7866 (m-30) REVERT: H 308 TYR cc_start: 0.9061 (m-80) cc_final: 0.8702 (m-10) REVERT: H 320 LYS cc_start: 0.9242 (tppt) cc_final: 0.8816 (tppt) REVERT: H 328 LYS cc_start: 0.8690 (mtpp) cc_final: 0.8387 (mtpt) REVERT: H 331 ASN cc_start: 0.8886 (p0) cc_final: 0.8476 (p0) REVERT: H 397 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8770 (tm-30) REVERT: H 446 ARG cc_start: 0.9280 (tmm-80) cc_final: 0.8701 (tpp80) REVERT: H 508 MET cc_start: 0.8986 (mtp) cc_final: 0.8695 (tpp) REVERT: J 172 ASP cc_start: 0.8850 (t0) cc_final: 0.8465 (t70) REVERT: J 196 ASP cc_start: 0.8112 (t70) cc_final: 0.7842 (p0) REVERT: J 213 GLN cc_start: 0.8859 (mm110) cc_final: 0.8535 (mm-40) REVERT: J 215 PHE cc_start: 0.8824 (m-80) cc_final: 0.8391 (m-80) REVERT: J 232 ASP cc_start: 0.9693 (m-30) cc_final: 0.9244 (m-30) REVERT: J 233 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8877 (mt-10) REVERT: J 236 GLU cc_start: 0.9608 (mm-30) cc_final: 0.9157 (mm-30) REVERT: J 245 LYS cc_start: 0.8884 (mtmm) cc_final: 0.8669 (mmmm) REVERT: J 303 GLU cc_start: 0.9256 (tm-30) cc_final: 0.9045 (tm-30) REVERT: J 320 LYS cc_start: 0.9193 (tppp) cc_final: 0.8814 (tppt) REVERT: J 347 GLN cc_start: 0.8700 (mp10) cc_final: 0.8141 (mp10) REVERT: J 407 MET cc_start: 0.8808 (tmm) cc_final: 0.8448 (tmm) REVERT: J 421 GLU cc_start: 0.8913 (pt0) cc_final: 0.8385 (pt0) REVERT: J 499 MET cc_start: 0.9047 (tpt) cc_final: 0.8531 (tpt) REVERT: L 172 ASP cc_start: 0.8015 (t0) cc_final: 0.7657 (t0) REVERT: L 194 MET cc_start: 0.7121 (tpt) cc_final: 0.4968 (pmm) REVERT: L 213 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8438 (mm-40) REVERT: L 235 TYR cc_start: 0.8967 (t80) cc_final: 0.8622 (t80) REVERT: L 236 GLU cc_start: 0.9382 (mm-30) cc_final: 0.9011 (tm-30) REVERT: L 241 GLN cc_start: 0.7760 (mp10) cc_final: 0.7296 (mp10) REVERT: L 271 GLN cc_start: 0.7137 (tt0) cc_final: 0.6777 (tt0) REVERT: L 285 GLN cc_start: 0.8990 (mm-40) cc_final: 0.8680 (mm-40) REVERT: L 320 LYS cc_start: 0.9210 (tppt) cc_final: 0.8787 (tppt) REVERT: L 331 ASN cc_start: 0.8907 (p0) cc_final: 0.8527 (p0) REVERT: L 333 MET cc_start: 0.9001 (mmp) cc_final: 0.8460 (mmp) REVERT: L 347 GLN cc_start: 0.8784 (mp10) cc_final: 0.8340 (pm20) REVERT: L 353 GLU cc_start: 0.9433 (mt-10) cc_final: 0.9168 (mt-10) REVERT: L 381 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8601 (tm-30) REVERT: L 423 THR cc_start: 0.8822 (p) cc_final: 0.8570 (t) REVERT: L 446 ARG cc_start: 0.9227 (tmm-80) cc_final: 0.8725 (tpp80) REVERT: D 602 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.5237 (pp30) outliers start: 189 outliers final: 149 residues processed: 1857 average time/residue: 0.1946 time to fit residues: 591.8697 Evaluate side-chains 1913 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 1752 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 510 ASN Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 187 GLN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 283 CYS Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 510 ASN Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 498 MET Chi-restraints excluded: chain D residue 510 ASN Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 312 GLU Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 458 SER Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 496 MET Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain G residue 240 LYS Chi-restraints excluded: chain G residue 277 ASP Chi-restraints excluded: chain G residue 283 CYS Chi-restraints excluded: chain G residue 312 GLU Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 361 PHE Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain G residue 380 SER Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 469 SER Chi-restraints excluded: chain G residue 498 MET Chi-restraints excluded: chain G residue 505 LEU Chi-restraints excluded: chain G residue 522 VAL Chi-restraints excluded: chain G residue 523 SER Chi-restraints excluded: chain I residue 266 CYS Chi-restraints excluded: chain I residue 289 LYS Chi-restraints excluded: chain I residue 302 THR Chi-restraints excluded: chain I residue 419 SER Chi-restraints excluded: chain I residue 423 THR Chi-restraints excluded: chain I residue 428 SER Chi-restraints excluded: chain I residue 442 ILE Chi-restraints excluded: chain I residue 484 VAL Chi-restraints excluded: chain I residue 510 ASN Chi-restraints excluded: chain K residue 194 MET Chi-restraints excluded: chain K residue 240 LYS Chi-restraints excluded: chain K residue 283 CYS Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain K residue 325 GLU Chi-restraints excluded: chain K residue 361 PHE Chi-restraints excluded: chain K residue 381 GLU Chi-restraints excluded: chain K residue 400 CYS Chi-restraints excluded: chain K residue 403 GLU Chi-restraints excluded: chain K residue 419 SER Chi-restraints excluded: chain K residue 423 THR Chi-restraints excluded: chain K residue 430 MET Chi-restraints excluded: chain K residue 505 LEU Chi-restraints excluded: chain K residue 523 SER Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 325 GLU Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 245 LYS Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain H residue 325 GLU Chi-restraints excluded: chain H residue 360 GLN Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 407 MET Chi-restraints excluded: chain H residue 408 VAL Chi-restraints excluded: chain H residue 421 GLU Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 458 SER Chi-restraints excluded: chain H residue 461 HIS Chi-restraints excluded: chain H residue 496 MET Chi-restraints excluded: chain H residue 510 ASN Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 231 ILE Chi-restraints excluded: chain J residue 325 GLU Chi-restraints excluded: chain J residue 381 GLU Chi-restraints excluded: chain J residue 429 VAL Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain L residue 231 ILE Chi-restraints excluded: chain L residue 253 LEU Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 362 LEU Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 458 SER Chi-restraints excluded: chain L residue 467 ASP Chi-restraints excluded: chain L residue 496 MET Chi-restraints excluded: chain L residue 510 ASN Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain D residue 602 GLN Chi-restraints excluded: chain E residue 602 GLN Chi-restraints excluded: chain F residue 602 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 264 optimal weight: 0.8980 chunk 338 optimal weight: 6.9990 chunk 286 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 308 optimal weight: 9.9990 chunk 449 optimal weight: 0.9990 chunk 337 optimal weight: 1.9990 chunk 285 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 255 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 HIS ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 GLN C 351 ASN ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 ASN ** E 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN F 360 GLN F 519 HIS ** H 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 471 GLN ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 241 GLN J 360 GLN ** J 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 519 HIS L 306 HIS L 471 GLN L 516 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.155822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.117387 restraints weight = 64708.414| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.91 r_work: 0.3215 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36972 Z= 0.135 Angle : 0.656 10.540 49932 Z= 0.333 Chirality : 0.044 0.237 5544 Planarity : 0.004 0.046 6408 Dihedral : 4.935 52.510 4929 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.26 % Favored : 93.66 % Rotamer: Outliers : 4.20 % Allowed : 26.89 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.13), residues: 4620 helix: 1.22 (0.11), residues: 2388 sheet: -0.37 (0.30), residues: 360 loop : -0.20 (0.16), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 217 TYR 0.029 0.002 TYR J 293 PHE 0.022 0.001 PHE K 415 TRP 0.012 0.001 TRP G 501 HIS 0.008 0.001 HIS J 157 Details of bonding type rmsd covalent geometry : bond 0.00314 (36972) covalent geometry : angle 0.65568 (49932) hydrogen bonds : bond 0.03009 ( 1700) hydrogen bonds : angle 4.79625 ( 5193) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9240 Ramachandran restraints generated. 4620 Oldfield, 0 Emsley, 4620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9240 Ramachandran restraints generated. 4620 Oldfield, 0 Emsley, 4620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1975 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 1806 time to evaluate : 1.087 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: A 164 LYS cc_start: 0.9369 (mtmt) cc_final: 0.9075 (mtmm) REVERT: A 194 MET cc_start: 0.6568 (tpp) cc_final: 0.5515 (tpp) REVERT: A 213 GLN cc_start: 0.9076 (mm-40) cc_final: 0.8663 (mm-40) REVERT: A 236 GLU cc_start: 0.9662 (mm-30) cc_final: 0.9361 (mm-30) REVERT: A 277 ASP cc_start: 0.9110 (m-30) cc_final: 0.8832 (p0) REVERT: A 293 TYR cc_start: 0.9438 (t80) cc_final: 0.8866 (t80) REVERT: A 306 HIS cc_start: 0.9009 (m-70) cc_final: 0.8703 (m-70) REVERT: A 320 LYS cc_start: 0.9459 (tppt) cc_final: 0.8983 (tppt) REVERT: A 357 TYR cc_start: 0.9370 (t80) cc_final: 0.9074 (t80) REVERT: A 360 GLN cc_start: 0.9419 (tm130) cc_final: 0.9061 (tm-30) REVERT: A 361 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.8456 (t80) REVERT: A 365 MET cc_start: 0.9470 (ttm) cc_final: 0.8902 (tmm) REVERT: A 415 PHE cc_start: 0.9464 (m-80) cc_final: 0.9099 (m-80) REVERT: A 421 GLU cc_start: 0.8800 (pt0) cc_final: 0.8405 (pt0) REVERT: A 434 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8889 (pp) REVERT: A 445 GLU cc_start: 0.9348 (mt-10) cc_final: 0.9012 (mt-10) REVERT: A 448 LEU cc_start: 0.9539 (mt) cc_final: 0.9239 (mt) REVERT: A 454 ARG cc_start: 0.9062 (ttp80) cc_final: 0.8721 (tpt170) REVERT: A 455 ASN cc_start: 0.9292 (m-40) cc_final: 0.9067 (m-40) REVERT: A 498 MET cc_start: 0.8870 (ttm) cc_final: 0.8615 (ttm) REVERT: A 499 MET cc_start: 0.9106 (tpp) cc_final: 0.8708 (tpp) REVERT: B 196 ASP cc_start: 0.7571 (t70) cc_final: 0.7236 (t0) REVERT: B 225 MET cc_start: 0.9445 (mmp) cc_final: 0.9158 (mmp) REVERT: B 234 LEU cc_start: 0.9708 (mt) cc_final: 0.9490 (mt) REVERT: B 235 TYR cc_start: 0.9399 (t80) cc_final: 0.8338 (t80) REVERT: B 236 GLU cc_start: 0.9530 (mm-30) cc_final: 0.9053 (mm-30) REVERT: B 252 GLN cc_start: 0.8441 (tp40) cc_final: 0.7475 (tp-100) REVERT: B 282 PHE cc_start: 0.9030 (p90) cc_final: 0.8681 (p90) REVERT: B 285 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8331 (mm-40) REVERT: B 293 TYR cc_start: 0.9358 (t80) cc_final: 0.9091 (t80) REVERT: B 297 VAL cc_start: 0.9698 (t) cc_final: 0.9408 (m) REVERT: B 331 ASN cc_start: 0.9251 (p0) cc_final: 0.9035 (p0) REVERT: B 379 GLN cc_start: 0.9166 (mm110) cc_final: 0.8844 (mm-40) REVERT: B 396 LYS cc_start: 0.9169 (tttp) cc_final: 0.8939 (tttp) REVERT: B 407 MET cc_start: 0.8889 (tmm) cc_final: 0.8520 (tmm) REVERT: B 414 TYR cc_start: 0.9565 (t80) cc_final: 0.8946 (t80) REVERT: B 421 GLU cc_start: 0.8999 (pt0) cc_final: 0.8568 (pt0) REVERT: B 425 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8580 (mp0) REVERT: B 436 ASN cc_start: 0.8975 (t0) cc_final: 0.8718 (t0) REVERT: B 454 ARG cc_start: 0.9171 (ttp80) cc_final: 0.8879 (ttp80) REVERT: B 520 ASP cc_start: 0.8945 (m-30) cc_final: 0.8572 (m-30) REVERT: C 164 LYS cc_start: 0.9307 (mtmt) cc_final: 0.9059 (mtpp) REVERT: C 172 ASP cc_start: 0.8828 (t0) cc_final: 0.7949 (t70) REVERT: C 175 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8525 (pp) REVERT: C 179 MET cc_start: 0.7751 (ptp) cc_final: 0.7084 (ptp) REVERT: C 213 GLN cc_start: 0.8962 (tp-100) cc_final: 0.8712 (tp-100) REVERT: C 227 PHE cc_start: 0.9612 (t80) cc_final: 0.9310 (t80) REVERT: C 246 VAL cc_start: 0.8424 (OUTLIER) cc_final: 0.7740 (t) REVERT: C 277 ASP cc_start: 0.9061 (m-30) cc_final: 0.8770 (p0) REVERT: C 347 GLN cc_start: 0.8848 (mp10) cc_final: 0.8373 (mp10) REVERT: C 387 ARG cc_start: 0.9223 (tpp80) cc_final: 0.8854 (tpp80) REVERT: C 415 PHE cc_start: 0.9516 (m-10) cc_final: 0.9213 (m-80) REVERT: C 421 GLU cc_start: 0.8703 (pt0) cc_final: 0.8420 (pt0) REVERT: C 434 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8809 (pp) REVERT: C 445 GLU cc_start: 0.9339 (mt-10) cc_final: 0.9076 (mt-10) REVERT: C 446 ARG cc_start: 0.9425 (tpp80) cc_final: 0.9087 (tpp80) REVERT: C 455 ASN cc_start: 0.9257 (m-40) cc_final: 0.8990 (m-40) REVERT: C 467 ASP cc_start: 0.9542 (p0) cc_final: 0.9008 (p0) REVERT: C 498 MET cc_start: 0.8852 (ttm) cc_final: 0.8649 (ttm) REVERT: C 499 MET cc_start: 0.8914 (tpp) cc_final: 0.8506 (tpp) REVERT: C 508 MET cc_start: 0.9341 (mtt) cc_final: 0.8974 (mtt) REVERT: D 140 GLU cc_start: 0.8710 (pm20) cc_final: 0.8353 (pp20) REVERT: D 196 ASP cc_start: 0.7166 (t0) cc_final: 0.6865 (t0) REVERT: D 212 THR cc_start: 0.9065 (p) cc_final: 0.8253 (p) REVERT: D 213 GLN cc_start: 0.9309 (mm110) cc_final: 0.9038 (mm-40) REVERT: D 224 PHE cc_start: 0.9035 (t80) cc_final: 0.8261 (m-80) REVERT: D 232 ASP cc_start: 0.9787 (m-30) cc_final: 0.9452 (m-30) REVERT: D 236 GLU cc_start: 0.9557 (mm-30) cc_final: 0.9178 (mm-30) REVERT: D 246 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.7837 (t) REVERT: D 249 TYR cc_start: 0.8549 (p90) cc_final: 0.8116 (p90) REVERT: D 260 LEU cc_start: 0.9450 (tp) cc_final: 0.9118 (tp) REVERT: D 285 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8368 (mm-40) REVERT: D 293 TYR cc_start: 0.9344 (t80) cc_final: 0.9095 (t80) REVERT: D 318 PHE cc_start: 0.9240 (p90) cc_final: 0.8989 (p90) REVERT: D 394 TYR cc_start: 0.9708 (t80) cc_final: 0.9334 (t80) REVERT: D 397 GLU cc_start: 0.9509 (tm-30) cc_final: 0.9174 (tm-30) REVERT: D 407 MET cc_start: 0.8849 (tmm) cc_final: 0.8455 (tmm) REVERT: D 421 GLU cc_start: 0.8861 (pt0) cc_final: 0.8382 (pt0) REVERT: D 454 ARG cc_start: 0.9136 (ttp80) cc_final: 0.8816 (ttp80) REVERT: D 506 ASP cc_start: 0.9583 (t70) cc_final: 0.8588 (p0) REVERT: D 520 ASP cc_start: 0.8919 (m-30) cc_final: 0.8467 (m-30) REVERT: E 172 ASP cc_start: 0.8879 (t0) cc_final: 0.8412 (t0) REVERT: E 183 ARG cc_start: 0.8754 (mmm-85) cc_final: 0.8392 (ttp-110) REVERT: E 194 MET cc_start: 0.8301 (tpp) cc_final: 0.8020 (tpt) REVERT: E 213 GLN cc_start: 0.9171 (mm110) cc_final: 0.8875 (mm110) REVERT: E 233 GLU cc_start: 0.9423 (tp30) cc_final: 0.9067 (tp30) REVERT: E 235 TYR