Starting phenix.real_space_refine on Wed Apr 17 04:17:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szj_40918/04_2024/8szj_40918.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szj_40918/04_2024/8szj_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szj_40918/04_2024/8szj_40918.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szj_40918/04_2024/8szj_40918.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szj_40918/04_2024/8szj_40918.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szj_40918/04_2024/8szj_40918.pdb" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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 Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 196": "OD1" <-> "OD2" Residue "E PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 269": "OD1" <-> "OD2" Residue "J TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/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: 18.19, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 13.48 Conformation dependent library (CDL) restraints added in 6.9 seconds 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: 4.29 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: 12.82 Time building geometry restraints manager: 14.55 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: 98.85 - 105.89: 904 105.89 - 112.94: 19608 112.94 - 119.98: 12942 119.98 - 127.02: 16080 127.02 - 134.06: 398 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 2.520 nonbonded pdb=" NH2 ARG D 387 " pdb=" O4 PO4 D 601 " model vdw 1.297 2.520 nonbonded pdb=" NH2 ARG H 387 " pdb=" O4 PO4 H 601 " model vdw 1.297 2.520 nonbonded pdb=" NH2 ARG I 387 " pdb=" O1 PO4 I 601 " model vdw 1.297 2.520 nonbonded pdb=" NH2 ARG G 387 " pdb=" O4 PO4 G 601 " model vdw 1.297 2.520 ... (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 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: 4.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 10.670 Check model and map are aligned: 0.540 Set scattering table: 0.320 Process input model: 90.900 Find NCS groups from input model: 2.520 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.050 ------------------------------------------------------------------------------- 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= 0.229 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (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 TRP 0.013 0.001 TRP B 501 HIS 0.006 0.001 HIS A 230 PHE 0.022 0.001 PHE K 227 TYR 0.019 0.001 TYR H 357 ARG 0.002 0.000 ARG J 272 *********************** 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 fitting. rotamer outliers: 6 poor density : 2221 time to evaluate : 4.107 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 379 GLN cc_start: 0.9251 (mm110) cc_final: 0.9035 (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: 0.8846 (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 379 GLN cc_start: 0.9233 (mm110) cc_final: 0.8943 (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: 0.8796 (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: 0.8312 (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: 0.8403 (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: 0.8876 (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: 0.8305 (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: 0.8702 (t0) REVERT: F 379 GLN cc_start: 0.9243 (mm110) cc_final: 0.8865 (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: 0.8215 (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: 0.8793 (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: 0.9161 (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: 0.8683 (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: 0.8506 (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 513 LYS cc_start: 0.7921 (mttt) cc_final: 0.7680 (mttm) outliers start: 6 outliers final: 3 residues processed: 2227 average time/residue: 0.5149 time to fit residues: 1823.5642 Evaluate side-chains 1834 residues out of total 4020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1831 time to evaluate : 3.791 ------------------------------------------------------------------------------- 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 385 optimal weight: 40.0000 chunk 345 optimal weight: 7.9990 chunk 191 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 233 optimal weight: 0.0870 chunk 184 optimal weight: 2.9990 chunk 357 optimal weight: 0.7980 chunk 138 optimal weight: 0.0470 chunk 217 optimal weight: 1.9990 chunk 266 optimal weight: 20.0000 chunk 414 optimal weight: 7.9990 overall best weight: 1.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN A 375 ASN A 475 HIS B 298 ASN B 351 ASN B 475 HIS C 213 GLN ** C 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN 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 516 HIS E 519 HIS G 207 ASN ** G 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 351 ASN G 360 GLN G 416 GLN I 187 GLN ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 271 GLN K 298 ASN ** K 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 351 ASN K 360 GLN ** K 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 36972 Z= 0.221 Angle : 0.604 9.362 49932 Z= 0.315 Chirality : 0.043 0.206 5544 Planarity : 0.005 0.055 6408 Dihedral : 4.986 63.775 4929 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.61 % Favored : 94.37 % Rotamer: Outliers : 3.13 % Allowed : 17.29 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.13), residues: 4620 helix: 1.06 (0.11), residues: 2388 sheet: -0.51 (0.29), residues: 384 loop : -0.44 (0.15), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 501 HIS 0.004 0.001 HIS E 516 PHE 0.030 0.001 PHE C 322 TYR 0.021 0.001 TYR B 249 ARG 0.006 0.000 ARG G 446 *********************** 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 2023 residues out of total 4020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1897 time to evaluate : 4.264 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: 0.9070 (mtmt) cc_final: 0.8852 (mtmm) REVERT: A 194 MET cc_start: 0.6511 (tpp) cc_final: 0.5714 (tpp) REVERT: A 213 GLN cc_start: 0.9099 (mm-40) cc_final: 0.8648 (mm-40) REVERT: A 216 ARG cc_start: 0.8857 (mtp180) cc_final: 0.8471 (mtp180) REVERT: A 218 LYS cc_start: 0.9464 (mmmt) cc_final: 0.9137 (mmmm) REVERT: A 236 GLU cc_start: 0.9601 (mm-30) cc_final: 0.9238 (mm-30) REVERT: A 245 LYS cc_start: 0.9243 (mmmt) cc_final: 0.9042 (tppt) REVERT: A 261 TRP cc_start: 0.9449 (t-100) cc_final: 0.9099 (t-100) REVERT: A 272 ARG cc_start: 0.8410 (ptm160) cc_final: 0.8103 (ptm160) REVERT: A 277 ASP cc_start: 0.9025 (m-30) cc_final: 0.8453 (p0) REVERT: A 279 LYS cc_start: 0.9656 (mmmt) cc_final: 0.9430 (mmmm) REVERT: A 285 GLN cc_start: 0.8407 (mm-40) cc_final: 0.8206 (mm-40) REVERT: A 293 TYR cc_start: 0.9057 (t80) cc_final: 0.8478 (t80) REVERT: A 306 HIS cc_start: 0.8697 (m-70) cc_final: 0.8317 (m-70) REVERT: A 320 LYS cc_start: 0.8942 (tppt) cc_final: 0.8346 (tppt) REVERT: A 347 GLN cc_start: 0.8660 (mp10) cc_final: 0.8435 (mp10) REVERT: A 365 MET cc_start: 0.9372 (ttm) cc_final: 0.8821 (tmm) REVERT: A 375 ASN cc_start: 0.8753 (t0) cc_final: 0.8323 (t0) REVERT: A 387 ARG cc_start: 0.8829 (tpp80) cc_final: 0.8545 (tpp80) REVERT: A 421 GLU cc_start: 0.8362 (pt0) cc_final: 0.7953 (pt0) REVERT: A 426 SER cc_start: 0.9585 (t) cc_final: 0.9322 (p) REVERT: A 445 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8732 (mt-10) REVERT: A 498 MET cc_start: 0.8177 (ttm) cc_final: 0.7537 (ttm) REVERT: A 499 MET cc_start: 0.8610 (tpp) cc_final: 0.8161 (tpp) REVERT: B 196 ASP cc_start: 0.7641 (t0) cc_final: 0.7138 (t70) REVERT: B 218 LYS cc_start: 0.9455 (mmmm) cc_final: 0.9041 (mtpp) REVERT: B 224 PHE cc_start: 0.9460 (t80) cc_final: 0.9240 (t80) REVERT: B 234 LEU cc_start: 0.9674 (mt) cc_final: 0.9406 (mt) REVERT: B 235 TYR cc_start: 0.9295 (t80) cc_final: 0.8467 (t80) REVERT: B 236 GLU cc_start: 0.9428 (mm-30) cc_final: 0.8969 (mm-30) REVERT: B 263 VAL cc_start: 0.9380 (t) cc_final: 0.9142 (p) REVERT: B 282 PHE cc_start: 0.8551 (p90) cc_final: 0.8135 (p90) REVERT: B 285 GLN cc_start: 0.8637 (mm-40) cc_final: 0.7879 (mm-40) REVERT: B 293 TYR cc_start: 0.9158 (t80) cc_final: 0.8889 (t80) REVERT: B 318 PHE cc_start: 0.9047 (p90) cc_final: 0.8779 (p90) REVERT: B 394 TYR cc_start: 0.9498 (t80) cc_final: 0.9180 (t80) REVERT: B 407 MET cc_start: 0.8604 (tmm) cc_final: 0.8106 (tmm) REVERT: B 421 GLU cc_start: 0.8535 (pt0) cc_final: 0.8080 (pt0) REVERT: B 424 CYS cc_start: 0.9013 (m) cc_final: 0.8728 (m) REVERT: B 426 SER cc_start: 0.9369 (t) cc_final: 0.9016 (p) REVERT: B 467 ASP cc_start: 0.9099 (OUTLIER) cc_final: 0.8729 (p0) REVERT: C 172 ASP cc_start: 0.8595 (t0) cc_final: 0.7711 (t0) REVERT: C 179 MET cc_start: 0.7696 (ptp) cc_final: 0.7025 (ptp) REVERT: C 272 ARG cc_start: 0.8345 (ptm160) cc_final: 0.8098 (ptm160) REVERT: C 277 ASP cc_start: 0.9093 (m-30) cc_final: 0.8499 (p0) REVERT: C 293 TYR cc_start: 0.9046 (t80) cc_final: 0.8501 (t80) REVERT: C 316 LEU cc_start: 0.9368 (mt) cc_final: 0.9095 (mt) REVERT: C 375 ASN cc_start: 0.8881 (t0) cc_final: 0.8586 (t0) REVERT: C 379 GLN cc_start: 0.9392 (mm110) cc_final: 0.9184 (mm110) REVERT: C 381 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8132 (tm-30) REVERT: C 407 MET cc_start: 0.8816 (tmm) cc_final: 0.8375 (tmm) REVERT: C 415 PHE cc_start: 0.9418 (m-10) cc_final: 0.8904 (m-80) REVERT: C 421 GLU cc_start: 0.8325 (pt0) cc_final: 0.8001 (pt0) REVERT: C 426 SER cc_start: 0.9537 (t) cc_final: 0.9302 (p) REVERT: C 445 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8737 (mt-10) REVERT: C 498 MET cc_start: 0.8230 (ttm) cc_final: 0.7679 (ttm) REVERT: C 499 MET cc_start: 0.8147 (tpp) cc_final: 0.7744 (tpp) REVERT: D 140 GLU cc_start: 0.8595 (pm20) cc_final: 0.8304 (pp20) REVERT: D 172 ASP cc_start: 0.8959 (t0) cc_final: 0.8744 (t0) REVERT: D 196 ASP cc_start: 0.7270 (t0) cc_final: 0.6866 (t0) REVERT: D 212 THR cc_start: 0.9059 (p) cc_final: 0.8224 (p) REVERT: D 213 GLN cc_start: 0.9182 (mm110) cc_final: 0.8957 (mm-40) REVERT: D 224 PHE cc_start: 0.9418 (t80) cc_final: 0.9188 (t80) REVERT: D 225 MET cc_start: 0.9411 (mmp) cc_final: 0.9200 (mmp) REVERT: D 232 ASP cc_start: 0.9656 (m-30) cc_final: 0.9145 (m-30) REVERT: D 236 GLU cc_start: 0.9498 (mm-30) cc_final: 0.9108 (mm-30) REVERT: D 249 TYR cc_start: 0.8461 (p90) cc_final: 0.8078 (p90) REVERT: D 260 LEU cc_start: 0.9467 (tp) cc_final: 0.9029 (tp) REVERT: D 261 TRP cc_start: 0.9112 (t-100) cc_final: 0.8897 (t-100) REVERT: D 263 VAL cc_start: 0.9439 (t) cc_final: 0.9124 (p) REVERT: D 277 ASP cc_start: 0.9151 (m-30) cc_final: 0.8922 (m-30) REVERT: D 285 GLN cc_start: 0.8607 (mm-40) cc_final: 0.7894 (mm-40) REVERT: D 293 TYR cc_start: 0.9112 (t80) cc_final: 0.8687 (t80) REVERT: D 303 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8784 (tm-30) REVERT: D 306 HIS cc_start: 0.8538 (m-70) cc_final: 0.8290 (m90) REVERT: D 318 PHE cc_start: 0.9134 (p90) cc_final: 0.8601 (p90) REVERT: D 344 LEU cc_start: 0.9528 (mt) cc_final: 0.9290 (mt) REVERT: D 394 TYR cc_start: 0.9508 (t80) cc_final: 0.9153 (t80) REVERT: D 397 GLU cc_start: 0.9186 (tm-30) cc_final: 0.8932 (tm-30) REVERT: D 421 GLU cc_start: 0.8391 (pt0) cc_final: 0.7808 (pt0) REVERT: D 436 ASN cc_start: 0.8542 (t0) cc_final: 0.8213 (t0) REVERT: D 454 ARG cc_start: 0.8884 (ttp80) cc_final: 0.8653 (ttp80) REVERT: D 499 MET cc_start: 0.7955 (tpp) cc_final: 0.7670 (tpp) REVERT: E 172 ASP cc_start: 0.8875 (t0) cc_final: 0.8334 (t0) REVERT: E 179 MET cc_start: 0.8850 (tpp) cc_final: 0.8490 (tpp) REVERT: E 183 ARG cc_start: 0.8937 (mmm-85) cc_final: 0.8640 (ttp-110) REVERT: E 213 GLN cc_start: 0.9144 (mm110) cc_final: 0.8813 (mm110) REVERT: E 233 GLU cc_start: 0.9404 (tp30) cc_final: 0.8892 (tp30) REVERT: E 271 GLN cc_start: 0.8281 (pt0) cc_final: 0.7733 (pt0) REVERT: E 272 ARG cc_start: 0.8673 (mtp180) cc_final: 0.8320 (mtp180) REVERT: E 279 LYS cc_start: 0.9465 (mmmt) cc_final: 0.9089 (mmmm) REVERT: E 323 LEU cc_start: 0.9231 (mp) cc_final: 0.8946 (mp) REVERT: E 331 ASN cc_start: 0.9048 (p0) cc_final: 0.8605 (p0) REVERT: E 365 MET cc_start: 0.9308 (ttm) cc_final: 0.9019 (ttm) REVERT: E 379 GLN cc_start: 0.8791 (mm110) cc_final: 0.6893 (tt0) REVERT: E 396 LYS cc_start: 0.9449 (tttt) cc_final: 0.9128 (tttm) REVERT: E 407 MET cc_start: 0.8724 (tmm) cc_final: 0.8347 (tmm) REVERT: E 421 GLU cc_start: 0.8591 (pt0) cc_final: 0.8227 (pt0) REVERT: E 424 CYS cc_start: 0.9186 (m) cc_final: 0.8923 (t) REVERT: E 426 SER cc_start: 0.9449 (t) cc_final: 0.9190 (p) REVERT: E 430 MET cc_start: 0.8860 (mmt) cc_final: 0.8551 (mmp) REVERT: E 455 ASN cc_start: 0.8991 (m-40) cc_final: 0.8514 (m-40) REVERT: E 465 MET cc_start: 0.9409 (tpp) cc_final: 0.9166 (mmm) REVERT: E 467 ASP cc_start: 0.8944 (m-30) cc_final: 0.8613 (m-30) REVERT: E 478 LEU cc_start: 0.9630 (mt) cc_final: 0.9419 (mt) REVERT: E 499 MET cc_start: 0.8382 (tpp) cc_final: 0.8055 (tpp) REVERT: E 517 PHE cc_start: 0.9344 (t80) cc_final: 0.9129 (t80) REVERT: E 520 ASP cc_start: 0.8962 (m-30) cc_final: 0.8756 (m-30) REVERT: G 179 MET cc_start: 0.9241 (tpp) cc_final: 0.8874 (tpp) REVERT: G 194 MET cc_start: 0.4486 (tpp) cc_final: 0.3956 (tpp) REVERT: G 227 PHE cc_start: 0.9620 (t80) cc_final: 0.9353 (t80) REVERT: G 232 ASP cc_start: 0.9618 (m-30) cc_final: 0.9114 (m-30) REVERT: G 235 TYR cc_start: 0.9349 (t80) cc_final: 0.9146 (t80) REVERT: G 236 GLU cc_start: 0.9544 (mm-30) cc_final: 0.9093 (mm-30) REVERT: G 240 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.9013 (mtmm) REVERT: G 261 TRP cc_start: 0.8796 (t-100) cc_final: 0.8477 (t-100) REVERT: G 271 GLN cc_start: 0.8608 (mt0) cc_final: 0.8386 (mt0) REVERT: G 277 ASP cc_start: 0.9251 (m-30) cc_final: 0.8808 (p0) REVERT: G 293 TYR cc_start: 0.9153 (t80) cc_final: 0.7418 (t80) REVERT: G 300 LEU cc_start: 0.9490 (mm) cc_final: 0.9218 (mt) REVERT: G 312 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8110 (mt-10) REVERT: G 317 ARG cc_start: 0.8485 (mmt90) cc_final: 0.8191 (mmt-90) REVERT: G 361 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8497 (t80) REVERT: G 382 ARG cc_start: 0.9484 (ttp80) cc_final: 0.9191 (mtp180) REVERT: G 421 GLU cc_start: 0.8159 (pt0) cc_final: 0.7912 (pt0) REVERT: G 424 CYS cc_start: 0.8941 (m) cc_final: 0.8289 (m) REVERT: G 436 ASN cc_start: 0.9190 (t0) cc_final: 0.8866 (t0) REVERT: G 451 GLU cc_start: 0.8183 (mp0) cc_final: 0.7943 (mp0) REVERT: G 454 ARG cc_start: 0.8859 (ttp80) cc_final: 0.8607 (ttp-110) REVERT: G 455 ASN cc_start: 0.9221 (m-40) cc_final: 0.8859 (m-40) REVERT: G 499 MET cc_start: 0.8559 (tpp) cc_final: 0.8261 (tpp) REVERT: G 516 HIS cc_start: 0.8020 (t-90) cc_final: 0.7364 (t-90) REVERT: I 140 GLU cc_start: 0.8686 (pm20) cc_final: 0.8300 (pp20) REVERT: I 172 ASP cc_start: 0.8886 (t0) cc_final: 0.8375 (t0) REVERT: I 194 MET cc_start: 0.7773 (tmm) cc_final: 0.7394 (tmm) REVERT: I 235 TYR cc_start: 0.8944 (t80) cc_final: 0.8562 (t80) REVERT: I 245 LYS cc_start: 0.8895 (mtmm) cc_final: 0.8678 (mmmm) REVERT: I 261 TRP cc_start: 0.9372 (t-100) cc_final: 0.8697 (t-100) REVERT: I 277 ASP cc_start: 0.8980 (m-30) cc_final: 0.8761 (p0) REVERT: I 279 LYS cc_start: 0.9494 (mmmt) cc_final: 0.9135 (mmmm) REVERT: I 331 ASN cc_start: 0.9067 (p0) cc_final: 0.8498 (p0) REVERT: I 375 ASN cc_start: 0.8507 (t0) cc_final: 0.8149 (m-40) REVERT: I 379 GLN cc_start: 0.8949 (mm110) cc_final: 0.6972 (tt0) REVERT: I 386 ASP cc_start: 0.8299 (m-30) cc_final: 0.7532 (m-30) REVERT: I 407 MET cc_start: 0.8698 (tmm) cc_final: 0.8319 (tmm) REVERT: I 421 GLU cc_start: 0.8575 (pt0) cc_final: 0.8149 (pt0) REVERT: I 426 SER cc_start: 0.9610 (t) cc_final: 0.9175 (p) REVERT: I 455 ASN cc_start: 0.8959 (m-40) cc_final: 0.8491 (m-40) REVERT: I 465 MET cc_start: 0.9395 (mmm) cc_final: 0.8726 (mmm) REVERT: I 467 ASP cc_start: 0.8687 (m-30) cc_final: 0.8354 (p0) REVERT: I 498 MET cc_start: 0.9014 (mtp) cc_final: 0.8762 (mtp) REVERT: I 499 MET cc_start: 0.8474 (tpp) cc_final: 0.8179 (tpp) REVERT: I 510 ASN cc_start: 0.8699 (m-40) cc_final: 0.8211 (m110) REVERT: I 520 ASP cc_start: 0.8985 (m-30) cc_final: 0.8766 (m-30) REVERT: K 219 PHE cc_start: 0.8074 (m-10) cc_final: 0.7749 (m-10) REVERT: K 232 ASP cc_start: 0.9588 (m-30) cc_final: 0.9314 (m-30) REVERT: K 235 TYR cc_start: 0.9319 (t80) cc_final: 0.9022 (t80) REVERT: K 236 GLU cc_start: 0.9524 (mm-30) cc_final: 0.9104 (mm-30) REVERT: K 293 TYR cc_start: 0.9124 (t80) cc_final: 0.7525 (t80) REVERT: K 318 PHE cc_start: 0.9183 (p90) cc_final: 0.8925 (p90) REVERT: K 331 ASN cc_start: 0.9378 (p0) cc_final: 0.8877 (p0) REVERT: K 333 MET cc_start: 0.9141 (mmp) cc_final: 0.8360 (mmp) REVERT: K 361 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.8454 (t80) REVERT: K 407 MET cc_start: 0.8632 (tmm) cc_final: 0.8352 (tmm) REVERT: K 416 GLN cc_start: 0.9436 (mt0) cc_final: 0.9214 (mt0) REVERT: K 424 CYS cc_start: 0.8689 (m) cc_final: 0.8401 (m) REVERT: K 436 ASN cc_start: 0.9191 (t0) cc_final: 0.8877 (t0) REVERT: K 451 GLU cc_start: 0.7967 (mp0) cc_final: 0.7715 (mp0) REVERT: K 454 ARG cc_start: 0.8885 (ttp80) cc_final: 0.8552 (ttp-110) REVERT: K 455 ASN cc_start: 0.9177 (m-40) cc_final: 0.8825 (m-40) REVERT: K 467 ASP cc_start: 0.9437 (p0) cc_final: 0.9025 (p0) REVERT: K 499 MET cc_start: 0.8305 (tpp) cc_final: 0.7949 (tpp) REVERT: K 501 TRP cc_start: 0.8830 (t-100) cc_final: 0.8191 (t-100) REVERT: K 508 MET cc_start: 0.8507 (mmm) cc_final: 0.8189 (mmm) REVERT: K 516 HIS cc_start: 0.8154 (t-90) cc_final: 0.7539 (t-90) REVERT: F 140 GLU cc_start: 0.8769 (pm20) cc_final: 0.8559 (pm20) REVERT: F 164 LYS cc_start: 0.9276 (mtmt) cc_final: 0.9010 (mtmm) REVERT: F 172 ASP cc_start: 0.8718 (t0) cc_final: 0.8490 (t0) REVERT: F 179 MET cc_start: 0.8737 (tpp) cc_final: 0.8313 (tpt) REVERT: F 196 ASP cc_start: 0.8315 (t70) cc_final: 0.8050 (t70) REVERT: F 213 GLN cc_start: 0.8883 (mm110) cc_final: 0.8496 (mm-40) REVERT: F 233 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8631 (mt-10) REVERT: F 236 GLU cc_start: 0.9442 (mm-30) cc_final: 0.8994 (mm-30) REVERT: F 252 GLN cc_start: 0.9139 (tp40) cc_final: 0.8795 (tp-100) REVERT: F 261 TRP cc_start: 0.9271 (t-100) cc_final: 0.9009 (t-100) REVERT: F 277 ASP cc_start: 0.9154 (OUTLIER) cc_final: 0.8437 (p0) REVERT: F 279 LYS cc_start: 0.9552 (mmmt) cc_final: 0.9060 (tppt) REVERT: F 285 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8643 (mm-40) REVERT: F 320 LYS cc_start: 0.8980 (tppt) cc_final: 0.8766 (tppt) REVERT: F 347 GLN cc_start: 0.8524 (mp10) cc_final: 0.8252 (mp10) REVERT: F 375 ASN cc_start: 0.9078 (t0) cc_final: 0.8525 (t0) REVERT: F 379 GLN cc_start: 0.9401 (mm110) cc_final: 0.8988 (mm110) REVERT: F 382 ARG cc_start: 0.9528 (ttp80) cc_final: 0.9271 (ttp80) REVERT: F 397 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8594 (tt0) REVERT: F 413 PHE cc_start: 0.8751 (t80) cc_final: 0.8260 (t80) REVERT: F 421 GLU cc_start: 0.8463 (pt0) cc_final: 0.7915 (pt0) REVERT: F 425 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8673 (mt-10) REVERT: F 430 MET cc_start: 0.8861 (mmt) cc_final: 0.8638 (mmp) REVERT: F 454 ARG cc_start: 0.9332 (ttp-110) cc_final: 0.9069 (ttp-110) REVERT: F 496 MET cc_start: 0.8480 (ppp) cc_final: 0.7807 (ppp) REVERT: F 498 MET cc_start: 0.8361 (mtp) cc_final: 0.8144 (mtp) REVERT: F 499 MET cc_start: 0.8568 (tpp) cc_final: 0.8092 (tpp) REVERT: H 194 MET cc_start: 0.7115 (tpp) cc_final: 0.6822 (tpp) REVERT: H 215 PHE cc_start: 0.8254 (m-80) cc_final: 0.7935 (m-80) REVERT: H 219 PHE cc_start: 0.8181 (m-10) cc_final: 0.7899 (m-10) REVERT: H 232 ASP cc_start: 0.9608 (m-30) cc_final: 0.9032 (m-30) REVERT: H 236 GLU cc_start: 0.9358 (mm-30) cc_final: 0.9023 (mm-30) REVERT: H 285 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8166 (mm-40) REVERT: H 293 TYR cc_start: 0.8943 (t80) cc_final: 0.8573 (t80) REVERT: H 308 TYR cc_start: 0.9127 (m-80) cc_final: 0.8665 (m-10) REVERT: H 320 LYS cc_start: 0.8917 (tppt) cc_final: 0.8575 (tppt) REVERT: H 328 LYS cc_start: 0.8852 (mtpp) cc_final: 0.8416 (mtpt) REVERT: H 346 LYS cc_start: 0.7985 (mtpp) cc_final: 0.7743 (ttmm) REVERT: H 347 GLN cc_start: 0.8887 (pm20) cc_final: 0.7922 (mp10) REVERT: H 353 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8931 (mt-10) REVERT: H 361 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8587 (t80) REVERT: H 378 PHE cc_start: 0.9436 (t80) cc_final: 0.9035 (t80) REVERT: H 382 ARG cc_start: 0.9456 (ttp80) cc_final: 0.8962 (ptm160) REVERT: H 397 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8722 (tm-30) REVERT: H 436 ASN cc_start: 0.8444 (t0) cc_final: 0.8206 (t0) REVERT: H 446 ARG cc_start: 0.9050 (tmm-80) cc_final: 0.8687 (tpp80) REVERT: H 455 ASN cc_start: 0.9032 (m-40) cc_final: 0.8772 (m-40) REVERT: H 499 MET cc_start: 0.8756 (tpp) cc_final: 0.7168 (tpp) REVERT: J 179 MET cc_start: 0.8781 (tmm) cc_final: 0.8412 (tmm) REVERT: J 180 ASP cc_start: 0.9349 (p0) cc_final: 0.8894 (p0) REVERT: J 196 ASP cc_start: 0.7749 (t70) cc_final: 0.7254 (p0) REVERT: J 215 PHE cc_start: 0.8776 (m-80) cc_final: 0.8251 (m-80) REVERT: J 233 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8547 (mt-10) REVERT: J 236 GLU cc_start: 0.9501 (mm-30) cc_final: 0.9219 (mm-30) REVERT: J 245 LYS cc_start: 0.8791 (mtmm) cc_final: 0.8516 (mmmm) REVERT: J 249 TYR cc_start: 0.8886 (p90) cc_final: 0.8555 (p90) REVERT: J 261 TRP cc_start: 0.9110 (t-100) cc_final: 0.8886 (t-100) REVERT: J 303 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8716 (tm-30) REVERT: J 320 LYS cc_start: 0.9158 (tppp) cc_final: 0.8795 (tppt) REVERT: J 413 PHE cc_start: 0.8903 (t80) cc_final: 0.8651 (t80) REVERT: J 421 GLU cc_start: 0.8579 (pt0) cc_final: 0.8058 (pt0) REVERT: J 430 MET cc_start: 0.8815 (mmt) cc_final: 0.8590 (mmp) REVERT: J 499 MET cc_start: 0.8950 (tpt) cc_final: 0.8169 (tpt) REVERT: L 172 ASP cc_start: 0.8446 (t0) cc_final: 0.8007 (t70) REVERT: L 194 MET cc_start: 0.6600 (tpt) cc_final: 0.4805 (pmm) REVERT: L 223 ASP cc_start: 0.8553 (p0) cc_final: 0.8310 (p0) REVERT: L 232 ASP cc_start: 0.9639 (m-30) cc_final: 0.9341 (m-30) REVERT: L 233 GLU cc_start: 0.9460 (mm-30) cc_final: 0.8893 (tp30) REVERT: L 236 GLU cc_start: 0.9329 (mm-30) cc_final: 0.8928 (mm-30) REVERT: L 241 GLN cc_start: 0.7585 (mp10) cc_final: 0.7122 (mp10) REVERT: L 260 LEU cc_start: 0.9486 (tp) cc_final: 0.9174 (tp) REVERT: L 285 GLN cc_start: 0.8598 (mm-40) cc_final: 0.8258 (mm-40) REVERT: L 320 LYS cc_start: 0.8899 (tppt) cc_final: 0.8506 (tppt) REVERT: L 331 ASN cc_start: 0.9138 (p0) cc_final: 0.8399 (p0) REVERT: L 333 MET cc_start: 0.8823 (mmp) cc_final: 0.7841 (mmp) REVERT: L 347 GLN cc_start: 0.8874 (pm20) cc_final: 0.7857 (mp10) REVERT: L 353 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8716 (mt-10) REVERT: L 378 PHE cc_start: 0.9444 (t80) cc_final: 0.9201 (t80) REVERT: L 426 SER cc_start: 0.9168 (t) cc_final: 0.8622 (p) REVERT: L 430 MET cc_start: 0.9097 (mpp) cc_final: 0.8823 (mpp) REVERT: L 455 ASN cc_start: 0.9041 (m-40) cc_final: 0.8741 (m-40) REVERT: D 602 GLN cc_start: 0.6232 (OUTLIER) cc_final: 0.5157 (pp30) outliers start: 126 outliers final: 88 residues processed: 1950 average time/residue: 0.4901 time to fit residues: 1543.7377 Evaluate side-chains 1887 residues out of total 4020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1792 time to evaluate : 4.145 ------------------------------------------------------------------------------- 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 408 VAL Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 327 ASP 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 B residue 511 SER Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 259 ASP 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 511 SER Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 