Starting phenix.real_space_refine on Thu Feb 5 05:27:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hew_52099/02_2026/9hew_52099.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hew_52099/02_2026/9hew_52099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hew_52099/02_2026/9hew_52099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hew_52099/02_2026/9hew_52099.map" model { file = "/net/cci-nas-00/data/ceres_data/9hew_52099/02_2026/9hew_52099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hew_52099/02_2026/9hew_52099.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 10094 2.51 5 N 2296 2.21 5 O 2569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15043 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2149 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 10, 'TRANS': 254} Chain breaks: 4 Chain: "B" Number of atoms: 2149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2149 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 10, 'TRANS': 254} Chain breaks: 4 Chain: "C" Number of atoms: 2149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2149 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 10, 'TRANS': 254} Chain breaks: 4 Chain: "D" Number of atoms: 2149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2149 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 10, 'TRANS': 254} Chain breaks: 4 Chain: "E" Number of atoms: 2149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2149 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 10, 'TRANS': 254} Chain breaks: 4 Chain: "F" Number of atoms: 2149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2149 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 10, 'TRANS': 254} Chain breaks: 4 Chain: "G" Number of atoms: 2149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2149 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 10, 'TRANS': 254} Chain breaks: 4 Time building chain proxies: 3.03, per 1000 atoms: 0.20 Number of scatterers: 15043 At special positions: 0 Unit cell: (109.12, 107.712, 111.936, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2569 8.00 N 2296 7.00 C 10094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 264 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 245 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 264 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 245 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 264 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 245 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 264 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 245 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 264 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 245 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 264 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 245 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 264 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 245 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 517.2 milliseconds 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3654 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 7 sheets defined 83.3% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 3.532A pdb=" N LEU A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU A 9 " --> pdb=" O HIS A 5 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 54 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 73 through 88 Processing helix chain 'A' and resid 101 through 131 Proline residue: A 110 - end of helix Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 155 Processing helix chain 'A' and resid 194 through 203 Processing helix chain 'A' and resid 206 through 238 removed outlier: 3.529A pdb=" N MET A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 268 through 294 removed outlier: 3.607A pdb=" N LEU A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Proline residue: A 288 - end of helix removed outlier: 3.820A pdb=" N PHE A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 299 Processing helix chain 'A' and resid 325 through 337 removed outlier: 3.535A pdb=" N LEU A 329 " --> pdb=" O ASN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 341 through 354 removed outlier: 3.566A pdb=" N CYS A 346 " --> pdb=" O LYS A 342 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 12 removed outlier: 3.861A pdb=" N GLU B 9 " --> pdb=" O HIS B 5 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR B 10 " --> pdb=" O LEU B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 54 Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 73 through 88 Processing helix chain 'B' and resid 101 through 131 Proline residue: B 110 - end of helix Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 155 Processing helix chain 'B' and resid 194 through 203 Processing helix chain 'B' and resid 206 through 238 removed outlier: 3.529A pdb=" N MET B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER B 238 " --> pdb=" O PHE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 255 removed outlier: 3.750A pdb=" N LYS B 253 