cc_start: 0.9087 (t80) cc_final: 0.8880 (t80) REVERT: E 271 GLN cc_start: 0.8536 (pt0) cc_final: 0.8165 (pt0) REVERT: E 279 LYS cc_start: 0.9510 (mmmt) cc_final: 0.9266 (mmmm) REVERT: E 322 PHE cc_start: 0.9389 (p90) cc_final: 0.9139 (p90) REVERT: E 331 ASN cc_start: 0.9093 (p0) cc_final: 0.8352 (p0) REVERT: E 365 MET cc_start: 0.9257 (ttm) cc_final: 0.8950 (ttm) REVERT: E 407 MET cc_start: 0.8877 (tmm) cc_final: 0.8540 (tmm) REVERT: E 421 GLU cc_start: 0.8811 (pt0) cc_final: 0.8534 (pt0) REVERT: E 424 CYS cc_start: 0.9453 (m) cc_final: 0.8856 (t) REVERT: E 426 SER cc_start: 0.9531 (t) cc_final: 0.9295 (p) REVERT: E 430 MET cc_start: 0.8887 (mmt) cc_final: 0.8636 (mmp) REVERT: E 455 ASN cc_start: 0.9129 (m-40) cc_final: 0.8740 (m-40) REVERT: E 467 ASP cc_start: 0.9132 (m-30) cc_final: 0.8727 (m-30) REVERT: E 508 MET cc_start: 0.9335 (ttm) cc_final: 0.8999 (tpp) REVERT: E 510 ASN cc_start: 0.9195 (m-40) cc_final: 0.8737 (m-40) REVERT: G 179 MET cc_start: 0.9370 (tpp) cc_final: 0.8733 (ptt) REVERT: G 181 MET cc_start: 0.9065 (tpp) cc_final: 0.8798 (mtm) REVERT: G 183 ARG cc_start: 0.9263 (mmm160) cc_final: 0.8879 (mmm160) REVERT: G 194 MET cc_start: 0.5337 (tpp) cc_final: 0.4934 (tpp) REVERT: G 227 PHE cc_start: 0.9590 (t80) cc_final: 0.9290 (t80) REVERT: G 232 ASP cc_start: 0.9788 (m-30) cc_final: 0.9315 (m-30) REVERT: G 235 TYR cc_start: 0.9223 (t80) cc_final: 0.8645 (t80) REVERT: G 236 GLU cc_start: 0.9616 (mm-30) cc_final: 0.9172 (mm-30) REVERT: G 240 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8930 (mtmm) REVERT: G 260 LEU cc_start: 0.9446 (tp) cc_final: 0.9096 (tt) REVERT: G 277 ASP cc_start: 0.9233 (m-30) cc_final: 0.8672 (p0) REVERT: G 293 TYR cc_start: 0.9246 (t80) cc_final: 0.7384 (t80) REVERT: G 300 LEU cc_start: 0.9576 (mm) cc_final: 0.9274 (mt) REVERT: G 312 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8336 (mt-10) REVERT: G 361 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8710 (t80) REVERT: G 382 ARG cc_start: 0.9612 (ttp80) cc_final: 0.9367 (mtp180) REVERT: G 421 GLU cc_start: 0.8935 (pt0) cc_final: 0.8697 (pt0) REVERT: G 424 CYS cc_start: 0.9225 (m) cc_final: 0.8841 (m) REVERT: G 436 ASN cc_start: 0.9416 (t0) cc_final: 0.9061 (t0) REVERT: G 446 ARG cc_start: 0.8435 (ttp80) cc_final: 0.7291 (ttp80) REVERT: G 451 GLU cc_start: 0.8807 (mp0) cc_final: 0.8404 (mp0) REVERT: G 454 ARG cc_start: 0.9195 (ttp80) cc_final: 0.8681 (ttp-110) REVERT: G 455 ASN cc_start: 0.9314 (m-40) cc_final: 0.8780 (m110) REVERT: G 499 MET cc_start: 0.9005 (tpp) cc_final: 0.8676 (tpp) REVERT: G 506 ASP cc_start: 0.9647 (t0) cc_final: 0.8694 (p0) REVERT: G 516 HIS cc_start: 0.8287 (t-90) cc_final: 0.7635 (t-90) REVERT: I 172 ASP cc_start: 0.8889 (t0) cc_final: 0.8626 (t0) REVERT: I 183 ARG cc_start: 0.9029 (mtp85) cc_final: 0.8296 (ptp-110) REVERT: I 194 MET cc_start: 0.7296 (tpp) cc_final: 0.6599 (tpp) REVERT: I 213 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8734 (tp40) REVERT: I 218 LYS cc_start: 0.9283 (mmmm) cc_final: 0.8963 (mtmm) REVERT: I 235 TYR cc_start: 0.8914 (t80) cc_final: 0.8638 (t80) REVERT: I 323 LEU cc_start: 0.9536 (mp) cc_final: 0.9312 (mp) REVERT: I 331 ASN cc_start: 0.9118 (p0) cc_final: 0.8448 (p0) REVERT: I 347 GLN cc_start: 0.8644 (mt0) cc_final: 0.8112 (mp10) REVERT: I 379 GLN cc_start: 0.8870 (mm110) cc_final: 0.6810 (tt0) REVERT: I 407 MET cc_start: 0.8906 (tmm) cc_final: 0.8549 (tmm) REVERT: I 421 GLU cc_start: 0.8870 (pt0) cc_final: 0.8554 (pt0) REVERT: I 426 SER cc_start: 0.9596 (t) cc_final: 0.9314 (p) REVERT: I 455 ASN cc_start: 0.9095 (m-40) cc_final: 0.8723 (m-40) REVERT: I 465 MET cc_start: 0.9556 (mmm) cc_final: 0.9329 (mmm) REVERT: I 467 ASP cc_start: 0.8778 (p0) cc_final: 0.8288 (p0) REVERT: I 494 ASN cc_start: 0.9364 (m-40) cc_final: 0.9053 (m-40) REVERT: I 520 ASP cc_start: 0.9042 (m-30) cc_final: 0.8827 (m-30) REVERT: K 179 MET cc_start: 0.9139 (tpp) cc_final: 0.8564 (tpp) REVERT: K 218 LYS cc_start: 0.9545 (mmmm) cc_final: 0.9343 (ttmm) REVERT: K 232 ASP cc_start: 0.9760 (m-30) cc_final: 0.9416 (m-30) REVERT: K 235 TYR cc_start: 0.9158 (t80) cc_final: 0.8523 (t80) REVERT: K 236 GLU cc_start: 0.9595 (mm-30) cc_final: 0.9149 (mm-30) REVERT: K 240 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.8718 (mtmm) REVERT: K 252 GLN cc_start: 0.8460 (tp40) cc_final: 0.8150 (tp-100) REVERT: K 260 LEU cc_start: 0.9396 (tp) cc_final: 0.9193 (tp) REVERT: K 293 TYR cc_start: 0.9289 (t80) cc_final: 0.7626 (t80) REVERT: K 312 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8403 (mt-10) REVERT: K 318 PHE cc_start: 0.9268 (p90) cc_final: 0.8914 (p90) REVERT: K 344 LEU cc_start: 0.9573 (mt) cc_final: 0.9362 (mp) REVERT: K 361 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8653 (t80) REVERT: K 407 MET cc_start: 0.8696 (tmm) cc_final: 0.8389 (tmm) REVERT: K 421 GLU cc_start: 0.8787 (pt0) cc_final: 0.8562 (pt0) REVERT: K 424 CYS cc_start: 0.8949 (m) cc_final: 0.8423 (m) REVERT: K 430 MET cc_start: 0.9303 (OUTLIER) cc_final: 0.8528 (mpp) REVERT: K 436 ASN cc_start: 0.9358 (t0) cc_final: 0.9003 (t0) REVERT: K 446 ARG cc_start: 0.8624 (ttp80) cc_final: 0.7555 (ttp80) REVERT: K 451 GLU cc_start: 0.8567 (mp0) cc_final: 0.8367 (mp0) REVERT: K 455 ASN cc_start: 0.9246 (m-40) cc_final: 0.8939 (m110) REVERT: K 467 ASP cc_start: 0.9386 (p0) cc_final: 0.8732 (p0) REVERT: K 508 MET cc_start: 0.8885 (mmm) cc_final: 0.8542 (mmm) REVERT: K 516 HIS cc_start: 0.8341 (t-90) cc_final: 0.7942 (t70) REVERT: F 140 GLU cc_start: 0.8792 (pm20) cc_final: 0.8536 (pm20) REVERT: F 172 ASP cc_start: 0.8780 (t0) cc_final: 0.8504 (t0) REVERT: F 196 ASP cc_start: 0.8027 (t70) cc_final: 0.7562 (t70) REVERT: F 212 THR cc_start: 0.9415 (p) cc_final: 0.8529 (t) REVERT: F 213 GLN cc_start: 0.8917 (mm110) cc_final: 0.8058 (mm110) REVERT: F 215 PHE cc_start: 0.8658 (m-80) cc_final: 0.8414 (m-80) REVERT: F 216 ARG cc_start: 0.8457 (mtp180) cc_final: 0.7438 (mtp180) REVERT: F 232 ASP cc_start: 0.9616 (m-30) cc_final: 0.9396 (m-30) REVERT: F 233 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8833 (mt-10) REVERT: F 236 GLU cc_start: 0.9599 (mm-30) cc_final: 0.9063 (mm-30) REVERT: F 252 GLN cc_start: 0.9216 (tp40) cc_final: 0.8949 (tp40) REVERT: F 299 ASP cc_start: 0.8964 (m-30) cc_final: 0.8742 (m-30) REVERT: F 323 LEU cc_start: 0.9540 (mp) cc_final: 0.9318 (mm) REVERT: F 382 ARG cc_start: 0.9480 (ttp80) cc_final: 0.8921 (mtp-110) REVERT: F 397 GLU cc_start: 0.9264 (tm-30) cc_final: 0.9036 (tm-30) REVERT: F 421 GLU cc_start: 0.8881 (pt0) cc_final: 0.8292 (pt0) REVERT: F 454 ARG cc_start: 0.9408 (ttp-110) cc_final: 0.9154 (ttp-110) REVERT: F 496 MET cc_start: 0.8572 (ppp) cc_final: 0.7734 (ppp) REVERT: F 499 MET cc_start: 0.8854 (tpp) cc_final: 0.8533 (tpp) REVERT: H 194 MET cc_start: 0.7357 (tpp) cc_final: 0.7014 (tpt) REVERT: H 215 PHE cc_start: 0.8329 (m-80) cc_final: 0.7965 (m-80) REVERT: H 218 LYS cc_start: 0.9302 (tptt) cc_final: 0.9088 (mtmm) REVERT: H 232 ASP cc_start: 0.9635 (m-30) cc_final: 0.9056 (m-30) REVERT: H 236 GLU cc_start: 0.9401 (mm-30) cc_final: 0.9046 (mm-30) REVERT: H 255 LYS cc_start: 0.9502 (mtmm) cc_final: 0.9208 (mtmm) REVERT: H 299 ASP cc_start: 0.8144 (m-30) cc_final: 0.7914 (m-30) REVERT: H 308 TYR cc_start: 0.9009 (m-80) cc_final: 0.8643 (m-10) REVERT: H 320 LYS cc_start: 0.9244 (tppt) cc_final: 0.8823 (tppt) REVERT: H 328 LYS cc_start: 0.8689 (mtpp) cc_final: 0.8397 (mtpt) REVERT: H 331 ASN cc_start: 0.8828 (p0) cc_final: 0.8454 (p0) REVERT: H 347 GLN cc_start: 0.8754 (mp10) cc_final: 0.8376 (pm20) REVERT: H 359 MET cc_start: 0.9525 (tpp) cc_final: 0.9312 (mmm) REVERT: H 397 GLU cc_start: 0.9092 (tm-30) cc_final: 0.8672 (tm-30) REVERT: H 446 ARG cc_start: 0.9306 (tmm-80) cc_final: 0.8753 (tpp80) REVERT: H 465 MET cc_start: 0.9378 (mmm) cc_final: 0.9104 (mmm) REVERT: H 471 GLN cc_start: 0.9282 (tp-100) cc_final: 0.8899 (mm110) REVERT: J 172 ASP cc_start: 0.8868 (t0) cc_final: 0.8436 (t70) REVERT: J 196 ASP cc_start: 0.8127 (t70) cc_final: 0.7909 (p0) REVERT: J 215 PHE cc_start: 0.8834 (m-80) cc_final: 0.8531 (m-80) REVERT: J 232 ASP cc_start: 0.9703 (m-30) cc_final: 0.9163 (m-30) REVERT: J 233 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8876 (mt-10) REVERT: J 236 GLU cc_start: 0.9625 (mm-30) cc_final: 0.9092 (mm-30) REVERT: J 245 LYS cc_start: 0.8873 (mtmm) cc_final: 0.8653 (mmmm) REVERT: J 303 GLU cc_start: 0.9284 (tm-30) cc_final: 0.9081 (tm-30) REVERT: J 320 LYS cc_start: 0.9212 (tppp) cc_final: 0.8817 (tppt) REVERT: J 347 GLN cc_start: 0.8685 (mp10) cc_final: 0.8056 (mp10) REVERT: J 397 GLU cc_start: 0.9188 (tm-30) cc_final: 0.8733 (tt0) REVERT: J 407 MET cc_start: 0.8744 (tmm) cc_final: 0.8374 (tmm) REVERT: J 421 GLU cc_start: 0.8883 (pt0) cc_final: 0.8296 (pt0) REVERT: J 499 MET cc_start: 0.9044 (tpt) cc_final: 0.8551 (tpt) REVERT: L 172 ASP cc_start: 0.7867 (t0) cc_final: 0.7589 (t0) REVERT: L 194 MET cc_start: 0.7007 (tpt) cc_final: 0.4823 (pmm) REVERT: L 218 LYS cc_start: 0.8710 (ttpp) cc_final: 0.8196 (ptmm) REVERT: L 235 TYR cc_start: 0.9002 (t80) cc_final: 0.8506 (t80) REVERT: L 236 GLU cc_start: 0.9372 (mm-30) cc_final: 0.9075 (tm-30) REVERT: L 255 LYS cc_start: 0.9485 (mtmm) cc_final: 0.9090 (mttt) REVERT: L 271 GLN cc_start: 0.7167 (tt0) cc_final: 0.6785 (tt0) REVERT: L 285 GLN cc_start: 0.9037 (mm-40) cc_final: 0.8777 (mm-40) REVERT: L 320 LYS cc_start: 0.9239 (tppt) cc_final: 0.8795 (tppt) REVERT: L 343 SER cc_start: 0.9407 (OUTLIER) cc_final: 0.9199 (p) REVERT: L 347 GLN cc_start: 0.8786 (mp10) cc_final: 0.8328 (pm20) REVERT: L 353 GLU cc_start: 0.9443 (mt-10) cc_final: 0.9160 (mt-10) REVERT: L 361 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.8248 (t80) REVERT: L 381 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8613 (tm-30) REVERT: L 446 ARG cc_start: 0.9222 (tmm-80) cc_final: 0.8734 (tpp80) REVERT: L 465 MET cc_start: 0.9408 (mmm) cc_final: 0.9126 (mmm) REVERT: D 602 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.5383 (pp30) outliers start: 169 outliers final: 128 residues processed: 1866 average time/residue: 0.2203 time to fit residues: 669.2339 Evaluate side-chains 1901 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 1756 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 510 ASN Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 187 GLN Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 283 CYS Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 510 ASN Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 498 MET Chi-restraints excluded: chain D residue 510 ASN Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 312 GLU Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 458 SER Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 496 MET Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain G residue 240 LYS Chi-restraints excluded: chain G residue 283 CYS Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 312 GLU Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 361 PHE Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain G residue 380 SER Chi-restraints excluded: chain G residue 381 GLU Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 469 SER Chi-restraints excluded: chain G residue 498 MET Chi-restraints excluded: chain G residue 505 LEU Chi-restraints excluded: chain G residue 522 VAL Chi-restraints excluded: chain I residue 302 THR Chi-restraints excluded: chain I residue 312 GLU Chi-restraints excluded: chain I residue 423 THR Chi-restraints excluded: chain I residue 428 SER Chi-restraints excluded: chain I residue 430 MET Chi-restraints excluded: chain I residue 445 GLU Chi-restraints excluded: chain I residue 469 SER Chi-restraints excluded: chain I residue 484 VAL Chi-restraints excluded: chain I residue 510 ASN Chi-restraints excluded: chain K residue 194 MET Chi-restraints excluded: chain K residue 231 ILE Chi-restraints excluded: chain K residue 240 LYS Chi-restraints excluded: chain K residue 283 CYS Chi-restraints excluded: chain K residue 312 GLU Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain K residue 325 GLU Chi-restraints excluded: chain K residue 361 PHE Chi-restraints excluded: chain K residue 400 CYS Chi-restraints excluded: chain K residue 403 GLU Chi-restraints excluded: chain K residue 423 THR Chi-restraints excluded: chain K residue 430 MET Chi-restraints excluded: chain K residue 505 LEU Chi-restraints excluded: chain K residue 523 SER Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 325 GLU Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 325 GLU Chi-restraints excluded: chain H residue 360 GLN Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 421 GLU Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain H residue 458 SER Chi-restraints excluded: chain H residue 467 ASP Chi-restraints excluded: chain H residue 496 MET Chi-restraints excluded: chain H residue 510 ASN Chi-restraints excluded: chain H residue 520 ASP Chi-restraints excluded: chain J residue 241 GLN Chi-restraints excluded: chain J residue 325 GLU Chi-restraints excluded: chain J residue 381 GLU Chi-restraints excluded: chain J residue 429 VAL Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain L residue 181 MET Chi-restraints excluded: chain L residue 231 ILE Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 343 SER Chi-restraints excluded: chain L residue 361 PHE Chi-restraints excluded: chain L residue 362 LEU Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 458 SER Chi-restraints excluded: chain L residue 467 ASP Chi-restraints excluded: chain L residue 496 MET Chi-restraints excluded: chain L residue 507 LYS Chi-restraints excluded: chain L residue 510 ASN Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain D residue 602 GLN Chi-restraints excluded: chain E residue 602 GLN Chi-restraints excluded: chain F residue 602 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 292 optimal weight: 2.9990 chunk 335 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 374 optimal weight: 3.9990 chunk 251 optimal weight: 3.9990 chunk 278 optimal weight: 0.9980 chunk 264 optimal weight: 4.9990 chunk 214 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 114 optimal weight: 20.0000 chunk 295 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN D 151 GLN ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 ASN ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 ASN ** E 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 HIS ** K 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 360 GLN F 388 ASN ** F 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 519 HIS ** H 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 241 GLN J 298 ASN J 360 GLN ** J 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 519 HIS ** L 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 335 ASN L 475 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.154087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.115369 restraints weight = 65244.969| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.91 r_work: 0.3186 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 36972 Z= 0.171 Angle : 0.696 12.129 49932 Z= 0.353 Chirality : 0.045 0.255 5544 Planarity : 0.005 0.046 6408 Dihedral : 5.004 51.253 4929 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.13 % Favored : 93.77 % Rotamer: Outliers : 4.60 % Allowed : 27.39 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.13), residues: 4620 helix: 1.15 (0.11), residues: 2388 sheet: -0.38 (0.30), residues: 360 loop : -0.21 (0.16), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 217 TYR 0.030 0.002 TYR J 293 PHE 0.034 0.001 PHE H 224 TRP 0.011 0.001 TRP D 261 HIS 0.009 0.001 HIS J 157 Details of bonding type rmsd covalent geometry : bond 0.00400 (36972) covalent geometry : angle 0.69607 (49932) hydrogen bonds : bond 0.03242 ( 1700) hydrogen bonds : angle 4.90179 ( 5193) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9240 Ramachandran restraints generated. 