312 GLU Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain G residue 240 LYS Chi-restraints excluded: chain G residue 242 SER 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 374 SER Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 462 SER Chi-restraints excluded: chain G residue 469 SER Chi-restraints excluded: chain G residue 505 LEU Chi-restraints excluded: chain G residue 511 SER Chi-restraints excluded: chain G residue 523 SER Chi-restraints excluded: chain I residue 207 ASN 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 484 VAL Chi-restraints excluded: chain I residue 511 SER Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 360 GLN Chi-restraints excluded: chain K residue 361 PHE Chi-restraints excluded: chain K residue 374 SER Chi-restraints excluded: chain K residue 469 SER Chi-restraints excluded: chain K residue 506 ASP Chi-restraints excluded: chain K residue 511 SER Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 277 ASP 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 F residue 458 SER Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 361 PHE Chi-restraints excluded: chain H residue 407 MET Chi-restraints excluded: chain H residue 426 SER 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 207 ASN 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 J residue 458 SER Chi-restraints excluded: chain J residue 467 ASP Chi-restraints excluded: chain J residue 484 VAL Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain L residue 231 ILE 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 230 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 344 optimal weight: 5.9990 chunk 281 optimal weight: 0.4980 chunk 114 optimal weight: 20.0000 chunk 414 optimal weight: 5.9990 chunk 448 optimal weight: 6.9990 chunk 369 optimal weight: 0.6980 chunk 411 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 332 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN A 360 GLN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 GLN D 455 ASN 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 519 HIS K 271 GLN K 298 ASN ** K 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 360 GLN F 510 ASN 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 379 GLN J 519 HIS L 213 GLN L 306 HIS ** L 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 36972 Z= 0.199 Angle : 0.594 9.629 49932 Z= 0.306 Chirality : 0.043 0.207 5544 Planarity : 0.004 0.049 6408 Dihedral : 4.919 64.056 4929 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.80 % Favored : 94.16 % Rotamer: Outliers : 4.03 % Allowed : 22.59 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.13), residues: 4620 helix: 1.20 (0.11), residues: 2400 sheet: -0.52 (0.29), residues: 384 loop : -0.30 (0.15), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 261 HIS 0.004 0.001 HIS E 330 PHE 0.027 0.001 PHE E 322 TYR 0.024 0.002 TYR C 235 ARG 0.011 0.000 ARG K 217 *********************** 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 2003 residues out of total 4020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1841 time to evaluate : 3.134 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: A 164 LYS cc_start: 0.9085 (mtmt) cc_final: 0.8856 (mtmm) REVERT: A 194 MET cc_start: 0.6498 (tpp) cc_final: 0.5723 (tpp) REVERT: A 213 GLN cc_start: 0.9096 (mm-40) cc_final: 0.8636 (mm-40) REVERT: A 236 GLU cc_start: 0.9617 (mm-30) cc_final: 0.9255 (mm-30) REVERT: A 245 LYS cc_start: 0.9212 (mmmt) cc_final: 0.8872 (tppt) REVERT: A 261 TRP cc_start: 0.9328 (t-100) cc_final: 0.8980 (t-100) REVERT: A 272 ARG cc_start: 0.8363 (ptm160) cc_final: 0.7955 (ptm160) REVERT: A 277 ASP cc_start: 0.8881 (m-30) cc_final: 0.8379 (p0) REVERT: A 293 TYR cc_start: 0.9068 (t80) cc_final: 0.8528 (t80) REVERT: A 306 HIS cc_start: 0.8671 (m-70) cc_final: 0.8303 (m-70) REVERT: A 320 LYS cc_start: 0.8994 (tppt) cc_final: 0.8560 (tppt) REVERT: A 365 MET cc_start: 0.9328 (ttm) cc_final: 0.8795 (tmm) REVERT: A 375 ASN cc_start: 0.8647 (t0) cc_final: 0.8305 (t0) REVERT: A 387 ARG cc_start: 0.8810 (tpp80) cc_final: 0.8502 (tpp80) REVERT: A 415 PHE cc_start: 0.9124 (m-80) cc_final: 0.8836 (m-80) REVERT: A 421 GLU cc_start: 0.8330 (pt0) cc_final: 0.7926 (pt0) REVERT: A 426 SER cc_start: 0.9534 (t) cc_final: 0.9304 (p) REVERT: A 445 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8725 (mt-10) REVERT: A 498 MET cc_start: 0.8181 (ttm) cc_final: 0.7752 (ttm) REVERT: A 499 MET cc_start: 0.8614 (tpp) cc_final: 0.8188 (tpp) REVERT: B 196 ASP cc_start: 0.7479 (t0) cc_final: 0.7212 (t70) REVERT: B 218 LYS cc_start: 0.9458 (mmmm) cc_final: 0.9024 (mtpp) REVERT: B 235 TYR cc_start: 0.9266 (t80) cc_final: 0.8386 (t80) REVERT: B 236 GLU cc_start: 0.9451 (mm-30) cc_final: 0.9113 (mm-30) REVERT: B 263 VAL cc_start: 0.9365 (t) cc_final: 0.9143 (p) REVERT: B 278 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8532 (t) REVERT: B 282 PHE cc_start: 0.8615 (p90) cc_final: 0.8207 (p90) REVERT: B 285 GLN cc_start: 0.8606 (mm-40) cc_final: 0.7886 (mm-40) REVERT: B 293 TYR cc_start: 0.9187 (t80) cc_final: 0.8971 (t80) REVERT: B 318 PHE cc_start: 0.9053 (p90) cc_final: 0.8814 (p90) REVERT: B 361 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8448 (t80) REVERT: B 394 TYR cc_start: 0.9420 (t80) cc_final: 0.9036 (t80) REVERT: B 396 LYS cc_start: 0.9213 (tttp) cc_final: 0.8903 (tttp) REVERT: B 407 MET cc_start: 0.8653 (tmm) cc_final: 0.8148 (tmm) REVERT: B 421 GLU cc_start: 0.8523 (pt0) cc_final: 0.8076 (pt0) REVERT: B 424 CYS cc_start: 0.9068 (m) cc_final: 0.8863 (m) REVERT: B 426 SER cc_start: 0.9372 (t) cc_final: 0.9077 (p) REVERT: B 467 ASP cc_start: 0.9164 (OUTLIER) cc_final: 0.8851 (p0) REVERT: C 172 ASP cc_start: 0.8678 (t0) cc_final: 0.7844 (t0) REVERT: C 179 MET cc_start: 0.7756 (ptp) cc_final: 0.7151 (ptp) REVERT: C 260 LEU cc_start: 0.9249 (mt) cc_final: 0.8912 (mt) REVERT: C 272 ARG cc_start: 0.8301 (ptm160) cc_final: 0.8054 (ptm160) REVERT: C 277 ASP cc_start: 0.8908 (m-30) cc_final: 0.8390 (p0) REVERT: C 365 MET cc_start: 0.9394 (ttm) cc_final: 0.8825 (tmm) REVERT: C 375 ASN cc_start: 0.8828 (t0) cc_final: 0.8528 (t0) REVERT: C 381 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8157 (tm-30) REVERT: C 387 ARG cc_start: 0.8922 (tpp80) cc_final: 0.8664 (tpp80) REVERT: C 407 MET cc_start: 0.8784 (tmm) cc_final: 0.8506 (tmm) REVERT: C 415 PHE cc_start: 0.9352 (m-10) cc_final: 0.8869 (m-80) REVERT: C 421 GLU cc_start: 0.8306 (pt0) cc_final: 0.7967 (pt0) REVERT: C 426 SER cc_start: 0.9549 (t) cc_final: 0.9303 (p) REVERT: C 445 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8687 (mt-10) REVERT: C 498 MET cc_start: 0.8115 (ttm) cc_final: 0.7751 (ttm) REVERT: C 499 MET cc_start: 0.8216 (tpp) cc_final: 0.7866 (tpp) REVERT: D 140 GLU cc_start: 0.8613 (pm20) cc_final: 0.8308 (pp20) REVERT: D 172 ASP cc_start: 0.8991 (t0) cc_final: 0.8782 (t0) REVERT: D 196 ASP cc_start: 0.6954 (t0) cc_final: 0.6638 (t0) REVERT: D 212 THR cc_start: 0.9041 (p) cc_final: 0.8204 (p) REVERT: D 213 GLN cc_start: 0.9203 (mm110) cc_final: 0.8925 (mm-40) REVERT: D 224 PHE cc_start: 0.9405 (t80) cc_final: 0.9200 (t80) REVERT: D 225 MET cc_start: 0.9395 (mmp) cc_final: 0.9158 (mmp) REVERT: D 232 ASP cc_start: 0.9707 (m-30) cc_final: 0.9155 (m-30) REVERT: D 236 GLU cc_start: 0.9514 (mm-30) cc_final: 0.9122 (mm-30) REVERT: D 241 GLN cc_start: 0.8197 (mp10) cc_final: 0.7759 (mp10) REVERT: D 249 TYR cc_start: 0.8467 (p90) cc_final: 0.8110 (p90) REVERT: D 263 VAL cc_start: 0.9447 (t) cc_final: 0.9140 (p) REVERT: D 285 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8020 (mm-40) REVERT: D 293 TYR cc_start: 0.9126 (t80) cc_final: 0.8715 (t80) REVERT: D 303 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8817 (tm-30) REVERT: D 306 HIS cc_start: 0.8556 (m-70) cc_final: 0.8355 (m90) REVERT: D 318 PHE cc_start: 0.9111 (p90) cc_final: 0.8679 (p90) REVERT: D 375 ASN cc_start: 0.8854 (t0) cc_final: 0.8564 (t0) REVERT: D 379 GLN cc_start: 0.9455 (mm-40) cc_final: 0.8975 (mm-40) REVERT: D 394 TYR cc_start: 0.9477 (t80) cc_final: 0.9117 (t80) REVERT: D 397 GLU cc_start: 0.9248 (tm-30) cc_final: 0.8950 (tm-30) REVERT: D 407 MET cc_start: 0.8583 (tmm) cc_final: 0.8131 (tmm) REVERT: D 421 GLU cc_start: 0.8357 (pt0) cc_final: 0.7814 (pt0) REVERT: D 454 ARG cc_start: 0.8929 (ttp80) cc_final: 0.8694 (ttp80) REVERT: D 471 GLN cc_start: 0.9496 (mm110) cc_final: 0.8856 (tp40) REVERT: E 172 ASP cc_start: 0.8905 (t0) cc_final: 0.8442 (t0) REVERT: E 213 GLN cc_start: 0.9151 (mm110) cc_final: 0.8886 (mm-40) REVERT: E 233 GLU cc_start: 0.9393 (tp30) cc_final: 0.9113 (tp30) REVERT: E 236 GLU cc_start: 0.9448 (mm-30) cc_final: 0.8946 (mm-30) REVERT: E 252 GLN cc_start: 0.9112 (tp40) cc_final: 0.8453 (tp40) REVERT: E 255 LYS cc_start: 0.9614 (mttt) cc_final: 0.9223 (mttm) REVERT: E 271 GLN cc_start: 0.8369 (pt0) cc_final: 0.7811 (pt0) REVERT: E 272 ARG cc_start: 0.8776 (mtp180) cc_final: 0.8524 (mtp180) REVERT: E 285 GLN cc_start: 0.8982 (mm-40) cc_final: 0.8766 (mm-40) REVERT: E 323 LEU cc_start: 0.9307 (mp) cc_final: 0.9054 (mp) REVERT: E 328 LYS cc_start: 0.8977 (mttt) cc_final: 0.8607 (mtpt) REVERT: E 331 ASN cc_start: 0.9017 (p0) cc_final: 0.8378 (p0) REVERT: E 365 MET cc_start: 0.9277 (ttm) cc_final: 0.8981 (tmm) REVERT: E 379 GLN cc_start: 0.8823 (mm110) cc_final: 0.6906 (tt0) REVERT: E 396 LYS cc_start: 0.9488 (tttt) cc_final: 0.9127 (tttm) REVERT: E 407 MET cc_start: 0.8785 (tmm) cc_final: 0.8400 (tmm) REVERT: E 421 GLU cc_start: 0.8619 (pt0) cc_final: 0.8273 (pt0) REVERT: E 424 CYS cc_start: 0.9195 (m) cc_final: 0.8924 (t) REVERT: E 426 SER cc_start: 0.9423 (t) cc_final: 0.9123 (p) REVERT: E 455 ASN cc_start: 0.8990 (m-40) cc_final: 0.8505 (m-40) REVERT: E 463 CYS cc_start: 0.8481 (p) cc_final: 0.8183 (p) REVERT: E 465 MET cc_start: 0.9405 (tpp) cc_final: 0.9158 (mmm) REVERT: E 467 ASP cc_start: 0.8956 (m-30) cc_final: 0.8507 (m-30) REVERT: E 478 LEU cc_start: 0.9620 (mt) cc_final: 0.9358 (mt) REVERT: E 496 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7247 (ppp) REVERT: G 179 MET cc_start: 0.9281 (tpp) cc_final: 0.8913 (tpp) REVERT: G 181 MET cc_start: 0.8353 (ttp) cc_final: 0.7975 (ttm) REVERT: G 194 MET cc_start: 0.4758 (tpp) cc_final: 0.4176 (tpp) REVERT: G 218 LYS cc_start: 0.9681 (mmmm) cc_final: 0.9194 (mtmm) REVERT: G 227 PHE cc_start: 0.9649 (t80) cc_final: 0.9362 (t80) REVERT: G 232 ASP cc_start: 0.9615 (m-30) cc_final: 0.9068 (m-30) REVERT: G 235 TYR cc_start: 0.9299 (t80) cc_final: 0.8919 (t80) REVERT: G 236 GLU cc_start: 0.9548 (mm-30) cc_final: 0.9129 (mm-30) REVERT: G 260 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.8843 (tp) REVERT: G 271 GLN cc_start: 0.8613 (mt0) cc_final: 0.8053 (mt0) REVERT: G 293 TYR cc_start: 0.9174 (t80) cc_final: 0.7518 (t80) REVERT: G 300 LEU cc_start: 0.9471 (mm) cc_final: 0.9182 (mt) REVERT: G 312 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8068 (mt-10) REVERT: G 320 LYS cc_start: 0.9221 (tppt) cc_final: 0.8971 (tppt) REVERT: G 361 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8530 (t80) REVERT: G 382 ARG cc_start: 0.9512 (ttp80) cc_final: 0.9188 (mtp180) REVERT: G 421 GLU cc_start: 0.8268 (pt0) cc_final: 0.7968 (pt0) REVERT: G 424 CYS cc_start: 0.8839 (m) cc_final: 0.8566 (m) REVERT: G 436 ASN cc_start: 0.9204 (t0) cc_final: 0.8899 (t0) REVERT: G 451 GLU cc_start: 0.8163 (mp0) cc_final: 0.7929 (mp0) REVERT: G 454 ARG cc_start: 0.8802 (ttp80) cc_final: 0.8594 (ttp-110) REVERT: G 455 ASN cc_start: 0.9228 (m-40) cc_final: 0.8880 (m110) REVERT: G 499 MET cc_start: 0.8504 (tpp) cc_final: 0.8274 (tpp) REVERT: G 516 HIS cc_start: 0.8173 (t-90) cc_final: 0.7581 (t-90) REVERT: I 140 GLU cc_start: 0.8659 (pm20) cc_final: 0.8252 (pp20) REVERT: I 172 ASP cc_start: 0.8851 (t0) cc_final: 0.8299 (t0) REVERT: I 183 ARG cc_start: 0.9049 (mtp85) cc_final: 0.8370 (ptp-110) REVERT: I 194 MET cc_start: 0.7827 (tmm) cc_final: 0.7457 (tmm) REVERT: I 213 GLN cc_start: 0.9179 (mm-40) cc_final: 0.8513 (mm110) REVERT: I 218 LYS cc_start: 0.9189 (mmmm) cc_final: 0.8680 (mtmm) REVERT: I 235 TYR cc_start: 0.8909 (t80) cc_final: 0.8545 (t80) REVERT: I 236 GLU cc_start: 0.9574 (mm-30) cc_final: 0.9134 (mm-30) REVERT: I 261 TRP cc_start: 0.9330 (t-100) cc_final: 0.8764 (t-100) REVERT: I 277 ASP cc_start: 0.9010 (m-30) cc_final: 0.8747 (p0) REVERT: I 279 LYS cc_start: 0.9481 (mmmt) cc_final: 0.9138 (mmmm) REVERT: I 331 ASN cc_start: 0.8946 (p0) cc_final: 0.8354 (p0) REVERT: I 379 GLN cc_start: 0.8789 (mm110) cc_final: 0.6891 (tt0) REVERT: I 386 ASP cc_start: 0.8265 (m-30) cc_final: 0.7266 (m-30) REVERT: I 407 MET cc_start: 0.8700 (tmm) cc_final: 0.8318 (tmm) REVERT: I 421 GLU cc_start: 0.8587 (pt0) cc_final: 0.8170 (pt0) REVERT: I 426 SER cc_start: 0.9530 (t) cc_final: 0.9160 (p) REVERT: I 455 ASN cc_start: 0.8957 (m-40) cc_final: 0.8494 (m-40) REVERT: I 465 MET cc_start: 0.9370 (mmm) cc_final: 0.8967 (tpp) REVERT: I 467 ASP cc_start: 0.8692 (m-30) cc_final: 0.8339 (p0) REVERT: I 520 ASP cc_start: 0.8969 (m-30) cc_final: 0.8748 (m-30) REVERT: K 179 MET cc_start: 0.9318 (tpp) cc_final: 0.8717 (tpp) REVERT: K 219 PHE cc_start: 0.8006 (m-10) cc_final: 0.7769 (m-10) REVERT: K 232 ASP cc_start: 0.9587 (m-30) cc_final: 0.9265 (m-30) REVERT: K 235 TYR cc_start: 0.9171 (t80) cc_final: 0.8674 (t80) REVERT: K 236 GLU cc_start: 0.9515 (mm-30) cc_final: 0.9097 (mm-30) REVERT: K 252 GLN cc_start: 0.8425 (tp-100) cc_final: 0.7961 (tp-100) REVERT: K 279 LYS cc_start: 0.9634 (mmmm) cc_final: 0.9401 (mmmm) REVERT: K 293 TYR cc_start: 0.9106 (t80) cc_final: 0.7449 (t80) REVERT: K 312 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: K 318 PHE cc_start: 0.9185 (p90) cc_final: 0.8938 (p90) REVERT: K 361 PHE cc_start: 0.9097 (OUTLIER) cc_final: 0.8462 (t80) REVERT: K 407 MET cc_start: 0.8562 (tmm) cc_final: 0.8267 (tmm) REVERT: K 421 GLU cc_start: 0.8398 (pt0) cc_final: 0.8141 (pt0) REVERT: K 424 CYS cc_start: 0.8752 (m) cc_final: 0.8471 (m) REVERT: K 436 ASN cc_start: 0.9254 (t0) cc_final: 0.8960 (t0) REVERT: K 446 ARG cc_start: 0.8236 (ttp80) cc_final: 0.6810 (ttp80) REVERT: K 454 ARG cc_start: 0.8829 (ttp80) cc_final: 0.8558 (ttp-110) REVERT: K 455 ASN cc_start: 0.9194 (m-40) cc_final: 0.8838 (m110) REVERT: K 501 TRP cc_start: 0.8824 (t-100) cc_final: 0.7901 (t-100) REVERT: K 508 MET cc_start: 0.8529 (mmm) cc_final: 0.8272 (mmm) REVERT: K 516 HIS cc_start: 0.8224 (t-90) cc_final: 0.7626 (t-90) REVERT: F 140 GLU cc_start: 0.8732 (pm20) cc_final: 0.8493 (pm20) REVERT: F 164 LYS cc_start: 0.9296 (mtmt) cc_final: 0.9036 (mtmm) REVERT: F 172 ASP cc_start: 0.8688 (t0) cc_final: 0.8483 (t0) REVERT: F 179 MET cc_start: 0.8717 (tpp) cc_final: 0.8254 (tpt) REVERT: F 194 MET cc_start: 0.6616 (tpp) cc_final: 0.6404 (tpp) REVERT: F 196 ASP cc_start: 0.8282 (t70) cc_final: 0.7857 (t70) REVERT: F 213 GLN cc_start: 0.8879 (mm110) cc_final: 0.8113 (mm-40) REVERT: F 216 ARG cc_start: 0.8501 (mtp180) cc_final: 0.7864 (mtp180) REVERT: F 233 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8628 (mt-10) REVERT: F 235 TYR cc_start: 0.9191 (t80) cc_final: 0.8974 (t80) REVERT: F 236 GLU cc_start: 0.9499 (mm-30) cc_final: 0.8840 (mm-30) REVERT: F 277 ASP cc_start: 0.9096 (OUTLIER) cc_final: 0.8249 (p0) REVERT: F 279 LYS cc_start: 0.9578 (mmmt) cc_final: 0.9066 (tppt) REVERT: F 285 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8584 (mm-40) REVERT: F 375 ASN cc_start: 0.9121 (t0) cc_final: 0.8764 (t0) REVERT: F 379 GLN cc_start: 0.9452 (mm110) cc_final: 0.9062 (mm110) REVERT: F 407 MET cc_start: 0.8485 (tmm) cc_final: 0.8239 (tmm) REVERT: F 421 GLU cc_start: 0.8539 (pt0) cc_final: 0.7983 (pt0) REVERT: F 425 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8666 (mt-10) REVERT: F 454 ARG cc_start: 0.9290 (ttp-110) cc_final: 0.9026 (ttp-110) REVERT: F 494 ASN cc_start: 0.9400 (m-40) cc_final: 0.9115 (m-40) REVERT: F 499 MET cc_start: 0.8611 (tpp) cc_final: 0.8234 (tpp) REVERT: H 194 MET cc_start: 0.7020 (tpp) cc_final: 0.6735 (tpp) REVERT: H 215 PHE cc_start: 0.8231 (m-80) cc_final: 0.7882 (m-80) REVERT: H 219 PHE cc_start: 0.8204 (m-10) cc_final: 0.7914 (m-10) REVERT: H 232 ASP cc_start: 0.9612 (m-30) cc_final: 0.9046 (m-30) REVERT: H 236 GLU cc_start: 0.9351 (mm-30) cc_final: 0.9005 (mm-30) REVERT: H 285 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8262 (mm-40) REVERT: H 293 TYR cc_start: 0.8913 (t80) cc_final: 0.8574 (t80) REVERT: H 308 TYR cc_start: 0.9106 (m-80) cc_final: 0.8620 (m-10) REVERT: H 320 LYS cc_start: 0.8932 (tppt) cc_final: 0.8548 (tppt) REVERT: H 328 LYS cc_start: 0.8834 (mtpp) cc_final: 0.8536 (mtpt) REVERT: H 346 LYS cc_start: 0.8356 (mtpp) cc_final: 0.8131 (mtpp) REVERT: H 347 GLN cc_start: 0.8907 (pm20) cc_final: 0.7887 (mp10) REVERT: H 353 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8835 (mt-10) REVERT: H 378 PHE cc_start: 0.9342 (t80) cc_final: 0.9096 (t80) REVERT: H 397 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8621 (tm-30) REVERT: H 436 ASN cc_start: 0.8412 (t0) cc_final: 0.8211 (t0) REVERT: H 440 CYS cc_start: 0.8669 (t) cc_final: 0.8217 (t) REVERT: H 446 ARG cc_start: 0.9159 (tmm-80) cc_final: 0.8708 (tpp80) REVERT: H 455 ASN cc_start: 0.9044 (m-40) cc_final: 0.8796 (m-40) REVERT: H 471 GLN cc_start: 0.9434 (tp-100) cc_final: 0.9164 (mm-40) REVERT: J 179 MET cc_start: 0.8715 (tmm) cc_final: 0.8500 (tmm) REVERT: J 180 ASP cc_start: 0.9353 (p0) cc_final: 0.8992 (p0) REVERT: J 196 ASP cc_start: 0.7683 (t70) cc_final: 0.7262 (p0) REVERT: J 215 PHE cc_start: 0.8870 (m-80) cc_final: 0.8480 (m-80) REVERT: J 233 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8527 (mt-10) REVERT: J 236 GLU cc_start: 0.9507 (mm-30) cc_final: 0.9209 (mm-30) REVERT: J 245 LYS cc_start: 0.8795 (mtmm) cc_final: 0.8534 (mmmm) REVERT: J 293 TYR cc_start: 0.8956 (t80) cc_final: 0.8729 (t80) REVERT: J 303 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8721 (tm-30) REVERT: J 320 LYS cc_start: 0.9122 (tppp) cc_final: 0.8782 (tppt) REVERT: J 347 GLN cc_start: 0.8468 (mp10) cc_final: 0.8164 (mp10) REVERT: J 375 ASN cc_start: 0.9043 (t0) cc_final: 0.8819 (t0) REVERT: J 407 MET cc_start: 0.8499 (tmm) cc_final: 0.8276 (tmm) REVERT: J 421 GLU cc_start: 0.8556 (pt0) cc_final: 0.8003 (pt0) REVERT: J 425 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8213 (mp0) REVERT: J 496 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7686 (ppp) REVERT: J 499 MET cc_start: 0.8932 (tpt) cc_final: 0.8193 (tpt) REVERT: L 144 PHE cc_start: 0.8282 (t80) cc_final: 0.7975 (t80) REVERT: L 172 ASP cc_start: 0.8452 (t0) cc_final: 0.8007 (t70) REVERT: L 194 MET cc_start: 0.6603 (tpt) cc_final: 0.4859 (pmm) REVERT: L 223 ASP cc_start: 0.8531 (p0) cc_final: 0.8280 (p0) REVERT: L 232 ASP cc_start: 0.9644 (m-30) cc_final: 0.9371 (m-30) REVERT: L 233 GLU cc_start: 0.9455 (mm-30) cc_final: 0.8881 (tp30) REVERT: L 236 GLU cc_start: 0.9310 (mm-30) cc_final: 0.8972 (mm-30) REVERT: L 285 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8283 (mm-40) REVERT: L 317 ARG cc_start: 0.8552 (mmt-90) cc_final: 0.8124 (mmt-90) REVERT: L 320 LYS cc_start: 0.8972 (tppt) cc_final: 0.8498 (tppt) REVERT: L 333 MET cc_start: 0.8792 (mmp) cc_final: 0.8106 (mmp) REVERT: L 347 GLN cc_start: 0.8917 (pm20) cc_final: 0.8667 (pm20) REVERT: L 353 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8744 (mt-10) REVERT: L 378 PHE cc_start: 0.9434 (t80) cc_final: 0.9180 (t80) REVERT: L 426 SER cc_start: 0.9086 (t) cc_final: 0.8577 (p) REVERT: L 430 MET cc_start: 0.9141 (mpp) cc_final: 0.8829 (mpp) REVERT: L 446 ARG cc_start: 0.9066 (tmm-80) cc_final: 0.8703 (tpp80) REVERT: D 602 GLN cc_start: 0.6390 (OUTLIER) cc_final: 0.5216 (pp30) outliers start: 162 outliers final: 120 residues processed: 1901 average time/residue: 0.4879 time to fit residues: 1496.0249 Evaluate side-chains 1890 residues out of total 4020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1759 time to evaluate : 4.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 314 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 412 ASP Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 278 THR 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 361 PHE Chi-restraints excluded: chain B residue 428 SER 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 511 SER Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 259 ASP 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 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 511 SER Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 510 ASN Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 283 CYS Chi-restraints excluded: chain E residue 312 GLU Chi-restraints excluded: chain E residue 386 ASP 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 458 SER Chi-restraints excluded: chain E residue 496 MET Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 266 CYS 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 374 SER Chi-restraints excluded: chain G residue 380 SER Chi-restraints excluded: chain G residue 386 ASP Chi-restraints excluded: chain G residue 419 SER Chi-restraints excluded: chain G residue 428 SER Chi-restraints excluded: chain G residue 458 SER Chi-restraints excluded: chain G residue 505 LEU Chi-restraints excluded: chain G residue 511 SER Chi-restraints excluded: chain G residue 522 VAL Chi-restraints excluded: chain I residue 207 ASN Chi-restraints excluded: chain I residue 266 CYS Chi-restraints excluded: chain I residue 283 CYS Chi-restraints excluded: chain I residue 286 SER 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 K residue 257 SER 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 374 SER Chi-restraints excluded: chain K residue 399 LYS Chi-restraints excluded: chain K residue 419 SER Chi-restraints excluded: chain K residue 458 SER Chi-restraints excluded: chain K residue 505 LEU Chi-restraints excluded: chain K residue 506 ASP 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 265 VAL Chi-restraints excluded: chain F residue 277 ASP 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 458 SER Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 231 ILE 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 423 THR 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 207 ASN Chi-restraints excluded: chain J residue 231 ILE Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 386 ASP Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 458 SER Chi-restraints excluded: chain J residue 467 ASP 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 266 CYS Chi-restraints excluded: chain L residue 360 GLN Chi-restraints excluded: chain L residue 362 LEU Chi-restraints excluded: chain L residue 408 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 409 optimal weight: 0.9980 chunk 311 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 197 optimal weight: 3.9990 chunk 278 optimal weight: 5.9990 chunk 416 optimal weight: 0.4980 chunk 440 optimal weight: 0.9980 chunk 217 optimal weight: 0.9990 chunk 394 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN C 375 ASN ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 298 ASN ** G 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 298 ASN ** K 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN F 360 GLN F 519 HIS ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 241 GLN J 252 GLN J 360 GLN J 519 HIS ** L 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 471 GLN L 475 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 36972 Z= 0.192 Angle : 0.596 9.800 49932 Z= 0.305 Chirality : 0.043 0.210 5544 Planarity : 0.004 0.047 6408 Dihedral : 4.853 62.768 4929 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.02 % Favored : 93.94 % Rotamer: Outliers : 4.73 % Allowed : 24.18 