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 294 removed outlier: 3.607A pdb=" N LEU B 274 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Proline residue: B 288 - end of helix removed outlier: 3.819A pdb=" N PHE B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 299 Processing helix chain 'B' and resid 325 through 337 removed outlier: 3.536A pdb=" N LEU B 329 " --> pdb=" O ASN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 341 through 354 removed outlier: 3.566A pdb=" N CYS B 346 " --> pdb=" O LYS B 342 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 12 removed outlier: 3.861A pdb=" N GLU C 9 " --> pdb=" O HIS C 5 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR C 10 " --> pdb=" O LEU C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 54 Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 73 through 88 Processing helix chain 'C' and resid 101 through 131 Proline residue: C 110 - end of helix Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 155 Processing helix chain 'C' and resid 194 through 203 Processing helix chain 'C' and resid 206 through 238 removed outlier: 3.529A pdb=" N MET C 210 " --> pdb=" O SER C 206 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER C 238 " --> pdb=" O PHE C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 255 Processing helix chain 'C' and resid 268 through 294 removed outlier: 3.608A pdb=" N LEU C 274 " --> pdb=" O GLY C 270 " (cutoff:3.500A) Proline residue: C 288 - end of helix removed outlier: 3.819A pdb=" N PHE C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 299 Processing helix chain 'C' and resid 325 through 337 removed outlier: 3.535A pdb=" N LEU C 329 " --> pdb=" O ASN C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 340 No H-bonds generated for 'chain 'C' and resid 338 through 340' Processing helix chain 'C' and resid 341 through 354 removed outlier: 3.565A pdb=" N CYS C 346 " --> pdb=" O LYS C 342 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL C 349 " --> pdb=" O LYS C 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 12 removed outlier: 3.862A pdb=" N GLU D 9 " --> pdb=" O HIS D 5 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR D 10 " --> pdb=" O LEU D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 54 Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 73 through 88 Processing helix chain 'D' and resid 101 through 131 Proline residue: D 110 - end of helix Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 155 Processing helix chain 'D' and resid 194 through 203 Processing helix chain 'D' and resid 206 through 238 removed outlier: 3.529A pdb=" N MET D 210 " --> pdb=" O SER D 206 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER D 238 " --> pdb=" O PHE D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 255 Processing helix chain 'D' and resid 268 through 294 removed outlier: 3.608A pdb=" N LEU D 274 " --> pdb=" O GLY D 270 " (cutoff:3.500A) Proline residue: D 288 - end of helix removed outlier: 3.819A pdb=" N PHE D 294 " --> pdb=" O VAL D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 299 Processing helix chain 'D' and resid 325 through 337 removed outlier: 3.534A pdb=" N LEU D 329 " --> pdb=" O ASN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 340 No H-bonds generated for 'chain 'D' and resid 338 through 340' Processing helix chain 'D' and resid 341 through 354 removed outlier: 3.566A pdb=" N CYS D 346 " --> pdb=" O LYS D 342 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL D 349 " --> pdb=" O LYS D 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 12 removed outlier: 3.862A pdb=" N GLU E 9 " --> pdb=" O HIS E 5 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR E 10 " --> pdb=" O LEU E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 54 Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 73 through 88 Processing helix chain 'E' and resid 101 through 131 Proline residue: E 110 - end of helix Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 155 Processing helix chain 'E' and resid 194 through 203 Processing helix chain 'E' and resid 206 through 238 removed outlier: 3.529A pdb=" N MET E 210 " --> pdb=" O SER E 206 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER E 238 " --> pdb=" O PHE E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 255 removed outlier: 3.750A pdb=" N LYS E 253 " --> pdb=" O GLY E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 294 removed outlier: 3.607A pdb=" N LEU E 274 " --> pdb=" O GLY E 270 " (cutoff:3.500A) Proline residue: E 288 - end of helix removed outlier: 3.819A pdb=" N PHE E 294 " --> pdb=" O VAL E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 299 Processing helix chain 'E' and resid 325 through 337 removed outlier: 3.534A pdb=" N LEU E 329 " --> pdb=" O ASN E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 340 No H-bonds generated for 'chain 'E' and resid 338 through 340' Processing helix chain 'E' and resid 341 through 354 removed outlier: 3.566A pdb=" N CYS E 346 " --> pdb=" O LYS E 342 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL E 349 " --> pdb=" O LYS E 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 12 removed outlier: 3.862A pdb=" N GLU F 9 " --> pdb=" O HIS F 5 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR F 10 " --> pdb=" O LEU F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 54 Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 56 through 60 Processing helix chain 'F' and resid 73 through 88 Processing helix chain 'F' and resid 101 through 131 Proline residue: F 110 - end of helix Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 155 Processing helix chain 'F' and resid 194 through 203 Processing helix chain 'F' and resid 206 through 238 removed outlier: 3.529A pdb=" N MET F 210 " --> pdb=" O SER F 206 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER F 238 " --> pdb=" O PHE F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 255 Processing helix chain 'F' and resid 268 through 294 removed outlier: 3.607A pdb=" N LEU F 274 " --> pdb=" O GLY F 270 " (cutoff:3.500A) Proline residue: F 288 - end of helix removed outlier: 3.819A pdb=" N PHE F 294 " --> pdb=" O VAL F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 299 Processing helix chain 'F' and resid 325 through 337 removed outlier: 3.534A pdb=" N LEU F 329 " --> pdb=" O ASN F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 340 No H-bonds generated for 'chain 'F' and resid 338 through 340' Processing helix chain 'F' and resid 341 through 354 removed outlier: 3.566A pdb=" N CYS F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL F 349 " --> pdb=" O LYS F 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 12 removed outlier: 3.861A pdb=" N GLU G 9 " --> pdb=" O HIS G 5 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR G 10 " --> pdb=" O LEU G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 54 Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 56 through 60 Processing helix chain 'G' and resid 73 through 88 Processing helix chain 'G' and resid 101 through 131 Proline residue: G 110 - end of helix Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 155 Processing helix chain 'G' and resid 194 through 203 Processing helix chain 'G' and resid 206 through 238 removed outlier: 3.530A pdb=" N MET G 210 " --> pdb=" O SER G 206 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER G 238 " --> pdb=" O PHE G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 255 Processing helix chain 'G' and resid 268 through 294 removed outlier: 3.608A pdb=" N LEU G 274 " --> pdb=" O GLY G 270 " (cutoff:3.500A) Proline residue: G 288 - end of helix removed outlier: 3.818A pdb=" N PHE G 294 " --> pdb=" O VAL G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 299 Processing helix chain 'G' and resid 325 through 337 removed outlier: 3.535A pdb=" N LEU G 329 " --> pdb=" O ASN G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 340 No H-bonds generated for 'chain 'G' and resid 338 through 340' Processing helix chain 'G' and resid 341 through 354 removed outlier: 3.567A pdb=" N CYS G 346 " --> pdb=" O LYS G 342 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL G 349 " --> pdb=" O LYS G 345 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66 1073 hydrogen bonds defined for protein. 3066 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: 2.33 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4361 1.35 - 1.46: 3783 1.46 - 1.58: 7158 1.58 - 1.70: 0 1.70 - 1.81: 105 Bond restraints: 15407 Sorted by residual: bond pdb=" CB CYS G 245 " pdb=" SG CYS G 245 " ideal model delta sigma weight residual 1.808 1.783 0.025 3.30e-02 9.18e+02 5.85e-01 bond pdb=" CB CYS E 245 " pdb=" SG CYS E 245 " ideal model delta sigma weight residual 1.808 1.783 0.025 3.30e-02 9.18e+02 5.81e-01 bond pdb=" CB CYS F 245 " pdb=" SG CYS F 245 " ideal model delta sigma weight residual 1.808 1.783 0.025 3.30e-02 9.18e+02 5.75e-01 bond pdb=" CB VAL A 269 " pdb=" CG2 VAL A 269 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.64e-01 bond pdb=" CB CYS B 245 " pdb=" SG CYS B 245 " ideal model delta sigma weight residual 1.808 1.783 0.025 3.30e-02 9.18e+02 5.61e-01 ... (remaining 15402 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 20637 2.33 - 4.66: 195 4.66 - 6.98: 49 6.98 - 9.31: 7 9.31 - 11.64: 7 Bond angle restraints: 20895 Sorted by residual: angle pdb=" CA LEU E 252 " pdb=" CB LEU E 252 " pdb=" CG LEU E 252 " ideal model delta sigma weight residual 116.30 104.66 11.64 3.50e+00 8.16e-02 1.11e+01 angle pdb=" CA LEU F 252 " pdb=" CB LEU F 252 " pdb=" CG LEU F 252 " ideal model delta sigma weight residual 116.30 104.68 11.62 3.50e+00 8.16e-02 1.10e+01 angle pdb=" CA LEU A 252 " pdb=" CB LEU A 252 " pdb=" CG LEU A 252 " ideal model delta sigma weight residual 116.30 104.69 11.61 3.50e+00 8.16e-02 1.10e+01 angle pdb=" CA LEU D 252 " pdb=" CB LEU D 252 " pdb=" CG LEU D 252 " ideal model delta sigma weight residual 116.30 104.69 11.61 3.50e+00 8.16e-02 1.10e+01 angle pdb=" CA LEU G 252 " pdb=" CB LEU G 252 " pdb=" CG LEU G 252 " ideal model delta sigma weight residual 116.30 104.70 11.60 