4620 Oldfield, 0 Emsley, 4620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9240 Ramachandran restraints generated. 4620 Oldfield, 0 Emsley, 4620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1971 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 1786 time to evaluate : 1.557 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: A 164 LYS cc_start: 0.9370 (mtmt) cc_final: 0.9051 (mtmm) REVERT: A 194 MET cc_start: 0.6767 (tpp) cc_final: 0.5733 (tpp) REVERT: A 213 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8675 (mm-40) REVERT: A 227 PHE cc_start: 0.9589 (t80) cc_final: 0.9359 (t80) REVERT: A 236 GLU cc_start: 0.9651 (mm-30) cc_final: 0.9365 (mm-30) REVERT: A 277 ASP cc_start: 0.9111 (m-30) cc_final: 0.8776 (p0) REVERT: A 293 TYR cc_start: 0.9445 (t80) cc_final: 0.8867 (t80) REVERT: A 306 HIS cc_start: 0.9033 (m-70) cc_final: 0.8745 (m-70) REVERT: A 331 ASN cc_start: 0.9210 (p0) cc_final: 0.8983 (p0) REVERT: A 347 GLN cc_start: 0.9002 (mp10) cc_final: 0.8719 (mp10) REVERT: A 357 TYR cc_start: 0.9424 (t80) cc_final: 0.8923 (t80) REVERT: A 360 GLN cc_start: 0.9436 (tm130) cc_final: 0.9094 (tm-30) REVERT: A 361 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.8446 (t80) REVERT: A 365 MET cc_start: 0.9434 (ttm) cc_final: 0.8836 (tmm) REVERT: A 375 ASN cc_start: 0.8931 (t0) cc_final: 0.8710 (t0) REVERT: A 379 GLN cc_start: 0.9623 (mm110) cc_final: 0.9207 (mm110) REVERT: A 407 MET cc_start: 0.8765 (tmm) cc_final: 0.8520 (tmm) REVERT: A 415 PHE cc_start: 0.9480 (m-80) cc_final: 0.9070 (m-80) REVERT: A 421 GLU cc_start: 0.8818 (pt0) cc_final: 0.8446 (pt0) REVERT: A 434 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8876 (pp) REVERT: A 445 GLU cc_start: 0.9367 (mt-10) cc_final: 0.9047 (mt-10) REVERT: A 448 LEU cc_start: 0.9566 (mt) cc_final: 0.9265 (mt) REVERT: A 454 ARG cc_start: 0.9078 (ttp80) cc_final: 0.8728 (tpt170) REVERT: A 455 ASN cc_start: 0.9289 (m-40) cc_final: 0.9063 (m-40) REVERT: A 498 MET cc_start: 0.8919 (ttm) cc_final: 0.8667 (ttm) REVERT: A 499 MET cc_start: 0.9071 (tpp) cc_final: 0.8690 (tpp) REVERT: A 500 CYS cc_start: 0.8624 (m) cc_final: 0.8367 (m) REVERT: B 196 ASP cc_start: 0.7590 (t70) cc_final: 0.7379 (t0) REVERT: B 225 MET cc_start: 0.9417 (mmp) cc_final: 0.9144 (mmp) REVERT: B 234 LEU cc_start: 0.9675 (mt) cc_final: 0.9438 (mt) REVERT: B 236 GLU cc_start: 0.9531 (mm-30) cc_final: 0.8964 (mm-30) REVERT: B 263 VAL cc_start: 0.9464 (t) cc_final: 0.9210 (p) REVERT: B 282 PHE cc_start: 0.9107 (p90) cc_final: 0.8719 (p90) REVERT: B 285 GLN cc_start: 0.9093 (mm-40) cc_final: 0.8366 (mm-40) REVERT: B 293 TYR cc_start: 0.9363 (t80) cc_final: 0.9073 (t80) REVERT: B 297 VAL cc_start: 0.9734 (t) cc_final: 0.9444 (m) REVERT: B 357 TYR cc_start: 0.9279 (t80) cc_final: 0.8893 (t80) REVERT: B 396 LYS cc_start: 0.9207 (tttp) cc_final: 0.8907 (tttp) REVERT: B 407 MET cc_start: 0.8881 (tmm) cc_final: 0.8580 (tmm) REVERT: B 421 GLU cc_start: 0.9011 (pt0) cc_final: 0.8588 (pt0) REVERT: B 436 ASN cc_start: 0.8983 (t0) cc_final: 0.8754 (t0) REVERT: B 454 ARG cc_start: 0.9194 (ttp80) cc_final: 0.8904 (ttp80) REVERT: B 520 ASP cc_start: 0.8975 (m-30) cc_final: 0.8571 (m-30) REVERT: C 164 LYS cc_start: 0.9309 (mtmt) cc_final: 0.9057 (mtpp) REVERT: C 172 ASP cc_start: 0.8902 (t0) cc_final: 0.7907 (t70) REVERT: C 175 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8574 (pp) REVERT: C 179 MET cc_start: 0.7792 (ptp) cc_final: 0.7102 (ptp) REVERT: C 227 PHE cc_start: 0.9612 (t80) cc_final: 0.9308 (t80) REVERT: C 246 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8006 (t) REVERT: C 277 ASP cc_start: 0.9034 (m-30) cc_final: 0.8648 (p0) REVERT: C 293 TYR cc_start: 0.9417 (t80) cc_final: 0.8856 (t80) REVERT: C 347 GLN cc_start: 0.8910 (mp10) cc_final: 0.8456 (mp10) REVERT: C 387 ARG cc_start: 0.9237 (tpp80) cc_final: 0.8982 (tpp80) REVERT: C 397 GLU cc_start: 0.9177 (tm-30) cc_final: 0.8838 (tm-30) REVERT: C 415 PHE cc_start: 0.9562 (m-10) cc_final: 0.9242 (m-80) REVERT: C 421 GLU cc_start: 0.8755 (pt0) cc_final: 0.8427 (pt0) REVERT: C 434 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8784 (pp) REVERT: C 445 GLU cc_start: 0.9329 (mt-10) cc_final: 0.9062 (mt-10) REVERT: C 455 ASN cc_start: 0.9277 (m-40) cc_final: 0.9012 (m-40) REVERT: C 467 ASP cc_start: 0.9528 (p0) cc_final: 0.8966 (p0) REVERT: C 498 MET cc_start: 0.8920 (ttm) cc_final: 0.8717 (ttm) REVERT: C 499 MET cc_start: 0.8932 (tpp) cc_final: 0.8514 (tpp) REVERT: C 508 MET cc_start: 0.9351 (mtt) cc_final: 0.8964 (mtt) REVERT: D 140 GLU cc_start: 0.8710 (pm20) cc_final: 0.8351 (pp20) REVERT: D 196 ASP cc_start: 0.7025 (t0) cc_final: 0.6693 (t0) REVERT: D 212 THR cc_start: 0.9062 (p) cc_final: 0.8223 (p) REVERT: D 213 GLN cc_start: 0.9304 (mm110) cc_final: 0.8932 (mm-40) REVERT: D 224 PHE cc_start: 0.9098 (t80) cc_final: 0.8256 (m-80) REVERT: D 232 ASP cc_start: 0.9799 (m-30) cc_final: 0.9460 (m-30) REVERT: D 236 GLU cc_start: 0.9557 (mm-30) cc_final: 0.9187 (mm-30) REVERT: D 246 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.7974 (t) REVERT: D 249 TYR cc_start: 0.8597 (p90) cc_final: 0.8233 (p90) REVERT: D 260 LEU cc_start: 0.9464 (tp) cc_final: 0.8872 (tp) REVERT: D 263 VAL cc_start: 0.9534 (t) cc_final: 0.9275 (p) REVERT: D 277 ASP cc_start: 0.9274 (m-30) cc_final: 0.8621 (p0) REVERT: D 285 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8334 (mm-40) REVERT: D 293 TYR cc_start: 0.9367 (t80) cc_final: 0.9115 (t80) REVERT: D 373 PHE cc_start: 0.8680 (t80) cc_final: 0.8313 (t80) REVERT: D 394 TYR cc_start: 0.9715 (t80) cc_final: 0.9439 (t80) REVERT: D 397 GLU cc_start: 0.9533 (tm-30) cc_final: 0.9201 (tm-30) REVERT: D 407 MET cc_start: 0.8830 (tmm) cc_final: 0.8538 (tmm) REVERT: D 421 GLU cc_start: 0.8822 (pt0) cc_final: 0.8349 (pt0) REVERT: D 454 ARG cc_start: 0.9146 (ttp80) cc_final: 0.8820 (ttp80) REVERT: D 506 ASP cc_start: 0.9574 (t70) cc_final: 0.8638 (p0) REVERT: D 508 MET cc_start: 0.9224 (mmm) cc_final: 0.8958 (mmm) REVERT: D 520 ASP cc_start: 0.8959 (m-30) cc_final: 0.8517 (m-30) REVERT: E 172 ASP cc_start: 0.8908 (t0) cc_final: 0.8505 (t0) REVERT: E 183 ARG cc_start: 0.8781 (mmm-85) cc_final: 0.8396 (ttp-110) REVERT: E 194 MET cc_start: 0.8403 (tpp) cc_final: 0.8105 (tpt) REVERT: E 213 GLN cc_start: 0.9169 (mm110) cc_final: 0.8800 (mm110) REVERT: E 233 GLU cc_start: 0.9443 (tp30) cc_final: 0.9079 (tp30) REVERT: E 279 LYS cc_start: 0.9501 (mmmt) cc_final: 0.9283 (mmmm) REVERT: E 331 ASN cc_start: 0.9154 (p0) cc_final: 0.8505 (p0) REVERT: E 365 MET cc_start: 0.9234 (ttm) cc_final: 0.8940 (ttm) REVERT: E 407 MET cc_start: 0.8935 (tmm) cc_final: 0.8577 (tmm) REVERT: E 421 GLU cc_start: 0.8829 (pt0) cc_final: 0.8567 (pt0) REVERT: E 426 SER cc_start: 0.9554 (t) cc_final: 0.9305 (p) REVERT: E 455 ASN cc_start: 0.9157 (m-40) cc_final: 0.8764 (m-40) REVERT: E 467 ASP cc_start: 0.9130 (m-30) cc_final: 0.8720 (m-30) REVERT: E 508 MET cc_start: 0.9432 (ttm) cc_final: 0.9044 (tpp) REVERT: E 520 ASP cc_start: 0.8956 (m-30) cc_final: 0.8432 (m-30) REVERT: G 179 MET cc_start: 0.9362 (tpp) cc_final: 0.8760 (ptt) REVERT: G 181 MET cc_start: 0.9133 (tpp) cc_final: 0.8817 (mtm) REVERT: G 183 ARG cc_start: 0.9250 (mmm160) cc_final: 0.8870 (mmm160) REVERT: G 194 MET cc_start: 0.5477 (tpp) cc_final: 0.5055 (tpp) REVERT: G 227 PHE cc_start: 0.9636 (t80) cc_final: 0.9352 (t80) REVERT: G 232 ASP cc_start: 0.9791 (m-30) cc_final: 0.9346 (m-30) REVERT: G 235 TYR cc_start: 0.9255 (t80) cc_final: 0.8654 (t80) REVERT: G 236 GLU cc_start: 0.9603 (mm-30) cc_final: 0.9178 (mm-30) REVERT: G 240 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8922 (mtmm) REVERT: G 260 LEU cc_start: 0.9451 (tp) cc_final: 0.9030 (tt) REVERT: G 277 ASP cc_start: 0.9274 (m-30) cc_final: 0.8583 (p0) REVERT: G 293 TYR cc_start: 0.9302 (t80) cc_final: 0.7476 (t80) REVERT: G 300 LEU cc_start: 0.9590 (mm) cc_final: 0.9238 (mt) REVERT: G 331 ASN cc_start: 0.9168 (p0) cc_final: 0.8914 (p0) REVERT: G 361 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8726 (t80) REVERT: G 370 TYR cc_start: 0.9157 (t80) cc_final: 0.8936 (t80) REVERT: G 382 ARG cc_start: 0.9617 (ttp80) cc_final: 0.9380 (mtp180) REVERT: G 421 GLU cc_start: 0.8914 (pt0) cc_final: 0.8609 (pt0) REVERT: G 424 CYS cc_start: 0.9230 (m) cc_final: 0.8851 (m) REVERT: G 436 ASN cc_start: 0.9370 (t0) cc_final: 0.9000 (t0) REVERT: G 446 ARG cc_start: 0.8467 (ttp80) cc_final: 0.7343 (ttp80) REVERT: G 451 GLU cc_start: 0.8804 (mp0) cc_final: 0.8364 (mp0) REVERT: G 454 ARG cc_start: 0.9198 (ttp80) cc_final: 0.8639 (ttp-110) REVERT: G 455 ASN cc_start: 0.9328 (m-40) cc_final: 0.8736 (m-40) REVERT: G 499 MET cc_start: 0.9034 (tpp) cc_final: 0.8751 (tpp) REVERT: G 516 HIS cc_start: 0.8358 (t-90) cc_final: 0.7692 (t-90) REVERT: I 172 ASP cc_start: 0.8979 (t0) cc_final: 0.8565 (t0) REVERT: I 183 ARG cc_start: 0.9071 (mtp85) cc_final: 0.8314 (ptp-110) REVERT: I 194 MET cc_start: 0.7413 (tpp) cc_final: 0.6687 (tpp) REVERT: I 213 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8665 (tp-100) REVERT: I 218 LYS cc_start: 0.9295 (mmmm) cc_final: 0.8966 (mtmm) REVERT: I 249 TYR cc_start: 0.9220 (p90) cc_final: 0.8989 (p90) REVERT: I 320 LYS cc_start: 0.9493 (tppt) cc_final: 0.8947 (tppt) REVERT: I 323 LEU cc_start: 0.9548 (mp) cc_final: 0.9334 (mp) REVERT: I 331 ASN cc_start: 0.9181 (p0) cc_final: 0.8534 (p0) REVERT: I 347 GLN cc_start: 0.8703 (mt0) cc_final: 0.8100 (mp10) REVERT: I 407 MET cc_start: 0.8953 (tmm) cc_final: 0.8577 (tmm) REVERT: I 421 GLU cc_start: 0.8854 (pt0) cc_final: 0.8558 (pt0) REVERT: I 426 SER cc_start: 0.9544 (t) cc_final: 0.9279 (p) REVERT: I 455 ASN cc_start: 0.9134 (m-40) cc_final: 0.8744 (m-40) REVERT: I 467 ASP cc_start: 0.8928 (p0) cc_final: 0.7507 (p0) REVERT: I 494 ASN cc_start: 0.9396 (m-40) cc_final: 0.9087 (m-40) REVERT: I 520 ASP cc_start: 0.9067 (m-30) cc_final: 0.8835 (m-30) REVERT: K 179 MET cc_start: 0.9120 (tpp) cc_final: 0.8499 (tpp) REVERT: K 232 ASP cc_start: 0.9756 (m-30) cc_final: 0.9397 (m-30) REVERT: K 235 TYR cc_start: 0.9155 (t80) cc_final: 0.8513 (t80) REVERT: K 236 GLU cc_start: 0.9597 (mm-30) cc_final: 0.9162 (mm-30) REVERT: K 240 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.8732 (mtmm) REVERT: K 260 LEU cc_start: 0.9460 (tp) cc_final: 0.9248 (tp) REVERT: K 293 TYR cc_start: 0.9305 (t80) cc_final: 0.7631 (t80) REVERT: K 331 ASN cc_start: 0.9210 (p0) cc_final: 0.8926 (p0) REVERT: K 344 LEU cc_start: 0.9580 (mt) cc_final: 0.9358 (mp) REVERT: K 361 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8666 (t80) REVERT: K 370 TYR cc_start: 0.9155 (t80) cc_final: 0.8953 (t80) REVERT: K 407 MET cc_start: 0.8685 (tmm) cc_final: 0.8335 (tmm) REVERT: K 421 GLU cc_start: 0.8879 (pt0) cc_final: 0.8590 (pt0) REVERT: K 424 CYS cc_start: 0.8968 (m) cc_final: 0.8442 (m) REVERT: K 430 MET cc_start: 0.9333 (OUTLIER) cc_final: 0.8743 (mpp) REVERT: K 436 ASN cc_start: 0.9384 (t0) cc_final: 0.9027 (t0) REVERT: K 446 ARG cc_start: 0.8651 (ttp80) cc_final: 0.7499 (ttp80) REVERT: K 451 GLU cc_start: 0.8539 (mp0) cc_final: 0.8331 (mp0) REVERT: K 455 ASN cc_start: 0.9266 (m-40) cc_final: 0.8976 (m110) REVERT: K 467 ASP cc_start: 0.9372 (p0) cc_final: 0.8566 (p0) REVERT: K 508 MET cc_start: 0.8922 (mmm) cc_final: 0.8555 (mmm) REVERT: K 516 HIS cc_start: 0.8324 (t-90) cc_final: 0.7742 (t-90) REVERT: K 520 ASP cc_start: 0.8984 (m-30) cc_final: 0.8521 (m-30) REVERT: F 140 GLU cc_start: 0.8643 (pm20) cc_final: 0.8408 (pm20) REVERT: F 172 ASP cc_start: 0.8812 (t0) cc_final: 0.8551 (t0) REVERT: F 194 MET cc_start: 0.6200 (tpp) cc_final: 0.5801 (tpp) REVERT: F 196 ASP cc_start: 0.7786 (t70) cc_final: 0.7271 (t70) REVERT: F 212 THR cc_start: 0.9414 (p) cc_final: 0.8629 (t) REVERT: F 213 GLN cc_start: 0.8799 (mm110) cc_final: 0.7721 (mm110) REVERT: F 215 PHE cc_start: 0.8735 (m-80) cc_final: 0.8448 (m-80) REVERT: F 216 ARG cc_start: 0.8482 (mtp180) cc_final: 0.7528 (mtp180) REVERT: F 233 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8854 (mt-10) REVERT: F 236 GLU cc_start: 0.9606 (mm-30) cc_final: 0.9078 (mm-30) REVERT: F 252 GLN cc_start: 0.9247 (tp40) cc_final: 0.8982 (tp40) REVERT: F 279 LYS cc_start: 0.9624 (mmmt) cc_final: 0.9299 (mmmt) REVERT: F 299 ASP cc_start: 0.8991 (m-30) cc_final: 0.8752 (m-30) REVERT: F 382 ARG cc_start: 0.9486 (ttp80) cc_final: 0.9156 (mtp-110) REVERT: F 421 GLU cc_start: 0.8922 (pt0) cc_final: 0.8356 (pt0) REVERT: F 499 MET cc_start: 0.8853 (tpp) cc_final: 0.8545 (tpp) REVERT: H 194 MET cc_start: 0.7416 (tpp) cc_final: 0.7077 (tpt) REVERT: H 232 ASP cc_start: 0.9642 (m-30) cc_final: 0.9111 (m-30) REVERT: H 236 GLU cc_start: 0.9415 (mm-30) cc_final: 0.9044 (mm-30) REVERT: H 252 GLN cc_start: 0.8845 (tp-100) cc_final: 0.7822 (tp-100) REVERT: H 255 LYS cc_start: 0.9518 (mtmm) cc_final: 0.8891 (mttt) REVERT: H 293 TYR cc_start: 0.8970 (t80) cc_final: 0.8739 (t80) REVERT: H 308 TYR cc_start: 0.9066 (m-80) cc_final: 0.8707 (m-10) REVERT: H 320 LYS cc_start: 0.9261 (tppt) cc_final: 0.8823 (tppt) REVERT: H 328 LYS cc_start: 0.8696 (mtpp) cc_final: 0.8407 (mtpt) REVERT: H 331 ASN cc_start: 0.8863 (p0) cc_final: 0.8588 (p0) REVERT: H 333 MET cc_start: 0.8820 (mmp) cc_final: 0.8305 (mmp) REVERT: H 347 GLN cc_start: 0.8810 (mp10) cc_final: 0.8452 (pm20) REVERT: H 360 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8953 (pp30) REVERT: H 397 GLU cc_start: 0.9114 (tm-30) cc_final: 0.8767 (tm-30) REVERT: H 446 ARG cc_start: 0.9340 (tmm-80) cc_final: 0.8808 (tpp80) REVERT: H 465 MET cc_start: 0.9441 (mmm) cc_final: 0.9043 (mmm) REVERT: J 172 ASP cc_start: 0.8894 (t0) cc_final: 0.8483 (t70) REVERT: J 215 PHE cc_start: 0.8887 (m-80) cc_final: 0.8610 (m-80) REVERT: J 232 ASP cc_start: 0.9713 (m-30) cc_final: 0.9171 (m-30) REVERT: J 233 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8903 (mt-10) REVERT: J 236 GLU cc_start: 0.9637 (mm-30) cc_final: 0.9136 (mm-30) REVERT: J 303 GLU cc_start: 0.9303 (tm-30) cc_final: 0.9092 (tm-30) REVERT: J 320 LYS cc_start: 0.9240 (tppp) cc_final: 0.8846 (tppt) REVERT: J 347 GLN cc_start: 0.8721 (mp10) cc_final: 0.8406 (mp10) REVERT: J 407 MET cc_start: 0.8787 (tmm) cc_final: 0.8260 (tmm) REVERT: J 421 GLU cc_start: 0.8889 (pt0) cc_final: 0.8317 (pt0) REVERT: J 499 MET cc_start: 0.9036 (tpt) cc_final: 0.8538 (tpt) REVERT: J 510 ASN cc_start: 0.8223 (m110) cc_final: 0.7906 (m110) REVERT: L 172 ASP cc_start: 0.8044 (t0) cc_final: 0.7692 (t0) REVERT: L 194 MET cc_start: 0.6127 (tpt) cc_final: 0.4425 (pmm) REVERT: L 218 LYS cc_start: 0.8703 (ttpp) cc_final: 0.8187 (ptmm) REVERT: L 235 TYR cc_start: 0.9032 (t80) cc_final: 0.8599 (t80) REVERT: L 236 GLU cc_start: 0.9356 (mm-30) cc_final: 0.9082 (tm-30) REVERT: L 252 GLN cc_start: 0.8905 (tp40) cc_final: 0.8254 (tp-100) REVERT: L 255 LYS cc_start: 0.9499 (mtmm) cc_final: 0.9026 (mttt) REVERT: L 285 GLN cc_start: 0.9070 (mm-40) cc_final: 0.8775 (mm-40) REVERT: L 320 LYS cc_start: 0.9240 (tppt) cc_final: 0.8776 (tppt) REVERT: L 331 ASN cc_start: 0.8949 (p0) cc_final: 0.8657 (p0) REVERT: L 353 GLU cc_start: 0.9455 (mt-10) cc_final: 0.9167 (mt-10) REVERT: L 361 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8226 (t80) REVERT: L 381 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8566 (tm-30) REVERT: L 446 ARG cc_start: 0.9241 (tmm-80) cc_final: 0.8727 (tpp80) REVERT: L 508 MET cc_start: 0.9059 (mmm) cc_final: 0.8849 (tpp) REVERT: D 602 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.5797 (pp30) outliers start: 185 outliers final: 150 residues processed: 1849 average time/residue: 0.2122 time to fit residues: 641.3568 Evaluate side-chains 1908 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 1744 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 510 ASN Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 187 GLN Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 283 CYS Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 510 ASN Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 498 MET Chi-restraints excluded: chain D residue 510 ASN Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 231 ILE Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 312 GLU Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 458 SER Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 496 MET Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain G residue 240 LYS Chi-restraints excluded: chain G residue 283 CYS Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 361 PHE Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain G residue 380 SER Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 419 SER Chi-restraints excluded: chain G residue 469 SER Chi-restraints excluded: chain G residue 498 MET Chi-restraints excluded: chain G residue 505 LEU Chi-restraints excluded: chain G residue 522 VAL Chi-restraints excluded: chain I residue 140 GLU Chi-restraints excluded: chain I residue 225 MET Chi-restraints excluded: chain I residue 236 GLU Chi-restraints excluded: chain I residue 289 LYS Chi-restraints excluded: chain I residue 302 THR Chi-restraints excluded: chain I residue 312 GLU Chi-restraints excluded: chain I residue 419 SER Chi-restraints excluded: chain I residue 423 THR Chi-restraints excluded: chain I residue 428 SER Chi-restraints excluded: chain I residue 430 MET Chi-restraints excluded: chain I residue 469 SER Chi-restraints excluded: chain I residue 484 VAL Chi-restraints excluded: chain I residue 510 ASN Chi-restraints excluded: chain K residue 194 MET Chi-restraints excluded: chain K residue 231 ILE Chi-restraints excluded: chain K residue 240 LYS Chi-restraints excluded: chain K residue 283 CYS Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain K residue 325 GLU Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 361 PHE Chi-restraints excluded: chain K residue 400 CYS Chi-restraints excluded: chain K residue 403 GLU Chi-restraints excluded: chain K residue 419 SER Chi-restraints excluded: chain K residue 423 THR Chi-restraints excluded: chain K residue 430 MET Chi-restraints excluded: chain K residue 505 LEU Chi-restraints excluded: chain K residue 523 SER Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 325 GLU Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain H residue 325 GLU Chi-restraints excluded: chain H residue 360 GLN Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 421 GLU Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain H residue 458 SER Chi-restraints excluded: chain H residue 467 ASP Chi-restraints excluded: chain H residue 496 MET Chi-restraints excluded: chain H residue 510 ASN Chi-restraints excluded: chain J residue 231 ILE Chi-restraints excluded: chain J residue 325 GLU Chi-restraints excluded: chain J residue 380 SER Chi-restraints excluded: chain J residue 381 GLU Chi-restraints excluded: chain J residue 429 VAL Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain L residue 231 ILE Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 343 SER Chi-restraints excluded: chain L residue 361 PHE Chi-restraints excluded: chain L residue 362 LEU Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 458 SER Chi-restraints excluded: chain L residue 467 ASP Chi-restraints excluded: chain L residue 496 MET Chi-restraints excluded: chain L residue 507 LYS Chi-restraints excluded: chain L residue 510 ASN Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain D residue 602 GLN Chi-restraints excluded: chain E residue 602 GLN Chi-restraints excluded: chain F residue 602 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 72 optimal weight: 0.9990 chunk 255 optimal weight: 0.9990 chunk 435 optimal weight: 0.2980 chunk 135 optimal weight: 2.9990 chunk 245 optimal weight: 0.8980 chunk 150 optimal weight: 0.6980 chunk 205 optimal weight: 0.7980 chunk 443 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 332 optimal weight: 1.9990 chunk 399 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN B 213 GLN ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN ** C 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 HIS E 351 ASN ** E 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 298 ASN K 271 GLN K 375 ASN F 298 ASN F 360 GLN F 388 ASN F 519 HIS ** H 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 471 GLN ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 360 GLN ** J 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 388 ASN ** J 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.156827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.118471 restraints weight = 64614.228| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 3.90 r_work: 0.3229 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 36972 Z= 0.133 Angle : 0.706 13.163 49932 Z= 0.354 Chirality : 0.045 0.274 5544 Planarity : 0.004 0.046 6408 Dihedral : 5.009 51.629 4929 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.39 % Favored : 93.53 % Rotamer: Outliers : 3.93 % Allowed : 29.03 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.13), residues: 4620 helix: 1.11 (0.11), residues: 2388 sheet: -0.32 (0.29), residues: 360 loop : -0.22 (0.16), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 446 TYR 0.029 0.001 TYR J 293 PHE 0.049 0.001 PHE H 224 TRP 0.012 0.001 TRP K 466 HIS 0.009 0.001 HIS J 157 Details of bonding type rmsd covalent geometry : bond 0.00314 (36972) covalent geometry : angle 0.70628 (49932) hydrogen bonds : bond 0.03016 ( 1700) hydrogen bonds : angle 4.87284 ( 5193) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9240 Ramachandran restraints generated. 4620 Oldfield, 0 Emsley, 4620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9240 Ramachandran restraints generated. 4620 Oldfield, 0 Emsley, 4620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1952 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 1794 time to evaluate : 1.341 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: A 194 MET cc_start: 0.6752 (tpp) cc_final: 0.5687 (tpp) REVERT: A 213 GLN cc_start: 0.9107 (mm-40) cc_final: 0.8678 (mm-40) REVERT: A 227 PHE cc_start: 0.9534 (t80) cc_final: 0.9272 (t80) REVERT: A 236 GLU cc_start: 0.9665 (mm-30) cc_final: 0.9417 (mm-30) REVERT: A 277 ASP cc_start: 0.9092 (m-30) cc_final: 0.8813 (p0) REVERT: A 293 TYR cc_start: 0.9433 (t80) cc_final: 0.8860 (t80) REVERT: A 306 HIS cc_start: 0.9012 (m-70) cc_final: 0.8656 (m-70) REVERT: A 357 TYR cc_start: 0.9388 (t80) cc_final: 0.9109 (t80) REVERT: A 360 GLN cc_start: 0.9429 (tm130) cc_final: 0.9072 (tm-30) REVERT: A 361 PHE cc_start: 0.9238 (OUTLIER) cc_final: 0.8454 (t80) REVERT: A 365 MET cc_start: 0.9414 (ttm) cc_final: 0.8850 (tmm) REVERT: A 415 PHE cc_start: 0.9440 (m-80) cc_final: 0.9005 (m-80) REVERT: A 421 GLU cc_start: 0.8798 (pt0) cc_final: 0.8421 (pt0) REVERT: A 434 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8878 (pp) REVERT: A 445 GLU cc_start: 0.9343 (mt-10) cc_final: 0.9054 (mt-10) REVERT: A 448 LEU cc_start: 0.9533 (mt) cc_final: 0.9253 (mt) REVERT: A 454 ARG cc_start: 0.9050 (ttp80) cc_final: 0.8713 (tpt170) REVERT: A 455 ASN cc_start: 0.9285 (m-40) cc_final: 0.9060 (m-40) REVERT: A 498 MET cc_start: 0.8835 (ttm) cc_final: 0.8583 (ttm) REVERT: A 499 MET cc_start: 0.9071 (tpp) cc_final: 0.8707 (tpp) REVERT: A 500 CYS cc_start: 0.8661 (m) cc_final: 0.8381 (m) REVERT: B 196 ASP cc_start: 0.7518 (t70) cc_final: 0.7188 (t0) REVERT: B 234 LEU cc_start: 0.9733 (mt) cc_final: 0.9501 (mt) REVERT: B 235 TYR cc_start: 0.9407 (t80) cc_final: 0.8430 (t80) REVERT: B 236 GLU cc_start: 0.9535 (mm-30) cc_final: 0.9047 (mm-30) REVERT: B 282 PHE cc_start: 0.9057 (p90) cc_final: 0.8713 (p90) REVERT: B 285 GLN cc_start: 0.9069 (mm-40) cc_final: 0.8378 (mm-40) REVERT: B 293 TYR cc_start: 0.9358 (t80) cc_final: 0.9056 (t80) REVERT: B 297 VAL cc_start: 0.9686 (t) cc_final: 0.9386 (m) REVERT: B 396 LYS cc_start: 0.9120 (tttp) cc_final: 0.8918 (tttp) REVERT: B 407 MET cc_start: 0.8846 (tmm) cc_final: 0.8595 (tmm) REVERT: B 414 TYR cc_start: 0.9551 (t80) cc_final: 0.8920 (t80) REVERT: B 421 GLU cc_start: 0.8917 (pt0) cc_final: 0.8555 (pt0) REVERT: B 436 ASN cc_start: 0.8930 (t0) cc_final: 0.8685 (t0) REVERT: B 454 ARG cc_start: 0.9162 (ttp80) cc_final: 0.8871 (ttp80) REVERT: B 520 ASP cc_start: 0.8953 (m-30) cc_final: 0.8555 (m-30) REVERT: C 164 LYS cc_start: 0.9312 (mtmt) cc_final: 0.9061 (mtpp) REVERT: C 175 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8340 (pp) REVERT: C 179 MET cc_start: 0.7706 (ptp) cc_final: 0.7057 (ptp) REVERT: C 227 PHE cc_start: 0.9608 (t80) cc_final: 0.9335 (t80) REVERT: C 246 VAL cc_start: 0.8439 (OUTLIER) cc_final: 0.7901 (t) REVERT: C 249 TYR cc_start: 0.8811 (p90) cc_final: 0.8378 (p90) REVERT: C 277 ASP cc_start: 0.9069 (m-30) cc_final: 0.8782 (p0) REVERT: C 347 GLN cc_start: 0.8930 (mp10) cc_final: 0.8475 (mp10) REVERT: C 365 MET cc_start: 0.9495 (ttm) cc_final: 0.8954 (tmm) REVERT: C 375 ASN cc_start: 0.9038 (t0) cc_final: 0.8822 (t0) REVERT: C 379 GLN cc_start: 0.9563 (mm110) cc_final: 0.9292 (mm110) REVERT: C 387 ARG cc_start: 0.9189 (tpp80) cc_final: 0.8954 (tpp80) REVERT: C 397 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8777 (tm-30) REVERT: C 421 GLU cc_start: 0.8740 (pt0) cc_final: 0.8396 (pt0) REVERT: C 434 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8761 (pp) REVERT: C 445 GLU cc_start: 0.9325 (mt-10) cc_final: 0.9066 (mt-10) REVERT: C 455 ASN cc_start: 0.9245 (m-40) cc_final: 0.8987 (m-40) REVERT: C 467 ASP cc_start: 0.9510 (p0) cc_final: 0.8731 (p0) REVERT: C 496 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.7327 (ppp) REVERT: C 499 MET cc_start: 0.8921 (tpp) cc_final: 0.8520 (tpp) REVERT: C 508 MET cc_start: 0.9361 (mtt) cc_final: 0.8789 (mtt) REVERT: D 140 GLU cc_start: 0.8677 (pm20) cc_final: 0.8359 (pp20) REVERT: D 196 ASP cc_start: 0.7254 (t0) cc_final: 0.6939 (t0) REVERT: D 212 THR cc_start: 0.9116 (p) cc_final: 0.8318 (p) REVERT: D 213 GLN cc_start: 0.9298 (mm110) cc_final: 0.8928 (mm-40) REVERT: D 232 ASP cc_start: 0.9798 (m-30) cc_final: 0.9458 (m-30) REVERT: D 236 GLU cc_start: 0.9552 (mm-30) cc_final: 0.9173 (mm-30) REVERT: D 246 VAL cc_start: 0.8472 (OUTLIER) cc_final: 0.7795 (t) REVERT: D 249 TYR cc_start: 0.8490 (p90) cc_final: 0.8022 (p90) REVERT: D 260 LEU cc_start: 0.9451 (tp) cc_final: 0.8874 (tp) REVERT: D 277 ASP cc_start: 0.9228 (m-30) cc_final: 0.8763 (p0) REVERT: D 285 GLN cc_start: 0.8940 (mm-40) cc_final: 0.8294 (mm-40) REVERT: D 293 TYR cc_start: 0.9360 (t80) cc_final: 0.9148 (t80) REVERT: D 318 PHE cc_start: 0.9093 (p90) cc_final: 0.8764 (p90) REVERT: D 373 PHE cc_start: 0.8572 (t80) cc_final: 0.8327 (t80) REVERT: D 382 ARG cc_start: 0.9337 (ttp80) cc_final: 0.9003 (mtp-110) REVERT: D 394 TYR cc_start: 0.9716 (t80) cc_final: 0.9395 (t80) REVERT: D 397 GLU cc_start: 0.9478 (tm-30) cc_final: 0.9132 (tm-30) REVERT: D 407 MET cc_start: 0.8832 (tmm) cc_final: 0.8528 (tmm) REVERT: D 421 GLU cc_start: 0.8841 (pt0) cc_final: 0.8355 (pt0) REVERT: D 454 ARG cc_start: 0.9129 (ttp80) cc_final: 0.8807 (ttp80) REVERT: D 506 ASP cc_start: 0.9548 (t70) cc_final: 0.8741 (p0) REVERT: D 508 MET cc_start: 0.9172 (mmm) cc_final: 0.8878 (mmm) REVERT: D 520 ASP cc_start: 0.8901 (m-30) cc_final: 0.8451 (m-30) REVERT: E 172 ASP cc_start: 0.8959 (t0) cc_final: 0.8538 (t0) REVERT: E 213 GLN cc_start: 0.9164 (mm110) cc_final: 0.8876 (mm110) REVERT: E 223 ASP cc_start: 0.9075 (t0) cc_final: 0.8868 (t0) REVERT: E 271 GLN cc_start: 0.8634 (pt0) cc_final: 0.8262 (pt0) REVERT: E 321 LEU cc_start: 0.9501 (pt) cc_final: 0.9101 (pp) REVERT: E 331 ASN cc_start: 0.9126 (p0) cc_final: 0.8390 (p0) REVERT: E 382 ARG cc_start: 0.9647 (ttp80) cc_final: 0.9132 (mtp85) REVERT: E 407 MET cc_start: 0.8859 (tmm) cc_final: 0.8518 (tmm) REVERT: E 421 GLU cc_start: 0.8801 (pt0) cc_final: 0.8545 (pt0) REVERT: E 426 SER cc_start: 0.9548 (t) cc_final: 0.9163 (p) REVERT: E 455 ASN cc_start: 0.9125 (m-40) cc_final: 0.8750 (m-40) REVERT: E 508 MET cc_start: 0.9462 (ttm) cc_final: 0.9027 (tpp) REVERT: E 520 ASP cc_start: 0.8965 (m-30) cc_final: 0.8432 (m-30) REVERT: G 181 MET cc_start: 0.9152 (tpp) cc_final: 0.8902 (mtm) REVERT: G 194 MET cc_start: 0.5539 (tpp) cc_final: 0.5077 (tpp) REVERT: G 227 PHE cc_start: 0.9578 (t80) cc_final: 0.9260 (t80) REVERT: G 232 ASP cc_start: 0.9803 (m-30) cc_final: 0.9240 (m-30) REVERT: G 235 TYR cc_start: 0.9259 (t80) cc_final: 0.8646 (t80) REVERT: G 236 GLU cc_start: 0.9606 (mm-30) cc_final: 0.9141 (mm-30) REVERT: G 240 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.8979 (mtmm) REVERT: G 249 TYR cc_start: 0.7996 (p90) cc_final: 0.7533 (p90) REVERT: G 293 TYR cc_start: 0.9238 (t80) cc_final: 0.7382 (t80) REVERT: G 300 LEU cc_start: 0.9592 (mm) cc_final: 0.9297 (mt) REVERT: G 361 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8688 (t80) REVERT: G 370 TYR cc_start: 0.9118 (t80) cc_final: 0.8913 (t80) REVERT: G 421 GLU cc_start: 0.8918 (pt0) cc_final: 0.8624 (pt0) REVERT: G 424 CYS cc_start: 0.9080 (m) cc_final: 0.8740 (m) REVERT: G 436 ASN cc_start: 0.9420 (t0) cc_final: 0.9070 (t0) REVERT: G 446 ARG cc_start: 0.8450 (ttp80) cc_final: 0.7307 (ttp80) REVERT: G 451 GLU cc_start: 0.8787 (mp0) cc_final: 0.8397 (mp0) REVERT: G 454 ARG cc_start: 0.9184 (ttp80) cc_final: 0.8639 (ttp-110) REVERT: G 455 ASN cc_start: 0.9312 (m-40) cc_final: 0.8754 (m110) REVERT: G 499 MET cc_start: 0.9011 (tpp) cc_final: 0.8672 (tpp) REVERT: G 516 HIS cc_start: 0.8273 (t-90) cc_final: 0.7632 (t-90) REVERT: I 172 ASP cc_start: 0.8930 (t0) cc_final: 0.8482 (t0) REVERT: I 183 ARG cc_start: 0.9085 (mtp85) cc_final: 0.8304 (ptp-110) REVERT: I 194 MET cc_start: 0.7346 (tpp) cc_final: 0.6658 (tpp) REVERT: I 213 GLN cc_start: 0.9161 (mm-40) cc_final: 0.8643 (tp-100) REVERT: I 218 LYS cc_start: 0.9290 (mmmm) cc_final: 0.8885 (mtmm) REVERT: I 249 TYR cc_start: 0.9174 (p90) cc_final: 0.8899 (p90) REVERT: I 320 LYS cc_start: 0.9432 (tppt) cc_final: 0.8819 (tppt) REVERT: I 323 LEU cc_start: 0.9535 (mp) cc_final: 0.9313 (mp) REVERT: I 331 ASN cc_start: 0.9137 (p0) cc_final: 0.8480 (p0) REVERT: I 347 GLN cc_start: 0.8623 (mt0) cc_final: 0.8004 (mp10) REVERT: I 382 ARG cc_start: 0.9622 (ttp80) cc_final: 0.9097 (mtp85) REVERT: I 407 MET cc_start: 0.8911 (tmm) cc_final: 0.8529 (tmm) REVERT: I 421 GLU cc_start: 0.8855 (pt0) cc_final: 0.8568 (pt0) REVERT: I 426 SER cc_start: 0.9559 (t) cc_final: 0.9228 (p) REVERT: I 455 ASN cc_start: 0.9136 (m-40) cc_final: 0.8747 (m-40) REVERT: I 467 ASP cc_start: 0.9045 (p0) cc_final: 0.8316 (p0) REVERT: I 494 ASN cc_start: 0.9413 (m-40) cc_final: 0.9115 (m-40) REVERT: I 506 ASP cc_start: 0.9459 (t70) cc_final: 0.8489 (p0) REVERT: I 520 ASP cc_start: 0.9033 (m-30) cc_final: 0.8821 (m-30) REVERT: K 179 MET cc_start: 0.9037 (tpp) cc_final: 0.8448 (tpp) REVERT: K 232 ASP cc_start: 0.9757 (m-30) cc_final: 0.9415 (m-30) REVERT: K 235 TYR cc_start: 0.9126 (t80) cc_final: 0.8480 (t80) REVERT: K 236 GLU cc_start: 0.9596 (mm-30) cc_final: 0.9241 (mm-30) REVERT: K 260 LEU cc_start: 0.9429 (tp) cc_final: 0.9024 (tp) REVERT: K 277 ASP cc_start: 0.9345 (OUTLIER) cc_final: 0.8939 (p0) REVERT: K 293 TYR cc_start: 0.9267 (t80) cc_final: 0.7592 (t80) REVERT: K 344 LEU cc_start: 0.9569 (mt) cc_final: 0.9359 (mp) REVERT: K 361 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.8735 (t80) REVERT: K 407 MET cc_start: 0.8682 (tmm) cc_final: 0.8388 (tmm) REVERT: K 421 GLU cc_start: 0.8848 (pt0) cc_final: 0.8553 (pt0) REVERT: K 424 CYS cc_start: 0.9018 (m) cc_final: 0.8433 (m) REVERT: K 430 MET cc_start: 0.9290 (OUTLIER) cc_final: 0.8557 (mpp) REVERT: K 436 ASN cc_start: 0.9345 (t0) cc_final: 0.8972 (t0) REVERT: K 446 ARG cc_start: 0.8635 (ttp80) cc_final: 0.7445 (ttp80) REVERT: K 455 ASN cc_start: 0.9251 (m-40) cc_final: 0.8942 (m110) REVERT: K 467 ASP cc_start: 0.9344 (p0) cc_final: 0.8569 (p0) REVERT: K 510 ASN cc_start: 0.8850 (m-40) cc_final: 0.8462 (m-40) REVERT: K 516 HIS cc_start: 0.8307 (t-90) cc_final: 0.7917 (t70) REVERT: K 520 ASP cc_start: 0.8993 (m-30) cc_final: 0.8720 (m-30) REVERT: F 140 GLU cc_start: 0.8706 (pm20) cc_final: 0.8470 (pm20) REVERT: F 172 ASP cc_start: 0.8811 (t0) cc_final: 0.8514 (t70) REVERT: F 177 GLU cc_start: 0.8931 (pp20) cc_final: 0.8666 (pp20) REVERT: F 194 MET cc_start: 0.6494 (tpp) cc_final: 0.6261 (tpp) REVERT: F 196 ASP cc_start: 0.8021 (t70) cc_final: 0.7505 (t70) REVERT: F 212 THR cc_start: 0.9420 (p) cc_final: 0.8637 (t) REVERT: F 213 GLN cc_start: 0.8790 (mm110) cc_final: 0.7706 (mm110) REVERT: F 215 PHE cc_start: 0.8715 (m-80) cc_final: 0.8423 (m-80) REVERT: F 216 ARG cc_start: 0.8474 (mtp180) cc_final: 0.7505 (mtp180) REVERT: F 232 ASP cc_start: 0.9659 (m-30) cc_final: 0.9404 (m-30) REVERT: F 233 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8795 (mt-10) REVERT: F 236 GLU cc_start: 0.9601 (mm-30) cc_final: 0.9147 (mm-30) REVERT: F 252 GLN cc_start: 0.9142 (tp40) cc_final: 0.8863 (tp40) REVERT: F 265 VAL cc_start: 0.9434 (t) cc_final: 0.9171 (t) REVERT: F 299 ASP cc_start: 0.9021 (m-30) cc_final: 0.8704 (m-30) REVERT: F 323 LEU cc_start: 0.9523 (mp) cc_final: 0.9317 (mm) REVERT: F 382 ARG cc_start: 0.9487 (ttp80) cc_final: 0.8934 (mtp-110) REVERT: F 421 GLU cc_start: 0.8909 (pt0) cc_final: 0.8309 (pt0) REVERT: F 496 MET cc_start: 0.8627 (ppp) cc_final: 0.7731 (ppp) REVERT: F 499 MET cc_start: 0.8836 (tpp) cc_final: 0.8541 (tpp) REVERT: H 194 MET cc_start: 0.7470 (tpp) cc_final: 0.7171 (tpt) REVERT: H 213 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8364 (mm-40) REVERT: H 232 ASP cc_start: 0.9634 (m-30) cc_final: 0.9115 (m-30) REVERT: H 236 GLU cc_start: 0.9401 (mm-30) cc_final: 0.9037 (mm-30) REVERT: H 249 TYR cc_start: 0.8465 (p90) cc_final: 0.8187 (p90) REVERT: H 255 LYS cc_start: 0.9535 (mtmm) cc_final: 0.8997 (mttt) REVERT: H 280 VAL cc_start: 0.9161 (t) cc_final: 0.8894 (p) REVERT: H 293 TYR cc_start: 0.8953 (t80) cc_final: 0.8680 (t80) REVERT: H 308 TYR cc_start: 0.9030 (m-80) cc_final: 0.8645 (m-10) REVERT: H 320 LYS cc_start: 0.9250 (tppt) cc_final: 0.8809 (tppt) REVERT: H 328 LYS cc_start: 0.8702 (mtpp) cc_final: 0.8384 (mtpt) REVERT: H 331 ASN cc_start: 0.8911 (p0) cc_final: 0.8607 (p0) REVERT: H 333 MET cc_start: 0.8743 (mmp) cc_final: 0.8282 (mmp) REVERT: H 347 GLN cc_start: 0.8856 (mp10) cc_final: 0.8503 (pm20) REVERT: H 360 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8929 (pp30) REVERT: H 378 PHE cc_start: 0.8974 (t80) cc_final: 0.8680 (t80) REVERT: H 397 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8795 (tm-30) REVERT: H 446 ARG cc_start: 0.9293 (tmm-80) cc_final: 0.8789 (tpp80) REVERT: H 455 ASN cc_start: 0.8806 (m-40) cc_final: 0.8565 (m-40) REVERT: H 465 MET cc_start: 0.9444 (mmm) cc_final: 0.9057 (mmm) REVERT: J 172 ASP cc_start: 0.8923 (t0) cc_final: 0.8482 (t70) REVERT: J 213 GLN cc_start: 0.8957 (tp40) cc_final: 0.8662 (tp-100) REVERT: J 215 PHE cc_start: 0.8854 (m-80) cc_final: 0.8584 (m-80) REVERT: J 216 ARG cc_start: 0.8752 (mtp-110) cc_final: 0.8493 (mtm110) REVERT: J 232 ASP cc_start: 0.9705 (m-30) cc_final: 0.9141 (m-30) REVERT: J 236 GLU cc_start: 0.9631 (mm-30) cc_final: 0.9164 (mm-30) REVERT: J 303 GLU cc_start: 0.9347 (tm-30) cc_final: 0.9133 (tm-30) REVERT: J 320 LYS cc_start: 0.9170 (tppp) cc_final: 0.8784 (tppt) REVERT: J 407 MET cc_start: 0.8693 (tmm) cc_final: 0.8155 (tmm) REVERT: J 418 CYS cc_start: 0.9059 (m) cc_final: 0.8485 (t) REVERT: J 421 GLU cc_start: 0.8882 (pt0) cc_final: 0.8296 (pt0) REVERT: J 499 MET cc_start: 0.9112 (tpt) cc_final: 0.8612 (tpt) REVERT: L 194 MET cc_start: 0.6218 (tpt) cc_final: 0.4467 (pmm) REVERT: L 218 LYS cc_start: 0.8707 (ttpp) cc_final: 0.7947 (ptmm) REVERT: L 223 ASP cc_start: 0.8827 (p0) cc_final: 0.8529 (p0) REVERT: L 235 TYR cc_start: 0.8971 (t80) cc_final: 0.8427 (t80) REVERT: L 236 GLU cc_start: 0.9349 (mm-30) cc_final: 0.9077 (tm-30) REVERT: L 252 GLN cc_start: 0.8836 (tp40) cc_final: 0.8437 (tp-100) REVERT: L 255 LYS cc_start: 0.9492 (mtmm) cc_final: 0.9227 (mtmm) REVERT: L 280 VAL cc_start: 0.9154 (t) cc_final: 0.8862 (p) REVERT: L 285 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8804 (mm-40) REVERT: L 320 LYS cc_start: 0.9230 (tppt) cc_final: 0.8792 (tppt) REVERT: L 331 ASN cc_start: 0.8905 (p0) cc_final: 0.8605 (p0) REVERT: L 349 VAL cc_start: 0.8925 (OUTLIER) cc_final: 0.8672 (p) REVERT: L 353 GLU cc_start: 0.9440 (mt-10) cc_final: 0.9131 (mt-10) REVERT: L 361 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8125 (t80) REVERT: L 381 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8569 (tm-30) REVERT: L 425 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8231 (mp0) REVERT: L 446 ARG cc_start: 0.9219 (tmm-80) cc_final: 0.8727 (tpp80) REVERT: L 455 ASN cc_start: 0.8861 (m-40) cc_final: 0.8557 (m-40) REVERT: L 465 MET cc_start: 0.9358 (mmm) cc_final: 0.9135 (mmm) REVERT: L 508 MET cc_start: 0.9098 (mmm) cc_final: 0.8870 (tpp) REVERT: D 602 GLN cc_start: 0.6933 (OUTLIER) cc_final: 0.5161 (pp30) outliers start: 158 outliers final: 119 residues processed: 1849 average time/residue: 0.2054 time to fit residues: 620.8426 Evaluate side-chains 1903 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 1768 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 510 ASN Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 187 GLN Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 283 CYS Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 510 ASN Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 498 MET Chi-restraints excluded: chain D residue 510 ASN Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 312 GLU Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 458 SER Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 496 MET Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain G residue 240 LYS Chi-restraints excluded: chain G residue 283 CYS Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 361 PHE Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain G residue 380 SER Chi-restraints excluded: chain G residue 381 GLU Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 469 SER Chi-restraints excluded: chain G residue 505 LEU Chi-restraints excluded: chain G residue 522 VAL Chi-restraints excluded: chain I residue 225 MET Chi-restraints excluded: chain I residue 236 GLU Chi-restraints excluded: chain I residue 289 LYS Chi-restraints excluded: chain I residue 302 THR Chi-restraints excluded: chain I residue 312 GLU Chi-restraints excluded: chain I residue 353 GLU Chi-restraints excluded: chain I residue 423 THR Chi-restraints excluded: chain I residue 428 SER Chi-restraints excluded: chain I residue 484 VAL Chi-restraints excluded: chain K residue 194 MET Chi-restraints excluded: chain K residue 221 ILE Chi-restraints excluded: chain K residue 277 ASP Chi-restraints excluded: chain K residue 283 CYS Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain K residue 325 GLU Chi-restraints excluded: chain K residue 361 PHE Chi-restraints excluded: chain K residue 400 CYS Chi-restraints excluded: chain K residue 403 GLU Chi-restraints excluded: chain K residue 419 SER Chi-restraints excluded: chain K residue 423 THR Chi-restraints excluded: chain K residue 430 MET Chi-restraints excluded: chain K residue 505 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 325 GLU Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain H residue 325 GLU Chi-restraints excluded: chain H residue 360 GLN Chi-restraints excluded: chain H residue 421 GLU Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain H residue 458 SER Chi-restraints excluded: chain H residue 496 MET Chi-restraints excluded: chain H residue 505 LEU Chi-restraints excluded: chain H residue 510 ASN Chi-restraints excluded: chain J residue 196 ASP Chi-restraints excluded: chain J residue 231 ILE Chi-restraints excluded: chain J residue 325 GLU Chi-restraints excluded: chain J residue 381 GLU Chi-restraints excluded: chain J residue 417 LEU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 349 VAL Chi-restraints excluded: chain L residue 361 PHE Chi-restraints excluded: chain L residue 362 LEU Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 458 SER Chi-restraints excluded: chain L residue 496 MET Chi-restraints excluded: chain L residue 507 LYS Chi-restraints excluded: chain L residue 510 ASN Chi-restraints excluded: chain L residue 520 ASP Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain D residue 602 GLN Chi-restraints excluded: chain E residue 602 GLN Chi-restraints excluded: chain F residue 602 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 395 optimal weight: 0.9990 chunk 437 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 231 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 153 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN ** C 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 HIS ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 ASN ** E 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 271 GLN ** K 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 461 HIS ** K 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 ASN F 379 GLN F 388 ASN F 519 HIS ** H 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 324 ASN H 335 ASN H 471 GLN ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 HIS J 213 GLN J 241 GLN ** J 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 519 HIS ** L 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.155982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.117535 restraints weight = 65022.462| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.90 r_work: 0.3219 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 36972 Z= 0.154 Angle : 0.742 13.872 49932 Z= 0.371 Chirality : 0.046 0.291 5544 Planarity : 0.005 0.054 6408 Dihedral : 5.064 50.078 4929 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.17 % Favored : 93.72 % Rotamer: Outliers : 4.13 % Allowed : 29.95 % Favored : 65.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.13), residues: 4620 helix: 1.03 (0.11), residues: 2400 sheet: -0.27 (0.29), residues: 360 loop : -0.21 (0.16), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 446 TYR 0.027 0.002 TYR F 293 PHE 0.026 0.001 PHE K 415 TRP 0.017 0.001 TRP G 501 HIS 0.009 0.001 HIS J 157 Details of bonding type rmsd covalent geometry : bond 0.00365 (36972) covalent geometry : angle 0.74189 (49932) hydrogen bonds : bond 0.03121 ( 1700) hydrogen bonds : angle 4.93491 ( 5193) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9240 Ramachandran restraints generated. 