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.13), residues: 4620 helix: 1.32 (0.11), residues: 2376 sheet: -0.40 (0.30), residues: 384 loop : -0.10 (0.16), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 501 HIS 0.003 0.001 HIS J 230 PHE 0.029 0.001 PHE I 322 TYR 0.023 0.001 TYR F 293 ARG 0.007 0.000 ARG K 217 *********************** 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 2019 residues out of total 4020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1829 time to evaluate : 4.304 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: A 164 LYS cc_start: 0.9103 (mtmt) cc_final: 0.8881 (mtmm) REVERT: A 194 MET cc_start: 0.6488 (tpp) cc_final: 0.5644 (tpp) REVERT: A 213 GLN cc_start: 0.9069 (mm-40) cc_final: 0.8630 (mm-40) REVERT: A 236 GLU cc_start: 0.9609 (mm-30) cc_final: 0.9257 (mm-30) REVERT: A 245 LYS cc_start: 0.9179 (mmmt) cc_final: 0.8841 (tppt) REVERT: A 272 ARG cc_start: 0.8348 (ptm160) cc_final: 0.7918 (ptm160) REVERT: A 293 TYR cc_start: 0.9109 (t80) cc_final: 0.8548 (t80) REVERT: A 306 HIS cc_start: 0.8680 (m-70) cc_final: 0.8337 (m-70) REVERT: A 320 LYS cc_start: 0.9034 (tppt) cc_final: 0.8620 (tppt) REVERT: A 351 ASN cc_start: 0.9009 (m-40) cc_final: 0.8777 (m-40) REVERT: A 360 GLN cc_start: 0.9256 (tm130) cc_final: 0.8919 (tm-30) REVERT: A 365 MET cc_start: 0.9295 (ttm) cc_final: 0.8737 (tmm) REVERT: A 415 PHE cc_start: 0.9178 (m-80) cc_final: 0.8902 (m-80) REVERT: A 421 GLU cc_start: 0.8349 (pt0) cc_final: 0.7857 (pt0) REVERT: A 426 SER cc_start: 0.9539 (t) cc_final: 0.9324 (p) REVERT: A 445 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8785 (mt-10) REVERT: A 498 MET cc_start: 0.8077 (ttm) cc_final: 0.7680 (ttm) REVERT: A 499 MET cc_start: 0.8634 (tpp) cc_final: 0.8221 (tpp) REVERT: B 196 ASP cc_start: 0.7323 (t0) cc_final: 0.7063 (t70) REVERT: B 218 LYS cc_start: 0.9477 (mmmm) cc_final: 0.8752 (mmmm) REVERT: B 232 ASP cc_start: 0.9694 (m-30) cc_final: 0.9213 (m-30) REVERT: B 236 GLU cc_start: 0.9491 (mm-30) cc_final: 0.9074 (mm-30) REVERT: B 263 VAL cc_start: 0.9353 (t) cc_final: 0.9147 (p) REVERT: B 282 PHE cc_start: 0.8771 (p90) cc_final: 0.8337 (p90) REVERT: B 285 GLN cc_start: 0.8614 (mm-40) cc_final: 0.7915 (mm-40) REVERT: B 293 TYR cc_start: 0.9159 (t80) cc_final: 0.8908 (t80) REVERT: B 297 VAL cc_start: 0.9667 (t) cc_final: 0.9348 (m) REVERT: B 318 PHE cc_start: 0.9046 (p90) cc_final: 0.8816 (p90) REVERT: B 361 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.8496 (t80) REVERT: B 375 ASN cc_start: 0.8758 (t0) cc_final: 0.8448 (t0) REVERT: B 394 TYR cc_start: 0.9355 (t80) cc_final: 0.9086 (t80) REVERT: B 396 LYS cc_start: 0.9162 (tttp) cc_final: 0.8932 (tttp) REVERT: B 407 MET cc_start: 0.8694 (tmm) cc_final: 0.8233 (tmm) REVERT: B 421 GLU cc_start: 0.8528 (pt0) cc_final: 0.8091 (pt0) REVERT: B 424 CYS cc_start: 0.9094 (m) cc_final: 0.8695 (m) REVERT: B 426 SER cc_start: 0.9403 (t) cc_final: 0.9119 (p) REVERT: B 467 ASP cc_start: 0.9215 (OUTLIER) cc_final: 0.8954 (p0) REVERT: C 172 ASP cc_start: 0.8721 (t0) cc_final: 0.7926 (t0) REVERT: C 175 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8355 (pp) REVERT: C 179 MET cc_start: 0.7741 (ptp) cc_final: 0.6996 (ptp) REVERT: C 194 MET cc_start: 0.9036 (tpp) cc_final: 0.8444 (tpp) REVERT: C 213 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8536 (tp-100) REVERT: C 227 PHE cc_start: 0.9598 (t80) cc_final: 0.9355 (t80) REVERT: C 252 GLN cc_start: 0.9315 (tp40) cc_final: 0.9056 (tp40) REVERT: C 272 ARG cc_start: 0.8310 (ptm160) cc_final: 0.8052 (ptm160) REVERT: C 347 GLN cc_start: 0.8292 (mp10) cc_final: 0.7918 (mp10) REVERT: C 365 MET cc_start: 0.9379 (ttm) cc_final: 0.8770 (tmm) REVERT: C 381 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8066 (tm-30) REVERT: C 415 PHE cc_start: 0.9398 (m-10) cc_final: 0.8908 (m-80) REVERT: C 421 GLU cc_start: 0.8272 (pt0) cc_final: 0.7928 (pt0) REVERT: C 426 SER cc_start: 0.9543 (t) cc_final: 0.9309 (p) REVERT: C 445 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8705 (mt-10) REVERT: C 467 ASP cc_start: 0.9208 (p0) cc_final: 0.8424 (p0) REVERT: C 498 MET cc_start: 0.8114 (ttm) cc_final: 0.7789 (ttm) REVERT: C 499 MET cc_start: 0.8233 (tpp) cc_final: 0.7889 (tpp) REVERT: C 508 MET cc_start: 0.8985 (mtt) cc_final: 0.8598 (mtt) REVERT: D 140 GLU cc_start: 0.8611 (pm20) cc_final: 0.8312 (pp20) REVERT: D 172 ASP cc_start: 0.9004 (t0) cc_final: 0.8801 (t0) REVERT: D 196 ASP cc_start: 0.6962 (t0) cc_final: 0.6654 (t0) REVERT: D 212 THR cc_start: 0.8952 (p) cc_final: 0.8002 (p) REVERT: D 213 GLN cc_start: 0.9300 (mm110) cc_final: 0.8998 (mm-40) REVERT: D 225 MET cc_start: 0.9375 (mmp) cc_final: 0.9165 (mmp) REVERT: D 232 ASP cc_start: 0.9742 (m-30) cc_final: 0.9181 (m-30) REVERT: D 236 GLU cc_start: 0.9520 (mm-30) cc_final: 0.9117 (mm-30) REVERT: D 246 VAL cc_start: 0.8448 (OUTLIER) cc_final: 0.7839 (t) REVERT: D 249 TYR cc_start: 0.8466 (p90) cc_final: 0.8157 (p90) REVERT: D 260 LEU cc_start: 0.9419 (tp) cc_final: 0.9096 (tp) REVERT: D 263 VAL cc_start: 0.9443 (t) cc_final: 0.9156 (p) REVERT: D 285 GLN cc_start: 0.8624 (mm-40) cc_final: 0.7983 (mm-40) REVERT: D 293 TYR cc_start: 0.9122 (t80) cc_final: 0.8827 (t80) REVERT: D 303 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8911 (tm-30) REVERT: D 318 PHE cc_start: 0.9105 (p90) cc_final: 0.8691 (p90) REVERT: D 394 TYR cc_start: 0.9500 (t80) cc_final: 0.9121 (t80) REVERT: D 397 GLU cc_start: 0.9296 (tm-30) cc_final: 0.8947 (tm-30) REVERT: D 407 MET cc_start: 0.8666 (tmm) cc_final: 0.8296 (tmm) REVERT: D 421 GLU cc_start: 0.8412 (pt0) cc_final: 0.7869 (pt0) REVERT: D 454 ARG cc_start: 0.8908 (ttp80) cc_final: 0.8647 (ttp80) REVERT: D 471 GLN cc_start: 0.9511 (mm110) cc_final: 0.9255 (mm-40) REVERT: E 172 ASP cc_start: 0.8926 (t0) cc_final: 0.8469 (t0) REVERT: E 213 GLN cc_start: 0.9143 (mm110) cc_final: 0.8867 (mm110) REVERT: E 233 GLU cc_start: 0.9385 (tp30) cc_final: 0.9079 (tp30) REVERT: E 236 GLU cc_start: 0.9474 (mm-30) cc_final: 0.8932 (mm-30) REVERT: E 271 GLN cc_start: 0.8378 (pt0) cc_final: 0.7789 (pt0) REVERT: E 272 ARG cc_start: 0.8793 (mtp180) cc_final: 0.8540 (mtp180) REVERT: E 279 LYS cc_start: 0.9454 (mmmt) cc_final: 0.9118 (mmmm) REVERT: E 323 LEU cc_start: 0.9387 (mp) cc_final: 0.9173 (mp) REVERT: E 331 ASN cc_start: 0.8989 (p0) cc_final: 0.8257 (p0) REVERT: E 365 MET cc_start: 0.9238 (ttm) cc_final: 0.8964 (ttm) REVERT: E 379 GLN cc_start: 0.8867 (mm110) cc_final: 0.6902 (tt0) REVERT: E 396 LYS cc_start: 0.9506 (tttt) cc_final: 0.9273 (ttmm) REVERT: E 407 MET cc_start: 0.8802 (tmm) cc_final: 0.8527 (tmm) REVERT: E 418 CYS cc_start: 0.9153 (m) cc_final: 0.8461 (t) REVERT: E 421 GLU cc_start: 0.8621 (pt0) cc_final: 0.8278 (pt0) REVERT: E 424 CYS cc_start: 0.9209 (m) cc_final: 0.8776 (t) REVERT: E 426 SER cc_start: 0.9449 (t) cc_final: 0.9190 (p) REVERT: E 430 MET cc_start: 0.8776 (mmt) cc_final: 0.8512 (mmp) REVERT: E 455 ASN cc_start: 0.8984 (m-40) cc_final: 0.8516 (m-40) REVERT: E 463 CYS cc_start: 0.8407 (p) cc_final: 0.8019 (p) REVERT: E 467 ASP cc_start: 0.8981 (m-30) cc_final: 0.8552 (m-30) REVERT: E 478 LEU cc_start: 0.9622 (mt) cc_final: 0.9378 (mt) REVERT: G 179 MET cc_start: 0.9274 (tpp) cc_final: 0.8923 (tpp) REVERT: G 181 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7994 (ttm) REVERT: G 194 MET cc_start: 0.4833 (tpp) cc_final: 0.4570 (tpp) REVERT: G 218 LYS cc_start: 0.9664 (mmmm) cc_final: 0.9231 (mtmm) REVERT: G 227 PHE cc_start: 0.9645 (t80) cc_final: 0.9346 (t80) REVERT: G 232 ASP cc_start: 0.9641 (m-30) cc_final: 0.9081 (m-30) REVERT: G 235 TYR cc_start: 0.9212 (t80) cc_final: 0.8719 (t80) REVERT: G 236 GLU cc_start: 0.9541 (mm-30) cc_final: 0.9126 (mm-30) REVERT: G 252 GLN cc_start: 0.8836 (tp40) cc_final: 0.8623 (tp-100) REVERT: G 271 GLN cc_start: 0.8575 (mt0) cc_final: 0.7982 (mt0) REVERT: G 293 TYR cc_start: 0.9160 (t80) cc_final: 0.7528 (t80) REVERT: G 300 LEU cc_start: 0.9478 (mm) cc_final: 0.9181 (mt) REVERT: G 312 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8074 (mt-10) REVERT: G 320 LYS cc_start: 0.9204 (tppt) cc_final: 0.8953 (tppt) REVERT: G 328 LYS cc_start: 0.8845 (mtpt) cc_final: 0.8576 (mtpp) REVERT: G 361 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.8536 (t80) REVERT: G 382 ARG cc_start: 0.9485 (ttp80) cc_final: 0.9201 (mtp180) REVERT: G 421 GLU cc_start: 0.8413 (pt0) cc_final: 0.8140 (pt0) REVERT: G 424 CYS cc_start: 0.8935 (m) cc_final: 0.8588 (m) REVERT: G 436 ASN cc_start: 0.9191 (t0) cc_final: 0.8882 (t0) REVERT: G 451 GLU cc_start: 0.8178 (mp0) cc_final: 0.7954 (mp0) REVERT: G 454 ARG cc_start: 0.8802 (ttp80) cc_final: 0.8598 (ttp-110) REVERT: G 455 ASN cc_start: 0.9229 (m-40) cc_final: 0.8878 (m110) REVERT: G 516 HIS cc_start: 0.8203 (t-90) cc_final: 0.7602 (t-90) REVERT: I 140 GLU cc_start: 0.8659 (pm20) cc_final: 0.8318 (pp20) REVERT: I 172 ASP cc_start: 0.8893 (t0) cc_final: 0.8348 (t0) REVERT: I 183 ARG cc_start: 0.9053 (mtp85) cc_final: 0.8356 (ptp-110) REVERT: I 218 LYS cc_start: 0.9202 (mmmm) cc_final: 0.8930 (mtpp) REVERT: I 235 TYR cc_start: 0.8878 (t80) cc_final: 0.8625 (t80) REVERT: I 236 GLU cc_start: 0.9579 (mm-30) cc_final: 0.9128 (mm-30) REVERT: I 252 GLN cc_start: 0.8955 (tp40) cc_final: 0.8671 (tp40) REVERT: I 261 TRP cc_start: 0.9260 (t-100) cc_final: 0.8876 (t-100) REVERT: I 277 ASP cc_start: 0.8966 (m-30) cc_final: 0.8758 (p0) REVERT: I 331 ASN cc_start: 0.8921 (p0) cc_final: 0.8407 (p0) REVERT: I 379 GLN cc_start: 0.8822 (mm110) cc_final: 0.6840 (tt0) REVERT: I 407 MET cc_start: 0.8727 (tmm) cc_final: 0.8340 (tmm) REVERT: I 421 GLU cc_start: 0.8598 (pt0) cc_final: 0.8214 (pt0) REVERT: I 426 SER cc_start: 0.9525 (t) cc_final: 0.9149 (p) REVERT: I 455 ASN cc_start: 0.8961 (m-40) cc_final: 0.8499 (m-40) REVERT: I 465 MET cc_start: 0.9359 (mmm) cc_final: 0.9068 (mmm) REVERT: I 467 ASP cc_start: 0.8682 (m-30) cc_final: 0.8337 (p0) REVERT: I 520 ASP cc_start: 0.8969 (m-30) cc_final: 0.8753 (m-30) REVERT: K 179 MET cc_start: 0.9343 (tpp) cc_final: 0.8791 (tpp) REVERT: K 218 LYS cc_start: 0.9223 (mmmm) cc_final: 0.8821 (mtmm) REVERT: K 219 PHE cc_start: 0.8024 (m-10) cc_final: 0.7817 (m-10) REVERT: K 232 ASP cc_start: 0.9586 (m-30) cc_final: 0.9274 (m-30) REVERT: K 235 TYR cc_start: 0.9114 (t80) cc_final: 0.8536 (t80) REVERT: K 236 GLU cc_start: 0.9511 (mm-30) cc_final: 0.9110 (mm-30) REVERT: K 293 TYR cc_start: 0.9085 (t80) cc_final: 0.7407 (t80) REVERT: K 312 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7630 (mt-10) REVERT: K 318 PHE cc_start: 0.9192 (p90) cc_final: 0.8927 (p90) REVERT: K 333 MET cc_start: 0.9103 (mmp) cc_final: 0.8531 (mmp) REVERT: K 361 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8528 (t80) REVERT: K 407 MET cc_start: 0.8561 (tmm) cc_final: 0.8247 (tmm) REVERT: K 416 GLN cc_start: 0.9405 (mt0) cc_final: 0.9078 (mt0) REVERT: K 421 GLU cc_start: 0.8399 (pt0) cc_final: 0.8141 (pt0) REVERT: K 424 CYS cc_start: 0.8776 (m) cc_final: 0.8374 (m) REVERT: K 436 ASN cc_start: 0.9247 (t0) cc_final: 0.8972 (t0) REVERT: K 446 ARG cc_start: 0.8331 (ttp80) cc_final: 0.6952 (ttp80) REVERT: K 455 ASN cc_start: 0.9185 (m-40) cc_final: 0.8841 (m110) REVERT: K 467 ASP cc_start: 0.9451 (p0) cc_final: 0.8727 (p0) REVERT: K 508 MET cc_start: 0.8697 (mmm) cc_final: 0.8307 (mmm) REVERT: K 516 HIS cc_start: 0.8196 (t-90) cc_final: 0.7605 (t-90) REVERT: F 140 GLU cc_start: 0.8764 (pm20) cc_final: 0.8496 (pm20) REVERT: F 164 LYS cc_start: 0.9294 (mtmt) cc_final: 0.9029 (mtmm) REVERT: F 179 MET cc_start: 0.8721 (tpp) cc_final: 0.8515 (tpp) REVERT: F 194 MET cc_start: 0.6837 (tpp) cc_final: 0.6593 (tpp) REVERT: F 196 ASP cc_start: 0.8401 (t70) cc_final: 0.7963 (t70) REVERT: F 213 GLN cc_start: 0.8861 (mm110) cc_final: 0.8076 (mm-40) REVERT: F 216 ARG cc_start: 0.8520 (mtp180) cc_final: 0.7853 (mtp180) REVERT: F 233 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8597 (mt-10) REVERT: F 235 TYR cc_start: 0.9151 (t80) cc_final: 0.8914 (t80) REVERT: F 236 GLU cc_start: 0.9468 (mm-30) cc_final: 0.9073 (mm-30) REVERT: F 252 GLN cc_start: 0.9157 (tp40) cc_final: 0.8928 (tp40) REVERT: F 277 ASP cc_start: 0.9079 (OUTLIER) cc_final: 0.8231 (p0) REVERT: F 279 LYS cc_start: 0.9579 (mmmt) cc_final: 0.9068 (tppt) REVERT: F 285 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8540 (mm-40) REVERT: F 347 GLN cc_start: 0.8455 (mp10) cc_final: 0.8200 (mp10) REVERT: F 379 GLN cc_start: 0.9445 (mm110) cc_final: 0.9165 (mm110) REVERT: F 382 ARG cc_start: 0.9398 (ttp80) cc_final: 0.9025 (mtp-110) REVERT: F 421 GLU cc_start: 0.8542 (pt0) cc_final: 0.7973 (pt0) REVERT: F 425 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8647 (mt-10) REVERT: F 454 ARG cc_start: 0.9291 (ttp-110) cc_final: 0.9027 (ttp-110) REVERT: F 506 ASP cc_start: 0.9309 (t70) cc_final: 0.7986 (p0) REVERT: H 172 ASP cc_start: 0.8377 (t0) cc_final: 0.8127 (t0) REVERT: H 194 MET cc_start: 0.6950 (tpp) cc_final: 0.6658 (tpp) REVERT: H 215 PHE cc_start: 0.8357 (m-80) cc_final: 0.7977 (m-80) REVERT: H 219 PHE cc_start: 0.8255 (m-10) cc_final: 0.7984 (m-10) REVERT: H 232 ASP cc_start: 0.9606 (m-30) cc_final: 0.9057 (m-30) REVERT: H 236 GLU cc_start: 0.9354 (mm-30) cc_final: 0.9043 (mm-30) REVERT: H 293 TYR cc_start: 0.8906 (t80) cc_final: 0.8585 (t80) REVERT: H 308 TYR cc_start: 0.9069 (m-80) cc_final: 0.8562 (m-10) REVERT: H 320 LYS cc_start: 0.8958 (tppt) cc_final: 0.8554 (tppt) REVERT: H 328 LYS cc_start: 0.8836 (mtpp) cc_final: 0.8543 (mtpt) REVERT: H 331 ASN cc_start: 0.9010 (OUTLIER) cc_final: 0.8255 (p0) REVERT: H 353 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8740 (mt-10) REVERT: H 378 PHE cc_start: 0.9326 (t80) cc_final: 0.9068 (t80) REVERT: H 397 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8588 (tm-30) REVERT: H 440 CYS cc_start: 0.8637 (t) cc_final: 0.8185 (t) REVERT: H 446 ARG cc_start: 0.9171 (tmm-80) cc_final: 0.8740 (tpp80) REVERT: H 455 ASN cc_start: 0.9085 (m-40) cc_final: 0.8813 (m-40) REVERT: H 471 GLN cc_start: 0.9429 (tp-100) cc_final: 0.8941 (tp-100) REVERT: J 172 ASP cc_start: 0.8874 (t0) cc_final: 0.8663 (t70) REVERT: J 180 ASP cc_start: 0.9362 (p0) cc_final: 0.9035 (p0) REVERT: J 196 ASP cc_start: 0.7914 (t70) cc_final: 0.7595 (p0) REVERT: J 213 GLN cc_start: 0.8647 (mm110) cc_final: 0.8337 (tp40) REVERT: J 215 PHE cc_start: 0.8874 (m-80) cc_final: 0.8540 (m-80) REVERT: J 216 ARG cc_start: 0.8616 (mtp180) cc_final: 0.8384 (mtp180) REVERT: J 233 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8589 (mt-10) REVERT: J 236 GLU cc_start: 0.9513 (mm-30) cc_final: 0.9193 (mm-30) REVERT: J 245 LYS cc_start: 0.8792 (mtmm) cc_final: 0.8537 (mmmm) REVERT: J 303 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8779 (tm-30) REVERT: J 320 LYS cc_start: 0.9119 (tppp) cc_final: 0.8759 (tppt) REVERT: J 347 GLN cc_start: 0.8544 (mp10) cc_final: 0.8191 (mp10) REVERT: J 379 GLN cc_start: 0.9571 (mm-40) cc_final: 0.9354 (mm110) REVERT: J 407 MET cc_start: 0.8517 (tmm) cc_final: 0.8247 (tmm) REVERT: J 421 GLU cc_start: 0.8519 (pt0) cc_final: 0.7940 (pt0) REVERT: J 454 ARG cc_start: 0.9274 (ttp-110) cc_final: 0.9021 (ttp-110) REVERT: J 499 MET cc_start: 0.8885 (tpt) cc_final: 0.8300 (tpt) REVERT: L 172 ASP cc_start: 0.8391 (t0) cc_final: 0.8094 (t0) REVERT: L 182 LEU cc_start: 0.8950 (mt) cc_final: 0.8716 (mt) REVERT: L 194 MET cc_start: 0.6479 (tpt) cc_final: 0.4797 (pmm) REVERT: L 213 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8299 (mm-40) REVERT: L 223 ASP cc_start: 0.8503 (p0) cc_final: 0.8241 (p0) REVERT: L 232 ASP cc_start: 0.9640 (m-30) cc_final: 0.9342 (m-30) REVERT: L 233 GLU cc_start: 0.9444 (mm-30) cc_final: 0.8855 (tp30) REVERT: L 235 TYR cc_start: 0.9062 (t80) cc_final: 0.8774 (t80) REVERT: L 236 GLU cc_start: 0.9312 (mm-30) cc_final: 0.8978 (mm-30) REVERT: L 241 GLN cc_start: 0.7841 (mp10) cc_final: 0.7473 (mp10) REVERT: L 271 GLN cc_start: 0.7429 (tt0) cc_final: 0.7040 (tt0) REVERT: L 285 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8308 (mm-40) REVERT: L 320 LYS cc_start: 0.9006 (tppt) cc_final: 0.8584 (tppt) REVERT: L 331 ASN cc_start: 0.8970 (OUTLIER) cc_final: 0.8196 (p0) REVERT: L 333 MET cc_start: 0.8836 (mmp) cc_final: 0.7717 (mmp) REVERT: L 347 GLN cc_start: 0.8947 (pm20) cc_final: 0.8732 (pm20) REVERT: L 353 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8713 (mt-10) REVERT: L 426 SER cc_start: 0.9056 (t) cc_final: 0.8504 (p) REVERT: L 430 MET cc_start: 0.9141 (mpp) cc_final: 0.8765 (mpp) REVERT: L 446 ARG cc_start: 0.9121 (tmm-80) cc_final: 0.8813 (tpp80) REVERT: L 455 ASN cc_start: 0.8981 (m-40) cc_final: 0.8628 (m-40) REVERT: D 602 GLN cc_start: 0.6573 (OUTLIER) cc_final: 0.5402 (pp30) outliers start: 190 outliers final: 142 residues processed: 1898 average time/residue: 0.4867 time to fit residues: 1495.3965 Evaluate side-chains 1918 residues out of total 4020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1763 time to evaluate : 4.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 259 ASP 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 386 ASP Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 408 VAL 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 231 ILE Chi-restraints excluded: chain B residue 278 THR 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 361 PHE 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 511 SER Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain C residue 259 ASP 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 511 SER Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 325 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 510 ASN Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 289 LYS Chi-restraints excluded: chain E residue 312 GLU Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 458 SER Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain E residue 496 MET Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain G residue 181 MET Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 298 ASN 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 374 SER Chi-restraints excluded: chain G residue 380 SER Chi-restraints excluded: chain G residue 386 ASP Chi-restraints excluded: chain G residue 400 CYS Chi-restraints excluded: chain G residue 419 SER Chi-restraints excluded: chain G residue 458 SER Chi-restraints excluded: chain G residue 498 MET Chi-restraints excluded: chain G residue 505 LEU Chi-restraints excluded: chain G residue 511 SER Chi-restraints excluded: chain G residue 522 VAL Chi-restraints excluded: chain G residue 523 SER Chi-restraints excluded: chain I residue 207 ASN Chi-restraints excluded: chain I residue 266 CYS Chi-restraints excluded: chain I residue 283 CYS Chi-restraints excluded: chain I residue 286 SER 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 484 VAL Chi-restraints excluded: chain I residue 511 SER Chi-restraints excluded: chain K residue 257 SER 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 419 SER Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 458 SER Chi-restraints excluded: chain K residue 505 LEU Chi-restraints excluded: chain K residue 506 ASP 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 231 ILE Chi-restraints excluded: chain F residue 277 ASP 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 F residue 458 SER Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 331 ASN 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 423 THR Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 458 SER Chi-restraints excluded: chain H residue 467 ASP Chi-restraints excluded: chain H residue 510 ASN Chi-restraints excluded: chain H residue 512 VAL Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 231 ILE Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 380 SER Chi-restraints excluded: chain J residue 386 ASP Chi-restraints excluded: chain J residue 429 VAL Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 458 SER Chi-restraints excluded: chain J residue 467 ASP 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 331 ASN 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 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 367 optimal weight: 0.5980 chunk 250 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 328 optimal weight: 0.0470 chunk 181 optimal weight: 1.9990 chunk 376 optimal weight: 0.6980 chunk 304 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 225 optimal weight: 0.8980 chunk 395 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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** A 455 ASN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN D 298 ASN ** D 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 271 GLN K 298 ASN ** K 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 375 ASN F 360 GLN F 519 HIS ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36972 Z= 0.177 Angle : 0.621 10.287 49932 Z= 0.312 Chirality : 0.043 0.235 5544 Planarity : 0.004 0.049 6408 Dihedral : 4.797 61.256 4929 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.04 % Favored : 93.90 % Rotamer: Outliers : 4.38 % Allowed : 26.27 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.13), residues: 4620 helix: 1.30 (0.11), residues: 2388 sheet: -0.38 (0.30), residues: 384 loop : -0.09 (0.16), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 501 HIS 0.003 0.001 HIS D 157 PHE 0.023 0.001 PHE E 322 TYR 0.028 0.001 TYR E 357 ARG 0.008 0.000 ARG K 217 *********************** 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 1992 residues out of total 4020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1816 time to evaluate : 4.079 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: 0.9147 (mtmt) cc_final: 0.8908 (mtmm) REVERT: A 194 MET cc_start: 0.6450 (tpp) cc_final: 0.5555 (tpp) REVERT: A 213 GLN cc_start: 0.9094 (mm-40) cc_final: 0.8635 (mm-40) REVERT: A 236 GLU cc_start: 0.9620 (mm-30) cc_final: 0.9354 (mm-30) REVERT: A 245 LYS cc_start: 0.9166 (mmmt) cc_final: 0.8849 (tppt) REVERT: A 272 ARG cc_start: 0.8288 (ptm160) cc_final: 0.7887 (ptm160) REVERT: A 293 TYR cc_start: 0.9090 (t80) cc_final: 0.8601 (t80) REVERT: A 306 HIS cc_start: 0.8641 (m-70) cc_final: 0.8321 (m-70) REVERT: A 320 LYS cc_start: 0.9033 (tppt) cc_final: 0.8615 (tppt) REVERT: A 357 TYR cc_start: 0.8818 (t80) cc_final: 0.8529 (t80) REVERT: A 360 GLN cc_start: 0.9260 (tm130) cc_final: 0.8910 (tm-30) REVERT: A 407 MET cc_start: 0.8351 (tmm) cc_final: 0.8032 (tmm) REVERT: A 415 PHE cc_start: 0.9166 (m-80) cc_final: 0.8872 (m-80) REVERT: A 421 GLU cc_start: 0.8358 (pt0) cc_final: 0.7868 (pt0) REVERT: A 426 SER cc_start: 0.9533 (t) cc_final: 0.9301 (p) REVERT: A 434 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8645 (pp) REVERT: A 445 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8770 (mt-10) REVERT: A 499 MET cc_start: 0.8631 (tpp) cc_final: 0.8215 (tpp) REVERT: B 196 ASP cc_start: 0.7206 (t0) cc_final: 0.6960 (t70) REVERT: B 213 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8607 (tp-100) REVERT: B 218 LYS cc_start: 0.9548 (mmmm) cc_final: 0.8897 (mtmm) REVERT: B 232 ASP cc_start: 0.9698 (m-30) cc_final: 0.9161 (m-30) REVERT: B 233 GLU cc_start: 0.9538 (tp30) cc_final: 0.8990 (tp30) REVERT: B 236 GLU cc_start: 0.9484 (mm-30) cc_final: 0.9069 (mm-30) REVERT: B 252 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.8074 (tt0) REVERT: B 282 PHE cc_start: 0.8739 (p90) cc_final: 0.8277 (p90) REVERT: B 285 GLN cc_start: 0.8589 (mm-40) cc_final: 0.7914 (mm-40) REVERT: B 293 TYR cc_start: 0.9133 (t80) cc_final: 0.8922 (t80) REVERT: B 297 VAL cc_start: 0.9662 (t) cc_final: 0.9352 (m) REVERT: B 331 ASN cc_start: 0.9135 (OUTLIER) cc_final: 0.8637 (p0) REVERT: B 361 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8494 (t80) REVERT: B 394 TYR cc_start: 0.9325 (t80) cc_final: 0.9045 (t80) REVERT: B 407 MET cc_start: 0.8600 (tmm) cc_final: 0.8178 (tmm) REVERT: B 421 GLU cc_start: 0.8537 (pt0) cc_final: 0.8107 (pt0) REVERT: B 424 CYS cc_start: 0.9056 (m) cc_final: 0.8709 (m) REVERT: B 426 SER cc_start: 0.9430 (t) cc_final: 0.9173 (p) REVERT: B 467 ASP cc_start: 0.9266 (OUTLIER) cc_final: 0.9037 (p0) REVERT: C 172 ASP cc_start: 0.8780 (t0) cc_final: 0.7780 (t70) REVERT: C 175 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8449 (pp) REVERT: C 179 MET cc_start: 0.7827 (ptp) cc_final: 0.7077 (ptp) REVERT: C 194 MET cc_start: 0.9042 (tpp) cc_final: 0.8442 (tpp) REVERT: C 213 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8559 (tp40) REVERT: C 227 PHE cc_start: 0.9622 (t80) cc_final: 0.9355 (t80) REVERT: C 246 VAL cc_start: 0.7991 (OUTLIER) cc_final: 0.7288 (t) REVERT: C 252 GLN cc_start: 0.9258 (tp40) cc_final: 0.8970 (tp40) REVERT: C 272 ARG cc_start: 0.8312 (ptm160) cc_final: 0.8064 (ptm160) REVERT: C 277 ASP cc_start: 0.8843 (m-30) cc_final: 0.8426 (p0) REVERT: C 375 ASN cc_start: 0.8828 (t0) cc_final: 0.8416 (t0) REVERT: C 421 GLU cc_start: 0.8252 (pt0) cc_final: 0.7908 (pt0) REVERT: C 426 SER cc_start: 0.9543 (t) cc_final: 0.9323 (p) REVERT: C 445 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8711 (mt-10) REVERT: C 467 ASP cc_start: 0.9425 (p0) cc_final: 0.8495 (p0) REVERT: C 498 MET cc_start: 0.8046 (ttm) cc_final: 0.7788 (ttm) REVERT: C 499 MET cc_start: 0.8232 (tpp) cc_final: 0.7906 (tpp) REVERT: C 508 MET cc_start: 0.9077 (mtt) cc_final: 0.8442 (mtt) REVERT: D 140 GLU cc_start: 0.8663 (pm20) cc_final: 0.8368 (pp20) REVERT: D 172 ASP cc_start: 0.8968 (t0) cc_final: 0.8624 (t70) REVERT: D 212 THR cc_start: 0.9010 (p) cc_final: 0.8122 (p) REVERT: D 213 GLN cc_start: 0.9193 (mm110) cc_final: 0.8901 (mm-40) REVERT: D 232 ASP cc_start: 0.9755 (m-30) cc_final: 0.9191 (m-30) REVERT: D 236 GLU cc_start: 0.9517 (mm-30) cc_final: 0.9110 (mm-30) REVERT: D 246 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.7722 (t) REVERT: D 260 LEU cc_start: 0.9427 (tp) cc_final: 0.9070 (tp) REVERT: D 279 LYS cc_start: 0.9651 (mmmm) cc_final: 0.9366 (mmmm) REVERT: D 293 TYR cc_start: 0.9086 (t80) cc_final: 0.8799 (t80) REVERT: D 303 GLU cc_start: 0.9170 (tm-30) cc_final: 0.8937 (tm-30) REVERT: D 306 HIS cc_start: 0.8683 (m90) cc_final: 0.8404 (m170) REVERT: D 318 PHE cc_start: 0.9114 (p90) cc_final: 0.8714 (p90) REVERT: D 331 ASN cc_start: 0.9143 (OUTLIER) cc_final: 0.8579 (p0) REVERT: D 394 TYR cc_start: 0.9476 (t80) cc_final: 0.9110 (t80) REVERT: D 397 GLU cc_start: 0.9344 (tm-30) cc_final: 0.8975 (tm-30) REVERT: D 407 MET cc_start: 0.8568 (tmm) cc_final: 0.8279 (tmm) REVERT: D 414 TYR cc_start: 0.9257 (t80) cc_final: 0.8680 (t80) REVERT: D 421 GLU cc_start: 0.8440 (pt0) cc_final: 0.7885 (pt0) REVERT: D 436 ASN cc_start: 0.8646 (t0) cc_final: 0.8372 (t0) REVERT: D 454 ARG cc_start: 0.8970 (ttp80) cc_final: 0.8687 (ttp80) REVERT: D 471 GLN cc_start: 0.9530 (mm110) cc_final: 0.9295 (mm110) REVERT: D 508 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8645 (tpp) REVERT: E 172 ASP cc_start: 0.8942 (t0) cc_final: 0.8659 (t0) REVERT: E 213 GLN cc_start: 0.9133 (mm110) cc_final: 0.8859 (mm110) REVERT: E 236 GLU cc_start: 0.9479 (mm-30) cc_final: 0.8919 (mm-30) REVERT: E 271 GLN cc_start: 0.8286 (pt0) cc_final: 0.7829 (pt0) REVERT: E 272 ARG cc_start: 0.8783 (mtp180) cc_final: 0.8573 (mtp180) REVERT: E 279 LYS cc_start: 0.9447 (mmmt) cc_final: 0.9119 (mmmm) REVERT: E 323 LEU cc_start: 0.9436 (mp) cc_final: 0.9201 (mp) REVERT: E 331 ASN cc_start: 0.8891 (p0) cc_final: 0.8053 (p0) REVERT: E 365 MET cc_start: 0.9209 (ttm) cc_final: 0.8865 (ttm) REVERT: E 379 GLN cc_start: 0.8835 (mm110) cc_final: 0.6830 (tt0) REVERT: E 396 LYS cc_start: 0.9522 (tttt) cc_final: 0.9112 (tttm) REVERT: E 407 MET cc_start: 0.8794 (tmm) cc_final: 0.8385 (tmm) REVERT: E 418 CYS cc_start: 0.9171 (m) cc_final: 0.8536 (t) REVERT: E 421 GLU cc_start: 0.8629 (pt0) cc_final: 0.8301 (pt0) REVERT: E 424 CYS cc_start: 0.9191 (m) cc_final: 0.8796 (t) REVERT: E 426 SER cc_start: 0.9428 (t) cc_final: 0.9167 (p) REVERT: E 430 MET cc_start: 0.8717 (mmt) cc_final: 0.8455 (mmp) REVERT: E 455 ASN cc_start: 0.8983 (m-40) cc_final: 0.8521 (m-40) REVERT: E 463 CYS cc_start: 0.8335 (p) cc_final: 0.7913 (p) REVERT: E 467 ASP cc_start: 0.8927 (m-30) cc_final: 0.8583 (m-30) REVERT: E 478 LEU cc_start: 0.9622 (mt) cc_final: 0.9385 (mt) REVERT: G 179 MET cc_start: 0.9264 (tpp) cc_final: 0.8907 (tpp) REVERT: G 181 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8264 (ttp) REVERT: G 194 MET cc_start: 0.4834 (tpp) cc_final: 0.4513 (tpp) REVERT: G 218 LYS cc_start: 0.9656 (mmmm) cc_final: 0.9225 (mtmm) REVERT: G 227 PHE cc_start: 0.9634 (t80) cc_final: 0.9353 (t80) REVERT: G 232 ASP cc_start: 0.9625 (m-30) cc_final: 0.9077 (m-30) REVERT: G 235 TYR cc_start: 0.9208 (t80) cc_final: 0.8670 (t80) REVERT: G 236 GLU cc_start: 0.9552 (mm-30) cc_final: 0.9162 (mm-30) REVERT: G 293 TYR cc_start: 0.9087 (t80) cc_final: 0.7436 (t80) REVERT: G 298 ASN cc_start: 0.9475 (OUTLIER) cc_final: 0.9186 (t0) REVERT: G 300 LEU cc_start: 0.9488 (mm) cc_final: 0.9178 (mt) REVERT: G 312 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8048 (mt-10) REVERT: G 320 LYS cc_start: 0.9179 (tppt) cc_final: 0.8860 (tppt) REVERT: G 361 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8624 (t80) REVERT: G 382 ARG cc_start: 0.9493 (ttp80) cc_final: 0.9230 (mtp180) REVERT: G 421 GLU cc_start: 0.8408 (pt0) cc_final: 0.8131 (pt0) REVERT: G 424 CYS cc_start: 0.8933 (m) cc_final: 0.8676 (m) REVERT: G 436 ASN cc_start: 0.9231 (t0) cc_final: 0.8970 (t0) REVERT: G 446 ARG cc_start: 0.8090 (ttp80) cc_final: 0.7154 (tmt-80) REVERT: G 451 GLU cc_start: 0.8115 (mp0) cc_final: 0.7906 (mp0) REVERT: G 455 ASN cc_start: 0.9233 (m-40) cc_final: 0.8718 (m110) REVERT: G 516 HIS cc_start: 0.8200 (t-90) cc_final: 0.7594 (t-90) REVERT: I 140 GLU cc_start: 0.8736 (pm20) cc_final: 0.8390 (pp20) REVERT: I 172 ASP cc_start: 0.8990 (t0) cc_final: 0.8659 (t0) REVERT: I 183 ARG cc_start: 0.9103 (mtp85) cc_final: 0.8384 (ptp-110) REVERT: I 194 MET cc_start: 0.7161 (tpp) cc_final: 0.6490 (tpp) REVERT: I 213 GLN cc_start: 0.9194 (mm-40) cc_final: 0.8713 (tp40) REVERT: I 218 LYS cc_start: 0.9250 (mmmm) cc_final: 0.8886 (mtmm) REVERT: I 235 TYR cc_start: 0.8834 (t80) cc_final: 0.8618 (t80) REVERT: I 236 GLU cc_start: 0.9583 (mm-30) cc_final: 0.9117 (mm-30) REVERT: I 261 TRP cc_start: 0.9198 (t-100) cc_final: 0.8874 (t-100) REVERT: I 277 ASP cc_start: 0.8957 (m-30) cc_final: 0.8580 (p0) REVERT: I 331 ASN cc_start: 0.8981 (p0) cc_final: 0.8426 (p0) REVERT: I 379 GLN cc_start: 0.8853 (mm110) cc_final: 0.6808 (tt0) REVERT: I 407 MET cc_start: 0.8715 (tmm) cc_final: 0.8332 (tmm) REVERT: I 421 GLU cc_start: 0.8595 (pt0) cc_final: 0.8215 (pt0) REVERT: I 426 SER cc_start: 0.9577 (t) cc_final: 0.9234 (p) REVERT: I 455 ASN cc_start: 0.8959 (m-40) cc_final: 0.8494 (m-40) REVERT: I 465 MET cc_start: 0.9363 (mmm) cc_final: 0.9119 (mmm) REVERT: I 467 ASP cc_start: 0.8730 (m-30) cc_final: 0.8330 (p0) REVERT: I 494 ASN cc_start: 0.9309 (m110) cc_final: 0.9038 (m110) REVERT: I 520 ASP cc_start: 0.8944 (m-30) cc_final: 0.8738 (m-30) REVERT: K 179 MET cc_start: 0.9305 (tpp) cc_final: 0.8743 (tpp) REVERT: K 213 GLN cc_start: 0.8985 (mm110) cc_final: 0.8057 (mm110) REVERT: K 218 LYS cc_start: 0.9346 (mmmm) cc_final: 0.9074 (mtmm) REVERT: K 232 ASP cc_start: 0.9580 (m-30) cc_final: 0.9280 (m-30) REVERT: K 235 TYR cc_start: 0.9081 (t80) cc_final: 0.8522 (t80) REVERT: K 236 GLU cc_start: 0.9509 (mm-30) cc_final: 0.9141 (mm-30) REVERT: K 293 TYR cc_start: 0.9084 (t80) cc_final: 0.7445 (t80) REVERT: K 312 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7694 (mt-10) REVERT: K 361 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8534 (t80) REVERT: K 407 MET cc_start: 0.8534 (tmm) cc_final: 0.8256 (tmm) REVERT: K 416 GLN cc_start: 0.9348 (mt0) cc_final: 0.9027 (mt0) REVERT: K 421 GLU cc_start: 0.8372 (pt0) cc_final: 0.8111 (pt0) REVERT: K 424 CYS cc_start: 0.8762 (m) cc_final: 0.8390 (m) REVERT: K 430 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8441 (mpp) REVERT: K 436 ASN cc_start: 0.9207 (t0) cc_final: 0.8931 (t0) REVERT: K 446 ARG cc_start: 0.8347 (ttp80) cc_final: 0.7098 (ttp80) REVERT: K 455 ASN cc_start: 0.9198 (m-40) cc_final: 0.8677 (m110) REVERT: K 516 HIS cc_start: 0.8166 (t-90) cc_final: 0.7534 (t-90) REVERT: F 140 GLU cc_start: 0.8771 (pm20) cc_final: 0.8448 (pm20) REVERT: F 194 MET cc_start: 0.6911 (tpp) cc_final: 0.6682 (tpp) REVERT: F 196 ASP cc_start: 0.8187 (t70) cc_final: 0.7718 (t70) REVERT: F 213 GLN cc_start: 0.8969 (mm110) cc_final: 0.8160 (mm-40) REVERT: F 216 ARG cc_start: 0.8494 (mtp180) cc_final: 0.7836 (mtp180) REVERT: F 233 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8567 (mt-10) REVERT: F 236 GLU cc_start: 0.9458 (mm-30) cc_final: 0.8877 (mm-30) REVERT: F 277 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8213 (p0) REVERT: F 279 LYS cc_start: 0.9578 (mmmt) cc_final: 0.9067 (tppt) REVERT: F 347 GLN cc_start: 0.8449 (mp10) cc_final: 0.8116 (mp10) REVERT: F 365 MET cc_start: 0.9201 (ttm) cc_final: 0.8847 (ttp) REVERT: F 375 ASN cc_start: 0.9076 (t0) cc_final: 0.8621 (t0) REVERT: F 379 GLN cc_start: 0.9431 (mm110) cc_final: 0.9035 (mm110) REVERT: F 382 ARG cc_start: 0.9411 (ttp80) cc_final: 0.9049 (mtp-110) REVERT: F 421 GLU cc_start: 0.8545 (pt0) cc_final: 0.7970 (pt0) REVERT: F 425 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8644 (mt-10) REVERT: F 454 ARG cc_start: 0.9294 (ttp-110) cc_final: 0.9057 (ttp-110) REVERT: F 506 ASP cc_start: 0.9300 (t70) cc_final: 0.7977 (p0) REVERT: F 512 VAL cc_start: 0.8266 (m) cc_final: 0.7553 (t) REVERT: H 194 MET cc_start: 0.6717 (tpp) cc_final: 0.5913 (tpt) REVERT: H 213 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8248 (mm-40) REVERT: H 215 PHE cc_start: 0.8309 (m-80) cc_final: 0.8046 (m-80) REVERT: H 232 ASP cc_start: 0.9599 (m-30) cc_final: 0.9036 (m-30) REVERT: H 236 GLU cc_start: 0.9355 (mm-30) cc_final: 0.9042 (mm-30) REVERT: H 252 GLN cc_start: 0.8299 (tp40) cc_final: 0.7888 (tp40) REVERT: H 255 LYS cc_start: 0.9465 (mttp) cc_final: 0.9192 (mttp) REVERT: H 293 TYR cc_start: 0.8855 (t80) cc_final: 0.8567 (t80) REVERT: H 308 TYR cc_start: 0.9055 (m-80) cc_final: 0.8527 (m-10) REVERT: H 320 LYS cc_start: 0.8988 (tppt) cc_final: 0.8582 (tppt) REVERT: H 328 LYS cc_start: 0.8852 (mtpp) cc_final: 0.8548 (mtpt) REVERT: H 331 ASN cc_start: 0.8987 (OUTLIER) cc_final: 0.8332 (p0) REVERT: H 347 GLN cc_start: 0.8792 (mp10) cc_final: 0.8496 (pm20) REVERT: H 353 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8681 (mt-10) REVERT: H 378 PHE cc_start: 0.9332 (t80) cc_final: 0.9093 (t80) REVERT: H 396 LYS cc_start: 0.8961 (tttt) cc_final: 0.8751 (tttm) REVERT: H 397 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8634 (tm-30) REVERT: H 440 CYS cc_start: 0.8550 (t) cc_final: 0.8084 (t) REVERT: H 446 ARG cc_start: 0.9171 (tmm-80) cc_final: 0.8751 (tpp80) REVERT: H 455 ASN cc_start: 0.9081 (m-40) cc_final: 0.8802 (m-40) REVERT: H 508 MET cc_start: 0.8481 (tpt) cc_final: 0.8263 (tpt) REVERT: J 172 ASP cc_start: 0.8918 (t0) cc_final: 0.8684 (t70) REVERT: J 180 ASP cc_start: 0.9342 (p0) cc_final: 0.9127 (p0) REVERT: J 196 ASP cc_start: 0.7911 (t70) cc_final: 0.7670 (p0) REVERT: J 213 GLN cc_start: 0.8878 (mm110) cc_final: 0.8607 (tp-100) REVERT: J 215 PHE cc_start: 0.8823 (m-80) cc_final: 0.8576 (m-80) REVERT: J 232 ASP cc_start: 0.9465 (m-30) cc_final: 0.9261 (m-30) REVERT: J 233 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8559 (mt-10) REVERT: J 236 GLU cc_start: 0.9504 (mm-30) cc_final: 0.9193 (mm-30) REVERT: J 245 LYS cc_start: 0.8773 (mtmm) cc_final: 0.8516 (mmmm) REVERT: J 303 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8765 (tm-30) REVERT: J 320 LYS cc_start: 0.9075 (tppp) cc_final: 0.8729 (tppt) REVERT: J 347 GLN cc_start: 0.8547 (mp10) cc_final: 0.8136 (mp10) REVERT: J 382 ARG cc_start: 0.9024 (ptm-80) cc_final: 0.8822 (ptm160) REVERT: J 407 MET cc_start: 0.8480 (tmm) cc_final: 0.8225 (tmm) REVERT: J 421 GLU cc_start: 0.8494 (pt0) cc_final: 0.7899 (pt0) REVERT: J 448 LEU cc_start: 0.9218 (mt) cc_final: 0.9003 (mt) REVERT: J 454 ARG cc_start: 0.9288 (ttp-110) cc_final: 0.9014 (ttp-110) REVERT: J 499 MET cc_start: 0.8869 (tpt) cc_final: 0.8221 (tpt) REVERT: J 510 ASN cc_start: 0.7954 (m-40) cc_final: 0.7654 (m110) REVERT: L 172 ASP cc_start: 0.8420 (t0) cc_final: 0.8174 (t0) REVERT: L 194 MET cc_start: 0.6470 (tpt) cc_final: 0.4806 (pmm) REVERT: L 213 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8299 (mm-40) REVERT: L 223 ASP cc_start: 0.8508 (p0) cc_final: 0.8270 (p0) REVERT: L 241 GLN cc_start: 0.7679 (mp10) cc_final: 0.7292 (mp10) REVERT: L 271 GLN cc_start: 0.7358 (tt0) cc_final: 0.6978 (tt0) REVERT: L 285 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8328 (mm-40) REVERT: L 320 LYS cc_start: 0.9003 (tppt) cc_final: 0.8578 (tppt) REVERT: L 331 ASN cc_start: 0.8962 (OUTLIER) cc_final: 0.8226 (p0) REVERT: L 353 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8691 (mt-10) REVERT: L 361 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.8116 (t80) REVERT: L 394 TYR cc_start: 0.9318 (t80) cc_final: 0.9070 (t80) REVERT: L 423 THR cc_start: 0.8929 (p) cc_final: 0.8695 (t) REVERT: L 426 SER cc_start: 0.9051 (t) cc_final: 0.8571 (p) REVERT: L 430 MET cc_start: 0.9141 (mpp) cc_final: 0.8754 (mpp) REVERT: L 446 ARG cc_start: 0.9095 (tmm-80) cc_final: 0.8824 (tpp80) REVERT: L 455 ASN cc_start: 0.8970 (m-40) cc_final: 0.8592 (m-40) REVERT: L 516 HIS cc_start: 0.8042 (t-170) cc_final: 0.7808 (t-170) REVERT: D 602 GLN cc_start: 0.6661 (OUTLIER) cc_final: 0.5104 (pp30) outliers start: 176 outliers final: 119 residues processed: 1881 average time/residue: 0.5060 time to fit residues: 1550.7884 Evaluate side-chains 1905 residues out of total 4020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1764 time to evaluate : 4.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 259 ASP 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 400 CYS Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 412 ASP 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 252 GLN Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 278 THR 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 331 ASN Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 428 SER 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 C residue 175 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 283 CYS 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 166 THR Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 298 ASN Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 510 ASN Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 289 LYS Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 458 SER Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain E residue 496 MET Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain G residue 181 MET Chi-restraints excluded: chain G residue 242 SER Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 277 ASP Chi-restraints excluded: chain G residue 283 CYS Chi-restraints excluded: chain G residue 298 ASN Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 326 ASP Chi-restraints excluded: chain G residue 361 PHE Chi-restraints excluded: chain G residue 380 SER Chi-restraints excluded: chain G residue 381 GLU Chi-restraints excluded: chain G residue 386 ASP Chi-restraints excluded: chain G residue 400 CYS Chi-restraints excluded: chain G residue 458 SER Chi-restraints excluded: chain G residue 462 SER Chi-restraints excluded: chain G residue 505 LEU Chi-restraints excluded: chain G residue 522 VAL Chi-restraints excluded: chain I residue 286 SER Chi-restraints excluded: chain I residue 289 LYS Chi-restraints excluded: chain I residue 312 GLU Chi-restraints excluded: chain I residue 386 ASP Chi-restraints excluded: chain I residue 419 SER Chi-restraints excluded: chain I residue 428 SER Chi-restraints excluded: chain I residue 484 VAL Chi-restraints excluded: chain I residue 510 ASN Chi-restraints excluded: chain K residue 257 SER Chi-restraints excluded: chain K residue 283 CYS Chi-restraints excluded: chain K residue 312 GLU 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 419 SER Chi-restraints excluded: chain K residue 430 MET Chi-restraints excluded: chain K residue 458 SER Chi-restraints excluded: chain K residue 505 LEU Chi-restraints excluded: chain K residue 511 SER Chi-restraints excluded: chain K residue 523 SER Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 277 ASP 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 458 SER Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 331 ASN Chi-restraints excluded: chain H residue 360 GLN Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 426 SER Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 467 ASP Chi-restraints excluded: chain H residue 510 ASN Chi-restraints excluded: chain H residue 512 VAL Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 386 ASP Chi-restraints excluded: chain J residue 429 VAL Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 458 SER Chi-restraints excluded: chain J residue 467 ASP 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 331 ASN 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 148 optimal weight: 5.9990 chunk 396 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 258 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 441 optimal weight: 0.0970 chunk 366 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 231 optimal weight: 6.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 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 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 516 HIS K 271 GLN K 298 ASN ** K 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN F 360 GLN F 519 HIS ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 471 GLN ** H 516 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 519 HIS ** L 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 471 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 36972 Z= 0.247 Angle : 0.658 11.564 49932 Z= 0.332 Chirality : 0.044 0.259 5544 Planarity : 0.004 0.047 6408 Dihedral : 4.911 64.192 4929 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.32 % Favored : 93.59 % Rotamer: Outliers : 5.52 % Allowed : 26.27 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.13), residues: 4620 helix: 1.27 (0.11), residues: 2400 sheet: -0.48 (0.30), residues: 360 loop : -0.25 (0.15), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 501 HIS 0.004 0.001 HIS F 475 PHE 0.039 0.001 PHE B 224 TYR 0.028 0.002 TYR J 293 ARG 0.005 0.000 ARG D 317 *********************** 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 2010 residues out of total 4020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1788 time to evaluate : 4.342 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: 0.9210 (mtmt) cc_final: 0.8962 (mtmm) REVERT: A 177 GLU cc_start: 0.8733 (pp20) cc_final: 0.8501 (pp20) REVERT: A 194 MET cc_start: 0.6618 (tpp) cc_final: 0.5638 (tpp) REVERT: A 213 GLN cc_start: 0.9107 (mm-40) cc_final: 0.8655 (mm-40) REVERT: A 236 GLU cc_start: 0.9622 (mm-30) cc_final: 0.9276 (mm-30) REVERT: A 245 LYS cc_start: 0.9210 (mmmt) cc_final: 0.8821 (tppt) REVERT: A 252 GLN cc_start: 0.9298 (tp40) cc_final: 0.9033 (tp40) REVERT: A 272 ARG cc_start: 0.8354 (ptm160) cc_final: 0.8026 (ptm160) REVERT: A 293 TYR cc_start: 0.9114 (t80) cc_final: 0.8640 (t80) REVERT: A 306 HIS cc_start: 0.8711 (m-70) cc_final: 0.8440 (m-70) REVERT: A 320 LYS cc_start: 0.9067 (tppt) cc_final: 0.8681 (tppt) REVERT: A 360 GLN cc_start: 0.9284 (tm130) cc_final: 0.8954 (tm-30) REVERT: A 361 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8235 (t80) REVERT: A 375 ASN cc_start: 0.8827 (t0) cc_final: 0.8330 (t0) REVERT: A 415 PHE cc_start: 0.9225 (m-80) cc_final: 0.8889 (m-80) REVERT: A 421 GLU cc_start: 0.8356 (pt0) cc_final: 0.7887 (pt0) REVERT: A 434 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8661 (pp) REVERT: A 445 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8737 (mt-10) REVERT: A 498 MET cc_start: 0.8184 (ttm) cc_final: 0.7842 (ttm) REVERT: A 499 MET cc_start: 0.8219 (tpp) cc_final: 0.7868 (tpp) REVERT: A 500 CYS cc_start: 0.7870 (m) cc_final: 0.7508 (m) REVERT: B 196 ASP cc_start: 0.7388 (t0) cc_final: 0.7053 (t0) REVERT: B 213 GLN cc_start: 0.9094 (mm110) cc_final: 0.8564 (tp-100) REVERT: B 218 LYS cc_start: 0.9557 (mmmm) cc_final: 0.8897 (mtmm) REVERT: B 232 ASP cc_start: 0.9728 (m-30) cc_final: 0.9175 (m-30) REVERT: B 236 GLU cc_start: 0.9498 (mm-30) cc_final: 0.9073 (mm-30) REVERT: B 263 VAL cc_start: 0.9335 (t) cc_final: 0.9053 (p) REVERT: B 285 GLN cc_start: 0.8661 (mm-40) cc_final: 0.7949 (mm-40) REVERT: B 293 TYR cc_start: 0.9169 (t80) cc_final: 0.8957 (t80) REVERT: B 297 VAL cc_start: 0.9674 (t) cc_final: 0.9349 (m) REVERT: B 331 ASN cc_start: 0.9149 (OUTLIER) cc_final: 0.8915 (p0) REVERT: B 361 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8535 (t80) REVERT: B 394 TYR cc_start: 0.9395 (t80) cc_final: 0.9126 (t80) REVERT: B 407 MET cc_start: 0.8611 (tmm) cc_final: 0.8287 (tmm) REVERT: B 421 GLU cc_start: 0.8505 (pt0) cc_final: 0.7996 (pt0) REVERT: B 424 CYS cc_start: 0.9076 (m) cc_final: 0.8549 (t) REVERT: B 426 SER cc_start: 0.9457 (t) cc_final: 0.9200 (p) REVERT: C 172 ASP cc_start: 0.8811 (t0) cc_final: 0.8049 (t0) REVERT: C 175 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8390 (pp) REVERT: C 179 MET cc_start: 0.7848 (ptp) cc_final: 0.7141 (ptp) REVERT: C 194 MET cc_start: 0.9090 (tpp) cc_final: 0.8492 (tpp) REVERT: C 227 PHE cc_start: 0.9669 (t80) cc_final: 0.9369 (t80) REVERT: C 246 VAL cc_start: 0.8072 (OUTLIER) cc_final: 0.7536 (t) REVERT: C 272 ARG cc_start: 0.8301 (ptm160) cc_final: 0.8095 (ptm160) REVERT: C 293 TYR cc_start: 0.9159 (t80) cc_final: 0.8742 (t80) REVERT: C 365 MET cc_start: 0.9434 (ttm) cc_final: 0.8777 (tmm) REVERT: C 375 ASN cc_start: 0.8933 (t0) cc_final: 0.8568 (t0) REVERT: C 381 GLU cc_start: 0.9128 (tm-30) cc_final: 0.8579 (tm-30) REVERT: C 415 PHE cc_start: 0.9119 (m-80) cc_final: 0.8279 (m-80) REVERT: C 421 GLU cc_start: 0.8230 (pt0) cc_final: 0.7865 (pt0) REVERT: C 426 SER cc_start: 0.9513 (t) cc_final: 0.9262 (p) REVERT: C 430 MET cc_start: 0.8385 (mmp) cc_final: 0.7622 (mmp) REVERT: C 434 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8591 (pp) REVERT: C 445 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8746 (mt-10) REVERT: C 467 ASP cc_start: 0.9439 (p0) cc_final: 0.8662 (p0) REVERT: C 498 MET cc_start: 0.8161 (ttm) cc_final: 0.7854 (ttm) REVERT: C 499 MET cc_start: 0.8256 (tpp) cc_final: 0.7909 (tpp) REVERT: C 508 MET cc_start: 0.9122 (mtt) cc_final: 0.8668 (mtt) REVERT: D 140 GLU cc_start: 0.8714 (pm20) cc_final: 0.8393 (pp20) REVERT: D 172 ASP cc_start: 0.9039 (t0) cc_final: 0.8664 (t70) REVERT: D 236 GLU cc_start: 0.9534 (mm-30) cc_final: 0.9139 (mm-30) REVERT: D 241 GLN cc_start: 0.8270 (mp10) cc_final: 0.7908 (mp10) REVERT: D 246 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.7757 (t) REVERT: D 260 LEU cc_start: 0.9427 (tp) cc_final: 0.9041 (tp) REVERT: D 263 VAL cc_start: 0.9412 (t) cc_final: 0.9158 (p) REVERT: D 279 LYS cc_start: 0.9666 (mmmm) cc_final: 0.9396 (mmmm) REVERT: D 285 GLN cc_start: 0.8611 (mm-40) cc_final: 0.7899 (mm-40) REVERT: D 293 TYR cc_start: 0.9088 (t80) cc_final: 0.8844 (t80) REVERT: D 303 GLU cc_start: 0.9233 (tm-30) cc_final: 0.8989 (tm-30) REVERT: D 306 HIS cc_start: 0.8725 (m90) cc_final: 0.8452 (m170) REVERT: D 318 PHE cc_start: 0.9148 (p90) cc_final: 0.8803 (p90) REVERT: D 331 ASN cc_start: 