3.50e+00 8.16e-02 1.10e+01 ... (remaining 20890 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 8513 17.72 - 35.44: 496 35.44 - 53.16: 109 53.16 - 70.87: 38 70.87 - 88.59: 14 Dihedral angle restraints: 9170 sinusoidal: 3591 harmonic: 5579 Sorted by residual: dihedral pdb=" CA LEU G 239 " pdb=" C LEU G 239 " pdb=" N SER G 240 " pdb=" CA SER G 240 " ideal model delta harmonic sigma weight residual -180.00 -151.68 -28.32 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA LEU F 239 " pdb=" C LEU F 239 " pdb=" N SER F 240 " pdb=" CA SER F 240 " ideal model delta harmonic sigma weight residual -180.00 -151.68 -28.32 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA LEU D 239 " pdb=" C LEU D 239 " pdb=" N SER D 240 " pdb=" CA SER D 240 " ideal model delta harmonic sigma weight residual 180.00 -151.68 -28.32 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 9167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1457 0.028 - 0.056: 624 0.056 - 0.085: 287 0.085 - 0.113: 91 0.113 - 0.141: 26 Chirality restraints: 2485 Sorted by residual: chirality pdb=" CA ILE F 258 " pdb=" N ILE F 258 " pdb=" C ILE F 258 " pdb=" CB ILE F 258 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE D 258 " pdb=" N ILE D 258 " pdb=" C ILE D 258 " pdb=" CB ILE D 258 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ILE G 258 " pdb=" N ILE G 258 " pdb=" C ILE G 258 " pdb=" CB ILE G 258 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 ... (remaining 2482 not shown) Planarity restraints: 2478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 67 " 0.018 2.00e-02 2.50e+03 1.23e-02 2.66e+00 pdb=" CG PHE G 67 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE G 67 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE G 67 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE G 67 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE G 67 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE G 67 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 67 " -0.017 2.00e-02 2.50e+03 1.22e-02 2.60e+00 pdb=" CG PHE C 67 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE C 67 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE C 67 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 67 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE C 67 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 67 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 67 " 0.017 2.00e-02 2.50e+03 1.22e-02 2.59e+00 pdb=" CG PHE F 67 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE F 67 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE F 67 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE F 67 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE F 67 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE F 67 " 0.002 2.00e-02 2.50e+03 ... (remaining 2475 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 175 2.63 - 3.20: 14687 3.20 - 3.77: 25157 3.77 - 4.33: 33256 4.33 - 4.90: 55443 Nonbonded interactions: 128718 Sorted by model distance: nonbonded pdb=" OH TYR A 111 " pdb=" O LEU B 52 " model vdw 2.068 3.040 nonbonded pdb=" OH TYR F 111 " pdb=" O LEU G 52 " model vdw 2.068 3.040 nonbonded pdb=" OH TYR D 111 " pdb=" O LEU E 52 " model vdw 2.071 3.040 nonbonded pdb=" OH TYR C 111 " pdb=" O LEU D 52 " model vdw 2.072 3.040 nonbonded pdb=" OH TYR E 111 " pdb=" O LEU F 52 " model vdw 2.074 3.040 ... (remaining 128713 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.620 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15421 Z= 0.118 Angle : 0.697 11.639 20923 Z= 0.371 Chirality : 0.040 0.141 2485 Planarity : 0.004 0.029 2478 Dihedral : 13.492 88.592 5474 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.14 % Favored : 96.47 % Rotamer: Outliers : 1.24 % Allowed : 4.13 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.19), residues: 1785 helix: 0.37 (0.13), residues: 1288 sheet: -0.20 (0.60), residues: 84 loop : -0.17 (0.36), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG B 128 TYR 0.017 0.004 TYR D 150 PHE 0.024 0.002 PHE G 67 TRP 0.025 0.003 TRP A 104 HIS 0.005 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00265 (15407) covalent geometry : angle 0.69401 (20895) SS BOND : bond 0.00228 ( 14) SS BOND : angle 1.82760 ( 28) hydrogen bonds : bond 0.17950 ( 1073) hydrogen bonds : angle 6.80223 ( 3066) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 885 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASP cc_start: 0.8792 (m-30) cc_final: 0.8477 (m-30) REVERT: A 108 PHE cc_start: 0.9174 (m-80) cc_final: 0.8942 (m-80) REVERT: A 130 SER cc_start: 0.9006 (t) cc_final: 0.8697 (t) REVERT: A 141 PHE cc_start: 0.8838 (t80) cc_final: 0.8443 (t80) REVERT: A 236 LEU cc_start: 0.8606 (tp) cc_final: 0.8324 (tp) REVERT: A 255 ASP cc_start: 0.8994 (t0) cc_final: 0.8196 (t70) REVERT: A 258 ILE cc_start: 0.9482 (mt) cc_final: 0.8460 (mt) REVERT: A 265 LYS cc_start: 0.9167 (tttt) cc_final: 0.8491 (tppp) REVERT: A 273 GLN cc_start: 0.7624 (tt0) cc_final: 0.6966 (mt0) REVERT: B 35 ASP cc_start: 0.8778 (m-30) cc_final: 0.8363 (m-30) REVERT: B 56 