4620 Oldfield, 0 Emsley, 4620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9240 Ramachandran restraints generated. 4620 Oldfield, 0 Emsley, 4620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1945 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 1779 time to evaluate : 1.417 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: A 194 MET cc_start: 0.6794 (tpp) cc_final: 0.5692 (tpp) REVERT: A 213 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8607 (mm-40) REVERT: A 227 PHE cc_start: 0.9547 (t80) cc_final: 0.9279 (t80) REVERT: A 236 GLU cc_start: 0.9685 (mm-30) cc_final: 0.9440 (mm-30) REVERT: A 277 ASP cc_start: 0.9117 (m-30) cc_final: 0.8801 (p0) REVERT: A 293 TYR cc_start: 0.9442 (t80) cc_final: 0.8874 (t80) REVERT: A 306 HIS cc_start: 0.9052 (m-70) cc_final: 0.8725 (m-70) REVERT: A 347 GLN cc_start: 0.8944 (mp10) cc_final: 0.8631 (mp10) REVERT: A 357 TYR cc_start: 0.9404 (t80) cc_final: 0.8903 (t80) REVERT: A 360 GLN cc_start: 0.9435 (tm130) cc_final: 0.9086 (tm-30) REVERT: A 361 PHE cc_start: 0.9270 (OUTLIER) cc_final: 0.8437 (t80) REVERT: A 365 MET cc_start: 0.9428 (ttm) cc_final: 0.8884 (tmm) REVERT: A 415 PHE cc_start: 0.9455 (m-80) cc_final: 0.8962 (m-80) REVERT: A 421 GLU cc_start: 0.8817 (pt0) cc_final: 0.8442 (pt0) REVERT: A 434 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8846 (pp) REVERT: A 445 GLU cc_start: 0.9349 (mt-10) cc_final: 0.9062 (mt-10) REVERT: A 448 LEU cc_start: 0.9562 (mt) cc_final: 0.9289 (mt) REVERT: A 454 ARG cc_start: 0.9053 (ttp80) cc_final: 0.8810 (ttp-110) REVERT: A 498 MET cc_start: 0.8879 (ttm) cc_final: 0.8621 (ttm) REVERT: A 499 MET cc_start: 0.9066 (tpp) cc_final: 0.8694 (tpp) REVERT: A 500 CYS cc_start: 0.8641 (m) cc_final: 0.8368 (m) REVERT: B 178 CYS cc_start: 0.8861 (m) cc_final: 0.8656 (m) REVERT: B 196 ASP cc_start: 0.7506 (t70) cc_final: 0.7165 (t0) REVERT: B 213 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8501 (mm110) REVERT: B 234 LEU cc_start: 0.9666 (mt) cc_final: 0.9438 (mt) REVERT: B 235 TYR cc_start: 0.9377 (t80) cc_final: 0.8421 (t80) REVERT: B 236 GLU cc_start: 0.9554 (mm-30) cc_final: 0.9083 (mm-30) REVERT: B 249 TYR cc_start: 0.8339 (p90) cc_final: 0.7854 (p90) REVERT: B 282 PHE cc_start: 0.9088 (p90) cc_final: 0.8760 (p90) REVERT: B 285 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8338 (mm-40) REVERT: B 293 TYR cc_start: 0.9331 (t80) cc_final: 0.9023 (t80) REVERT: B 297 VAL cc_start: 0.9690 (t) cc_final: 0.9395 (m) REVERT: B 357 TYR cc_start: 0.9247 (t80) cc_final: 0.8875 (t80) REVERT: B 396 LYS cc_start: 0.9154 (tttp) cc_final: 0.8901 (tttp) REVERT: B 407 MET cc_start: 0.8864 (tmm) cc_final: 0.8583 (tmm) REVERT: B 414 TYR cc_start: 0.9551 (t80) cc_final: 0.8944 (t80) REVERT: B 421 GLU cc_start: 0.8890 (pt0) cc_final: 0.8544 (pt0) REVERT: B 436 ASN cc_start: 0.8946 (t0) cc_final: 0.8703 (t0) REVERT: B 454 ARG cc_start: 0.9163 (ttp80) cc_final: 0.8880 (ttp80) REVERT: B 520 ASP cc_start: 0.8959 (m-30) cc_final: 0.8550 (m-30) REVERT: C 164 LYS cc_start: 0.9327 (mtmt) cc_final: 0.9091 (mtpp) REVERT: C 175 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8369 (pp) REVERT: C 179 MET cc_start: 0.7733 (ptp) cc_final: 0.7080 (ptp) REVERT: C 227 PHE cc_start: 0.9613 (t80) cc_final: 0.9341 (t80) REVERT: C 246 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8031 (t) REVERT: C 249 TYR cc_start: 0.8895 (p90) cc_final: 0.8585 (p90) REVERT: C 277 ASP cc_start: 0.9029 (m-30) cc_final: 0.8652 (p0) REVERT: C 293 TYR cc_start: 0.9394 (t80) cc_final: 0.8859 (t80) REVERT: C 347 GLN cc_start: 0.8993 (mp10) cc_final: 0.8348 (mp10) REVERT: C 365 MET cc_start: 0.9488 (ttm) cc_final: 0.8948 (tmm) REVERT: C 397 GLU cc_start: 0.9190 (tm-30) cc_final: 0.8789 (tm-30) REVERT: C 421 GLU cc_start: 0.8761 (pt0) cc_final: 0.8405 (pt0) REVERT: C 434 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8781 (pp) REVERT: C 445 GLU cc_start: 0.9319 (mt-10) cc_final: 0.9071 (mt-10) REVERT: C 455 ASN cc_start: 0.9257 (m-40) cc_final: 0.9011 (m-40) REVERT: C 467 ASP cc_start: 0.9516 (p0) cc_final: 0.8952 (p0) REVERT: C 496 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.7358 (ppp) REVERT: C 499 MET cc_start: 0.9086 (tpp) cc_final: 0.8683 (tpp) REVERT: C 508 MET cc_start: 0.9394 (mtt) cc_final: 0.8996 (mtt) REVERT: D 140 GLU cc_start: 0.8672 (pm20) cc_final: 0.8359 (pp20) REVERT: D 196 ASP cc_start: 0.7209 (t0) cc_final: 0.6909 (t0) REVERT: D 232 ASP cc_start: 0.9803 (m-30) cc_final: 0.9463 (m-30) REVERT: D 236 GLU cc_start: 0.9561 (mm-30) cc_final: 0.9180 (mm-30) REVERT: D 246 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.7859 (t) REVERT: D 249 TYR cc_start: 0.8526 (p90) cc_final: 0.8069 (p90) REVERT: D 260 LEU cc_start: 0.9488 (tp) cc_final: 0.8901 (tp) REVERT: D 263 VAL cc_start: 0.9526 (t) cc_final: 0.9264 (p) REVERT: D 277 ASP cc_start: 0.9253 (m-30) cc_final: 0.8607 (p0) REVERT: D 285 GLN cc_start: 0.8970 (mm-40) cc_final: 0.8307 (mm-40) REVERT: D 293 TYR cc_start: 0.9362 (t80) cc_final: 0.9147 (t80) REVERT: D 373 PHE cc_start: 0.8574 (t80) cc_final: 0.8290 (t80) REVERT: D 382 ARG cc_start: 0.9332 (ttp80) cc_final: 0.9003 (mtp-110) REVERT: D 394 TYR cc_start: 0.9725 (t80) cc_final: 0.9459 (t80) REVERT: D 397 GLU cc_start: 0.9491 (tm-30) cc_final: 0.9158 (tm-30) REVERT: D 407 MET cc_start: 0.8836 (tmm) cc_final: 0.8530 (tmm) REVERT: D 421 GLU cc_start: 0.8858 (pt0) cc_final: 0.8359 (pt0) REVERT: D 454 ARG cc_start: 0.9139 (ttp80) cc_final: 0.8811 (ttp80) REVERT: D 467 ASP cc_start: 0.9374 (OUTLIER) cc_final: 0.8545 (p0) REVERT: D 506 ASP cc_start: 0.9553 (t70) cc_final: 0.8702 (p0) REVERT: D 508 MET cc_start: 0.9181 (mmm) cc_final: 0.7388 (mmm) REVERT: D 520 ASP cc_start: 0.8903 (m-30) cc_final: 0.8460 (m-30) REVERT: E 172 ASP cc_start: 0.8823 (t0) cc_final: 0.8420 (t0) REVERT: E 183 ARG cc_start: 0.8897 (mmm-85) cc_final: 0.8576 (ttp-110) REVERT: E 213 GLN cc_start: 0.9153 (mm110) cc_final: 0.8787 (mm110) REVERT: E 223 ASP cc_start: 0.9050 (t0) cc_final: 0.8828 (t0) REVERT: E 233 GLU cc_start: 0.9473 (tp30) cc_final: 0.8829 (tp30) REVERT: E 271 GLN cc_start: 0.8674 (pt0) cc_final: 0.8369 (pt0) REVERT: E 321 LEU cc_start: 0.9517 (pt) cc_final: 0.9094 (pp) REVERT: E 331 ASN cc_start: 0.9118 (p0) cc_final: 0.8419 (p0) REVERT: E 382 ARG cc_start: 0.9651 (ttp80) cc_final: 0.9128 (mtp85) REVERT: E 407 MET cc_start: 0.8897 (tmm) cc_final: 0.8537 (tmm) REVERT: E 421 GLU cc_start: 0.8800 (pt0) cc_final: 0.8554 (pt0) REVERT: E 426 SER cc_start: 0.9431 (t) cc_final: 0.9161 (p) REVERT: E 436 ASN cc_start: 0.8768 (m-40) cc_final: 0.8545 (m-40) REVERT: E 455 ASN cc_start: 0.9128 (m-40) cc_final: 0.8755 (m-40) REVERT: E 520 ASP cc_start: 0.9011 (m-30) cc_final: 0.8469 (m-30) REVERT: G 179 MET cc_start: 0.9256 (tpp) cc_final: 0.9014 (tpp) REVERT: G 181 MET cc_start: 0.9189 (tpp) cc_final: 0.8969 (mtm) REVERT: G 194 MET cc_start: 0.5693 (tpp) cc_final: 0.5213 (tpp) REVERT: G 227 PHE cc_start: 0.9576 (t80) cc_final: 0.9241 (t80) REVERT: G 232 ASP cc_start: 0.9808 (m-30) cc_final: 0.9234 (m-30) REVERT: G 235 TYR cc_start: 0.9248 (t80) cc_final: 0.8622 (t80) REVERT: G 236 GLU cc_start: 0.9612 (mm-30) cc_final: 0.9151 (mm-30) REVERT: G 240 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.8961 (mtmm) REVERT: G 249 TYR cc_start: 0.7984 (p90) cc_final: 0.7456 (p90) REVERT: G 293 TYR cc_start: 0.9280 (t80) cc_final: 0.7465 (t80) REVERT: G 300 LEU cc_start: 0.9603 (mm) cc_final: 0.9251 (mt) REVERT: G 361 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8664 (t80) REVERT: G 370 TYR cc_start: 0.9141 (t80) cc_final: 0.8921 (t80) REVERT: G 421 GLU cc_start: 0.8894 (pt0) cc_final: 0.8593 (pt0) REVERT: G 424 CYS cc_start: 0.9181 (m) cc_final: 0.8825 (m) REVERT: G 436 ASN cc_start: 0.9429 (t0) cc_final: 0.9081 (t0) REVERT: G 446 ARG cc_start: 0.8479 (ttp80) cc_final: 0.7292 (ttp80) REVERT: G 451 GLU cc_start: 0.8820 (mp0) cc_final: 0.8378 (mp0) REVERT: G 454 ARG cc_start: 0.9192 (ttp80) cc_final: 0.8634 (ttp-110) REVERT: G 455 ASN cc_start: 0.9318 (m-40) cc_final: 0.8705 (m-40) REVERT: G 499 MET cc_start: 0.9004 (tpp) cc_final: 0.8656 (tpp) REVERT: G 506 ASP cc_start: 0.9559 (t0) cc_final: 0.8481 (p0) REVERT: G 516 HIS cc_start: 0.8300 (t-90) cc_final: 0.7709 (t-90) REVERT: I 172 ASP cc_start: 0.8876 (t0) cc_final: 0.8436 (t0) REVERT: I 183 ARG cc_start: 0.9073 (mtp85) cc_final: 0.8301 (ptp-110) REVERT: I 194 MET cc_start: 0.7379 (tpp) cc_final: 0.6694 (tpp) REVERT: I 213 GLN cc_start: 0.9165 (mm-40) cc_final: 0.8638 (tp-100) REVERT: I 218 LYS cc_start: 0.9284 (mmmm) cc_final: 0.8880 (mtmm) REVERT: I 320 LYS cc_start: 0.9416 (tppt) cc_final: 0.8840 (tppt) REVERT: I 323 LEU cc_start: 0.9546 (mp) cc_final: 0.9340 (mp) REVERT: I 331 ASN cc_start: 0.9131 (p0) cc_final: 0.8481 (p0) REVERT: I 347 GLN cc_start: 0.8575 (mt0) cc_final: 0.7989 (mp10) REVERT: I 382 ARG cc_start: 0.9646 (ttp80) cc_final: 0.9139 (mtp85) REVERT: I 407 MET cc_start: 0.8944 (tmm) cc_final: 0.8552 (tmm) REVERT: I 421 GLU cc_start: 0.8873 (pt0) cc_final: 0.8593 (pt0) REVERT: I 426 SER cc_start: 0.9552 (t) cc_final: 0.9260 (p) REVERT: I 449 SER cc_start: 0.8901 (OUTLIER) cc_final: 0.8643 (t) REVERT: I 455 ASN cc_start: 0.9121 (m-40) cc_final: 0.8759 (m-40) REVERT: I 494 ASN cc_start: 0.9403 (m-40) cc_final: 0.9115 (m-40) REVERT: I 506 ASP cc_start: 0.9486 (t70) cc_final: 0.8449 (p0) REVERT: I 508 MET cc_start: 0.8793 (ttm) cc_final: 0.8478 (ttm) REVERT: I 520 ASP cc_start: 0.9040 (m-30) cc_final: 0.8812 (m-30) REVERT: K 179 MET cc_start: 0.8995 (tpp) cc_final: 0.8404 (tpp) REVERT: K 232 ASP cc_start: 0.9766 (m-30) cc_final: 0.9405 (m-30) REVERT: K 235 TYR cc_start: 0.9113 (t80) cc_final: 0.8475 (t80) REVERT: K 236 GLU cc_start: 0.9570 (mm-30) cc_final: 0.9212 (mm-30) REVERT: K 260 LEU cc_start: 0.9434 (tp) cc_final: 0.9011 (tp) REVERT: K 277 ASP cc_start: 0.9358 (m-30) cc_final: 0.8996 (p0) REVERT: K 293 TYR cc_start: 0.9271 (t80) cc_final: 0.7597 (t80) REVERT: K 331 ASN cc_start: 0.9155 (p0) cc_final: 0.8872 (p0) REVERT: K 344 LEU cc_start: 0.9573 (mt) cc_final: 0.9359 (mp) REVERT: K 361 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8746 (t80) REVERT: K 407 MET cc_start: 0.8697 (tmm) cc_final: 0.8357 (tmm) REVERT: K 421 GLU cc_start: 0.8783 (pt0) cc_final: 0.8557 (pt0) REVERT: K 424 CYS cc_start: 0.8986 (m) cc_final: 0.8376 (t) REVERT: K 430 MET cc_start: 0.9316 (OUTLIER) cc_final: 0.8564 (mpp) REVERT: K 436 ASN cc_start: 0.9340 (t0) cc_final: 0.8978 (t0) REVERT: K 446 ARG cc_start: 0.8686 (ttp80) cc_final: 0.7490 (ttp80) REVERT: K 455 ASN cc_start: 0.9239 (m-40) cc_final: 0.8970 (m110) REVERT: K 516 HIS cc_start: 0.8279 (t-90) cc_final: 0.7885 (t70) REVERT: K 520 ASP cc_start: 0.8995 (m-30) cc_final: 0.8743 (m-30) REVERT: F 140 GLU cc_start: 0.8698 (pm20) cc_final: 0.8436 (pm20) REVERT: F 172 ASP cc_start: 0.8775 (t0) cc_final: 0.8467 (t70) REVERT: F 194 MET cc_start: 0.6839 (tpp) cc_final: 0.6563 (tpp) REVERT: F 196 ASP cc_start: 0.8045 (t70) cc_final: 0.7539 (t70) REVERT: F 212 THR cc_start: 0.9419 (p) cc_final: 0.8641 (t) REVERT: F 213 GLN cc_start: 0.8778 (mm110) cc_final: 0.7723 (mm110) REVERT: F 215 PHE cc_start: 0.8732 (m-80) cc_final: 0.8441 (m-80) REVERT: F 216 ARG cc_start: 0.8432 (mtp180) cc_final: 0.7481 (mtp180) REVERT: F 232 ASP cc_start: 0.9655 (m-30) cc_final: 0.9407 (m-30) REVERT: F 233 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8814 (mt-10) REVERT: F 236 GLU cc_start: 0.9623 (mm-30) cc_final: 0.9174 (mm-30) REVERT: F 252 GLN cc_start: 0.9212 (tp40) cc_final: 0.8916 (tp40) REVERT: F 299 ASP cc_start: 0.8983 (m-30) cc_final: 0.8691 (m-30) REVERT: F 323 LEU cc_start: 0.9528 (mp) cc_final: 0.9313 (mm) REVERT: F 382 ARG cc_start: 0.9463 (ttp80) cc_final: 0.9125 (mtp-110) REVERT: F 421 GLU cc_start: 0.8920 (pt0) cc_final: 0.8337 (pt0) REVERT: F 499 MET cc_start: 0.8874 (tpp) cc_final: 0.8577 (tpp) REVERT: H 194 MET cc_start: 0.7490 (tpp) cc_final: 0.7174 (tpt) REVERT: H 213 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8529 (mm-40) REVERT: H 232 ASP cc_start: 0.9635 (m-30) cc_final: 0.9148 (m-30) REVERT: H 236 GLU cc_start: 0.9410 (mm-30) cc_final: 0.9050 (mm-30) REVERT: H 255 LYS cc_start: 0.9519 (mtmm) cc_final: 0.9079 (mttt) REVERT: H 272 ARG cc_start: 0.8839 (ttp80) cc_final: 0.8553 (ttp80) REVERT: H 280 VAL cc_start: 0.9189 (t) cc_final: 0.8934 (p) REVERT: H 293 TYR cc_start: 0.8952 (t80) cc_final: 0.8667 (t80) REVERT: H 308 TYR cc_start: 0.9026 (m-80) cc_final: 0.8557 (m-10) REVERT: H 320 LYS cc_start: 0.9272 (tppt) cc_final: 0.8820 (tppt) REVERT: H 328 LYS cc_start: 0.8659 (mtpp) cc_final: 0.8284 (mtpt) REVERT: H 331 ASN cc_start: 0.8925 (p0) cc_final: 0.8617 (p0) REVERT: H 333 MET cc_start: 0.8804 (mmp) cc_final: 0.8440 (mmp) REVERT: H 347 GLN cc_start: 0.8880 (mp10) cc_final: 0.8542 (pm20) REVERT: H 357 TYR cc_start: 0.8222 (t80) cc_final: 0.7849 (t80) REVERT: H 360 GLN cc_start: 0.9170 (mm110) cc_final: 0.8949 (pp30) REVERT: H 378 PHE cc_start: 0.8990 (t80) cc_final: 0.8713 (t80) REVERT: H 397 GLU cc_start: 0.9140 (tm-30) cc_final: 0.8844 (tm-30) REVERT: H 446 ARG cc_start: 0.9297 (tmm-80) cc_final: 0.8801 (tpp80) REVERT: H 455 ASN cc_start: 0.8804 (m-40) cc_final: 0.8573 (m-40) REVERT: H 465 MET cc_start: 0.9446 (mmm) cc_final: 0.9044 (mmm) REVERT: H 471 GLN cc_start: 0.9369 (tp-100) cc_final: 0.9135 (mm110) REVERT: H 482 SER cc_start: 0.9058 (t) cc_final: 0.8843 (t) REVERT: J 172 ASP cc_start: 0.8875 (t0) cc_final: 0.8498 (t70) REVERT: J 213 GLN cc_start: 0.8954 (tp-100) cc_final: 0.8605 (tp40) REVERT: J 215 PHE cc_start: 0.8831 (m-80) cc_final: 0.8588 (m-80) REVERT: J 218 LYS cc_start: 0.9281 (mmmm) cc_final: 0.9059 (mtmt) REVERT: J 232 ASP cc_start: 0.9645 (m-30) cc_final: 0.8989 (m-30) REVERT: J 236 GLU cc_start: 0.9657 (mm-30) cc_final: 0.9169 (mm-30) REVERT: J 303 GLU cc_start: 0.9357 (tm-30) cc_final: 0.9132 (tm-30) REVERT: J 320 LYS cc_start: 0.9182 (tppp) cc_final: 0.8803 (tppt) REVERT: J 407 MET cc_start: 0.8765 (tmm) cc_final: 0.8227 (tmm) REVERT: J 418 CYS cc_start: 0.9142 (m) cc_final: 0.8541 (t) REVERT: J 421 GLU cc_start: 0.8903 (pt0) cc_final: 0.8323 (pt0) REVERT: J 499 MET cc_start: 0.9050 (tpt) cc_final: 0.8552 (tpt) REVERT: L 194 MET cc_start: 0.6352 (tpt) cc_final: 0.4516 (pmm) REVERT: L 218 LYS cc_start: 0.8863 (ttpp) cc_final: 0.8358 (ptmm) REVERT: L 223 