0.9125 (OUTLIER) cc_final: 0.8837 (p0) REVERT: D 379 GLN cc_start: 0.9482 (mm-40) cc_final: 0.8969 (mm-40) REVERT: D 394 TYR cc_start: 0.9510 (t80) cc_final: 0.9166 (t80) REVERT: D 397 GLU cc_start: 0.9361 (tm-30) cc_final: 0.8994 (tm-30) REVERT: D 407 MET cc_start: 0.8602 (tmm) cc_final: 0.8353 (tmm) REVERT: D 414 TYR cc_start: 0.9279 (t80) cc_final: 0.8569 (t80) REVERT: D 421 GLU cc_start: 0.8365 (pt0) cc_final: 0.7852 (pt0) REVERT: D 454 ARG cc_start: 0.8999 (ttp80) cc_final: 0.8739 (ttp80) REVERT: D 471 GLN cc_start: 0.9540 (mm110) cc_final: 0.9237 (mm110) REVERT: E 172 ASP cc_start: 0.8973 (t0) cc_final: 0.8513 (t0) REVERT: E 233 GLU cc_start: 0.9416 (tp30) cc_final: 0.9072 (tp30) REVERT: E 236 GLU cc_start: 0.9473 (mm-30) cc_final: 0.9245 (mm-30) REVERT: E 271 GLN cc_start: 0.8541 (pt0) cc_final: 0.8106 (pt0) REVERT: E 279 LYS cc_start: 0.9450 (mmmt) cc_final: 0.9145 (mmmm) REVERT: E 285 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8697 (mm-40) REVERT: E 318 PHE cc_start: 0.8959 (p90) cc_final: 0.8746 (p90) REVERT: E 331 ASN cc_start: 0.8995 (p0) cc_final: 0.8010 (p0) REVERT: E 365 MET cc_start: 0.9179 (ttm) cc_final: 0.8782 (ttm) REVERT: E 379 GLN cc_start: 0.8828 (mm110) cc_final: 0.6871 (tt0) REVERT: E 396 LYS cc_start: 0.9518 (tttt) cc_final: 0.9315 (tttm) REVERT: E 407 MET cc_start: 0.8851 (tmm) cc_final: 0.8438 (tmm) REVERT: E 421 GLU cc_start: 0.8631 (pt0) cc_final: 0.8320 (pt0) REVERT: E 424 CYS cc_start: 0.9262 (m) cc_final: 0.8778 (t) REVERT: E 426 SER cc_start: 0.9447 (t) cc_final: 0.9194 (p) REVERT: E 430 MET cc_start: 0.8845 (mmt) cc_final: 0.8585 (mmp) REVERT: E 455 ASN cc_start: 0.8998 (m-40) cc_final: 0.8532 (m-40) REVERT: E 463 CYS cc_start: 0.8428 (p) cc_final: 0.7994 (p) REVERT: E 465 MET cc_start: 0.9436 (mmm) cc_final: 0.9110 (mmm) REVERT: E 467 ASP cc_start: 0.8892 (m-30) cc_final: 0.8510 (m-30) REVERT: E 478 LEU cc_start: 0.9636 (mt) cc_final: 0.9373 (mt) REVERT: G 179 MET cc_start: 0.9252 (tpp) cc_final: 0.8881 (tpp) REVERT: G 181 MET cc_start: 0.8629 (ttp) cc_final: 0.8190 (ttm) REVERT: G 194 MET cc_start: 0.5000 (tpp) cc_final: 0.4646 (tpp) REVERT: G 227 PHE cc_start: 0.9628 (t80) cc_final: 0.9312 (t80) REVERT: G 232 ASP cc_start: 0.9662 (m-30) cc_final: 0.9071 (m-30) REVERT: G 235 TYR cc_start: 0.9204 (t80) cc_final: 0.8686 (t80) REVERT: G 236 GLU cc_start: 0.9555 (mm-30) cc_final: 0.9187 (mm-30) REVERT: G 245 LYS cc_start: 0.9014 (mmmm) cc_final: 0.8813 (mmmm) REVERT: G 293 TYR cc_start: 0.9168 (t80) cc_final: 0.7547 (t80) REVERT: G 300 LEU cc_start: 0.9484 (mm) cc_final: 0.9174 (mt) REVERT: G 312 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8078 (mt-10) REVERT: G 320 LYS cc_start: 0.9224 (tppt) cc_final: 0.8908 (tppt) REVERT: G 333 MET cc_start: 0.9212 (mmp) cc_final: 0.8559 (mmp) REVERT: G 361 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8662 (t80) REVERT: G 382 ARG cc_start: 0.9515 (ttp80) cc_final: 0.9209 (mtp180) REVERT: G 421 GLU cc_start: 0.8293 (pt0) cc_final: 0.8006 (pt0) REVERT: G 424 CYS cc_start: 0.8994 (m) cc_final: 0.8633 (m) REVERT: G 436 ASN cc_start: 0.9208 (t0) cc_final: 0.8946 (t0) REVERT: G 446 ARG cc_start: 0.8238 (ttp80) cc_final: 0.7750 (ttp80) REVERT: G 451 GLU cc_start: 0.8259 (mp0) cc_final: 0.7988 (mp0) REVERT: G 455 ASN cc_start: 0.9241 (m-40) cc_final: 0.8887 (m110) REVERT: G 499 MET cc_start: 0.8496 (tpp) cc_final: 0.8236 (tpp) REVERT: G 516 HIS cc_start: 0.8187 (t-90) cc_final: 0.7486 (t-90) REVERT: I 140 GLU cc_start: 0.8739 (pm20) cc_final: 0.8387 (pp20) REVERT: I 172 ASP cc_start: 0.9049 (t0) cc_final: 0.8582 (t0) REVERT: I 183 ARG cc_start: 0.9095 (mtp85) cc_final: 0.8431 (ptp-110) REVERT: I 194 MET cc_start: 0.7352 (tpp) cc_final: 0.6685 (tpp) REVERT: I 213 GLN cc_start: 0.9211 (mm-40) cc_final: 0.8677 (tp-100) REVERT: I 218 LYS cc_start: 0.9274 (mmmm) cc_final: 0.8881 (mtmm) REVERT: I 235 TYR cc_start: 0.8857 (t80) cc_final: 0.8609 (t80) REVERT: I 236 GLU cc_start: 0.9592 (mm-30) cc_final: 0.9143 (mm-30) REVERT: I 261 TRP cc_start: 0.9206 (t-100) cc_final: 0.8805 (t-100) REVERT: I 277 ASP cc_start: 0.8942 (m-30) cc_final: 0.8619 (p0) REVERT: I 323 LEU cc_start: 0.9429 (mp) cc_final: 0.9143 (mp) REVERT: I 331 ASN cc_start: 0.8985 (p0) cc_final: 0.8451 (p0) REVERT: I 379 GLN cc_start: 0.8851 (mm110) cc_final: 0.6881 (tt0) REVERT: I 407 MET cc_start: 0.8781 (tmm) cc_final: 0.8373 (tmm) REVERT: I 421 GLU cc_start: 0.8604 (pt0) cc_final: 0.8263 (pt0) REVERT: I 426 SER cc_start: 0.9535 (t) cc_final: 0.9182 (p) REVERT: I 455 ASN cc_start: 0.8974 (m-40) cc_final: 0.8496 (m-40) REVERT: I 465 MET cc_start: 0.9403 (mmm) cc_final: 0.9168 (mmm) REVERT: I 467 ASP cc_start: 0.8756 (m-30) cc_final: 0.8492 (p0) REVERT: I 494 ASN cc_start: 0.9340 (m110) cc_final: 0.9007 (m-40) REVERT: I 520 ASP cc_start: 0.8940 (m-30) cc_final: 0.8694 (m-30) REVERT: K 179 MET cc_start: 0.9343 (tpp) cc_final: 0.8810 (tpp) REVERT: K 213 GLN cc_start: 0.9008 (mm110) cc_final: 0.8253 (mm110) REVERT: K 218 LYS cc_start: 0.9402 (mmmm) cc_final: 0.9116 (mtmm) REVERT: K 232 ASP cc_start: 0.9620 (m-30) cc_final: 0.9286 (m-30) REVERT: K 235 TYR cc_start: 0.9072 (t80) cc_final: 0.8501 (t80) REVERT: K 236 GLU cc_start: 0.9512 (mm-30) cc_final: 0.9166 (mm-30) REVERT: K 293 TYR cc_start: 0.9126 (t80) cc_final: 0.7443 (t80) REVERT: K 312 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7692 (mt-10) REVERT: K 361 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.8655 (t80) REVERT: K 370 TYR cc_start: 0.8975 (t80) cc_final: 0.8706 (t80) REVERT: K 407 MET cc_start: 0.8641 (tmm) cc_final: 0.8275 (tmm) REVERT: K 416 GLN cc_start: 0.9370 (mt0) cc_final: 0.9075 (mt0) REVERT: K 421 GLU cc_start: 0.8387 (pt0) cc_final: 0.8046 (pt0) REVERT: K 424 CYS cc_start: 0.8782 (m) cc_final: 0.8391 (m) REVERT: K 430 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8669 (mpp) REVERT: K 436 ASN cc_start: 0.9238 (t0) cc_final: 0.8971 (t0) REVERT: K 446 ARG cc_start: 0.8338 (ttp80) cc_final: 0.7205 (ttp80) REVERT: K 455 ASN cc_start: 0.9203 (m-40) cc_final: 0.8857 (m110) REVERT: K 467 ASP cc_start: 0.9455 (OUTLIER) cc_final: 0.9115 (p0) REVERT: K 516 HIS cc_start: 0.8245 (t-90) cc_final: 0.7560 (t-90) REVERT: F 140 GLU cc_start: 0.8664 (pm20) cc_final: 0.8365 (pm20) REVERT: F 194 MET cc_start: 0.7189 (tpp) cc_final: 0.6957 (tpp) REVERT: F 196 ASP cc_start: 0.8389 (t70) cc_final: 0.7939 (t70) REVERT: F 213 GLN cc_start: 0.8964 (mm110) cc_final: 0.8144 (mm-40) REVERT: F 215 PHE cc_start: 0.8740 (m-80) cc_final: 0.8503 (m-80) REVERT: F 216 ARG cc_start: 0.8507 (mtp180) cc_final: 0.7870 (mtp180) REVERT: F 233 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8611 (mt-10) REVERT: F 236 GLU cc_start: 0.9475 (mm-30) cc_final: 0.8899 (mm-30) REVERT: F 277 ASP cc_start: 0.9136 (OUTLIER) cc_final: 0.8393 (p0) REVERT: F 279 LYS cc_start: 0.9573 (mmmt) cc_final: 0.9061 (tppt) REVERT: F 347 GLN cc_start: 0.8516 (mp10) cc_final: 0.8133 (mp10) REVERT: F 379 GLN cc_start: 0.9457 (mm110) cc_final: 0.9188 (mm110) REVERT: F 382 ARG cc_start: 0.9419 (ttp80) cc_final: 0.9119 (mtp-110) REVERT: F 421 GLU cc_start: 0.8605 (pt0) cc_final: 0.8018 (pt0) REVERT: F 425 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8660 (mt-10) REVERT: F 454 ARG cc_start: 0.9296 (ttp-110) cc_final: 0.9014 (ttp-110) REVERT: F 499 MET cc_start: 0.8459 (tpp) cc_final: 0.8187 (tpp) REVERT: F 517 PHE cc_start: 0.9446 (t80) cc_final: 0.9242 (t80) REVERT: H 194 MET cc_start: 0.6679 (tpp) cc_final: 0.5813 (tpt) REVERT: H 213 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8510 (mm-40) REVERT: H 215 PHE cc_start: 0.8318 (m-80) cc_final: 0.7883 (m-80) REVERT: H 232 ASP cc_start: 0.9608 (m-30) cc_final: 0.9061 (m-30) REVERT: H 236 GLU cc_start: 0.9352 (mm-30) cc_final: 0.8992 (mm-30) REVERT: H 252 GLN cc_start: 0.8439 (tp40) cc_final: 0.8009 (tp-100) REVERT: H 255 LYS cc_start: 0.9488 (mttp) cc_final: 0.9243 (mtmm) REVERT: H 293 TYR cc_start: 0.8834 (t80) cc_final: 0.8555 (t80) REVERT: H 308 TYR cc_start: 0.9127 (m-80) cc_final: 0.8590 (m-10) REVERT: H 320 LYS cc_start: 0.9048 (tppt) cc_final: 0.8641 (tppt) REVERT: H 328 LYS cc_start: 0.8842 (mtpp) cc_final: 0.8501 (mtpt) REVERT: H 331 ASN cc_start: 0.9016 (OUTLIER) cc_final: 0.8422 (p0) REVERT: H 396 LYS cc_start: 0.9058 (tttt) cc_final: 0.8832 (tttm) REVERT: H 397 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8808 (tm-30) REVERT: H 440 CYS cc_start: 0.8479 (t) cc_final: 0.8013 (t) REVERT: H 446 ARG cc_start: 0.9139 (tmm-80) cc_final: 0.8724 (tpp80) REVERT: H 455 ASN cc_start: 0.9020 (m-40) cc_final: 0.8735 (m-40) REVERT: H 471 GLN cc_start: 0.9422 (tp-100) cc_final: 0.9058 (mm-40) REVERT: H 508 MET cc_start: 0.8433 (tpt) cc_final: 0.8204 (tpt) REVERT: J 180 ASP cc_start: 0.9348 (p0) cc_final: 0.9145 (p0) REVERT: J 215 PHE cc_start: 0.8875 (m-80) cc_final: 0.8638 (m-80) REVERT: J 232 ASP cc_start: 0.9483 (m-30) cc_final: 0.9176 (m-30) REVERT: J 233 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8600 (mt-10) REVERT: J 236 GLU cc_start: 0.9501 (mm-30) cc_final: 0.9140 (mm-30) REVERT: J 245 LYS cc_start: 0.8773 (mtmm) cc_final: 0.8565 (mmmm) REVERT: J 277 ASP cc_start: 0.9056 (OUTLIER) cc_final: 0.8360 (p0) REVERT: J 303 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8811 (tm-30) REVERT: J 320 LYS cc_start: 0.9147 (tppp) cc_final: 0.8732 (tppt) REVERT: J 347 GLN cc_start: 0.8627 (mp10) cc_final: 0.8193 (mp10) REVERT: J 382 ARG cc_start: 0.9010 (ptm-80) cc_final: 0.8810 (ptm160) REVERT: J 407 MET cc_start: 0.8598 (tmm) cc_final: 0.8252 (tmm) REVERT: J 421 GLU cc_start: 0.8540 (pt0) cc_final: 0.7942 (pt0) REVERT: J 454 ARG cc_start: 0.9300 (ttp-110) cc_final: 0.9056 (ttp-110) REVERT: J 499 MET cc_start: 0.8894 (tpt) cc_final: 0.8216 (tpt) REVERT: L 172 ASP cc_start: 0.8553 (t0) cc_final: 0.8197 (t0) REVERT: L 194 MET cc_start: 0.6545 (tpt) cc_final: 0.4833 (pmm) REVERT: L 218 LYS cc_start: 0.8718 (ttpp) cc_final: 0.8200 (ptmm) REVERT: L 233 GLU cc_start: 0.9446 (mm-30) cc_final: 0.8873 (tp30) REVERT: L 285 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8306 (mm-40) REVERT: L 320 LYS cc_start: 0.9064 (tppt) cc_final: 0.8589 (tppt) REVERT: L 331 ASN cc_start: 0.9004 (OUTLIER) cc_final: 0.8557 (p0) REVERT: L 361 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.8082 (t80) REVERT: L 387 ARG cc_start: 0.9143 (mmm-85) cc_final: 0.8847 (mmm-85) REVERT: L 446 ARG cc_start: 0.9098 (tmm-80) cc_final: 0.8794 (tpp80) REVERT: D 602 GLN cc_start: 0.6783 (OUTLIER) cc_final: 0.5268 (pp30) outliers start: 222 outliers final: 158 residues processed: 1870 average time/residue: 0.5150 time to fit residues: 1571.3434 Evaluate side-chains 1910 residues out of total 4020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1732 time to evaluate : 4.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 259 ASP 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 361 PHE 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 434 LEU Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 278 THR 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 331 ASN Chi-restraints excluded: chain B residue 361 PHE 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 231 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 259 ASP 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 434 LEU 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 166 THR Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain D residue 331 ASN 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 510 ASN Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 289 LYS Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 312 GLU Chi-restraints excluded: chain E residue 386 ASP 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 462 SER Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 496 MET Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain G residue 242 SER Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 283 CYS Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 326 ASP Chi-restraints excluded: chain G residue 361 PHE Chi-restraints excluded: chain G residue 374 SER Chi-restraints excluded: chain G residue 380 SER Chi-restraints excluded: chain G residue 381 GLU Chi-restraints excluded: chain G residue 384 SER Chi-restraints excluded: chain G residue 386 ASP Chi-restraints excluded: chain G residue 419 SER Chi-restraints excluded: chain G residue 458 SER Chi-restraints excluded: chain G residue 462 SER Chi-restraints excluded: chain G residue 505 LEU Chi-restraints excluded: chain G residue 523 SER Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 207 ASN Chi-restraints excluded: chain I residue 266 CYS Chi-restraints excluded: chain I residue 283 CYS Chi-restraints excluded: chain I residue 286 SER 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 386 ASP Chi-restraints excluded: chain I residue 419 SER 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 I residue 511 SER Chi-restraints excluded: chain K residue 172 ASP 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 386 ASP Chi-restraints excluded: chain K residue 419 SER Chi-restraints excluded: chain K residue 430 MET Chi-restraints excluded: chain K residue 458 SER Chi-restraints excluded: chain K residue 467 ASP Chi-restraints excluded: chain K residue 505 LEU Chi-restraints excluded: chain K residue 511 SER 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 277 ASP 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 F residue 458 SER Chi-restraints excluded: chain H residue 141 ASP 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 218 LYS Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 331 ASN Chi-restraints excluded: chain H residue 360 GLN Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 420 ILE 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 467 ASP Chi-restraints excluded: chain H residue 510 ASN Chi-restraints excluded: chain H residue 512 VAL Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 231 ILE Chi-restraints excluded: chain J residue 277 ASP Chi-restraints excluded: chain J residue 325 GLU Chi-restraints excluded: chain J residue 380 SER Chi-restraints excluded: chain J residue 386 ASP Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 458 SER Chi-restraints excluded: chain J residue 467 ASP 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 331 ASN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 425 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 251 optimal weight: 0.9990 chunk 322 optimal weight: 0.6980 chunk 249 optimal weight: 0.0070 chunk 371 optimal weight: 4.9990 chunk 246 optimal weight: 1.9990 chunk 439 optimal weight: 0.6980 chunk 275 optimal weight: 0.5980 chunk 267 optimal weight: 8.9990 chunk 202 optimal weight: 5.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 ASN G 298 ASN ** G 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 271 GLN K 375 ASN F 252 GLN F 360 GLN F 519 HIS H 324 ASN ** H 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 519 HIS L 306 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 36972 Z= 0.185 Angle : 0.658 12.351 49932 Z= 0.327 Chirality : 0.044 0.255 5544 Planarity : 0.004 0.046 6408 Dihedral : 4.874 65.690 4929 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.95 % Favored : 93.98 % Rotamer: Outliers : 4.33 % Allowed : 28.68 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.13), residues: 4620 helix: 1.29 (0.11), residues: 2388 sheet: -0.33 (0.30), residues: 384 loop : -0.06 (0.16), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 501 HIS 0.005 0.001 HIS F 475 PHE 0.055 0.001 PHE D 224 TYR 0.026 0.001 TYR J 293 ARG 0.008 0.000 ARG I 446 *********************** 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 1976 residues out of total 4020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1802 time to evaluate : 4.434 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: 0.9278 (mtmt) cc_final: 0.9004 (mtmm) REVERT: A 177 GLU cc_start: 0.8735 (pp20) cc_final: 0.8485 (pp20) REVERT: A 194 MET cc_start: 0.6552 (tpp) cc_final: 0.5590 (tpp) REVERT: A 213 GLN cc_start: 0.9109 (mm-40) cc_final: 0.8649 (mm-40) REVERT: A 236 GLU cc_start: 0.9617 (mm-30) cc_final: 0.9325 (mm-30) REVERT: A 245 LYS cc_start: 0.9039 (mmmt) cc_final: 0.8644 (tppt) REVERT: A 252 GLN cc_start: 0.9219 (tp40) cc_final: 0.8961 (tp40) REVERT: A 260 LEU cc_start: 0.9057 (mt) cc_final: 0.8825 (mp) REVERT: A 272 ARG cc_start: 0.8283 (ptm160) cc_final: 0.7958 (ptm160) REVERT: A 277 ASP cc_start: 0.8878 (m-30) cc_final: 0.8575 (p0) REVERT: A 293 TYR cc_start: 0.9104 (t80) cc_final: 0.8689 (t80) REVERT: A 306 HIS cc_start: 0.8657 (m-70) cc_final: 0.8352 (m-70) REVERT: A 320 LYS cc_start: 0.9047 (tppt) cc_final: 0.8644 (tppt) REVERT: A 357 TYR cc_start: 0.8795 (t80) cc_final: 0.8509 (t80) REVERT: A 360 GLN cc_start: 0.9280 (tm130) cc_final: 0.8909 (tm-30) REVERT: A 365 MET cc_start: 0.9383 (ttm) cc_final: 0.8694 (tmm) REVERT: A 375 ASN cc_start: 0.8760 (t0) cc_final: 0.8347 (t0) REVERT: A 415 PHE cc_start: 0.9185 (m-80) cc_final: 0.8817 (m-80) REVERT: A 421 GLU cc_start: 0.8404 (pt0) cc_final: 0.7941 (pt0) REVERT: A 434 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8608 (pp) REVERT: A 445 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8788 (mt-10) REVERT: A 499 MET cc_start: 0.8465 (tpp) cc_final: 0.8110 (tpp) REVERT: A 500 CYS cc_start: 0.7911 (m) cc_final: 0.7563 (m) REVERT: B 196 ASP cc_start: 0.7289 (t0) cc_final: 0.6964 (t0) REVERT: B 213 GLN cc_start: 0.9059 (mm110) cc_final: 0.8526 (tp-100) REVERT: B 218 LYS cc_start: 0.9586 (mmmm) cc_final: 0.9132 (mtmm) REVERT: B 232 ASP cc_start: 0.9732 (m-30) cc_final: 0.9165 (m-30) REVERT: B 236 GLU cc_start: 0.9492 (mm-30) cc_final: 0.9066 (mm-30) REVERT: B 285 GLN cc_start: 0.8582 (mm-40) cc_final: 0.7936 (mm-40) REVERT: B 297 VAL cc_start: 0.9671 (t) cc_final: 0.9369 (m) REVERT: B 331 ASN cc_start: 0.9097 (OUTLIER) cc_final: 0.8832 (p0) REVERT: B 361 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.8558 (t80) REVERT: B 394 TYR cc_start: 0.9310 (t80) cc_final: 0.9011 (t80) REVERT: B 407 MET cc_start: 0.8521 (tmm) cc_final: 0.8263 (tmm) REVERT: B 421 GLU cc_start: 0.8551 (pt0) cc_final: 0.8167 (pt0) REVERT: B 424 CYS cc_start: 0.9065 (m) cc_final: 0.8840 (m) REVERT: B 426 SER cc_start: 0.9455 (t) cc_final: 0.9204 (p) REVERT: B 467 ASP cc_start: 0.9260 (OUTLIER) cc_final: 0.8935 (p0) REVERT: C 172 ASP cc_start: 0.8838 (t0) cc_final: 0.7880 (t70) REVERT: C 175 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8461 (pp) REVERT: C 179 MET cc_start: 0.7743 (ptp) cc_final: 0.7045 (ptp) REVERT: C 194 MET cc_start: 0.9072 (tpp) cc_final: 0.8484 (tpp) REVERT: C 213 GLN cc_start: 0.9008 (tp40) cc_final: 0.8764 (tp40) REVERT: C 227 PHE cc_start: 0.9663 (t80) cc_final: 0.9325 (t80) REVERT: C 246 VAL cc_start: 0.7992 (OUTLIER) cc_final: 0.7413 (t) REVERT: C 260 LEU cc_start: 0.9065 (mt) cc_final: 0.8763 (mp) REVERT: C 272 ARG cc_start: 0.8264 (ptm160) cc_final: 0.8036 (ptm160) REVERT: C 277 ASP cc_start: 0.8892 (m-30) cc_final: 0.8610 (p0) REVERT: C 375 ASN cc_start: 0.8857 (t0) cc_final: 0.8496 (t0) REVERT: C 381 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8529 (tm-30) REVERT: C 415 PHE cc_start: 0.9024 (m-80) cc_final: 0.8118 (m-10) REVERT: C 416 GLN cc_start: 0.9085 (mt0) cc_final: 0.8861 (mt0) REVERT: C 421 GLU cc_start: 0.8230 (pt0) cc_final: 0.7882 (pt0) REVERT: C 426 SER cc_start: 0.9515 (t) cc_final: 0.9296 (p) REVERT: C 445 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8732 (mt-10) REVERT: C 467 ASP cc_start: 0.9444 (p0) cc_final: 0.8395 (p0) REVERT: C 498 MET cc_start: 0.8013 (ttm) cc_final: 0.7787 (ttm) REVERT: C 508 MET cc_start: 0.9146 (mtt) cc_final: 0.8478 (mtt) REVERT: D 140 GLU cc_start: 0.8686 (pm20) cc_final: 0.8370 (pp20) REVERT: D 172 ASP cc_start: 0.9045 (t0) cc_final: 0.8676 (t70) REVERT: D 213 GLN cc_start: 0.9203 (mm110) cc_final: 0.8942 (mm-40) REVERT: D 224 PHE cc_start: 0.9092 (t80) cc_final: 0.8690 (t80) REVERT: D 232 ASP cc_start: 0.9763 (m-30) cc_final: 0.9424 (m-30) REVERT: D 236 GLU cc_start: 0.9528 (mm-30) cc_final: 0.9139 (mm-30) REVERT: D 246 VAL cc_start: 0.8308 (OUTLIER) cc_final: 0.7657 (t) REVERT: D 260 LEU cc_start: 0.9434 (tp) cc_final: 0.8746 (tp) REVERT: D 277 ASP cc_start: 0.9142 (m-30) cc_final: 0.8678 (p0) REVERT: D 279 LYS cc_start: 0.9665 (mmmm) cc_final: 0.9390 (mmmm) REVERT: D 293 TYR cc_start: 0.9090 (t80) cc_final: 0.8863 (t80) REVERT: D 303 GLU cc_start: 0.9237 (tm-30) cc_final: 0.8976 (tm-30) REVERT: D 379 GLN cc_start: 0.9502 (mm-40) cc_final: 0.9040 (mm-40) REVERT: D 394 TYR cc_start: 0.9492 (t80) cc_final: 0.9137 (t80) REVERT: D 397 GLU cc_start: 0.9328 (tm-30) cc_final: 0.8947 (tm-30) REVERT: D 414 TYR cc_start: 0.9235 (t80) cc_final: 0.8498 (t80) REVERT: D 421 GLU cc_start: 0.8396 (pt0) cc_final: 0.7882 (pt0) REVERT: D 436 ASN cc_start: 0.8674 (t0) cc_final: 0.8410 (t0) REVERT: D 454 ARG cc_start: 0.8989 (ttp80) cc_final: 0.8739 (ttp80) REVERT: E 172 ASP cc_start: 0.8946 (t0) cc_final: 0.8467 (t0) REVERT: E 183 ARG cc_start: 0.8821 (mmm-85) cc_final: 0.8462 (ttp-110) REVERT: E 213 GLN cc_start: 0.9215 (mm110) cc_final: 0.8929 (mm-40) REVERT: E 271 GLN cc_start: 0.8395 (pt0) cc_final: 0.7920 (pt0) REVERT: E 331 ASN cc_start: 0.8901 (p0) cc_final: 0.7994 (p0) REVERT: E 365 MET cc_start: 0.9129 (ttm) cc_final: 0.8718 (ttm) REVERT: E 379 GLN cc_start: 0.8832 (mm110) cc_final: 0.6752 (tt0) REVERT: E 382 ARG cc_start: 0.9519 (ttp80) cc_final: 0.9014 (mtp85) REVERT: E 396 LYS cc_start: 0.9489 (tttt) cc_final: 0.9256 (ttmm) REVERT: E 407 MET cc_start: 0.8793 (tmm) cc_final: 0.8479 (tmm) REVERT: E 421 GLU cc_start: 0.8634 (pt0) cc_final: 0.8333 (pt0) REVERT: E 424 CYS cc_start: 0.9272 (m) cc_final: 0.8734 (t) REVERT: E 426 SER cc_start: 0.9452 (t) cc_final: 0.9211 (p) REVERT: E 430 MET cc_start: 0.8785 (mmt) cc_final: 0.8561 (mmp) REVERT: E 455 ASN cc_start: 0.8969 (m-40) cc_final: 0.8517 (m-40) REVERT: E 463 CYS cc_start: 0.8147 (p) cc_final: 0.7867 (p) REVERT: E 478 LEU cc_start: 0.9623 (mt) cc_final: 0.9356 (mt) REVERT: E 520 ASP cc_start: 0.8832 (m-30) cc_final: 0.8337 (m-30) REVERT: G 179 MET cc_start: 0.9244 (tpp) cc_final: 0.8858 (tpp) REVERT: G 181 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8285 (ttm) REVERT: G 194 MET cc_start: 0.5083 (tpp) cc_final: 0.4710 (tpp) REVERT: G 227 PHE cc_start: 0.9629 (t80) cc_final: 0.9305 (t80) REVERT: G 232 ASP cc_start: 0.9644 (m-30) cc_final: 0.9059 (m-30) REVERT: G 235 TYR cc_start: 0.9215 (t80) cc_final: 0.8730 (t80) REVERT: G 236 GLU cc_start: 0.9556 (mm-30) cc_final: 0.9178 (mm-30) REVERT: G 293 TYR cc_start: 0.9078 (t80) cc_final: 0.7488 (t80) REVERT: G 300 LEU cc_start: 0.9511 (mm) cc_final: 0.9201 (mt) REVERT: G 312 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8035 (mt-10) REVERT: G 320 LYS cc_start: 0.9156 (tppt) cc_final: 0.8868 (tppt) REVERT: G 382 ARG cc_start: 0.9478 (ttp80) cc_final: 0.9249 (mtp180) REVERT: G 407 MET cc_start: 0.8495 (tmm) cc_final: 0.8223 (tmm) REVERT: G 421 GLU cc_start: 0.8235 (pt0) cc_final: 0.7952 (pt0) REVERT: G 424 CYS cc_start: 0.8994 (m) cc_final: 0.8641 (m) REVERT: G 436 ASN cc_start: 0.9231 (t0) cc_final: 0.8975 (t0) REVERT: G 446 ARG cc_start: 0.8303 (ttp80) cc_final: 0.7127 (ttp80) REVERT: G 451 GLU cc_start: 0.8178 (mp0) cc_final: 0.7916 (mp0) REVERT: G 454 ARG cc_start: 0.8840 (ttp-110) cc_final: 0.8578 (ttp-110) REVERT: G 455 ASN cc_start: 0.9251 (m-40) cc_final: 0.8697 (m110) REVERT: G 499 MET cc_start: 0.8493 (tpp) cc_final: 0.8213 (tpp) REVERT: G 516 HIS cc_start: 0.8094 (t-90) cc_final: 0.7451 (t-90) REVERT: I 140 GLU cc_start: 0.8726 (pm20) cc_final: 0.8400 (pp20) REVERT: I 172 ASP cc_start: 0.9025 (t0) cc_final: 0.8539 (t0) REVERT: I 