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7527 (tp40) REVERT: B 130 SER cc_start: 0.8992 (t) cc_final: 0.8685 (t) REVERT: B 138 ASP cc_start: 0.9223 (m-30) cc_final: 0.8994 (m-30) REVERT: B 141 PHE cc_start: 0.8843 (t80) cc_final: 0.8557 (t80) REVERT: B 236 LEU cc_start: 0.8611 (tp) cc_final: 0.8336 (tp) REVERT: B 255 ASP cc_start: 0.8965 (t0) cc_final: 0.8245 (t70) REVERT: B 258 ILE cc_start: 0.9468 (mt) cc_final: 0.8541 (mt) REVERT: B 265 LYS cc_start: 0.9161 (tttt) cc_final: 0.8925 (tppp) REVERT: B 273 GLN cc_start: 0.7517 (tt0) cc_final: 0.6862 (mt0) REVERT: C 35 ASP cc_start: 0.8792 (m-30) cc_final: 0.8412 (m-30) REVERT: C 56 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7434 (tp40) REVERT: C 130 SER cc_start: 0.8967 (t) cc_final: 0.8668 (t) REVERT: C 138 ASP cc_start: 0.9257 (m-30) cc_final: 0.9022 (m-30) REVERT: C 141 PHE cc_start: 0.8890 (t80) cc_final: 0.8396 (t80) REVERT: C 236 LEU cc_start: 0.8608 (tp) cc_final: 0.8327 (tp) REVERT: C 255 ASP cc_start: 0.8944 (t0) cc_final: 0.8228 (t70) REVERT: C 258 ILE cc_start: 0.9462 (mt) cc_final: 0.8443 (mt) REVERT: C 265 LYS cc_start: 0.9175 (tttt) cc_final: 0.8941 (tppp) REVERT: C 273 GLN cc_start: 0.7545 (tt0) cc_final: 0.7181 (tt0) REVERT: C 274 LEU cc_start: 0.9095 (tp) cc_final: 0.8891 (tp) REVERT: D 35 ASP cc_start: 0.8795 (m-30) cc_final: 0.8393 (m-30) REVERT: D 56 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7433 (tp40) REVERT: D 108 PHE cc_start: 0.9130 (m-80) cc_final: 0.8924 (m-80) REVERT: D 130 SER cc_start: 0.8950 (t) cc_final: 0.8640 (t) REVERT: D 138 ASP cc_start: 0.9220 (m-30) cc_final: 0.8923 (m-30) REVERT: D 236 LEU cc_start: 0.8647 (tp) cc_final: 0.8389 (tp) REVERT: D 241 ASP cc_start: 0.7529 (p0) cc_final: 0.7285 (p0) REVERT: D 255 ASP cc_start: 0.8941 (t0) cc_final: 0.8501 (t70) REVERT: D 265 LYS cc_start: 0.9161 (tttt) cc_final: 0.8880 (tppp) REVERT: D 273 GLN cc_start: 0.7583 (tt0) cc_final: 0.6950 (mt0) REVERT: E 35 ASP cc_start: 0.8747 (m-30) cc_final: 0.8362 (m-30) REVERT: E 56 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7544 (tp40) REVERT: E 121 TYR cc_start: 0.9008 (t80) cc_final: 0.8560 (t80) REVERT: E 125 LEU cc_start: 0.9472 (tp) cc_final: 0.9143 (tp) REVERT: E 130 SER cc_start: 0.8899 (t) cc_final: 0.8601 (t) REVERT: E 236 LEU cc_start: 0.8577 (tp) cc_final: 0.8318 (tp) REVERT: E 255 ASP cc_start: 0.8958 (t0) cc_final: 0.8428 (t70) REVERT: E 265 LYS cc_start: 0.9149 (tttt) cc_final: 0.8878 (tppp) REVERT: E 273 GLN cc_start: 0.7607 (tt0) cc_final: 0.7243 (tt0) REVERT: F 35 ASP cc_start: 0.8779 (m-30) cc_final: 0.8364 (m-30) REVERT: F 56 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7567 (tp40) REVERT: F 130 SER cc_start: 0.8912 (t) cc_final: 0.8621 (t) REVERT: F 236 LEU cc_start: 0.8612 (tp) cc_final: 0.8348 (tp) REVERT: F 255 ASP cc_start: 0.8985 (t0) cc_final: 0.8615 (t70) REVERT: F 265 LYS cc_start: 0.9173 (tttt) cc_final: 0.8917 (tppp) REVERT: F 273 GLN cc_start: 0.7593 (tt0) cc_final: 0.6934 (mt0) REVERT: G 35 ASP cc_start: 0.8746 (m-30) cc_final: 0.8364 (m-30) REVERT: G 56 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7524 (tp40) REVERT: G 111 TYR cc_start: 0.8471 (m-10) cc_final: 0.8236 (m-10) REVERT: G 130 SER cc_start: 0.9037 (t) cc_final: 0.8733 (t) REVERT: G 138 ASP cc_start: 0.9225 (m-30) cc_final: 0.8941 (m-30) REVERT: G 236 LEU cc_start: 0.8599 (tp) cc_final: 0.8355 (tp) REVERT: G 255 ASP cc_start: 0.8997 (t0) cc_final: 0.8278 (t0) REVERT: G 258 ILE cc_start: 0.9479 (mt) cc_final: 0.8486 (mt) REVERT: G 265 LYS cc_start: 0.9175 (tttt) cc_final: 0.8942 (tppp) REVERT: G 273 GLN cc_start: 0.7501 (tt0) cc_final: 0.7044 (mt0) outliers start: 21 outliers final: 0 residues processed: 885 average time/residue: 0.1020 time to fit residues: 136.4115 Evaluate side-chains 595 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 589 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain G residue 56 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 279 ASN A 352 ASN B 204 ASN B 279 ASN C 204 ASN C 279 ASN C 352 ASN D 204 ASN D 279 ASN D 352 ASN E 279 ASN F 204 ASN F 279 ASN F 352 ASN G 204 ASN G 279 ASN G 337 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.088702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.069968 restraints weight = 45560.472| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 4.30 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 15421 Z= 0.275 Angle : 0.836 12.101 20923 Z= 0.406 Chirality : 0.046 0.186 2485 Planarity : 0.004 0.028 2478 Dihedral : 6.854 81.216 1985 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.39 % Allowed : 1.23 % Favored : 98.38 % Rotamer: Outliers : 6.26 % Allowed : 16.06 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.20), residues: 1785 helix: 1.64 (0.14), residues: 1358 sheet: -0.55 (0.64), residues: 84 loop : -0.25 (0.39), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG A 75 TYR 0.014 0.002 TYR B 10 PHE 0.022 0.002 PHE B 333 TRP 0.023 0.003 TRP F 104 HIS 0.004 0.001 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00604 (15407) covalent geometry : angle 0.83206 (20895) SS BOND : bond 0.00823 ( 14) SS BOND : angle 2.38125 ( 28) hydrogen bonds : bond 0.05268 ( 1073) hydrogen bonds : angle 4.91716 ( 3066) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 648 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASP cc_start: 0.8856 (m-30) cc_final: 0.8510 (m-30) REVERT: A 75 ARG cc_start: 0.9233 (ttm-80) cc_final: 0.9010 (ttm-80) REVERT: A 196 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8368 (tt0) REVERT: A 199 LEU cc_start: 0.9722 (mt) cc_final: 0.9450 (pp) REVERT: A 204 ASN cc_start: 0.8866 (OUTLIER) cc_final: 0.8575 (p0) REVERT: A 236 LEU cc_start: 0.8687 (tp) cc_final: 0.8444 (tp) REVERT: A 255 ASP cc_start: 0.9333 (t0) cc_final: 0.9060 (t70) REVERT: A 263 GLN cc_start: 0.8385 (tt0) cc_final: 0.7746 (mt0) REVERT: A 273 GLN cc_start: 0.7458 (tt0) cc_final: 0.6990 (tt0) REVERT: A 340 GLU cc_start: 0.8159 (tp30) cc_final: 0.7918 (mp0) REVERT: A 348 LYS cc_start: 0.9641 (pttm) cc_final: 0.9186 (pttp) REVERT: B 35 ASP cc_start: 0.8915 (m-30) cc_final: 0.8573 (m-30) REVERT: B 56 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7728 (mm-40) REVERT: B 63 GLN cc_start: 0.8525 (mp10) cc_final: 0.8304 (mp10) REVERT: B 68 SER cc_start: 0.9393 (OUTLIER) cc_final: 0.8962 (t) REVERT: B 199 LEU cc_start: 0.9725 (mt) cc_final: 0.9457 (pp) REVERT: B 204 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.8572 (p0) REVERT: B 236 LEU cc_start: 0.8792 (tp) cc_final: 0.8536 (tp) REVERT: B 255 ASP cc_start: 0.9318 (t0) cc_final: 0.9036 (t70) REVERT: B 273 GLN cc_start: 0.7445 (tt0) cc_final: 0.6904 (tt0) REVERT: B 348 LYS cc_start: 0.9635 (pttm) cc_final: 0.9274 (pttp) REVERT: C 35 ASP cc_start: 0.8895 (m-30) cc_final: 0.8562 (m-30) REVERT: C 51 SER cc_start: 0.9508 (m) cc_final: 0.9077 (p) REVERT: C 56 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7929 (mm-40) REVERT: C 75 ARG cc_start: 0.9167 (ttm-80) cc_final: 0.8488 (mmm-85) REVERT: C 134 HIS cc_start: 0.8432 (m-70) cc_final: 0.8187 (m170) REVERT: C 196 GLU cc_start: 0.8316 (tt0) cc_final: 0.8082 (mt-10) REVERT: C 199 LEU cc_start: 0.9701 (mt) cc_final: 0.9416 (pp) REVERT: C 204 ASN cc_start: 0.8818 (OUTLIER) cc_final: 0.8554 (p0) REVERT: C 236 LEU cc_start: 0.8712 (tp) cc_final: 0.8474 (tp) REVERT: C 255 ASP cc_start: 0.9281 (t0) cc_final: 0.8990 (t70) REVERT: C 265 LYS cc_start: 0.9097 (tttt) cc_final: 0.8851 (tppp) REVERT: C 273 GLN cc_start: 0.7366 (tt0) cc_final: 0.6877 (tt0) REVERT: C 274 LEU cc_start: 0.9211 (tp) cc_final: 0.8891 (tp) REVERT: C 348 LYS cc_start: 0.9608 (pttm) cc_final: 0.9137 (pttp) REVERT: D 35 ASP cc_start: 0.8914 (m-30) cc_final: 0.8620 (m-30) REVERT: D 59 SER cc_start: 0.9254 (t) cc_final: 0.9039 (p) REVERT: D 68 SER cc_start: 0.9343 (OUTLIER) cc_final: 0.8909 (t) REVERT: D 74 TRP cc_start: 0.8047 (OUTLIER) cc_final: 0.7641 (t-100) REVERT: D 75 ARG cc_start: 0.9178 (ttm-80) cc_final: 0.8412 (mmm-85) REVERT: D 81 ASP cc_start: 0.9060 (m-30) cc_final: 0.8815 (m-30) REVERT: D 199 LEU cc_start: 0.9732 (mt) cc_final: 0.9447 (pp) REVERT: D 204 ASN cc_start: 0.8834 (OUTLIER) cc_final: 0.8584 (p0) REVERT: D 255 ASP cc_start: 0.9433 (t0) cc_final: 0.9194 (t0) REVERT: D 263 GLN cc_start: 0.8443 (tt0) cc_final: 0.7703 (mt0) REVERT: D 273 GLN cc_start: 0.7351 (tt0) cc_final: 0.6887 (tt0) REVERT: E 35 ASP cc_start: 0.8828 (m-30) cc_final: 0.8500 (m-30) REVERT: E 56 GLN cc_start: 0.8319 (tp40) cc_final: 0.8116 (mm-40) REVERT: E 68 SER cc_start: 0.9374 (OUTLIER) cc_final: 0.8920 (t) REVERT: E 75 ARG cc_start: 0.9175 (ttm-80) cc_final: 0.8364 (mmm-85) REVERT: E 81 ASP cc_start: 0.9060 (m-30) cc_final: 0.8754 (m-30) REVERT: E 199 LEU cc_start: 0.9732 (mt) cc_final: 0.9464 (pp) REVERT: E 236 LEU cc_start: 0.8682 (tp) cc_final: 0.8417 (tp) REVERT: E 251 VAL cc_start: 0.8953 (OUTLIER) cc_final: 0.8668 (p) REVERT: E 255 ASP cc_start: 0.9349 (t0) cc_final: 0.9129 (t0) REVERT: E 263 GLN cc_start: 0.8461 (tt0) cc_final: 0.7770 (mt0) REVERT: E 273 GLN cc_start: 0.7433 (tt0) cc_final: 0.6904 (tt0) REVERT: E 340 GLU cc_start: 0.8112 (tp30) cc_final: 0.7878 (mp0) REVERT: E 348 LYS cc_start: 0.9627 (pttm) cc_final: 0.9204 (pttp) REVERT: F 35 ASP cc_start: 0.8847 (m-30) cc_final: 0.8514 (m-30) REVERT: F 37 MET cc_start: 0.9157 (tpt) cc_final: 0.8658 (tpp) REVERT: F 56 GLN cc_start: 0.8273 (tp40) cc_final: 0.8025 (mm-40) REVERT: F 75 ARG cc_start: 0.9267 (ttm-80) cc_final: 0.8661 (tpp80) REVERT: F 81 ASP cc_start: 0.9007 (m-30) cc_final: 0.8635 (m-30) REVERT: F 204 ASN cc_start: 0.8868 (OUTLIER) cc_final: 0.8582 (p0) REVERT: F 236 LEU cc_start: 0.8741 (tp) cc_final: 0.8488 (tp) REVERT: F 255 ASP cc_start: 0.9318 (t0) cc_final: 0.9018 (t70) REVERT: F 273 GLN cc_start: 0.7521 (tt0) cc_final: 0.6975 (tt0) REVERT: F 340 GLU cc_start: 0.8107 (tp30) cc_final: 0.7854 (mp0) REVERT: F 348 LYS cc_start: 0.9626 (pttm) cc_final: 0.9195 (pttp) REVERT: G 35 ASP cc_start: 0.8883 (m-30) cc_final: 0.8540 (m-30) REVERT: G 56 GLN cc_start: 0.8298 (tp40) cc_final: 0.8062 (mm-40) REVERT: G 68 SER cc_start: 0.9374 (OUTLIER) cc_final: 0.8885 (t) REVERT: G 81 ASP cc_start: 