ASP cc_start: 0.8788 (p0) cc_final: 0.8468 (p0) REVERT: L 235 TYR cc_start: 0.8960 (t80) cc_final: 0.8403 (t80) REVERT: L 236 GLU cc_start: 0.9354 (mm-30) cc_final: 0.9080 (tm-30) REVERT: L 280 VAL cc_start: 0.9170 (t) cc_final: 0.8832 (p) REVERT: L 285 GLN cc_start: 0.9072 (mm-40) cc_final: 0.8769 (mm-40) REVERT: L 320 LYS cc_start: 0.9234 (tppt) cc_final: 0.8772 (tppt) REVERT: L 331 ASN cc_start: 0.8905 (p0) cc_final: 0.8597 (p0) REVERT: L 333 MET cc_start: 0.8816 (mmp) cc_final: 0.8430 (mmm) REVERT: L 349 VAL cc_start: 0.8914 (OUTLIER) cc_final: 0.8656 (p) REVERT: L 353 GLU cc_start: 0.9433 (mt-10) cc_final: 0.9119 (mt-10) REVERT: L 361 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8100 (t80) REVERT: L 381 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8535 (tm-30) REVERT: L 425 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8180 (mp0) REVERT: L 446 ARG cc_start: 0.9251 (tmm-80) cc_final: 0.8769 (tpp80) REVERT: L 455 ASN cc_start: 0.8865 (m-40) cc_final: 0.8552 (m-40) REVERT: L 465 MET cc_start: 0.9423 (mmm) cc_final: 0.9157 (mmm) REVERT: L 508 MET cc_start: 0.9101 (mmm) cc_final: 0.8820 (tpp) REVERT: D 602 GLN cc_start: 0.7039 (OUTLIER) cc_final: 0.5378 (pp30) outliers start: 166 outliers final: 140 residues processed: 1835 average time/residue: 0.2188 time to fit residues: 658.7276 Evaluate side-chains 1911 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 1755 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 187 GLN Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 283 CYS Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 510 ASN Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 498 MET Chi-restraints excluded: chain D residue 510 ASN Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 312 GLU Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 458 SER Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 496 MET Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain G residue 240 LYS Chi-restraints excluded: chain G residue 283 CYS Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 361 PHE Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain G residue 380 SER Chi-restraints excluded: chain G residue 381 GLU Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 419 SER Chi-restraints excluded: chain G residue 469 SER Chi-restraints excluded: chain G residue 505 LEU Chi-restraints excluded: chain I residue 140 GLU Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 225 MET Chi-restraints excluded: chain I residue 236 GLU Chi-restraints excluded: chain I residue 289 LYS Chi-restraints excluded: chain I residue 302 THR Chi-restraints excluded: chain I residue 312 GLU Chi-restraints excluded: chain I residue 353 GLU Chi-restraints excluded: chain I residue 423 THR Chi-restraints excluded: chain I residue 428 SER Chi-restraints excluded: chain I residue 449 SER Chi-restraints excluded: chain I residue 484 VAL Chi-restraints excluded: chain I residue 510 ASN Chi-restraints excluded: chain I residue 511 SER Chi-restraints excluded: chain K residue 194 MET Chi-restraints excluded: chain K residue 283 CYS Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain K residue 325 GLU Chi-restraints excluded: chain K residue 361 PHE Chi-restraints excluded: chain K residue 400 CYS Chi-restraints excluded: chain K residue 403 GLU Chi-restraints excluded: chain K residue 419 SER Chi-restraints excluded: chain K residue 423 THR Chi-restraints excluded: chain K residue 430 MET Chi-restraints excluded: chain K residue 505 LEU Chi-restraints excluded: chain K residue 523 SER Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 325 GLU Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 218 LYS Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain H residue 325 GLU Chi-restraints excluded: chain H residue 408 VAL Chi-restraints excluded: chain H residue 421 GLU Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain H residue 458 SER Chi-restraints excluded: chain H residue 467 ASP Chi-restraints excluded: chain H residue 496 MET Chi-restraints excluded: chain H residue 505 LEU Chi-restraints excluded: chain H residue 510 ASN Chi-restraints excluded: chain H residue 520 ASP Chi-restraints excluded: chain J residue 196 ASP Chi-restraints excluded: chain J residue 231 ILE Chi-restraints excluded: chain J residue 325 GLU Chi-restraints excluded: chain J residue 381 GLU Chi-restraints excluded: chain J residue 417 LEU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 231 ILE Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 349 VAL Chi-restraints excluded: chain L residue 361 PHE Chi-restraints excluded: chain L residue 362 LEU Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 458 SER Chi-restraints excluded: chain L residue 496 MET Chi-restraints excluded: chain L residue 507 LYS Chi-restraints excluded: chain L residue 510 ASN Chi-restraints excluded: chain L residue 520 ASP Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain D residue 602 GLN Chi-restraints excluded: chain E residue 602 GLN Chi-restraints excluded: chain F residue 602 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 198 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 239 optimal weight: 0.9980 chunk 328 optimal weight: 2.9990 chunk 390 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 408 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN ** C 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 ASN E 375 ASN ** E 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 519 HIS ** K 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 ASN F 388 ASN ** F 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 519 HIS H 298 ASN ** H 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 510 ASN H 519 HIS ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 HIS J 241 GLN ** J 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 519 HIS ** L 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.156914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.118705 restraints weight = 64955.057| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.92 r_work: 0.3235 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 36972 Z= 0.146 Angle : 0.757 13.524 49932 Z= 0.377 Chirality : 0.046 0.278 5544 Planarity : 0.005 0.049 6408 Dihedral : 5.077 53.975 4929 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.32 % Favored : 93.57 % Rotamer: Outliers : 3.93 % Allowed : 30.45 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.13), residues: 4620 helix: 1.00 (0.11), residues: 2400 sheet: -0.20 (0.29), residues: 384 loop : -0.22 (0.16), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 446 TYR 0.024 0.001 TYR E 357 PHE 0.067 0.001 PHE B 224 TRP 0.024 0.002 TRP G 501 HIS 0.009 0.001 HIS J 157 Details of bonding type rmsd covalent geometry : bond 0.00346 (36972) covalent geometry : angle 0.75728 (49932) hydrogen bonds : bond 0.03095 ( 1700) hydrogen bonds : angle 4.95934 ( 5193) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9240 Ramachandran restraints generated. 4620 Oldfield, 0 Emsley, 4620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9240 Ramachandran restraints generated. 4620 Oldfield, 0 Emsley, 4620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1949 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 1791 time to evaluate : 1.406 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: A 194 MET cc_start: 0.6852 (tpp) cc_final: 0.5643 (tpp) REVERT: A 213 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8548 (mm-40) REVERT: A 227 PHE cc_start: 0.9545 (t80) cc_final: 0.9272 (t80) REVERT: A 236 GLU cc_start: 0.9676 (mm-30) cc_final: 0.9431 (mm-30) REVERT: A 250 ILE cc_start: 0.9174 (mt) cc_final: 0.8960 (mt) REVERT: A 277 ASP cc_start: 0.9115 (m-30) cc_final: 0.8803 (p0) REVERT: A 293 TYR cc_start: 0.9418 (t80) cc_final: 0.8849 (t80) REVERT: A 306 HIS cc_start: 0.9055 (m-70) cc_final: 0.8710 (m-70) REVERT: A 357 TYR cc_start: 0.9393 (t80) cc_final: 0.8903 (t80) REVERT: A 360 GLN cc_start: 0.9429 (tm130) cc_final: 0.9082 (tm-30) REVERT: A 361 PHE cc_start: 0.9260 (OUTLIER) cc_final: 0.8439 (t80) REVERT: A 365 MET cc_start: 0.9434 (ttm) cc_final: 0.8872 (tmm) REVERT: A 415 PHE cc_start: 0.9451 (m-80) cc_final: 0.9017 (m-80) REVERT: A 421 GLU cc_start: 0.8820 (pt0) cc_final: 0.8466 (pt0) REVERT: A 434 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8834 (pp) REVERT: A 445 GLU cc_start: 0.9305 (mt-10) cc_final: 0.9049 (mt-10) REVERT: A 448 LEU cc_start: 0.9555 (mt) cc_final: 0.9281 (mt) REVERT: A 498 MET cc_start: 0.8841 (ttm) cc_final: 0.8588 (ttm) REVERT: A 499 MET cc_start: 0.9071 (tpp) cc_final: 0.8705 (tpp) REVERT: A 500 CYS cc_start: 0.8655 (m) cc_final: 0.8376 (m) REVERT: B 140 GLU cc_start: 0.9160 (pm20) cc_final: 0.7938 (tt0) REVERT: B 178 CYS cc_start: 0.8710 (m) cc_final: 0.8402 (m) REVERT: B 196 ASP cc_start: 0.7664 (t70) cc_final: 0.7339 (t0) REVERT: B 217 ARG cc_start: 0.8269 (tpm170) cc_final: 0.8032 (tpm170) REVERT: B 234 LEU cc_start: 0.9657 (mt) cc_final: 0.9457 (mt) REVERT: B 235 TYR cc_start: 0.9360 (t80) cc_final: 0.8427 (t80) REVERT: B 236 GLU cc_start: 0.9543 (mm-30) cc_final: 0.9239 (mm-30) REVERT: B 249 TYR cc_start: 0.8454 (p90) cc_final: 0.7969 (p90) REVERT: B 272 ARG cc_start: 0.9103 (ptp90) cc_final: 0.8799 (ptp-170) REVERT: B 282 PHE cc_start: 0.9071 (p90) cc_final: 0.8735 (p90) REVERT: B 285 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8354 (mm-40) REVERT: B 293 TYR cc_start: 0.9325 (t80) cc_final: 0.9037 (t80) REVERT: B 297 VAL cc_start: 0.9691 (t) cc_final: 0.9402 (m) REVERT: B 382 ARG cc_start: 0.9352 (ttp80) cc_final: 0.9145 (mtp-110) REVERT: B 396 LYS cc_start: 0.9140 (tttp) cc_final: 0.8901 (tttp) REVERT: B 407 MET cc_start: 0.8831 (tmm) cc_final: 0.8546 (tmm) REVERT: B 414 TYR cc_start: 0.9549 (t80) cc_final: 0.8935 (t80) REVERT: B 421 GLU cc_start: 0.8865 (pt0) cc_final: 0.8561 (pt0) REVERT: B 436 ASN cc_start: 0.8929 (t0) cc_final: 0.8696 (t0) REVERT: B 454 ARG cc_start: 0.9229 (ttp80) cc_final: 0.8930 (ttp80) REVERT: C 164 LYS cc_start: 0.9330 (mtmt) cc_final: 0.9089 (mtpp) REVERT: C 175 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8378 (pp) REVERT: C 179 MET cc_start: 0.7771 (ptp) cc_final: 0.7193 (ptp) REVERT: C 246 VAL cc_start: 0.8434 (OUTLIER) cc_final: 0.7914 (t) REVERT: C 249 TYR cc_start: 0.8868 (p90) cc_final: 0.8165 (p90) REVERT: C 250 ILE cc_start: 0.9016 (mt) cc_final: 0.8632 (mt) REVERT: C 260 LEU cc_start: 0.9368 (mt) cc_final: 0.9116 (mp) REVERT: C 277 ASP cc_start: 0.9086 (m-30) cc_final: 0.8705 (p0) REVERT: C 347 GLN cc_start: 0.8982 (mp10) cc_final: 0.8296 (mp10) REVERT: C 365 MET cc_start: 0.9484 (ttm) cc_final: 0.8932 (tmm) REVERT: C 397 GLU cc_start: 0.9181 (tm-30) cc_final: 0.8794 (tm-30) REVERT: C 416 GLN cc_start: 0.9256 (mt0) cc_final: 0.8851 (mt0) REVERT: C 421 GLU cc_start: 0.8742 (pt0) cc_final: 0.8375 (pt0) REVERT: C 434 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8745 (pp) REVERT: C 445 GLU cc_start: 0.9290 (mt-10) cc_final: 0.9066 (mt-10) REVERT: C 446 ARG cc_start: 0.9371 (tpp80) cc_final: 0.8842 (tpp80) REVERT: C 455 ASN cc_start: 0.9239 (m-40) cc_final: 0.8997 (m-40) REVERT: C 467 ASP cc_start: 0.9512 (p0) cc_final: 0.8913 (p0) REVERT: C 496 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.7122 (ppp) REVERT: C 499 MET cc_start: 0.9054 (tpp) cc_final: 0.8635 (tpp) REVERT: C 500 CYS cc_start: 0.8555 (m) cc_final: 0.8327 (m) REVERT: C 508 MET cc_start: 0.9389 (mtt) cc_final: 0.8981 (mtt) REVERT: D 140 GLU cc_start: 0.8674 (pm20) cc_final: 0.8410 (pp20) REVERT: D 196 ASP cc_start: 0.7451 (t0) cc_final: 0.7156 (t0) REVERT: D 232 ASP cc_start: 0.9800 (m-30) cc_final: 0.9458 (m-30) REVERT: D 236 GLU cc_start: 0.9555 (mm-30) cc_final: 0.9171 (mm-30) REVERT: D 246 VAL cc_start: 0.8427 (OUTLIER) cc_final: 0.7710 (t) REVERT: D 249 TYR cc_start: 0.8489 (p90) cc_final: 0.8048 (p90) REVERT: D 260 LEU cc_start: 0.9477 (tp) cc_final: 0.9097 (tp) REVERT: D 271 GLN cc_start: 0.7810 (pt0) cc_final: 0.7516 (pt0) REVERT: D 285 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8260 (mm-40) REVERT: D 293 TYR cc_start: 0.9364 (t80) cc_final: 0.9130 (t80) REVERT: D 360 GLN cc_start: 0.9271 (tm-30) cc_final: 0.8515 (tm-30) REVERT: D 373 PHE cc_start: 0.8674 (t80) cc_final: 0.8324 (t80) REVERT: D 394 TYR cc_start: 0.9713 (t80) cc_final: 0.9435 (t80) REVERT: D 397 GLU cc_start: 0.9497 (tm-30) cc_final: 0.9139 (tm-30) REVERT: D 407 MET cc_start: 0.8820 (tmm) cc_final: 0.8522 (tmm) REVERT: D 421 GLU cc_start: 0.8853 (pt0) cc_final: 0.8370 (pt0) REVERT: D 446 ARG cc_start: 0.8795 (tpp80) cc_final: 0.8318 (tpp80) REVERT: D 454 ARG cc_start: 0.9127 (ttp80) cc_final: 0.8795 (ttp80) REVERT: D 467 ASP cc_start: 0.9361 (OUTLIER) cc_final: 0.8539 (p0) REVERT: D 506 ASP cc_start: 0.9556 (t70) cc_final: 0.8690 (p0) REVERT: D 508 MET cc_start: 0.9167 (mmm) cc_final: 0.7479 (mmm) REVERT: D 520 ASP cc_start: 0.8901 (m-30) cc_final: 0.8454 (m-30) REVERT: E 172 ASP cc_start: 0.8877 (t0) cc_final: 0.8466 (t0) REVERT: E 183 ARG cc_start: 0.8919 (mmm-85) cc_final: 0.8563 (ttp-110) REVERT: E 213 GLN cc_start: 0.9163 (mm110) cc_final: 0.8871 (mm110) REVERT: E 223 ASP cc_start: 0.9034 (t0) cc_final: 0.8807 (t0) REVERT: E 233 GLU cc_start: 0.9467 (tp30) cc_final: 0.8822 (tp30) REVERT: E 271 GLN cc_start: 0.8676 (pt0) cc_final: 0.8376 (pt0) REVERT: E 331 ASN cc_start: 0.9112 (p0) cc_final: 0.8425 (p0) REVERT: E 382 ARG cc_start: 0.9655 (ttp80) cc_final: 0.9145 (mtp85) REVERT: E 407 MET cc_start: 0.8878 (tmm) cc_final: 0.8528 (tmm) REVERT: E 421 GLU cc_start: 0.8846 (pt0) cc_final: 0.8612 (pt0) REVERT: E 426 SER cc_start: 0.9454 (t) cc_final: 0.9184 (p) REVERT: E 436 ASN cc_start: 0.8803 (m-40) cc_final: 0.8589 (m-40) REVERT: E 455 ASN cc_start: 0.9122 (m-40) cc_final: 0.8779 (m-40) REVERT: E 508 MET cc_start: 0.9447 (ttm) cc_final: 0.9000 (tpp) REVERT: G 194 MET cc_start: 0.5824 (tpp) cc_final: 0.5370 (tpp) REVERT: G 227 PHE cc_start: 0.9552 (t80) cc_final: 0.9190 (t80) REVERT: G 232 ASP cc_start: 0.9811 (m-30) cc_final: 0.9244 (m-30) REVERT: G 235 TYR cc_start: 0.9215 (t80) cc_final: 0.8491 (t80) REVERT: G 236 GLU cc_start: 0.9599 (mm-30) cc_final: 0.9178 (mm-30) REVERT: G 240 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.8971 (mtmm) REVERT: G 249 TYR cc_start: 0.8040 (p90) cc_final: 0.7516 (p90) REVERT: G 293 TYR cc_start: 0.9253 (t80) cc_final: 0.7379 (t80) REVERT: G 300 LEU cc_start: 0.9585 (mm) cc_final: 0.9258 (mt) REVERT: G 370 TYR cc_start: 0.9162 (t80) cc_final: 0.8939 (t80) REVERT: G 421 GLU cc_start: 0.8846 (pt0) cc_final: 0.8554 (pt0) REVERT: G 424 CYS cc_start: 0.9211 (m) cc_final: 0.8884 (m) REVERT: G 436 ASN cc_start: 0.9402 (t0) cc_final: 0.9063 (t0) REVERT: G 446 ARG cc_start: 0.8500 (ttp80) cc_final: 0.7351 (ttp80) REVERT: G 451 GLU cc_start: 0.8819 (mp0) cc_final: 0.8433 (mp0) REVERT: G 454 ARG cc_start: 0.9184 (ttp80) cc_final: 0.8633 (ttp-110) REVERT: G 455 ASN cc_start: 0.9311 (m-40) cc_final: 0.8761 (m110) REVERT: G 499 MET cc_start: 0.9000 (tpp) cc_final: 0.8650 (tpp) REVERT: G 516 HIS cc_start: 0.8250 (t-90) cc_final: 0.7742 (t-90) REVERT: I 172 ASP cc_start: 0.8892 (t0) cc_final: 0.8454 (t0) REVERT: I 183 ARG cc_start: 0.9087 (mtp85) cc_final: 0.8288 (ptp-110) REVERT: I 194 MET cc_start: 0.7280 (tpp) cc_final: 0.6574 (tpp) REVERT: I 213 GLN cc_start: 0.9160 (mm-40) cc_final: 0.8565 (tp-100) REVERT: I 218 LYS cc_start: 0.9282 (mmmm) cc_final: 0.8690 (mtmm) REVERT: I 320 LYS cc_start: 0.9405 (tppt) cc_final: 0.8770 (tppt) REVERT: I 323 LEU cc_start: 0.9541 (mp) cc_final: 0.9329 (mp) REVERT: I 331 ASN cc_start: 0.9151 (p0) cc_final: 0.8513 (p0) REVERT: I 347 GLN cc_start: 0.8510 (mt0) cc_final: 0.7792 (mp10) REVERT: I 382 ARG cc_start: 0.9639 (ttp80) cc_final: 0.9123 (mtp85) REVERT: I 407 MET cc_start: 0.8896 (tmm) cc_final: 0.8502 (tmm) REVERT: I 421 GLU cc_start: 0.8878 (pt0) cc_final: 0.8609 (pt0) REVERT: I 426 SER cc_start: 0.9568 (t) cc_final: 0.9278 (p) REVERT: I 449 SER cc_start: 0.8900 (OUTLIER) cc_final: 0.8637 (t) REVERT: I 455 ASN cc_start: 0.9110 (m-40) cc_final: 0.8775 (m-40) REVERT: I 494 ASN cc_start: 0.9396 (m-40) cc_final: 0.9118 (m-40) REVERT: I 506 ASP cc_start: 0.9409 (t70) cc_final: 0.8782 (p0) REVERT: I 520 ASP cc_start: 0.9025 (m-30) cc_final: 0.8817 (m-30) REVERT: K 179 MET cc_start: 0.9006 (tpp) cc_final: 0.8451 (tpp) REVERT: K 232 ASP cc_start: 0.9769 (m-30) cc_final: 0.9416 (m-30) REVERT: K 235 TYR cc_start: 0.9105 (t80) cc_final: 0.8455 (t80) REVERT: K 236 GLU cc_start: 0.9577 (mm-30) cc_final: 0.9251 (mm-30) REVERT: K 260 LEU cc_start: 0.9434 (tp) cc_final: 0.9012 (tp) REVERT: K 277 ASP cc_start: 0.9341 (m-30) cc_final: 0.8995 (p0) REVERT: K 293 TYR cc_start: 0.9248 (t80) cc_final: 0.7583 (t80) REVERT: K 344 LEU cc_start: 0.9562 (mt) cc_final: 0.9356 (mp) REVERT: K 361 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.8714 (t80) REVERT: K 379 GLN cc_start: 0.9410 (mm-40) cc_final: 0.9083 (mm-40) REVERT: K 407 MET cc_start: 0.8663 (tmm) cc_final: 0.8320 (tmm) REVERT: K 421 GLU cc_start: 0.8795 (pt0) cc_final: 0.8575 (pt0) REVERT: K 424 CYS cc_start: 0.8964 (m) cc_final: 0.8393 (t) REVERT: K 430 MET cc_start: 0.9321 (OUTLIER) cc_final: 0.8601 (mpp) REVERT: K 436 ASN cc_start: 0.9330 (t0) cc_final: 0.8972 (t0) REVERT: K 446 ARG cc_start: 0.8649 (ttp80) cc_final: 0.8375 (ttp80) REVERT: K 455 ASN cc_start: 0.9228 (m-40) cc_final: 0.8961 (m110) REVERT: K 516 HIS cc_start: 0.8278 (t-90) cc_final: 0.7885 (t70) REVERT: K 520 ASP cc_start: 0.9005 (m-30) cc_final: 0.8739 (m-30) REVERT: F 140 GLU cc_start: 0.8708 (pm20) cc_final: 0.8439 (pm20) REVERT: F 172 ASP cc_start: 0.8815 (t0) cc_final: 0.8554 (t0) REVERT: F 194 MET cc_start: 0.7030 (tpp) cc_final: 0.6780 (tpp) REVERT: F 196 ASP cc_start: 0.8238 (t70) cc_final: 0.7829 (t70) REVERT: F 212 THR cc_start: 0.9425 (p) cc_final: 0.8723 (t) REVERT: F 213 GLN cc_start: 0.8782 (mm110) cc_final: 0.7706 (mm110) REVERT: F 215 PHE cc_start: 0.8734 (m-80) cc_final: 0.8501 (m-80) REVERT: F 216 ARG cc_start: 0.8451 (mtp180) cc_final: 0.7630 (mtp180) REVERT: F 217 ARG cc_start: 0.7837 (mmt180) cc_final: 0.6943 (mmm-85) REVERT: F 223 ASP cc_start: 0.8236 (p0) cc_final: 0.7914 (p0) REVERT: F 232 ASP cc_start: 0.9657 (m-30) cc_final: 0.9399 (m-30) REVERT: F 233 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8807 (mt-10) REVERT: F 236 GLU cc_start: 0.9620 (mm-30) cc_final: 0.9170 (mm-30) REVERT: F 252 GLN cc_start: 0.9174 (tp40) cc_final: 0.8862 (tp40) REVERT: F 299 ASP cc_start: 0.8995 (m-30) cc_final: 0.8671 (m-30) REVERT: F 323 LEU cc_start: 0.9533 (mp) cc_final: 0.9314 (mm) REVERT: F 379 GLN cc_start: 0.9596 (mm110) cc_final: 0.9212 (mm-40) REVERT: F 382 ARG cc_start: 0.9449 (ttp80) cc_final: 0.9047 (mtp-110) REVERT: F 413 PHE cc_start: 0.8686 (t80) cc_final: 0.8342 (t80) REVERT: F 421 GLU cc_start: 0.8924 (pt0) cc_final: 0.8341 (pt0) REVERT: F 499 MET cc_start: 0.8847 (tpp) cc_final: 0.8579 (tpp) REVERT: F 510 ASN cc_start: 0.8377 (m110) cc_final: 0.8176 (m110) REVERT: H 194 MET cc_start: 0.7504 (tpp) cc_final: 0.7177 (tpt) REVERT: H 213 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8536 (mm-40) REVERT: H 215 PHE cc_start: 0.8480 (m-80) cc_final: 0.8012 (m-80) REVERT: H 232 ASP cc_start: 0.9620 (m-30) cc_final: 0.9105 (m-30) REVERT: H 236 GLU cc_start: 0.9393 (mm-30) cc_final: 0.9052 (mm-30) REVERT: H 255 LYS cc_start: 0.9525 (mtmm) cc_final: 0.9042 (mttt) REVERT: H 271 GLN cc_start: 0.7552 (tt0) cc_final: 0.7070 (pt0) REVERT: H 280 VAL cc_start: 0.9307 (t) cc_final: 0.9081 (p) REVERT: H 293 TYR cc_start: 0.8888 (t80) cc_final: 0.8615 (t80) REVERT: H 308 TYR cc_start: 0.9059 (m-80) cc_final: 0.8486 (m-10) REVERT: H 320 LYS cc_start: 0.9252 (tppt) cc_final: 0.8791 (tppt) REVERT: H 328 LYS cc_start: 0.8748 (mtpp) cc_final: 0.8394 (mtpt) REVERT: H 331 ASN cc_start: 0.8929 (p0) cc_final: 0.8604 (p0) REVERT: H 333 MET cc_start: 0.8769 (mmp) cc_final: 0.8448 (mmp) REVERT: H 357 TYR cc_start: 0.8217 (t80) cc_final: 0.7844 (t80) REVERT: H 360 GLN cc_start: 0.9186 (mm110) cc_final: 0.8958 (pp30) REVERT: H 378 PHE cc_start: 0.8921 (t80) cc_final: 0.8667 (t80) REVERT: H 397 GLU cc_start: 0.9123 (tm-30) cc_final: 0.8825 (tm-30) REVERT: H 446 ARG cc_start: 0.9333 (tmm-80) cc_final: 0.8927 (tpp80) REVERT: H 455 ASN cc_start: 0.8752 (m-40) cc_final: 0.8520 (m-40) REVERT: H 465 MET cc_start: 0.9440 (mmm) cc_final: 0.9054 (mmm) REVERT: H 482 SER cc_start: 0.9097 (t) cc_final: 0.8870 (t) REVERT: J 172 ASP cc_start: 0.8891 (t0) cc_final: 0.8523 (t70) REVERT: J 213 GLN cc_start: 0.8983 (tp-100) cc_final: 0.8635 (tp-100) REVERT: J 215 PHE cc_start: 0.8809 (m-80) cc_final: 0.8565 (m-80) REVERT: J 218 LYS cc_start: 0.9303 (mmmm) cc_final: 0.9047 (mtmm) REVERT: J 232 ASP cc_start: 0.9672 (m-30) cc_final: 0.9022 (m-30) REVERT: J 236 GLU cc_start: 0.9656 (mm-30) cc_final: 0.9143 (mm-30) REVERT: J 303 GLU cc_start: 0.9383 (tm-30) cc_final: 0.9159 (tm-30) REVERT: J 320 LYS cc_start: 0.9169 (tppp) cc_final: 0.8777 (tppt) REVERT: J 375 ASN cc_start: 0.9071 (t0) cc_final: 0.8648 (t0) REVERT: J 379 GLN cc_start: 0.9587 (mm110) cc_final: 0.9291 (mm110) REVERT: J 407 MET cc_start: 0.8725 (tmm) cc_final: 0.8183 (tmm) REVERT: J 418 CYS cc_start: 0.9142 (m) cc_final: 0.8556 (t) REVERT: J 421 GLU cc_start: 0.8887 (pt0) cc_final: 0.8324 (pt0) REVERT: J 499 MET cc_start: 0.9071 (tpt) cc_final: 0.8611 (tpt) REVERT: J 512 VAL cc_start: 0.8114 (m) cc_final: 0.7495 (t) REVERT: L 194 MET cc_start: 0.6261 (tpt) cc_final: 0.4471 (pmm) REVERT: L 218 LYS cc_start: 0.8853 (ttpp) cc_final: 0.8351 (ptmm) REVERT: L 223 ASP cc_start: 0.8792 (p0) cc_final: 0.8480 (p0) REVERT: L 235 TYR cc_start: 0.8950 (t80) cc_final: 0.8395 (t80) REVERT: L 236 GLU cc_start: 0.9350 (mm-30) cc_final: 0.9079 (tm-30) REVERT: L 271 GLN cc_start: 0.7341 (tt0) cc_final: 0.6931 (tt0) REVERT: L 280 VAL cc_start: 0.9137 (t) cc_final: 0.8923 (p) REVERT: L 285 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8748 (mm-40) REVERT: L 320 LYS cc_start: 0.9247 (tppt) cc_final: 0.8784 (tppt) REVERT: L 331 ASN cc_start: 0.8899 (p0) cc_final: 0.8593 (p0) REVERT: L 333 MET cc_start: 0.8791 (mmp) cc_final: 0.8399 (mmm) REVERT: L 340 VAL cc_start: 0.8938 (t) cc_final: 0.8724 (m) REVERT: L 347 GLN cc_start: 0.8855 (mp10) cc_final: 0.8417 (pm20) REVERT: L 349 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8668 (p) REVERT: L 353 GLU cc_start: 0.9441 (mt-10) cc_final: 0.9128 (mt-10) REVERT: L 361 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.8042 (t80) REVERT: L 378 PHE cc_start: 0.9039 (t80) cc_final: 0.8755 (t80) REVERT: L 381 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8578 (tm-30) REVERT: L 446 ARG cc_start: 0.9240 (tmm-80) cc_final: 0.8768 (tpp80) REVERT: L 465 MET cc_start: 0.9440 (mmm) cc_final: 0.9169 (mmm) REVERT: D 602 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.5370 (pp30) outliers start: 158 outliers final: 133 residues processed: 1844 average time/residue: 0.2095 time to fit residues: 633.4671 Evaluate side-chains 1914 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 1766 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 507 LYS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 187 GLN Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 283 CYS Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 510 ASN Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 498 MET Chi-restraints excluded: chain D residue 507 LYS Chi-restraints excluded: chain D residue 510 ASN Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 312 GLU Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 458 SER Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 496 MET Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain G residue 240 LYS Chi-restraints excluded: chain G residue 283 CYS Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain G residue 380 SER Chi-restraints excluded: chain G residue 381 GLU Chi-restraints excluded: chain G residue 400 CYS Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 419 SER Chi-restraints excluded: chain G residue 469 SER Chi-restraints excluded: chain G residue 505 LEU Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 225 MET Chi-restraints excluded: chain I residue 236 GLU Chi-restraints excluded: chain I residue 289 LYS Chi-restraints excluded: chain I residue 302 THR Chi-restraints excluded: chain I residue 312 GLU Chi-restraints excluded: chain I residue 408 VAL Chi-restraints excluded: chain I residue 423 THR Chi-restraints excluded: chain I residue 428 SER Chi-restraints excluded: chain I residue 449 SER Chi-restraints excluded: chain I residue 484 VAL Chi-restraints excluded: chain I residue 510 ASN Chi-restraints excluded: chain K residue 194 MET Chi-restraints excluded: chain K residue 231 ILE Chi-restraints excluded: chain K residue 283 CYS Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain K residue 325 GLU Chi-restraints excluded: chain K residue 361 PHE Chi-restraints excluded: chain K residue 381 GLU Chi-restraints excluded: chain K residue 400 CYS Chi-restraints excluded: chain K residue 403 GLU Chi-restraints excluded: chain K residue 419 SER Chi-restraints excluded: chain K residue 423 THR Chi-restraints excluded: chain K residue 430 MET Chi-restraints excluded: chain K residue 505 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 325 GLU Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 298 ASN Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain H residue 325 GLU Chi-restraints excluded: chain H residue 421 GLU Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain H residue 458 SER Chi-restraints excluded: chain H residue 467 ASP Chi-restraints excluded: chain H residue 496 MET Chi-restraints excluded: chain H residue 505 LEU Chi-restraints excluded: chain H residue 510 ASN Chi-restraints excluded: chain H residue 520 ASP Chi-restraints excluded: chain J residue 231 ILE Chi-restraints excluded: chain J residue 325 GLU Chi-restraints excluded: chain J residue 381 GLU Chi-restraints excluded: chain J residue 417 LEU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain L residue 231 ILE Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 349 VAL Chi-restraints excluded: chain L residue 361 PHE Chi-restraints excluded: chain L residue 362 LEU Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 458 SER Chi-restraints excluded: chain L residue 496 MET Chi-restraints excluded: chain L residue 510 ASN Chi-restraints excluded: chain L residue 515 ILE Chi-restraints excluded: chain L residue 520 ASP Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain D residue 602 GLN Chi-restraints excluded: chain E residue 602 GLN Chi-restraints excluded: chain F residue 602 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 40 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 235 optimal weight: 0.0270 chunk 117 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 424 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 293 optimal weight: 0.7980 chunk 332 optimal weight: 0.0040 chunk 21 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 overall best weight: 0.5050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 ASN C 351 ASN ** C 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 GLN ** D 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 ASN ** E 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 271 GLN G 351 ASN K 351 ASN ** K 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 360 GLN ** F 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 GLN F 519 HIS H 298 ASN ** H 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 510 ASN ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 HIS J 241 GLN J 324 ASN ** J 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 519 HIS ** L 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 516 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.158744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.120561 restraints weight = 64264.254| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.93 r_work: 0.3263 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 36972 Z= 0.138 Angle : 0.768 16.754 49932 Z= 0.380 Chirality : 0.046 0.273 5544 Planarity : 0.005 0.047 6408 Dihedral : 5.065 55.614 4929 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.21 % Favored : 93.70 % Rotamer: Outliers : 3.58 % Allowed : 31.04 % Favored : 65.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.13), residues: 4620 helix: 0.97 (0.11), residues: 2400 sheet: -0.14 (0.29), residues: 384 loop : -0.23 (0.16), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 216 TYR 0.024 0.001 TYR E 357 PHE 0.069 0.001 PHE B 224 TRP 0.024 0.001 TRP G 261 HIS 0.009 0.001 HIS J 157 Details of bonding type rmsd covalent geometry : bond 0.00322 (36972) covalent geometry : angle 0.76784 (49932) hydrogen bonds : bond 0.02997 ( 1700) hydrogen bonds : angle 4.98490 ( 5193) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12714.73 seconds wall clock time: 217 minutes 45.23 seconds (13065.23 seconds total)