183 ARG cc_start: 0.9102 (mtp85) cc_final: 0.8429 (ptp-110) REVERT: I 194 MET cc_start: 0.7334 (tpp) cc_final: 0.6693 (tpp) REVERT: I 213 GLN cc_start: 0.9188 (mm-40) cc_final: 0.8668 (tp40) REVERT: I 218 LYS cc_start: 0.9267 (mmmm) cc_final: 0.8920 (mtmm) REVERT: I 236 GLU cc_start: 0.9590 (mm-30) cc_final: 0.9121 (mm-30) REVERT: I 249 TYR cc_start: 0.9174 (p90) cc_final: 0.8773 (p90) REVERT: I 261 TRP cc_start: 0.9155 (t-100) cc_final: 0.8841 (t-100) REVERT: I 277 ASP cc_start: 0.8947 (m-30) cc_final: 0.8602 (p0) REVERT: I 323 LEU cc_start: 0.9362 (mp) cc_final: 0.9135 (mp) REVERT: I 331 ASN cc_start: 0.8956 (p0) cc_final: 0.8378 (p0) REVERT: I 379 GLN cc_start: 0.8837 (mm110) cc_final: 0.6755 (tt0) REVERT: I 382 ARG cc_start: 0.9494 (ttp80) cc_final: 0.9014 (mtp85) REVERT: I 407 MET cc_start: 0.8718 (tmm) cc_final: 0.8329 (tmm) REVERT: I 421 GLU cc_start: 0.8631 (pt0) cc_final: 0.8295 (pt0) REVERT: I 426 SER cc_start: 0.9570 (t) cc_final: 0.9256 (p) REVERT: I 455 ASN cc_start: 0.8957 (m-40) cc_final: 0.8508 (m-40) REVERT: I 465 MET cc_start: 0.9372 (mmm) cc_final: 0.9164 (mmm) REVERT: I 467 ASP cc_start: 0.8764 (m-30) cc_final: 0.8468 (p0) REVERT: I 494 ASN cc_start: 0.9294 (m110) cc_final: 0.8950 (m-40) REVERT: I 520 ASP cc_start: 0.8899 (m-30) cc_final: 0.8680 (m-30) REVERT: K 179 MET cc_start: 0.9284 (tpp) cc_final: 0.8742 (tpp) REVERT: K 213 GLN cc_start: 0.9010 (mm110) cc_final: 0.8241 (mm110) REVERT: K 218 LYS cc_start: 0.9386 (mmmm) cc_final: 0.9051 (mtmm) REVERT: K 235 TYR cc_start: 0.9070 (t80) cc_final: 0.8460 (t80) REVERT: K 236 GLU cc_start: 0.9509 (mm-30) cc_final: 0.9150 (mm-30) REVERT: K 293 TYR cc_start: 0.9085 (t80) cc_final: 0.7449 (t80) REVERT: K 312 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: K 318 PHE cc_start: 0.9206 (p90) cc_final: 0.8844 (p90) REVERT: K 361 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8637 (t80) REVERT: K 370 TYR cc_start: 0.8928 (t80) cc_final: 0.8701 (t80) REVERT: K 407 MET cc_start: 0.8643 (tmm) cc_final: 0.8337 (tmm) REVERT: K 416 GLN cc_start: 0.9315 (mt0) cc_final: 0.9051 (mt0) REVERT: K 421 GLU cc_start: 0.8309 (pt0) cc_final: 0.7956 (pt0) REVERT: K 424 CYS cc_start: 0.8759 (m) cc_final: 0.8391 (m) REVERT: K 430 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8461 (mpp) REVERT: K 436 ASN cc_start: 0.9206 (t0) cc_final: 0.8928 (t0) REVERT: K 446 ARG cc_start: 0.8445 (ttp80) cc_final: 0.7366 (ttp80) REVERT: K 455 ASN cc_start: 0.9205 (m-40) cc_final: 0.8670 (m110) REVERT: K 467 ASP cc_start: 0.9454 (OUTLIER) cc_final: 0.9149 (p0) REVERT: K 516 HIS cc_start: 0.8077 (t-90) cc_final: 0.7394 (t-90) REVERT: F 140 GLU cc_start: 0.8665 (pm20) cc_final: 0.8326 (pm20) REVERT: F 194 MET cc_start: 0.7233 (tpp) cc_final: 0.7026 (tpp) REVERT: F 196 ASP cc_start: 0.8042 (t70) cc_final: 0.7593 (t70) REVERT: F 212 THR cc_start: 0.9455 (p) cc_final: 0.8463 (t) REVERT: F 213 GLN cc_start: 0.8981 (mm110) cc_final: 0.8072 (mm110) REVERT: F 215 PHE cc_start: 0.8664 (m-80) cc_final: 0.8446 (m-80) REVERT: F 216 ARG cc_start: 0.8507 (mtp180) cc_final: 0.7520 (mtp180) REVERT: F 233 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8579 (mt-10) REVERT: F 236 GLU cc_start: 0.9501 (mm-30) cc_final: 0.8970 (mm-30) REVERT: F 252 GLN cc_start: 0.9091 (tp40) cc_final: 0.8839 (tp40) REVERT: F 277 ASP cc_start: 0.9072 (OUTLIER) cc_final: 0.8193 (p0) REVERT: F 279 LYS cc_start: 0.9565 (mmmt) cc_final: 0.9055 (tppt) REVERT: F 347 GLN cc_start: 0.8455 (mp10) cc_final: 0.8064 (mp10) REVERT: F 382 ARG cc_start: 0.9412 (ttp80) cc_final: 0.9119 (mtp-110) REVERT: F 421 GLU cc_start: 0.8594 (pt0) cc_final: 0.7991 (pt0) REVERT: F 425 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8644 (mt-10) REVERT: F 454 ARG cc_start: 0.9282 (ttp-110) cc_final: 0.9004 (ttp-110) REVERT: F 510 ASN cc_start: 0.8381 (m110) cc_final: 0.8163 (m110) REVERT: H 194 MET cc_start: 0.6776 (tpp) cc_final: 0.6389 (tpt) REVERT: H 213 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8551 (mm-40) REVERT: H 215 PHE cc_start: 0.8306 (m-80) cc_final: 0.7900 (m-80) REVERT: H 232 ASP cc_start: 0.9586 (m-30) cc_final: 0.9031 (m-30) REVERT: H 233 GLU cc_start: 0.9367 (tt0) cc_final: 0.9112 (tt0) REVERT: H 236 GLU cc_start: 0.9336 (mm-30) cc_final: 0.8992 (mm-30) REVERT: H 308 TYR cc_start: 0.9062 (m-80) cc_final: 0.8570 (m-10) REVERT: H 320 LYS cc_start: 0.9027 (tppt) cc_final: 0.8616 (tppt) REVERT: H 328 LYS cc_start: 0.8913 (mtpp) cc_final: 0.8560 (mtpt) REVERT: H 331 ASN cc_start: 0.8970 (OUTLIER) cc_final: 0.8309 (p0) REVERT: H 333 MET cc_start: 0.8805 (mmp) cc_final: 0.8483 (mmp) REVERT: H 347 GLN cc_start: 0.8771 (mp10) cc_final: 0.8394 (pm20) REVERT: H 394 TYR cc_start: 0.9298 (t80) cc_final: 0.8864 (t80) REVERT: H 396 LYS cc_start: 0.9068 (tttt) cc_final: 0.8821 (tttm) REVERT: H 397 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8643 (tm-30) REVERT: H 440 CYS cc_start: 0.8543 (t) cc_final: 0.8143 (t) REVERT: H 446 ARG cc_start: 0.9078 (tmm-80) cc_final: 0.8742 (tpp80) REVERT: H 455 ASN cc_start: 0.9011 (m-40) cc_final: 0.8726 (m-40) REVERT: H 471 GLN cc_start: 0.9395 (tp-100) cc_final: 0.8973 (tp-100) REVERT: J 213 GLN cc_start: 0.8959 (tp40) cc_final: 0.8556 (tp40) REVERT: J 218 LYS cc_start: 0.9301 (mmmm) cc_final: 0.9037 (mtmm) REVERT: J 232 ASP cc_start: 0.9484 (m-30) cc_final: 0.9004 (m-30) REVERT: J 233 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8560 (mt-10) REVERT: J 236 GLU cc_start: 0.9469 (mm-30) cc_final: 0.9119 (mm-30) REVERT: J 245 LYS cc_start: 0.8752 (mtmm) cc_final: 0.8512 (mmmm) REVERT: J 279 LYS cc_start: 0.9549 (tppt) cc_final: 0.9302 (mmmt) REVERT: J 303 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8778 (tm-30) REVERT: J 320 LYS cc_start: 0.9082 (tppp) cc_final: 0.8589 (tppt) REVERT: J 347 GLN cc_start: 0.8594 (mp10) cc_final: 0.8133 (mp10) REVERT: J 382 ARG cc_start: 0.8864 (ptm-80) cc_final: 0.8642 (ptm160) REVERT: J 407 MET cc_start: 0.8470 (tmm) cc_final: 0.8221 (tmm) REVERT: J 418 CYS cc_start: 0.8931 (m) cc_final: 0.8069 (t) REVERT: J 421 GLU cc_start: 0.8462 (pt0) cc_final: 0.7834 (pt0) REVERT: J 499 MET cc_start: 0.8984 (tpt) cc_final: 0.8415 (tpt) REVERT: L 194 MET cc_start: 0.6565 (tpt) cc_final: 0.4863 (pmm) REVERT: L 218 LYS cc_start: 0.8719 (ttpp) cc_final: 0.8242 (ptmm) REVERT: L 223 ASP cc_start: 0.8497 (p0) cc_final: 0.8254 (p0) REVERT: L 285 GLN cc_start: 0.8524 (mm-40) cc_final: 0.8225 (mm-40) REVERT: L 320 LYS cc_start: 0.9047 (tppt) cc_final: 0.8604 (tppt) REVERT: L 331 ASN cc_start: 0.8955 (OUTLIER) cc_final: 0.8464 (p0) REVERT: L 361 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8001 (t80) REVERT: L 387 ARG cc_start: 0.9072 (mmm-85) cc_final: 0.8759 (mmm-85) REVERT: L 394 TYR cc_start: 0.9264 (t80) cc_final: 0.8936 (t80) REVERT: L 446 ARG cc_start: 0.9037 (tmm-80) cc_final: 0.8790 (tpp80) outliers start: 174 outliers final: 131 residues processed: 1861 average time/residue: 0.4881 time to fit residues: 1477.8407 Evaluate side-chains 1914 residues out of total 4020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1767 time to evaluate : 4.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 295 ILE 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 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 434 LEU Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain B residue 278 THR 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 331 ASN Chi-restraints excluded: chain B residue 361 PHE 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 165 SER Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 259 ASP 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 D residue 157 HIS Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 507 LYS Chi-restraints excluded: chain D residue 510 ASN Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain E residue 289 LYS Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 312 GLU Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 458 SER Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain E residue 496 MET Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 181 MET Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 283 CYS Chi-restraints excluded: chain G residue 298 ASN Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 326 ASP Chi-restraints excluded: chain G residue 380 SER Chi-restraints excluded: chain G residue 381 GLU Chi-restraints excluded: chain G residue 384 SER Chi-restraints excluded: chain G residue 386 ASP Chi-restraints excluded: chain G residue 458 SER Chi-restraints excluded: chain G residue 505 LEU Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 283 CYS Chi-restraints excluded: chain I residue 286 SER 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 386 ASP 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 I residue 511 SER Chi-restraints excluded: chain K residue 194 MET Chi-restraints excluded: chain K residue 257 SER 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 386 ASP Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 430 MET Chi-restraints excluded: chain K residue 458 SER Chi-restraints excluded: chain K residue 467 ASP Chi-restraints excluded: chain K residue 505 LEU Chi-restraints excluded: chain K residue 508 MET Chi-restraints excluded: chain K residue 523 SER Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 325 GLU 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 F residue 458 SER Chi-restraints excluded: chain H residue 141 ASP 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 246 VAL Chi-restraints excluded: chain H residue 331 ASN Chi-restraints excluded: chain H residue 360 GLN 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 467 ASP Chi-restraints excluded: chain H residue 507 LYS Chi-restraints excluded: chain H residue 510 ASN Chi-restraints excluded: chain H residue 520 ASP Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 196 ASP Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 241 GLN Chi-restraints excluded: chain J residue 386 ASP Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 458 SER Chi-restraints excluded: chain J residue 467 ASP Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 331 ASN Chi-restraints excluded: chain L residue 361 PHE Chi-restraints excluded: chain L residue 362 LEU Chi-restraints excluded: chain L residue 423 THR 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 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 271 optimal weight: 0.7980 chunk 175 optimal weight: 5.9990 chunk 262 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 279 optimal weight: 0.6980 chunk 299 optimal weight: 3.9990 chunk 217 optimal weight: 0.4980 chunk 40 optimal weight: 9.9990 chunk 345 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN C 360 GLN C 455 ASN ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN ** E 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 ASN E 436 ASN E 475 HIS G 271 GLN G 298 ASN ** G 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 375 ASN ** G 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 375 ASN ** F 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 519 HIS ** H 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 519 HIS ** 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 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 519 HIS L 306 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 36972 Z= 0.196 Angle : 0.688 12.005 49932 Z= 0.340 Chirality : 0.044 0.263 5544 Planarity : 0.004 0.047 6408 Dihedral : 4.866 63.491 4929 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.97 % Favored : 93.96 % Rotamer: Outliers : 4.35 % Allowed : 29.43 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.13), residues: 4620 helix: 1.23 (0.11), residues: 2400 sheet: -0.27 (0.30), residues: 384 loop : -0.02 (0.16), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 501 HIS 0.005 0.001 HIS J 475 PHE 0.045 0.001 PHE D 224 TYR 0.025 0.001 TYR J 293 ARG 0.008 0.000 ARG E 446 *********************** 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 1977 residues out of total 4020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1802 time to evaluate : 4.238 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: A 164 LYS cc_start: 0.9291 (mtmt) cc_final: 0.9017 (mtmm) REVERT: A 177 GLU cc_start: 0.8748 (pp20) cc_final: 0.8381 (pp20) REVERT: A 194 MET cc_start: 0.6572 (tpp) cc_final: 0.5553 (tpp) REVERT: A 213 GLN cc_start: 0.9099 (mm-40) cc_final: 0.8699 (mm-40) REVERT: A 219 PHE cc_start: 0.8533 (m-10) cc_final: 0.8181 (m-10) REVERT: A 236 GLU cc_start: 0.9615 (mm-30) cc_final: 0.9327 (mm-30) REVERT: A 245 LYS cc_start: 0.9122 (mmmt) cc_final: 0.8739 (tppt) REVERT: A 260 LEU cc_start: 0.9071 (mt) cc_final: 0.8802 (mp) REVERT: A 272 ARG cc_start: 0.8239 (ptm160) cc_final: 0.7923 (ptm160) REVERT: A 277 ASP cc_start: 0.8887 (m-30) cc_final: 0.8583 (p0) REVERT: A 293 TYR cc_start: 0.9110 (t80) cc_final: 0.8611 (t80) REVERT: A 306 HIS cc_start: 0.8685 (m-70) cc_final: 0.8335 (m-70) REVERT: A 320 LYS cc_start: 0.9025 (tppt) cc_final: 0.8564 (tppt) REVERT: A 357 TYR cc_start: 0.8757 (t80) cc_final: 0.8504 (t80) REVERT: A 360 GLN cc_start: 0.9261 (tm130) cc_final: 0.8936 (tm-30) REVERT: A 361 PHE cc_start: 0.9008 (OUTLIER) cc_final: 0.8128 (t80) REVERT: A 375 ASN cc_start: 0.8684 (t0) cc_final: 0.8378 (t0) REVERT: A 415 PHE cc_start: 0.9180 (m-80) cc_final: 0.8788 (m-80) REVERT: A 421 GLU cc_start: 0.8354 (pt0) cc_final: 0.7914 (pt0) REVERT: A 434 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8593 (pp) REVERT: A 445 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8787 (mt-10) REVERT: A 499 MET cc_start: 0.8449 (tpp) cc_final: 0.8112 (tpp) REVERT: A 500 CYS cc_start: 0.8216 (m) cc_final: 0.7922 (m) REVERT: B 196 ASP cc_start: 0.7275 (t0) cc_final: 0.7055 (t0) REVERT: B 213 GLN cc_start: 0.9028 (mm110) cc_final: 0.8508 (tp-100) REVERT: B 218 LYS cc_start: 0.9579 (mmmm) cc_final: 0.9127 (mtmm) REVERT: B 236 GLU cc_start: 0.9495 (mm-30) cc_final: 0.9066 (mm-30) REVERT: B 285 GLN cc_start: 0.8564 (mm-40) cc_final: 0.7934 (mm-40) REVERT: B 293 TYR cc_start: 0.9019 (t80) cc_final: 0.8798 (t80) REVERT: B 361 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.8550 (t80) REVERT: B 373 PHE cc_start: 0.8533 (t80) cc_final: 0.8065 (t80) REVERT: B 394 TYR cc_start: 0.9339 (t80) cc_final: 0.9085 (t80) REVERT: B 407 MET cc_start: 0.8539 (tmm) cc_final: 0.8264 (tmm) REVERT: B 421 GLU cc_start: 0.8551 (pt0) cc_final: 0.8167 (pt0) REVERT: B 424 CYS cc_start: 0.9038 (m) cc_final: 0.8794 (m) REVERT: B 426 SER cc_start: 0.9460 (t) cc_final: 0.9203 (p) REVERT: B 467 ASP cc_start: 0.9273 (OUTLIER) cc_final: 0.8945 (p0) REVERT: C 172 ASP cc_start: 0.8855 (t0) cc_final: 0.7905 (t70) REVERT: C 175 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8475 (pp) REVERT: C 179 MET cc_start: 0.7799 (ptp) cc_final: 0.7078 (ptp) REVERT: C 213 GLN cc_start: 0.9031 (tp40) cc_final: 0.8683 (tp-100) REVERT: C 246 VAL cc_start: 0.8146 (OUTLIER) cc_final: 0.7642 (t) REVERT: C 260 LEU cc_start: 0.9085 (mt) cc_final: 0.8806 (mp) REVERT: C 272 ARG cc_start: 0.8324 (ptm160) cc_final: 0.8116 (ptm160) REVERT: C 277 ASP cc_start: 0.8914 (m-30) cc_final: 0.8629 (p0) REVERT: C 375 ASN cc_start: 0.8904 (t0) cc_final: 0.8413 (t0) REVERT: C 381 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8257 (tm-30) REVERT: C 415 PHE cc_start: 0.9070 (m-80) cc_final: 0.8093 (m-80) REVERT: C 421 GLU cc_start: 0.8255 (pt0) cc_final: 0.7883 (pt0) REVERT: C 434 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8405 (pp) REVERT: C 445 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8753 (mt-10) REVERT: C 455 ASN cc_start: 0.9097 (m-40) cc_final: 0.8859 (m110) REVERT: C 467 ASP cc_start: 0.9445 (p0) cc_final: 0.8433 (p0) REVERT: C 498 MET cc_start: 0.8305 (ttm) cc_final: 0.8063 (ttm) REVERT: C 508 MET cc_start: 0.9163 (mtt) cc_final: 0.8500 (mtt) REVERT: D 140 GLU cc_start: 0.8695 (pm20) cc_final: 0.8377 (pp20) REVERT: D 172 ASP cc_start: 0.9046 (t0) cc_final: 0.8679 (t70) REVERT: D 216 ARG cc_start: 0.7252 (ptt180) cc_final: 0.6966 (ptt180) REVERT: D 224 PHE cc_start: 0.9102 (t80) cc_final: 0.8728 (t80) REVERT: D 232 ASP cc_start: 0.9763 (m-30) cc_final: 0.9424 (m-30) REVERT: D 236 GLU cc_start: 0.9530 (mm-30) cc_final: 0.9142 (mm-30) REVERT: D 241 GLN cc_start: 0.8247 (mp10) cc_final: 0.7849 (mp10) REVERT: D 246 VAL cc_start: 0.8298 (OUTLIER) cc_final: 0.7640 (t) REVERT: D 260 LEU cc_start: 0.9417 (tp) cc_final: 0.9010 (tp) REVERT: D 263 VAL cc_start: 0.9425 (t) cc_final: 0.9149 (p) REVERT: D 271 GLN cc_start: 0.6704 (pt0) cc_final: 0.6371 (pp30) REVERT: D 279 LYS cc_start: 0.9682 (mmmm) cc_final: 0.9361 (mmmm) REVERT: D 285 GLN cc_start: 0.8571 (mm-40) cc_final: 0.7760 (mm-40) REVERT: D 293 TYR cc_start: 0.9088 (t80) cc_final: 0.8880 (t80) REVERT: D 303 GLU cc_start: 0.9238 (tm-30) cc_final: 0.8960 (tm-30) REVERT: D 360 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8610 (pp30) REVERT: D 382 ARG cc_start: 0.9303 (ttp80) cc_final: 0.8934 (mtp-110) REVERT: D 394 TYR cc_start: 0.9469 (t80) cc_final: 0.9139 (t80) REVERT: D 397 GLU cc_start: 0.9314 (tm-30) cc_final: 0.9014 (tm-30) REVERT: D 414 TYR cc_start: 0.9195 (t80) cc_final: 0.8684 (t80) REVERT: D 421 GLU cc_start: 0.8435 (pt0) cc_final: 0.7900 (pt0) REVERT: D 454 ARG cc_start: 0.8941 (ttp80) cc_final: 0.8686 (ttp80) REVERT: D 471 GLN cc_start: 0.9523 (mm110) cc_final: 0.9300 (tp40) REVERT: E 172 ASP cc_start: 0.8911 (t0) cc_final: 0.8413 (t0) REVERT: E 181 MET cc_start: 0.7787 (tmm) cc_final: 0.7477 (tmm) REVERT: E 183 ARG cc_start: 0.8811 (mmm-85) cc_final: 0.8495 (mtm110) REVERT: E 213 GLN cc_start: 0.9190 (mm110) cc_final: 0.8920 (mm-40) REVERT: E 271 GLN cc_start: 0.8420 (pt0) cc_final: 0.7967 (pt0) REVERT: E 331 ASN cc_start: 0.8942 (p0) cc_final: 0.8026 (p0) REVERT: E 365 MET cc_start: 0.9129 (ttm) cc_final: 0.8720 (ttm) REVERT: E 379 GLN cc_start: 0.8831 (mm110) cc_final: 0.6797 (tt0) REVERT: E 382 ARG cc_start: 0.9520 (ttp80) cc_final: 0.8988 (mtp85) REVERT: E 396 LYS cc_start: 0.9476 (tttt) cc_final: 0.9238 (ttmm) REVERT: E 407 MET cc_start: 0.8839 (tmm) cc_final: 0.8512 (tmm) REVERT: E 421 GLU cc_start: 0.8643 (pt0) cc_final: 0.8354 (pt0) REVERT: E 424 CYS cc_start: 0.9262 (m) cc_final: 0.8760 (t) REVERT: E 426 SER cc_start: 0.9435 (t) cc_final: 0.9181 (p) REVERT: E 455 ASN cc_start: 0.8974 (m-40) cc_final: 0.8523 (m-40) REVERT: E 463 CYS cc_start: 0.8245 (p) cc_final: 0.7915 (p) REVERT: E 478 LEU cc_start: 0.9612 (mt) cc_final: 0.9337 (mt) REVERT: E 520 ASP cc_start: 0.8854 (m-30) cc_final: 0.8324 (m-30) REVERT: G 179 MET cc_start: 0.9218 (tpp) cc_final: 0.8825 (tpp) REVERT: G 194 MET cc_start: 0.5383 (tpp) cc_final: 0.4978 (tpp) REVERT: G 227 PHE cc_start: 0.9636 (t80) cc_final: 0.9312 (t80) REVERT: G 232 ASP cc_start: 0.9648 (m-30) cc_final: 0.9047 (m-30) REVERT: G 235 TYR cc_start: 0.9190 (t80) cc_final: 0.8678 (t80) REVERT: G 236 GLU cc_start: 0.9558 (mm-30) cc_final: 0.9178 (mm-30) REVERT: G 260 LEU cc_start: 0.9222 (tp) cc_final: 0.8727 (mt) REVERT: G 293 TYR cc_start: 0.9125 (t80) cc_final: 0.7368 (t80) REVERT: G 297 VAL cc_start: 0.9698 (t) cc_final: 0.9307 (m) REVERT: G 300 LEU cc_start: 0.9451 (mm) cc_final: 0.9096 (mt) REVERT: G 312 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8020 (mt-10) REVERT: G 320 LYS cc_start: 0.9101 (tppt) cc_final: 0.8533 (tppt) REVERT: G 328 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8561 (mtpp) REVERT: G 382 ARG cc_start: 0.9475 (ttp80) cc_final: 0.9272 (mtp180) REVERT: G 407 MET cc_start: 0.8460 (tmm) cc_final: 0.8179 (tmm) REVERT: G 421 GLU cc_start: 0.8240 (pt0) cc_final: 0.7967 (pt0) REVERT: G 424 CYS cc_start: 0.8966 (m) cc_final: 0.8659 (m) REVERT: G 436 ASN cc_start: 0.9210 (t0) cc_final: 0.8965 (t0) REVERT: G 446 ARG cc_start: 0.8406 (ttp80) cc_final: 0.7216 (ttp80) REVERT: G 451 GLU cc_start: 0.8182 (mp0) cc_final: 0.7919 (mp0) REVERT: G 455 ASN cc_start: 0.9234 (m-40) cc_final: 0.8666 (m110) REVERT: G 499 MET cc_start: 0.8495 (tpp) cc_final: 0.8218 (tpp) REVERT: G 516 HIS cc_start: 0.8101 (t-90) cc_final: 0.7482 (t-90) REVERT: I 140 GLU cc_start: 0.8806 (pm20) cc_final: 0.8454 (tm-30) REVERT: I 172 ASP cc_start: 0.9026 (t0) cc_final: 0.8528 (t0) REVERT: I 183 ARG cc_start: 0.9105 (mtp85) cc_final: 0.8414 (ptp-110) REVERT: I 194 MET cc_start: 0.7319 (tpp) cc_final: 0.6688 (tpp) REVERT: I 213 GLN cc_start: 0.9177 (mm-40) cc_final: 0.8666 (tp-100) REVERT: I 218 LYS cc_start: 0.9280 (mmmm) cc_final: 0.8924 (mtmm) REVERT: I 260 LEU cc_start: 0.9491 (mt) cc_final: 0.9211 (mm) REVERT: I 277 ASP cc_start: 0.8940 (m-30) cc_final: 0.8712 (p0) REVERT: I 323 LEU cc_start: 0.9433 (mp) cc_final: 0.9172 (mp) REVERT: I 331 ASN cc_start: 0.8953 (p0) cc_final: 0.8409 (p0) REVERT: I 379 GLN cc_start: 0.8832 (mm110) cc_final: 0.6822 (tt0) REVERT: I 382 ARG cc_start: 0.9496 (ttp80) cc_final: 0.9005 (mtp85) REVERT: I 407 MET cc_start: 0.8731 (tmm) cc_final: 0.8327 (tmm) REVERT: I 421 GLU cc_start: 0.8639 (pt0) cc_final: 0.8321 (pt0) REVERT: I 424 CYS cc_start: 0.9171 (m) cc_final: 0.8816 (t) REVERT: I 426 SER cc_start: 0.9596 (t) cc_final: 0.9286 (p) REVERT: I 455 ASN cc_start: 0.8964 (m-40) cc_final: 0.8508 (m-40) REVERT: I 465 MET cc_start: 0.9390 (mmm) cc_final: 0.9189 (mmm) REVERT: I 467 ASP cc_start: 0.8787 (m-30) cc_final: 0.8468 (p0) REVERT: I 494 ASN cc_start: 0.9327 (m110) cc_final: 0.9040 (m-40) REVERT: I 520 ASP cc_start: 0.8896 (m-30) cc_final: 0.8689 (m-30) REVERT: K 179 MET cc_start: 0.9289 (tpp) cc_final: 0.9079 (tpp) REVERT: K 213 GLN cc_start: 0.8997 (mm110) cc_final: 0.7816 (mm110) REVERT: K 235 TYR cc_start: 0.9043 (t80) cc_final: 0.8433 (t80) REVERT: K 236 GLU cc_start: 0.9506 (mm-30) cc_final: 0.9146 (mm-30) REVERT: K 260 LEU cc_start: 0.9221 (mt) cc_final: 0.8902 (mp) REVERT: K 293 TYR cc_start: 0.9073 (t80) cc_final: 0.7410 (t80) REVERT: K 312 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7720 (mt-10) REVERT: K 361 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.8605 (t80) REVERT: K 370 TYR cc_start: 0.8927 (t80) cc_final: 0.8709 (t80) REVERT: K 407 MET cc_start: 0.8580 (tmm) cc_final: 0.8295 (tmm) REVERT: K 416 GLN cc_start: 0.9320 (mt0) cc_final: 0.8956 (mt0) REVERT: K 421 GLU cc_start: 0.8375 (pt0) cc_final: 0.8016 (pt0) REVERT: K 424 CYS cc_start: 0.8776 (m) cc_final: 0.8395 (m) REVERT: K 436 ASN cc_start: 0.9183 (t0) cc_final: 0.8913 (t0) REVERT: K 446 ARG cc_start: 0.8358 (ttp80) cc_final: 0.7212 (ttp80) REVERT: K 455 ASN cc_start: 0.9208 (m-40) cc_final: 0.8670 (m110) REVERT: K 467 ASP cc_start: 0.9405 (OUTLIER) cc_final: 0.9103 (p0) REVERT: K 516 HIS cc_start: 0.8137 (t-90) cc_final: 0.7414 (t-90) REVERT: F 140 GLU cc_start: 0.8650 (pm20) cc_final: 0.8223 (pm20) REVERT: F 194 MET cc_start: 0.7380 (tpp) cc_final: 0.7162 (tpp) REVERT: F 196 ASP cc_start: 0.8294 (t70) cc_final: 0.7855 (t70) REVERT: F 212 THR cc_start: 0.9488 (p) cc_final: 0.8580 (t) REVERT: F 213 GLN cc_start: 0.8964 (mm110) cc_final: 0.8055 (mm110) REVERT: F 215 PHE cc_start: 0.8695 (m-80) cc_final: 0.8442 (m-80) REVERT: F 216 ARG cc_start: 0.8504 (mtp180) cc_final: 0.7511 (mtp180) REVERT: F 233 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8574 (mt-10) REVERT: F 236 GLU cc_start: 0.9489 (mm-30) cc_final: 0.8975 (mm-30) REVERT: F 272 ARG cc_start: 0.8816 (ttp-170) cc_final: 0.8571 (mtp180) REVERT: F 277 ASP cc_start: 0.9089 (OUTLIER) cc_final: 0.8217 (p0) REVERT: F 279 LYS cc_start: 0.9587 (mmmt) cc_final: 0.9228 (tppt) REVERT: F 293 TYR cc_start: 0.8841 (t80) cc_final: 0.8627 (t80) REVERT: F 347 GLN cc_start: 0.8453 (mp10) cc_final: 0.8031 (mp10) REVERT: F 382 ARG cc_start: 0.9401 (ttp80) cc_final: 0.9126 (mtp-110) REVERT: F 421 GLU cc_start: 0.8596 (pt0) cc_final: 0.7964 (pt0) REVERT: F 425 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8662 (mt-10) REVERT: F 454 ARG cc_start: 0.9284 (ttp-110) cc_final: 0.9020 (ttp-110) REVERT: F 510 ASN cc_start: 0.8173 (m110) cc_final: 0.7883 (m-40) REVERT: H 194 MET cc_start: 0.7022 (tpp) cc_final: 0.6686 (tpt) REVERT: H 215 PHE cc_start: 0.8303 (m-80) cc_final: 0.7891 (m-80) REVERT: H 232 ASP cc_start: 0.9571 (m-30) cc_final: 0.9040 (m-30) REVERT: H 233 GLU cc_start: 0.9381 (tt0) cc_final: 0.9138 (tt0) REVERT: H 235 TYR cc_start: 0.8965 (t80) cc_final: 0.8750 (t80) REVERT: H 236 GLU cc_start: 0.9314 (mm-30) cc_final: 0.8975 (mm-30) REVERT: H 320 LYS cc_start: 0.8942 (tppt) cc_final: 0.8528 (tppt) REVERT: H 331 ASN cc_start: 0.8934 (OUTLIER) cc_final: 0.8349 (p0) REVERT: H 333 MET cc_start: 0.8787 (mmp) cc_final: 0.8458 (mmp) REVERT: H 347 GLN cc_start: 0.8712 (mp10) cc_final: 0.8361 (pm20) REVERT: H 394 TYR cc_start: 0.9269 (t80) cc_final: 0.8833 (t80) REVERT: H 396 LYS cc_start: 0.9066 (tttt) cc_final: 0.8819 (tttm) REVERT: H 397 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8695 (tm-30) REVERT: H 440 CYS cc_start: 0.8378 (t) cc_final: 0.7886 (t) REVERT: H 446 ARG cc_start: 0.9126 (tmm-80) cc_final: 0.8860 (tpp80) REVERT: H 455 ASN cc_start: 0.9013 (m-40) cc_final: 0.8730 (m-40) REVERT: H 471 GLN cc_start: 0.9399 (tp-100) cc_final: 0.8898 (tp-100) REVERT: J 213 GLN cc_start: 0.8952 (tp40) cc_final: 0.8585 (tp40) REVERT: J 218 LYS cc_start: 0.9346 (mmmm) cc_final: 0.9057 (mtmm) REVERT: J 232 ASP cc_start: 0.9502 (m-30) cc_final: 0.8996 (m-30) REVERT: J 233 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8653 (mt-10) REVERT: J 236 GLU cc_start: 0.9457 (mm-30) cc_final: 0.9090 (mm-30) REVERT: J 277 ASP cc_start: 0.9056 (OUTLIER) cc_final: 0.8493 (p0) REVERT: J 279 LYS cc_start: 0.9532 (tppt) cc_final: 0.9282 (mmmt) REVERT: J 303 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8809 (tm-30) REVERT: J 320 LYS cc_start: 0.9090 (tppp) cc_final: 0.8599 (tppt) REVERT: J 347 GLN cc_start: 0.8607 (mp10) cc_final: 0.8379 (mp10) REVERT: J 379 GLN cc_start: 0.9548 (mm110) cc_final: 0.9281 (mm110) REVERT: J 407 MET cc_start: 0.8486 (tmm) cc_final: 0.8219 (tmm) REVERT: J 418 CYS cc_start: 0.8930 (m) cc_final: 0.8087 (t) REVERT: J 421 GLU cc_start: 0.8550 (pt0) cc_final: 0.7937 (pt0) REVERT: J 448 LEU cc_start: 0.9216 (mt) cc_final: 0.8997 (mt) REVERT: J 499 MET cc_start: 0.8986 (tpt) cc_final: 0.8411 (tpt) REVERT: L 172 ASP cc_start: 0.8460 (t0) cc_final: 0.8202 (t0) REVERT: L 194 MET cc_start: 0.6454 (tpt) cc_final: 0.4846 (pmm) REVERT: L 218 LYS cc_start: 0.8788 (ttpp) cc_final: 0.8264 (ptmm) REVERT: L 223 ASP cc_start: 0.8489 (p0) cc_final: 0.8245 (p0) REVERT: L 280 VAL cc_start: 0.9343 (t) cc_final: 0.9086 (p) REVERT: L 285 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8224 (mm-40) REVERT: L 320 LYS cc_start: 0.9040 (tppt) cc_final: 0.8609 (tppt) REVERT: L 331 ASN cc_start: 0.8927 (OUTLIER) cc_final: 0.8558 (p0) REVERT: L 361 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.7943 (t80) REVERT: L 387 ARG cc_start: 0.9062 (mmm-85) cc_final: 0.8802 (mmm-85) REVERT: L 394 TYR cc_start: 0.9242 (t80) cc_final: 0.8870 (t80) REVERT: L 446 ARG cc_start: 0.9037 (tmm-80) cc_final: 0.8800 (tpp80) REVERT: L 455 ASN cc_start: 0.8897 (m-40) cc_final: 0.8523 (m-40) outliers start: 175 outliers final: 136 residues processed: 1868 average time/residue: 0.4920 time to fit residues: 1490.4354 Evaluate side-chains 1892 residues out of total 4020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1740 time to evaluate : 4.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 295 ILE 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 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 434 LEU Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain B residue 278 THR 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 361 PHE 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 511 SER Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 259 ASP 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 434 LEU Chi-restraints excluded: chain C residue 458 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 C residue 513 LYS Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 325 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 507 LYS Chi-restraints excluded: chain D residue 510 ASN Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 289 LYS Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 312 GLU Chi-restraints excluded: chain E residue 386 ASP 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 496 MET Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 271 GLN Chi-restraints excluded: chain G residue 283 CYS Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 380 SER Chi-restraints excluded: chain G residue 381 GLU Chi-restraints excluded: chain G residue 386 ASP Chi-restraints excluded: chain G residue 458 SER Chi-restraints excluded: chain G residue 505 LEU Chi-restraints excluded: chain G residue 523 SER Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 225 MET Chi-restraints excluded: chain I residue 283 CYS Chi-restraints excluded: chain I residue 286 SER 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 386 ASP 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 I residue 511 SER Chi-restraints excluded: chain K residue 257 SER 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 410 ILE Chi-restraints excluded: chain K residue 458 SER Chi-restraints excluded: chain K residue 467 ASP Chi-restraints excluded: chain K residue 505 LEU Chi-restraints excluded: chain K residue 508 MET Chi-restraints excluded: chain K residue 511 SER Chi-restraints excluded: chain K residue 523 SER Chi-restraints excluded: chain F residue 277 ASP 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 F residue 458 SER Chi-restraints excluded: chain H residue 141 ASP 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 245 LYS Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 331 ASN Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 386 ASP 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 510 ASN Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 196 ASP Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 241 GLN Chi-restraints excluded: chain J residue 277 ASP Chi-restraints excluded: chain J residue 325 GLU Chi-restraints excluded: chain J residue 386 ASP Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 458 SER Chi-restraints excluded: chain J residue 467 ASP Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 331 ASN Chi-restraints excluded: chain L residue 361 PHE Chi-restraints excluded: chain L residue 362 LEU Chi-restraints excluded: chain L residue 423 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 399 optimal weight: 0.8980 chunk 421 optimal weight: 7.9990 chunk 384 optimal weight: 0.6980 chunk 409 optimal weight: 0.0770 chunk 420 optimal weight: 9.9990 chunk 246 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 321 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 370 optimal weight: 4.9990 chunk 387 optimal weight: 1.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 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 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN C 351 ASN ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 ASN ** G 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 461 HIS I 271 GLN ** K 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 510 ASN ** F 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 519 HIS ** H 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 510 ASN ** H 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 519 HIS L 306 HIS L 475 HIS ** L 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 36972 Z= 0.218 Angle : 0.717 14.381 49932 Z= 0.352 Chirality : 0.045 0.272 5544 Planarity : 0.004 0.047 6408 Dihedral : 4.904 63.825 4929 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.23 % Favored : 93.70 % Rotamer: Outliers : 4.35 % Allowed : 29.18 % Favored : 66.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.13), residues: 4620 helix: 1.25 (0.11), residues: 2388 sheet: -0.23 (0.30), residues: 384 loop : -0.07 (0.16), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 501 HIS 0.005 0.001 HIS F 330 PHE 0.041 0.001 PHE D 224 TYR 0.023 0.001 TYR J 293 ARG 0.007 0.000 ARG E 446 *********************** 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 1958 residues out of total 4020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1783 time to evaluate : 4.115 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: A 164 LYS cc_start: 0.9308 (mtmt) cc_final: 0.9039 (mtmm) REVERT: A 172 ASP cc_start: 0.9072 (t0) cc_final: 0.8793 (t70) REVERT: A 194 MET cc_start: 0.6388 (tpp) cc_final: 0.5309 (tpp) REVERT: A 213 GLN cc_start: 0.9094 (mm-40) cc_final: 0.8701 (mm-40) REVERT: A 219 PHE cc_start: 0.8563 (m-10) cc_final: 0.8289 (m-10) REVERT: A 236 GLU cc_start: 0.9617 (mm-30) cc_final: 0.9336 (mm-30) REVERT: A 245 LYS cc_start: 0.9049 (mmmt) cc_final: 0.8651 (tppt) REVERT: A 252 GLN cc_start: 0.9196 (tp40) cc_final: 0.8805 (tp40) REVERT: A 272 ARG cc_start: 0.8288 (ptm160) cc_final: 0.7979 (ptm160) REVERT: A 293 TYR cc_start: 0.9112 (t80) cc_final: 0.8610 (t80) REVERT: A 306 HIS cc_start: 0.8677 (m-70) cc_final: 0.8353 (m-70) REVERT: A 320 LYS cc_start: 0.8986 (tppt) cc_final: 0.8597 (tppt) REVERT: A 360 GLN cc_start: 0.9245 (tm130) cc_final: 0.8924 (tm-30) REVERT: A 361 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8174 (t80) REVERT: A 415 PHE cc_start: 0.9161 (m-80) cc_final: 0.8752 (m-80) REVERT: A 421 GLU cc_start: 0.8356 (pt0) cc_final: 0.7922 (pt0) REVERT: A 434 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8592 (pp) REVERT: A 445 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8799 (mt-10) REVERT: A 498 MET cc_start: 0.8149 (ttm) cc_final: 0.7674 (ttm) REVERT: A 499 MET cc_start: 0.8215 (tpp) cc_final: 0.7819 (tpp) REVERT: A 500 CYS cc_start: 0.8212 (m) cc_final: 0.8001 (m) REVERT: B 196 ASP cc_start: 0.7286 (t0) cc_final: 0.6939 (t0) REVERT: B 213 GLN cc_start: 0.9004 (mm110) cc_final: 0.8498 (tp-100) REVERT: B 218 LYS cc_start: 0.9575 (mmmm) cc_final: 0.9125 (mtmm) REVERT: B 236 GLU cc_start: 0.9499 (mm-30) cc_final: 0.9075 (mm-30) REVERT: B 285 GLN cc_start: 0.8569 (mm-40) cc_final: 0.7937 (mm-40) REVERT: B 293 TYR cc_start: 0.9008 (t80) cc_final: 0.8767 (t80) REVERT: B 361 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8560 (t80) REVERT: B 373 PHE cc_start: 0.8488 (t80) cc_final: 0.8063 (t80) REVERT: B 379 GLN cc_start: 0.9179 (mm-40) cc_final: 0.8973 (mm-40) REVERT: B 394 TYR cc_start: 0.9383 (t80) cc_final: 0.9155 (t80) REVERT: B 407 MET cc_start: 0.8568 (tmm) cc_final: 0.8281 (tmm) REVERT: B 421 GLU cc_start: 0.8537 (pt0) cc_final: 0.8165 (pt0) REVERT: B 424 CYS cc_start: 0.9042 (m) cc_final: 0.8793 (m) REVERT: B 426 SER cc_start: 0.9466 (t) cc_final: 0.9194 (p) REVERT: B 467 ASP cc_start: 0.9289 (OUTLIER) cc_final: 0.8977 (p0) REVERT: C 172 ASP cc_start: 0.8865 (t0) cc_final: 0.7923 (t70) REVERT: C 175 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8549 (pp) REVERT: C 179 MET cc_start: 0.7797 (ptp) cc_final: 0.7096 (ptp) REVERT: C 194 MET cc_start: 0.9128 (mtp) cc_final: 0.8686 (mmm) REVERT: C 213 GLN cc_start: 0.8954 (tp40) cc_final: 0.8696 (tp-100) REVERT: C 246 VAL cc_start: 0.8098 (OUTLIER) cc_final: 0.7577 (t) REVERT: C 260 LEU cc_start: 0.9096 (mt) cc_final: 0.8812 (mp) REVERT: C 272 ARG cc_start: 0.8319 (ptm160) cc_final: 0.8114 (ptm160) REVERT: C 277 ASP cc_start: 0.8928 (m-30) cc_final: 0.8639 (p0) REVERT: C 375 ASN cc_start: 0.9000 (t0) cc_final: 0.8659 (t0) REVERT: C 381 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8236 (tm-30) REVERT: C 415 PHE cc_start: 0.9082 (m-80) cc_final: 0.8258 (m-80) REVERT: C 421 GLU cc_start: 0.8275 (pt0) cc_final: 0.7908 (pt0) REVERT: C 434 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8431 (pp) REVERT: C 445 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8752 (mt-10) REVERT: C 455 ASN cc_start: 0.9105 (m-40) cc_final: 0.8864 (m110) REVERT: C 467 ASP cc_start: 0.9449 (p0) cc_final: 0.8580 (p0) REVERT: C 508 MET cc_start: 0.9159 (mtt) cc_final: 0.8679 (mtt) REVERT: D 140 GLU cc_start: 0.8706 (pm20) cc_final: 0.8382 (pp20) REVERT: D 172 ASP cc_start: 0.9035 (t0) cc_final: 0.8662 (t70) REVERT: D 216 ARG cc_start: 0.7254 (ptt180) cc_final: 0.6971 (ptt180) REVERT: D 236 GLU cc_start: 0.9532 (mm-30) cc_final: 0.9149 (mm-30) REVERT: D 246 VAL cc_start: 0.8289 (OUTLIER) cc_final: 0.7629 (t) REVERT: D 260 LEU cc_start: 0.9406 (tp) cc_final: 0.8998 (tp) REVERT: D 263 VAL cc_start: 0.9419 (t) cc_final: 0.9160 (p) REVERT: D 279 LYS cc_start: 0.9681 (mmmm) cc_final: 0.9353 (mmmm) REVERT: D 285 GLN cc_start: 0.8504 (mm-40) cc_final: 0.7774 (mm-40) REVERT: D 293 TYR cc_start: 0.9101 (t80) cc_final: 0.8900 (t80) REVERT: D 303 GLU cc_start: 0.9257 (tm-30) cc_final: 0.8973 (tm-30) REVERT: D 318 PHE cc_start: 0.8956 (p90) cc_final: 0.8646 (p90) REVERT: D 360 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8629 (pp30) REVERT: D 382 ARG cc_start: 0.9327 (ttp80) cc_final: 0.8972 (mtp-110) REVERT: D 394 TYR cc_start: 0.9513 (t80) cc_final: 0.9212 (t80) REVERT: D 397 GLU cc_start: 0.9318 (tm-30) cc_final: 0.9026 (tm-30) REVERT: D 421 GLU cc_start: 0.8411 (pt0) cc_final: 0.7897 (pt0) REVERT: D 454 ARG cc_start: 0.8955 (ttp80) cc_final: 0.8690 (ttp80) REVERT: D 471 GLN cc_start: 0.9540 (mm110) cc_final: 0.9202 (tp40) REVERT: E 172 ASP cc_start: 0.8891 (t0) cc_final: 0.8398 (t0) REVERT: E 223 ASP cc_start: 0.9006 (t0) cc_final: 0.8793 (t0) REVERT: E 271 GLN cc_start: 0.8439 (pt0) cc_final: 0.8048 (pt0) REVERT: E 321 LEU cc_start: 0.9362 (pt) cc_final: 0.8963 (pp) REVERT: E 323 LEU cc_start: 0.9363 (mp) cc_final: 0.9121 (mp) REVERT: E 331 ASN cc_start: 0.8941 (p0) cc_final: 0.8035 (p0) REVERT: E 365 MET cc_start: 0.9329 (ttm) cc_final: 0.9050 (ttm) REVERT: E 379 GLN cc_start: 0.8802 (mm110) cc_final: 0.6842 (tt0) REVERT: E 382 ARG cc_start: 0.9531 (ttp80) cc_final: 0.8997 (mtp85) REVERT: E 396 LYS cc_start: 0.9472 (tttt) cc_final: 0.9045 (tttm) REVERT: E 407 MET cc_start: 0.8825 (tmm) cc_final: 0.8372 (tmm) REVERT: E 421 GLU cc_start: 0.8655 (pt0) cc_final: 0.8376 (pt0) REVERT: E 424 CYS cc_start: 0.9254 (m) cc_final: 0.8663 (t) REVERT: E 426 SER cc_start: 0.9483 (t) cc_final: 0.9211 (p) REVERT: E 455 ASN cc_start: 0.8977 (m-40) cc_final: 0.8522 (m-40) REVERT: E 463 CYS cc_start: 0.8231 (p) cc_final: 0.7945 (p) REVERT: E 467 ASP cc_start: 0.8563 (m-30) cc_final: 0.8159 (m-30) REVERT: E 478 LEU cc_start: 0.9632 (mt) cc_final: 0.9384 (mt) REVERT: G 194 MET cc_start: 0.5485 (tpp) cc_final: 0.5056 (tpp) REVERT: G 227 PHE cc_start: 0.9590 (t80) cc_final: 0.9285 (t80) REVERT: G 232 ASP cc_start: 0.9670 (m-30) cc_final: 0.9065 (m-30) REVERT: G 235 TYR cc_start: 0.9112 (t80) cc_final: 0.8566 (t80) REVERT: G 236 GLU cc_start: 0.9557 (mm-30) cc_final: 0.9176 (mm-30) REVERT: G 260 LEU cc_start: 0.9197 (tp) cc_final: 0.8808 (mt) REVERT: G 293 TYR cc_start: 0.9040 (t80) cc_final: 0.7492 (t80) REVERT: G 300 LEU cc_start: 0.9475 (mm) cc_final: 0.9143 (mt) REVERT: G 312 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8038 (mt-10) REVERT: G 320 LYS cc_start: 0.9105 (tppt) cc_final: 0.8573 (tppt) REVERT: G 362 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9285 (tt) REVERT: G 373 PHE cc_start: 0.8599 (t80) cc_final: 0.8245 (t80) REVERT: G 407 MET cc_start: 0.8476 (tmm) cc_final: 0.8229 (tmm) REVERT: G 421 GLU cc_start: 0.8248 (pt0) cc_final: 0.7980 (pt0) REVERT: G 424 CYS cc_start: 0.8920 (m) cc_final: 0.8584 (m) REVERT: G 436 ASN cc_start: 0.9231 (t0) cc_final: 0.8988 (t0) REVERT: G 446 ARG cc_start: 0.8387 (ttp80) cc_final: 0.7331 (ttp80) REVERT: G 451 GLU cc_start: 0.8255 (mp0) cc_final: 0.7984 (mp0) REVERT: G 455 ASN cc_start: 0.9235 (m-40) cc_final: 0.8680 (m110) REVERT: G 499 MET cc_start: 0.8469 (tpp) cc_final: 0.8225 (tpp) REVERT: G 506 ASP cc_start: 0.9505 (t0) cc_final: 0.8671 (p0) REVERT: G 510 ASN cc_start: 0.7713 (m110) cc_final: 0.7330 (m-40) REVERT: G 516 HIS cc_start: 0.8101 (t-90) cc_final: 0.7476 (t-90) REVERT: I 140 GLU cc_start: 0.8815 (pm20) cc_final: 0.8594 (tm-30) REVERT: I 172 ASP cc_start: 0.9021 (t0) cc_final: 0.8528 (t0) REVERT: I 183 ARG cc_start: 0.9113 (mtp85) cc_final: 0.8407 (ptp-110) REVERT: I 194 MET cc_start: 0.7304 (tpp) cc_final: 0.6673 (tpp) REVERT: I 213 GLN cc_start: 0.9179 (mm-40) cc_final: 0.8664 (tp-100) REVERT: I 218 LYS cc_start: 0.9268 (mmmm) cc_final: 0.8909 (mtmm) REVERT: I 260 LEU cc_start: 0.9483 (mt) cc_final: 0.9197 (mm) REVERT: I 277 ASP cc_start: 0.8942 (m-30) cc_final: 0.8596 (p0) REVERT: I 323 LEU cc_start: 0.9418 (mp) cc_final: 0.9212 (mp) REVERT: I 331 ASN cc_start: 0.8922 (p0) cc_final: 0.8373 (p0) REVERT: I 379 GLN cc_start: 0.8837 (mm110) cc_final: 0.6817 (tt0) REVERT: I 382 ARG cc_start: 0.9502 (ttp80) cc_final: 0.8948 (mtp85) REVERT: I 407 MET cc_start: 0.8739 (tmm) cc_final: 0.8329 (tmm) REVERT: I 421 GLU cc_start: 0.8646 (pt0) cc_final: 0.8338 (pt0) REVERT: I 426 SER cc_start: 0.9595 (t) cc_final: 0.9136 (p) REVERT: I 455 ASN cc_start: 0.8969 (m-40) cc_final: 0.8511 (m-40) REVERT: I 465 MET cc_start: 0.9375 (mmm) cc_final: 0.9173 (mmm) REVERT: I 467 ASP cc_start: 0.8821 (m-30) cc_final: 0.8472 (p0) REVERT: I 494 ASN cc_start: 0.9333 (m110) cc_final: 0.9061 (m-40) REVERT: I 520 ASP cc_start: 0.8910 (m-30) cc_final: 0.8688 (m-30) REVERT: K 179 MET cc_start: 0.9303 (tpp) cc_final: 0.8718 (tpp) REVERT: K 218 LYS cc_start: 0.8418 (mtmm) cc_final: 0.8115 (mtmm) REVERT: K 235 TYR cc_start: 0.9057 (t80) cc_final: 0.8395 (t80) REVERT: K 236 GLU cc_start: 0.9484 (mm-30) cc_final: 0.9122 (mm-30) REVERT: K 260 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8939 (mp) REVERT: K 293 TYR cc_start: 0.9096 (t80) cc_final: 0.7434 (t80) REVERT: K 312 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7720 (mt-10) REVERT: K 361 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8607 (t80) REVERT: K 370 TYR cc_start: 0.8944 (t80) cc_final: 0.8722 (t80) REVERT: K 407 MET cc_start: 0.8638 (tmm) cc_final: 0.8335 (tmm) REVERT: K 416 GLN cc_start: 0.9315 (mt0) cc_final: 0.9070 (mt0) REVERT: K 421 GLU cc_start: 0.8384 (pt0) cc_final: 0.8033 (pt0) REVERT: K 424 CYS cc_start: 0.8764 (m) cc_final: 0.8397 (m) REVERT: K 430 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8524 (mpp) REVERT: K 436 ASN cc_start: 0.9196 (t0) cc_final: 0.8929 (t0) REVERT: K 446 ARG cc_start: 0.8367 (ttp80) cc_final: 0.7148 (ttp80) REVERT: K 455 ASN cc_start: 0.9209 (m-40) cc_final: 0.8681 (m110) REVERT: K 467 ASP cc_start: 0.9365 (OUTLIER) cc_final: 0.9076 (p0) REVERT: K 516 HIS cc_start: 0.8117 (t-90) cc_final: 0.7419 (t-90) REVERT: F 140 GLU cc_start: 0.8665 (pm20) cc_final: 0.8203 (pm20) REVERT: F 194 MET cc_start: 0.7398 (tpp) cc_final: 0.7175 (tpp) REVERT: F 196 ASP cc_start: 0.8268 (t70) cc_final: 0.7831 (t70) REVERT: F 212 THR cc_start: 0.9488 (p) cc_final: 0.8581 (t) REVERT: F 213 GLN cc_start: 0.8961 (mm110) cc_final: 0.8060 (mm110) REVERT: F 215 PHE cc_start: 0.8746 (m-80) cc_final: 0.8495 (m-80) REVERT: F 216 ARG cc_start: 0.8519 (mtp180) cc_final: 0.7530 (mtp180) REVERT: F 233 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8572 (mt-10) REVERT: F 236 GLU cc_start: 0.9490 (mm-30) cc_final: 0.8950 (mm-30) REVERT: F 277 ASP cc_start: 0.9102 (OUTLIER) cc_final: 0.8217 (p0) REVERT: F 279 LYS cc_start: 0.9589 (mmmt) cc_final: 0.9224 (tppt) REVERT: F 293 TYR cc_start: 0.8867 (t80) cc_final: 0.8634 (t80) REVERT: F 347 GLN cc_start: 0.8475 (mp10) cc_final: 0.8037 (mp10) REVERT: F 379 GLN cc_start: 0.9459 (mm110) cc_final: 0.9206 (mm110) REVERT: F 382 ARG cc_start: 0.9386 (ttp80) cc_final: 0.9083 (mtp-110) REVERT: F 421 GLU cc_start: 0.8621 (pt0) cc_final: 0.8006 (pt0) REVERT: F 425 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8676 (mt-10) REVERT: F 454 ARG cc_start: 0.9285 (ttp-110) cc_final: 0.9017 (ttp-110) REVERT: F 499 MET cc_start: 0.8429 (tpp) cc_final: 0.8186 (tpp) REVERT: F 510 ASN cc_start: 0.8117 (m110) cc_final: 0.7778 (m-40) REVERT: H 194 MET cc_start: 0.7067 (tpp) cc_final: 0.6736 (tpt) REVERT: H 213 GLN cc_start: 0.8835 (mm-40) cc_final: 0.8601 (mm-40) REVERT: H 215 PHE cc_start: 0.8308 (m-80) cc_final: 0.7891 (m-80) REVERT: H 232 ASP cc_start: 0.9562 (m-30) cc_final: 0.9023 (m-30) REVERT: H 233 GLU cc_start: 0.9384 (tt0) cc_final: 0.9118 (tt0) REVERT: H 235 TYR cc_start: 0.8943 (t80) cc_final: 0.8730 (t80) REVERT: H 236 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8976 (mm-30) REVERT: H 320 LYS cc_start: 0.8951 (tppt) cc_final: 0.8564 (tppt) REVERT: H 331 ASN cc_start: 0.8949 (p0) cc_final: 0.8539 (p0) REVERT: H 396 LYS cc_start: 0.9102 (tttt) cc_final: 0.8856 (tttm) REVERT: H 397 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8781 (tm-30) REVERT: H 446 ARG cc_start: 0.9155 (tmm-80) cc_final: 0.8871 (tpp80) REVERT: H 455 ASN cc_start: 0.8983 (m-40) cc_final: 0.8701 (m-40) REVERT: H 471 GLN cc_start: 0.9399 (tp-100) cc_final: 0.8884 (tp-100) REVERT: J 218 LYS cc_start: 0.9335 (mmmm) cc_final: 0.9056 (mtmm) REVERT: J 232 ASP cc_start: 0.9504 (m-30) cc_final: 0.8997 (m-30) REVERT: J 233 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8665 (mt-10) REVERT: J 236 GLU cc_start: 0.9458 (mm-30) cc_final: 0.9107 (mm-30) REVERT: J 277 ASP cc_start: 0.9065 (OUTLIER) cc_final: 0.8302 (p0) REVERT: J 279 LYS cc_start: 0.9492 (tppt) cc_final: 0.9246 (tppt) REVERT: J 303 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8820 (tm-30) REVERT: J 320 LYS cc_start: 0.9077 (tppp) cc_final: 0.8583 (tppt) REVERT: J 347 GLN cc_start: 0.8637 (mp10) cc_final: 0.8404 (mp10) REVERT: J 407 MET cc_start: 0.8514 (tmm) cc_final: 0.8233 (tmm) REVERT: J 418 CYS cc_start: 0.8975 (m) cc_final: 0.8078 (t) REVERT: J 421 GLU cc_start: 0.8556 (pt0) cc_final: 0.7953 (pt0) REVERT: J 448 LEU cc_start: 0.9247 (mt) cc_final: 0.9032 (mt) REVERT: J 499 MET cc_start: 0.8934 (tpt) cc_final: 0.8329 (tpt) REVERT: L 172 ASP cc_start: 0.8458 (t0) cc_final: 0.8213 (t0) REVERT: L 194 MET cc_start: 0.6473 (tpt) cc_final: 0.4844 (pmm) REVERT: L 218 LYS cc_start: 0.8803 (ttpp) cc_final: 0.8283 (ptmm) REVERT: L 280 VAL cc_start: 0.9375 (t) cc_final: 0.9102 (p) REVERT: L 285 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8194 (mm-40) REVERT: L 320 LYS cc_start: 0.9060 (tppt) cc_final: 0.8625 (tppt) REVERT: L 331 ASN cc_start: 0.8937 (OUTLIER) cc_final: 0.8562 (p0) REVERT: L 361 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.7912 (t80) REVERT: L 446 ARG cc_start: 0.9042 (tmm-80) cc_final: 0.8804 (tpp80) REVERT: L 455 ASN cc_start: 0.8906 (m-40) cc_final: 0.8526 (m-40) REVERT: D 602 GLN cc_start: 0.6482 (OUTLIER) cc_final: 0.5234 (pp30) outliers start: 175 outliers final: 147 residues processed: 1844 average time/residue: 0.4461 time to fit residues: 1333.3522 Evaluate side-chains 1917 residues out of total 4020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1751 time to evaluate : 3.