0.9051 (m-30) cc_final: 0.8811 (m-30) REVERT: G 199 LEU cc_start: 0.9715 (mt) cc_final: 0.9423 (pp) REVERT: G 204 ASN cc_start: 0.8986 (OUTLIER) cc_final: 0.8701 (p0) REVERT: G 236 LEU cc_start: 0.8755 (tp) cc_final: 0.8505 (tp) REVERT: G 255 ASP cc_start: 0.9322 (t0) cc_final: 0.9015 (t70) REVERT: G 273 GLN cc_start: 0.7468 (tt0) cc_final: 0.6966 (tt0) REVERT: G 348 LYS cc_start: 0.9628 (pttm) cc_final: 0.9210 (pttp) outliers start: 106 outliers final: 61 residues processed: 704 average time/residue: 0.1045 time to fit residues: 112.4576 Evaluate side-chains 631 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 555 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 279 ASN Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 327 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 179 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 chunk 173 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN B 337 ASN B 352 ASN C 279 ASN C 337 ASN D 337 ASN E 134 HIS E 352 ASN F 134 HIS F 337 ASN G 279 ASN G 352 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.093177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.074584 restraints weight = 45276.616| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 4.44 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15421 Z= 0.148 Angle : 0.732 8.990 20923 Z= 0.353 Chirality : 0.043 0.175 2485 Planarity : 0.004 0.035 2478 Dihedral : 5.098 75.597 1973 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.39 % Allowed : 1.90 % Favored : 97.70 % Rotamer: Outliers : 3.96 % Allowed : 20.19 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.21), residues: 1785 helix: 2.01 (0.14), residues: 1344 sheet: -1.16 (0.57), residues: 84 loop : 0.03 (0.42), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 75 TYR 0.011 0.001 TYR B 121 PHE 0.026 0.002 PHE C 141 TRP 0.019 0.002 TRP B 74 HIS 0.003 0.001 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00325 (15407) covalent geometry : angle 0.72998 (20895) SS BOND : bond 0.00489 ( 14) SS BOND : angle 1.53971 ( 28) hydrogen bonds : bond 0.04450 ( 1073) hydrogen bonds : angle 4.61647 ( 3066) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 652 time to evaluate : 0.603 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: A 75 ARG cc_start: 0.9195 (ttm-80) cc_final: 0.8591 (mmm-85) REVERT: A 128 ARG cc_start: 0.9024 (mmt90) cc_final: 0.8793 (mmt90) REVERT: A 204 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8414 (p0) REVERT: A 236 LEU cc_start: 0.8377 (tp) cc_final: 0.8035 (tp) REVERT: A 255 ASP cc_start: 0.9332 (t0) cc_final: 0.9094 (t0) REVERT: A 263 GLN cc_start: 0.8169 (tt0) cc_final: 0.7745 (mt0) REVERT: A 265 LYS cc_start: 0.9174 (tttt) cc_final: 0.8946 (tppp) REVERT: A 273 GLN cc_start: 0.7354 (tt0) cc_final: 0.6933 (tt0) REVERT: A 344 TYR cc_start: 0.8028 (t80) cc_final: 0.7807 (t80) REVERT: A 348 LYS cc_start: 0.9631 (pttm) cc_final: 0.9152 (pttp) REVERT: B 35 ASP cc_start: 0.8796 (m-30) cc_final: 0.8528 (m-30) REVERT: B 56 GLN cc_start: 0.8023 (tp40) cc_final: 0.7655 (mm-40) REVERT: B 74 TRP cc_start: 0.8204 (t-100) cc_final: 0.7968 (t-100) REVERT: B 128 ARG cc_start: 0.9044 (mmt90) cc_final: 0.8825 (mmt90) REVERT: B 204 ASN cc_start: 0.8882 (OUTLIER) cc_final: 0.8394 (p0) REVERT: B 236 LEU cc_start: 0.8469 (tp) cc_final: 0.8147 (tp) REVERT: B 263 GLN cc_start: 0.8171 (tt0) cc_final: 0.7728 (mt0) REVERT: B 273 GLN cc_start: 0.7432 (tt0) cc_final: 0.6900 (mt0) REVERT: B 344 TYR cc_start: 0.8296 (t80) cc_final: 0.7847 (t80) REVERT: B 348 LYS cc_start: 0.9652 (pttm) cc_final: 0.9208 (pttt) REVERT: C 35 ASP cc_start: 0.8789 (m-30) cc_final: 0.8550 (m-30) REVERT: C 37 MET cc_start: 0.9109 (tpt) cc_final: 0.8649 (tpp) REVERT: C 51 SER cc_start: 0.9397 (m) cc_final: 0.8995 (p) REVERT: C 56 GLN cc_start: 0.8022 (tp40) cc_final: 0.7592 (mm-40) REVERT: C 75 ARG cc_start: 0.9120 (ttm-80) cc_final: 0.8489 (mmm-85) REVERT: C 199 LEU cc_start: 0.9693 (mt) cc_final: 0.9398 (pp) REVERT: C 204 ASN cc_start: 0.8933 (OUTLIER) cc_final: 0.8464 (p0) REVERT: C 236 LEU cc_start: 0.8458 (tp) cc_final: 0.8152 (tp) REVERT: C 255 ASP cc_start: 0.9294 (t0) cc_final: 0.9077 (t0) REVERT: C 273 GLN cc_start: 0.7325 (tt0) cc_final: 0.6936 (mt0) REVERT: C 274 LEU cc_start: 0.9038 (tp) cc_final: 0.8768 (tp) REVERT: C 340 GLU cc_start: 0.8069 (tp30) cc_final: 0.7737 (mp0) REVERT: D 35 ASP cc_start: 0.8788 (m-30) cc_final: 0.8545 (m-30) REVERT: D 56 GLN cc_start: 0.8180 (tp40) cc_final: 0.7927 (tp40) REVERT: D 74 TRP cc_start: 0.7858 (t60) cc_final: 0.7481 (t-100) REVERT: D 236 LEU cc_start: 0.8498 (tp) cc_final: 0.8132 (tp) REVERT: D 255 ASP cc_start: 0.9394 (t0) cc_final: 0.9182 (t0) REVERT: D 263 GLN cc_start: 0.8211 (tt0) cc_final: 0.7838 (mt0) REVERT: D 273 GLN cc_start: 0.7310 (tt0) cc_final: 0.6875 (tt0) REVERT: D 340 GLU cc_start: 0.8098 (tp30) cc_final: 0.7732 (mp0) REVERT: D 344 TYR cc_start: 0.8052 (t80) cc_final: 0.7596 (t80) REVERT: D 348 LYS cc_start: 0.9677 (pttm) cc_final: 0.9130 (pttt) REVERT: E 35 ASP cc_start: 0.8791 (m-30) cc_final: 0.8590 (m-30) REVERT: E 56 