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 259 ASP 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 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 434 LEU Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 322 PHE Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 381 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 467 ASP Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain C residue 175 LEU 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 259 ASP 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 434 LEU Chi-restraints excluded: chain C residue 458 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 C residue 511 SER 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 259 ASP Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 325 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 510 ASN Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 289 LYS Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 312 GLU Chi-restraints excluded: chain E residue 386 ASP 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 496 MET Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 271 GLN Chi-restraints excluded: chain G residue 283 CYS Chi-restraints excluded: chain G residue 314 SER 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 384 SER Chi-restraints excluded: chain G residue 386 ASP Chi-restraints excluded: chain G residue 458 SER Chi-restraints excluded: chain G residue 462 SER Chi-restraints excluded: chain G residue 505 LEU Chi-restraints excluded: chain G residue 523 SER Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 225 MET Chi-restraints excluded: chain I residue 283 CYS Chi-restraints excluded: chain I residue 286 SER 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 386 ASP 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 458 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 257 SER Chi-restraints excluded: chain K residue 260 LEU 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 386 ASP Chi-restraints excluded: chain K residue 419 SER Chi-restraints excluded: chain K residue 430 MET Chi-restraints excluded: chain K residue 458 SER Chi-restraints excluded: chain K residue 467 ASP Chi-restraints excluded: chain K residue 505 LEU Chi-restraints excluded: chain K residue 508 MET 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 277 ASP 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 412 ASP Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 458 SER Chi-restraints excluded: chain H residue 141 ASP 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 362 LEU Chi-restraints excluded: chain H residue 381 GLU Chi-restraints excluded: chain H residue 386 ASP 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 510 ASN Chi-restraints excluded: chain H residue 520 ASP Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 196 ASP Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 231 ILE Chi-restraints excluded: chain J residue 277 ASP Chi-restraints excluded: chain J residue 325 GLU Chi-restraints excluded: chain J residue 386 ASP Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 458 SER Chi-restraints excluded: chain J residue 467 ASP Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain L residue 231 ILE Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 331 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 408 optimal weight: ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 ASN ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 ASN G 271 GLN G 368 ASN ** G 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN ** F 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 519 HIS ** H 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 519 HIS L 306 HIS L 416 GLN ** L 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 36972 Z= 0.212 Angle : 0.732 14.558 49932 Z= 0.358 Chirality : 0.045 0.280 5544 Planarity : 0.004 0.048 6408 Dihedral : 4.909 63.281 4929 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.17 % Favored : 93.79 % Rotamer: Outliers : 4.25 % Allowed : 29.55 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.13), residues: 4620 helix: 1.22 (0.11), residues: 2388 sheet: -0.22 (0.30), residues: 384 loop : -0.08 (0.16), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 501 HIS 0.005 0.001 HIS J 475 PHE 0.043 0.001 PHE D 224 TYR 0.024 0.001 TYR G 249 ARG 0.008 0.001 ARG A 446 ********************** 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 fitting. rotamer outliers: 171 poor density : 1778 time to evaluate : 3.172 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: A 172 ASP cc_start: 0.9105 (t0) cc_final: 0.8815 (t70) REVERT: A 176 LYS cc_start: 0.9232 (ttpp) cc_final: 0.8961 (ttpp) REVERT: A 179 MET cc_start: 0.8433 (tmm) cc_final: 0.8093 (tmm) REVERT: A 194 MET cc_start: 0.6512 (tpp) cc_final: 0.5510 (tpp) REVERT: A 213 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8692 (mm-40) REVERT: A 219 PHE cc_start: 0.8534 (m-10) cc_final: 0.8244 (m-10) REVERT: A 236 GLU cc_start: 0.9617 (mm-30) cc_final: 0.9337 (mm-30) REVERT: A 245 LYS cc_start: 0.9008 (mmmt) cc_final: 0.8588 (tppt) REVERT: A 272 ARG cc_start: 0.8283 (ptm160) cc_final: 0.7975 (ptm160) REVERT: A 293 TYR cc_start: 0.9099 (t80) cc_final: 0.8598 (t80) REVERT: A 306 HIS cc_start: 0.8663 (m-70) cc_final: 0.8326 (m-70) REVERT: A 320 LYS cc_start: 0.9019 (tppt) cc_final: 0.8657 (tppt) REVERT: A 360 GLN cc_start: 0.9222 (tm130) cc_final: 0.8983 (tm-30) REVERT: A 361 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.8152 (t80) REVERT: A 415 PHE cc_start: 0.9172 (m-80) cc_final: 0.8715 (m-80) REVERT: A 421 GLU cc_start: 0.8373 (pt0) cc_final: 0.7938 (pt0) REVERT: A 434 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8577 (pp) REVERT: A 445 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8704 (mm-30) REVERT: A 454 ARG cc_start: 0.9228 (ttp-110) cc_final: 0.8647 (ttp-110) REVERT: A 498 MET cc_start: 0.8057 (ttm) cc_final: 0.7551 (ttm) REVERT: A 499 MET cc_start: 0.8219 (tpp) cc_final: 0.7825 (tpp) REVERT: A 500 CYS cc_start: 0.8215 (m) cc_final: 0.8006 (m) REVERT: B 196 ASP cc_start: 0.7268 (t0) cc_final: 0.7027 (t0) REVERT: B 213 GLN cc_start: 0.8965 (mm110) cc_final: 0.8470 (tp-100) REVERT: B 218 LYS cc_start: 0.9570 (mmmm) cc_final: 0.9126 (mtmm) REVERT: B 232 ASP cc_start: 0.9756 (m-30) cc_final: 0.9374 (m-30) REVERT: B 236 GLU cc_start: 0.9503 (mm-30) cc_final: 0.9092 (mm-30) REVERT: B 285 GLN cc_start: 0.8563 (mm-40) cc_final: 0.7934 (mm-40) REVERT: B 293 TYR cc_start: 0.8982 (t80) cc_final: 0.8727 (t80) REVERT: B 361 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8575 (t80) REVERT: B 379 GLN cc_start: 0.9240 (mm-40) cc_final: 0.8994 (mm-40) REVERT: B 394 TYR cc_start: 0.9387 (t80) cc_final: 0.9161 (t80) REVERT: B 407 MET cc_start: 0.8550 (tmm) cc_final: 0.8246 (tmm) REVERT: B 421 GLU cc_start: 0.8544 (pt0) cc_final: 0.8095 (pt0) REVERT: B 424 CYS cc_start: 0.9028 (m) cc_final: 0.8797 (m) REVERT: B 426 SER cc_start: 0.9450 (t) cc_final: 0.9198 (p) REVERT: C 172 ASP cc_start: 0.8876 (t0) cc_final: 0.7940 (t70) REVERT: C 175 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8559 (pp) REVERT: C 179 MET cc_start: 0.7807 (ptp) cc_final: 0.7063 (ptp) REVERT: C 194 MET cc_start: 0.9143 (mtp) cc_final: 0.8697 (mmm) REVERT: C 213 GLN cc_start: 0.8991 (tp40) cc_final: 0.8629 (tp-100) REVERT: C 246 VAL cc_start: 0.8125 (OUTLIER) cc_final: 0.7629 (t) REVERT: C 260 LEU cc_start: 0.9092 (mt) cc_final: 0.8807 (mp) REVERT: C 272 ARG cc_start: 0.8339 (ptm160) cc_final: 0.8137 (ptm160) REVERT: C 277 ASP cc_start: 0.8919 (m-30) cc_final: 0.8637 (p0) REVERT: C 375 ASN cc_start: 0.8998 (t0) cc_final: 0.8666 (t0) REVERT: C 381 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8195 (tm-30) REVERT: C 415 PHE cc_start: 0.9095 (m-80) cc_final: 0.8260 (m-80) REVERT: C 421 GLU cc_start: 0.8326 (pt0) cc_final: 0.7916 (pt0) REVERT: C 434 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8419 (pp) REVERT: C 445 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8739 (mt-10) REVERT: C 455 ASN cc_start: 0.9102 (m-40) cc_final: 0.8867 (m110) REVERT: C 467 ASP cc_start: 0.9472 (p0) cc_final: 0.8628 (p0) REVERT: C 508 MET cc_start: 0.9138 (mtt) cc_final: 0.8637 (mtt) REVERT: D 140 GLU cc_start: 0.8719 (pm20) cc_final: 0.8397 (pp20) REVERT: D 172 ASP cc_start: 0.9027 (t0) cc_final: 0.8658 (t70) REVERT: D 216 ARG cc_start: 0.7316 (ptt180) cc_final: 0.7029 (ptt180) REVERT: D 232 ASP cc_start: 0.9764 (m-30) cc_final: 0.9423 (m-30) REVERT: D 236 GLU cc_start: 0.9529 (mm-30) cc_final: 0.9149 (mm-30) REVERT: D 245 LYS cc_start: 0.9027 (mmtp) cc_final: 0.8786 (mmmm) REVERT: D 246 VAL cc_start: 0.8262 (OUTLIER) cc_final: 0.7616 (t) REVERT: D 260 LEU cc_start: 0.9394 (tp) cc_final: 0.9000 (tp) REVERT: D 263 VAL cc_start: 0.9420 (t) cc_final: 0.9145 (p) REVERT: D 279 LYS cc_start: 0.9653 (mmmm) cc_final: 0.9353 (mmmm) REVERT: D 285 GLN cc_start: 0.8559 (mm-40) cc_final: 0.7786 (mm-40) REVERT: D 303 GLU cc_start: 0.9305 (tm-30) cc_final: 0.9055 (tm-30) REVERT: D 360 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8613 (pp30) REVERT: D 373 PHE cc_start: 0.8759 (t80) cc_final: 0.8488 (t80) REVERT: D 394 TYR cc_start: 0.9518 (t80) cc_final: 0.9212 (t80) REVERT: D 397 GLU cc_start: 0.9317 (tm-30) cc_final: 0.9039 (tm-30) REVERT: D 414 TYR cc_start: 0.9209 (t80) cc_final: 0.8777 (t80) REVERT: D 421 GLU cc_start: 0.8413 (pt0) cc_final: 0.7896 (pt0) REVERT: D 454 ARG cc_start: 0.8890 (ttp80) cc_final: 0.8628 (ttp80) REVERT: D 471 GLN cc_start: 0.9537 (mm110) cc_final: 0.9202 (tp40) REVERT: E 172 ASP cc_start: 0.8896 (t0) cc_final: 0.8400 (t0) REVERT: E 183 ARG cc_start: 0.8820 (mmm-85) cc_final: 0.8428 (ttp-110) REVERT: E 213 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8674 (mm-40) REVERT: E 223 ASP cc_start: 0.8997 (t0) cc_final: 0.8777 (t0) REVERT: E 271 GLN cc_start: 0.8420 (pt0) cc_final: 0.8022 (pt0) REVERT: E 321 LEU cc_start: 0.9345 (pt) cc_final: 0.8916 (pp) REVERT: E 323 LEU cc_start: 0.9351 (mp) cc_final: 0.9113 (mp) REVERT: E 331 ASN cc_start: 0.8895 (p0) cc_final: 0.8007 (p0) REVERT: E 382 ARG cc_start: 0.9531 (ttp80) cc_final: 0.8999 (mtp85) REVERT: E 396 LYS cc_start: 0.9460 (tttt) cc_final: 0.9046 (tttm) REVERT: E 407 MET cc_start: 0.8817 (tmm) cc_final: 0.8356 (tmm) REVERT: E 421 GLU cc_start: 0.8661 (pt0) cc_final: 0.8391 (pt0) REVERT: E 424 CYS cc_start: 0.9244 (m) cc_final: 0.8678 (t) REVERT: E 426 SER cc_start: 0.9484 (t) cc_final: 0.9140 (p) REVERT: E 446 ARG cc_start: 0.9117 (tpp80) cc_final: 0.8799 (tpp80) REVERT: E 455 ASN cc_start: 0.8969 (m-40) cc_final: 0.8525 (m-40) REVERT: E 467 ASP cc_start: 0.8536 (m-30) cc_final: 0.8284 (m-30) REVERT: E 478 LEU cc_start: 0.9595 (mt) cc_final: 0.9294 (mt) REVERT: E 492 VAL cc_start: 0.9136 (t) cc_final: 0.8793 (m) REVERT: E 520 ASP cc_start: 0.8848 (m-30) cc_final: 0.8309 (m-30) REVERT: G 194 MET cc_start: 0.5545 (tpp) cc_final: 0.5119 (tpp) REVERT: G 232 ASP cc_start: 0.9666 (m-30) cc_final: 0.9052 (m-30) REVERT: G 235 TYR cc_start: 0.9098 (t80) cc_final: 0.8559 (t80) REVERT: G 236 GLU cc_start: 0.9518 (mm-30) cc_final: 0.9182 (mm-30) REVERT: G 260 LEU cc_start: 0.9171 (tp) cc_final: 0.8817 (mt) REVERT: G 293 TYR cc_start: 0.9135 (t80) cc_final: 0.7498 (t80) REVERT: G 300 LEU cc_start: 0.9529 (mm) cc_final: 0.9142 (mt) REVERT: G 312 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8002 (mt-10) REVERT: G 320 LYS cc_start: 0.9100 (tppt) cc_final: 0.8581 (tppt) REVERT: G 362 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9302 (tt) REVERT: G 379 GLN cc_start: 0.9502 (mm110) cc_final: 0.9254 (mm110) REVERT: G 407 MET cc_start: 0.8452 (tmm) cc_final: 0.8203 (tmm) REVERT: G 421 GLU cc_start: 0.8335 (pt0) cc_final: 0.8003 (pt0) REVERT: G 424 CYS cc_start: 0.8902 (m) cc_final: 0.8585 (m) REVERT: G 436 ASN cc_start: 0.9228 (t0) cc_final: 0.8988 (t0) REVERT: G 446 ARG cc_start: 0.8352 (ttp80) cc_final: 0.7278 (ttp80) REVERT: G 451 GLU cc_start: 0.8274 (mp0) cc_final: 0.7991 (mp0) REVERT: G 455 ASN cc_start: 0.9233 (m-40) cc_final: 0.8673 (m110) REVERT: G 499 MET cc_start: 0.8474 (tpp) cc_final: 0.8228 (tpp) REVERT: G 506 ASP cc_start: 0.9530 (t0) cc_final: 0.8652 (p0) REVERT: G 508 MET cc_start: 0.9021 (tpp) cc_final: 0.8550 (mmm) REVERT: G 510 ASN cc_start: 0.7567 (m110) cc_final: 0.7161 (m-40) REVERT: G 516 HIS cc_start: 0.8066 (t-90) cc_final: 0.7551 (t-90) REVERT: I 140 GLU cc_start: 0.8824 (pm20) cc_final: 0.8605 (tm-30) REVERT: I 172 ASP cc_start: 0.9012 (t0) cc_final: 0.8521 (t0) REVERT: I 183 ARG cc_start: 0.9111 (mtp85) cc_final: 0.8397 (ptp-110) REVERT: I 194 MET cc_start: 0.7293 (tpp) cc_final: 0.6665 (tpp) REVERT: I 213 GLN cc_start: 0.9184 (mm-40) cc_final: 0.8677 (tp-100) REVERT: I 218 LYS cc_start: 0.9257 (mmmm) cc_final: 0.8907 (mtmm) REVERT: I 260 LEU cc_start: 0.9487 (mt) cc_final: 0.9182 (mm) REVERT: I 323 LEU cc_start: 0.9417 (mp) cc_final: 0.9210 (mp) REVERT: I 331 ASN cc_start: 0.8902 (p0) cc_final: 0.8274 (p0) REVERT: I 379 GLN cc_start: 0.8777 (mm110) cc_final: 0.6783 (tt0) REVERT: I 382 ARG cc_start: 0.9524 (ttp80) cc_final: 0.9018 (mtp85) REVERT: I 407 MET cc_start: 0.8727 (tmm) cc_final: 0.8314 (tmm) REVERT: I 421 GLU cc_start: 0.8643 (pt0) cc_final: 0.8340 (pt0) REVERT: I 424 CYS cc_start: 0.9196 (m) cc_final: 0.8804 (t) REVERT: I 426 SER cc_start: 0.9486 (t) cc_final: 0.9105 (p) REVERT: I 455 ASN cc_start: 0.8973 (m-40) cc_final: 0.8516 (m-40) REVERT: I 465 MET cc_start: 0.9371 (mmm) cc_final: 0.9171 (mmm) REVERT: I 467 ASP cc_start: 0.8842 (m-30) cc_final: 0.8460 (p0) REVERT: I 494 ASN cc_start: 0.9338 (m110) cc_final: 0.9078 (m-40) REVERT: I 520 ASP cc_start: 0.8907 (m-30) cc_final: 0.8684 (m-30) REVERT: K 179 MET cc_start: 0.9291 (tpp) cc_final: 0.8832 (tpp) REVERT: K 235 TYR cc_start: 0.9050 (t80) cc_final: 0.8405 (t80) REVERT: K 236 GLU cc_start: 0.9482 (mm-30) cc_final: 0.9120 (mm-30) REVERT: K 260 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8936 (mp) REVERT: K 293 TYR cc_start: 0.9073 (t80) cc_final: 0.7390 (t80) REVERT: K 312 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7708 (mt-10) REVERT: K 361 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8618 (t80) REVERT: K 370 TYR cc_start: 0.8951 (t80) cc_final: 0.8733 (t80) REVERT: K 407 MET cc_start: 0.8653 (tmm) cc_final: 0.8337 (tmm) REVERT: K 416 GLN cc_start: 0.9332 (mt0) cc_final: 0.9100 (mt0) REVERT: K 421 GLU cc_start: 0.8383 (pt0) cc_final: 0.8037 (pt0) REVERT: K 424 CYS cc_start: 0.8730 (m) cc_final: 0.8301 (m) REVERT: K 430 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8466 (mpp) REVERT: K 436 ASN cc_start: 0.9187 (t0) cc_final: 0.8926 (t0) REVERT: K 446 ARG cc_start: 0.8414 (ttp80) cc_final: 0.7111 (ttp80) REVERT: K 455 ASN cc_start: 0.9207 (m-40) cc_final: 0.8622 (m-40) REVERT: K 467 ASP cc_start: 0.9362 (OUTLIER) cc_final: 0.9145 (p0) REVERT: K 516 HIS cc_start: 0.8052 (t-90) cc_final: 0.7438 (t-90) REVERT: F 140 GLU cc_start: 0.8672 (pm20) cc_final: 0.8182 (pm20) REVERT: F 194 MET cc_start: 0.7411 (tpp) cc_final: 0.7185 (tpp) REVERT: F 196 ASP cc_start: 0.8332 (t70) cc_final: 0.7955 (t70) REVERT: F 212 THR cc_start: 0.9491 (p) cc_final: 0.8596 (t) REVERT: F 213 GLN cc_start: 0.8963 (mm110) cc_final: 0.8053 (mm110) REVERT: F 216 ARG cc_start: 0.8527 (mtp180) cc_final: 0.7659 (mtp180) REVERT: F 217 ARG cc_start: 0.7901 (mmt180) cc_final: 0.6882 (mmm-85) REVERT: F 223 ASP cc_start: 0.8054 (p0) cc_final: 0.7775 (p0) REVERT: F 233 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8593 (mt-10) REVERT: F 236 GLU cc_start: 0.9491 (mm-30) cc_final: 0.9035 (mm-30) REVERT: F 277 ASP cc_start: 0.9100 (OUTLIER) cc_final: 0.8210 (p0) REVERT: F 279 LYS cc_start: 0.9589 (mmmt) cc_final: 0.9220 (tppt) REVERT: F 293 TYR cc_start: 0.8883 (t80) cc_final: 0.8611 (t80) REVERT: F 347 GLN cc_start: 0.8437 (mp10) cc_final: 0.7994 (mp10) REVERT: F 375 ASN cc_start: 0.8506 (t0) cc_final: 0.8305 (t160) REVERT: F 379 GLN cc_start: 0.9473 (mm110) cc_final: 0.9189 (mm110) REVERT: F 413 PHE cc_start: 0.8642 (t80) cc_final: 0.8292 (t80) REVERT: F 421 GLU cc_start: 0.8627 (pt0) cc_final: 0.8022 (pt0) REVERT: F 425 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8678 (mt-10) REVERT: F 454 ARG cc_start: 0.9279 (ttp-110) cc_final: 0.9013 (ttp-110) REVERT: F 510 ASN cc_start: 0.8083 (m110) cc_final: 0.7789 (m-40) REVERT: H 194 MET cc_start: 0.7110 (tpp) cc_final: 0.6778 (tpt) REVERT: H 213 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8598 (mm-40) REVERT: H 215 PHE cc_start: 0.8255 (m-80) cc_final: 0.7860 (m-80) REVERT: H 232 ASP cc_start: 0.9552 (m-30) cc_final: 0.9011 (m-30) REVERT: H 233 GLU cc_start: 0.9385 (tt0) cc_final: 0.9115 (tt0) REVERT: H 235 TYR cc_start: 0.8917 (t80) cc_final: 0.8706 (t80) REVERT: H 236 GLU cc_start: 0.9318 (mm-30) cc_final: 0.8973 (mm-30) REVERT: H 320 LYS cc_start: 0.8974 (tppt) cc_final: 0.8568 (tppt) REVERT: H 331 ASN cc_start: 0.8979 (OUTLIER) cc_final: 0.8559 (p0) REVERT: H 378 PHE cc_start: 0.9340 (t80) cc_final: 0.8824 (t80) REVERT: H 396 LYS cc_start: 0.9115 (tttt) cc_final: 0.8854 (tttm) REVERT: H 397 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8772 (tm-30) REVERT: H 446 ARG cc_start: 0.9158 (tmm-80) cc_final: 0.8843 (tpp80) REVERT: H 455 ASN cc_start: 0.8978 (m-40) cc_final: 0.8687 (m-40) REVERT: H 471 GLN cc_start: 0.9392 (tp-100) cc_final: 0.8873 (tp-100) REVERT: J 213 GLN cc_start: 0.8860 (tp40) cc_final: 0.8591 (tp40) REVERT: J 232 ASP cc_start: 0.9505 (m-30) cc_final: 0.8988 (m-30) REVERT: J 233 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8666 (mt-10) REVERT: J 236 GLU cc_start: 0.9477 (mm-30) cc_final: 0.9119 (mm-30) REVERT: J 249 TYR cc_start: 0.8945 (p90) cc_final: 0.8550 (p90) REVERT: J 277 ASP cc_start: 0.9025 (OUTLIER) cc_final: 0.8494 (p0) REVERT: J 279 LYS cc_start: 0.9465 (tppt) cc_final: 0.9223 (tppt) REVERT: J 303 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8838 (tm-30) REVERT: J 320 LYS cc_start: 0.9074 (tppp) cc_final: 0.8601 (tppt) REVERT: J 347 GLN cc_start: 0.8634 (mp10) cc_final: 0.8395 (mp10) REVERT: J 407 MET cc_start: 0.8519 (tmm) cc_final: 0.8228 (tmm) REVERT: J 418 CYS cc_start: 0.8940 (m) cc_final: 0.8097 (t) REVERT: J 421 GLU cc_start: 0.8549 (pt0) cc_final: 0.7910 (pt0) REVERT: J 448 LEU cc_start: 0.9230 (mt) cc_final: 0.9014 (mt) REVERT: J 499 MET cc_start: 0.8933 (tpt) cc_final: 0.8330 (tpt) REVERT: L 172 ASP cc_start: 0.8473 (t0) cc_final: 0.8229 (t0) REVERT: L 194 MET cc_start: 0.6236 (tpt) cc_final: 0.4651 (pmm) REVERT: L 218 LYS cc_start: 0.8808 (ttpp) cc_final: 0.8276 (ptmm) REVERT: L 280 VAL cc_start: 0.9374 (t) cc_final: 0.9111 (p) REVERT: L 285 GLN cc_start: 0.8467 (mm-40) cc_final: 0.8199 (mm-40) REVERT: L 320 LYS cc_start: 0.9018 (tppt) cc_final: 0.8557 (tppt) REVERT: L 331 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8550 (p0) REVERT: L 361 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.7984 (t80) REVERT: L 378 PHE cc_start: 0.9106 (t80) cc_final: 0.8815 (t80) REVERT: L 446 ARG cc_start: 0.9056 (tmm-80) cc_final: 0.8841 (tpp80) REVERT: L 455 ASN cc_start: 0.8874 (m-40) cc_final: 0.8556 (m-40) REVERT: D 602 GLN cc_start: 0.6488 (OUTLIER) cc_final: 0.4998 (pp30) outliers start: 171 outliers final: 142 residues processed: 1840 average time/residue: 0.4596 time to fit residues: 1386.4743 Evaluate side-chains 1922 residues out of total 4020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1761 time to evaluate : 4.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 259 ASP 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 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 434 LEU Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 322 PHE Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 361 PHE 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 511 SER Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 259 ASP 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 434 LEU Chi-restraints excluded: chain C residue 458 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 C residue 511 SER Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain D residue 381 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 510 ASN Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 289 LYS Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 312 GLU Chi-restraints excluded: chain E residue 386 ASP 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 496 MET Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 271 GLN 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 326 ASP 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 386 ASP Chi-restraints excluded: chain G residue 458 SER Chi-restraints excluded: chain G residue 505 LEU Chi-restraints excluded: chain G residue 522 VAL Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 225 MET Chi-restraints excluded: chain I residue 236 GLU Chi-restraints excluded: chain I residue 283 CYS Chi-restraints excluded: chain I residue 286 SER 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 386 ASP 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 458 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 257 SER Chi-restraints excluded: chain K residue 260 LEU 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 386 ASP Chi-restraints excluded: chain K residue 430 MET Chi-restraints excluded: chain K residue 458 SER Chi-restraints excluded: chain K residue 467 ASP Chi-restraints excluded: chain K residue 505 LEU Chi-restraints excluded: chain K residue 508 MET Chi-restraints excluded: chain K residue 523 SER Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 277 ASP 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 412 ASP Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 458 SER Chi-restraints excluded: chain H residue 141 ASP 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 325 GLU Chi-restraints excluded: chain H residue 331 ASN Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 381 GLU Chi-restraints excluded: chain H residue 386 ASP 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 J residue 141 ASP Chi-restraints excluded: chain J residue 196 ASP Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 231 ILE Chi-restraints excluded: chain J residue 277 ASP Chi-restraints excluded: chain J residue 325 GLU Chi-restraints excluded: chain J residue 386 ASP Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 458 SER Chi-restraints excluded: chain J residue 467 ASP Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain L residue 331 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 221 optimal weight: 0.9990 chunk 287 optimal weight: 4.9990 chunk 385 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 333 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 362 optimal weight: 0.0030 chunk 151 optimal weight: 4.9990 chunk 372 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN B 298 ASN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN C 519 HIS ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 ASN ** G 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 271 GLN ** G 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 461 HIS ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 519 HIS H 252 GLN ** H 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 519 HIS L 207 ASN ** L 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 475 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.158136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.119856 restraints weight = 65296.876| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 3.92 r_work: 0.3251 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 36972 Z= 0.223 Angle : 0.732 14.434 49932 Z= 0.360 Chirality : 0.045 0.268 5544 Planarity : 0.004 0.048 6408 Dihedral : 4.920 63.791 4929 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.23 % Favored : 93.70 % Rotamer: Outliers : 4.28 % Allowed : 29.85 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.13), residues: 4620 helix: 1.23 (0.11), residues: 2388 sheet: -0.18 (0.30), residues: 384 loop : -0.10 (0.16), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 501 HIS 0.007 0.001 HIS G 273 PHE 0.042 0.001 PHE D 224 TYR 0.025 0.002 TYR G 249 ARG 0.008 0.001 ARG A 446 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18791.76 seconds wall clock time: 519 minutes 17.80 seconds (31157.80 seconds total)