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7704 (mm-40) REVERT: E 75 ARG cc_start: 0.9200 (ttm-80) cc_final: 0.8432 (mmm-85) REVERT: E 128 ARG cc_start: 0.9050 (mmt90) cc_final: 0.8829 (mmt90) REVERT: E 196 GLU cc_start: 0.8565 (tt0) cc_final: 0.8307 (mt-10) REVERT: E 199 LEU cc_start: 0.9724 (mt) cc_final: 0.9468 (pp) REVERT: E 236 LEU cc_start: 0.8405 (tp) cc_final: 0.8063 (tp) REVERT: E 263 GLN cc_start: 0.8189 (tt0) cc_final: 0.7818 (mt0) REVERT: E 273 GLN cc_start: 0.7403 (tt0) cc_final: 0.6869 (mt0) REVERT: E 348 LYS cc_start: 0.9644 (pttm) cc_final: 0.9283 (ptpp) REVERT: F 35 ASP cc_start: 0.8669 (m-30) cc_final: 0.8449 (m-30) REVERT: F 37 MET cc_start: 0.9084 (tpt) cc_final: 0.8625 (tpt) REVERT: F 75 ARG cc_start: 0.9269 (ttm-80) cc_final: 0.8599 (mmm-85) REVERT: F 128 ARG cc_start: 0.9054 (mmt90) cc_final: 0.8837 (mmt90) REVERT: F 204 ASN cc_start: 0.8921 (OUTLIER) cc_final: 0.8391 (p0) REVERT: F 236 LEU cc_start: 0.8423 (tp) cc_final: 0.8081 (tp) REVERT: F 255 ASP cc_start: 0.9310 (t0) cc_final: 0.9067 (t0) REVERT: F 263 GLN cc_start: 0.8140 (tt0) cc_final: 0.7810 (mt0) REVERT: F 273 GLN cc_start: 0.7473 (tt0) cc_final: 0.6996 (mt0) REVERT: F 344 TYR cc_start: 0.7953 (t80) cc_final: 0.7750 (t80) REVERT: F 348 LYS cc_start: 0.9607 (pttm) cc_final: 0.9241 (pttp) REVERT: G 35 ASP cc_start: 0.8855 (m-30) cc_final: 0.8601 (m-30) REVERT: G 56 GLN cc_start: 0.8194 (tp40) cc_final: 0.7685 (mm-40) REVERT: G 74 TRP cc_start: 0.8473 (t60) cc_final: 0.7639 (t60) REVERT: G 81 ASP cc_start: 0.9053 (m-30) cc_final: 0.8806 (m-30) REVERT: G 128 ARG cc_start: 0.9026 (mmt90) cc_final: 0.8804 (mmt90) REVERT: G 204 ASN cc_start: 0.8983 (OUTLIER) cc_final: 0.8446 (p0) REVERT: G 233 TYR cc_start: 0.9141 (t80) cc_final: 0.8832 (t80) REVERT: G 236 LEU cc_start: 0.8461 (tp) cc_final: 0.8101 (tp) REVERT: G 255 ASP cc_start: 0.9310 (t0) cc_final: 0.9086 (t0) REVERT: G 263 GLN cc_start: 0.8157 (tt0) cc_final: 0.7798 (mt0) REVERT: G 265 LYS cc_start: 0.9236 (tttt) cc_final: 0.9033 (tppp) REVERT: G 273 GLN cc_start: 0.7347 (tt0) cc_final: 0.6906 (mt0) REVERT: G 348 LYS cc_start: 0.9613 (pttm) cc_final: 0.9221 (pttp) outliers start: 67 outliers final: 36 residues processed: 680 average time/residue: 0.1095 time to fit residues: 110.6625 Evaluate side-chains 626 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 584 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 352 ASN Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 352 ASN Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 352 ASN Chi-restraints excluded: chain F residue 134 HIS Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 352 ASN Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 279 ASN Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 352 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 61 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 161 optimal weight: 10.0000 chunk 138 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 180 optimal weight: 9.9990 chunk 139 optimal weight: 0.9980 chunk 178 optimal weight: 0.0060 chunk 27 optimal weight: 0.6980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS B 134 HIS C 134 HIS C 279 ASN D 204 ASN F 279 ASN G 134 HIS G 279 ASN G 352 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.097050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.078687 restraints weight = 44216.536| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 4.52 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.5940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15421 Z= 0.143 Angle : 0.729 8.603 20923 Z= 0.355 Chirality : 0.042 0.182 2485 Planarity : 0.004 0.029 2478 Dihedral : 4.138 25.673 1967 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.39 % Allowed : 1.29 % Favored : 98.32 % Rotamer: Outliers : 3.72 % Allowed : 25.32 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.21), residues: 1785 helix: 1.85 (0.14), residues: 1344 sheet: -1.34 (0.54), residues: 84 loop : 0.09 (0.40), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 75 TYR 0.019 0.001 TYR B 121 PHE 0.022 0.002 PHE C 141 TRP 0.014 0.002 TRP F 104 HIS 0.013 0.002 HIS F 134 Details of bonding type rmsd covalent geometry : bond 0.00314 (15407) covalent geometry : angle 0.72774 (20895) SS BOND : bond 0.00347 ( 14) SS BOND : angle 1.31080 ( 28) hydrogen bonds : bond 0.04207 ( 1073) hydrogen bonds : angle 4.55554 ( 3066) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 676 time to evaluate : 0.608 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: A 75 ARG cc_start: 0.9193 (ttm-80) cc_final: 0.8575 (mmm-85) REVERT: A 83 TYR cc_start: 0.9143 (t80) cc_final: 0.8838 (t80) REVERT: A 128 ARG cc_start: 0.9029 (mmt90) cc_final: 0.8796 (mmt90) REVERT: A 199 LEU cc_start: 0.9660 (OUTLIER) cc_final: 0.9414 (pp) REVERT: A 236 LEU cc_start: 0.8314 (tp) cc_final: 0.7952 (tp) REVERT: A 263 GLN cc_start: 0.8169 (tt0) cc_final: 0.7774 (mt0) REVERT: A 273 GLN cc_start: 0.7374 (tt0) cc_final: 0.6949 (mt0) REVERT: B 36 LYS cc_start: 0.8776 (tttt) cc_final: 0.8450 (tptp) REVERT: B 51 SER cc_start: 0.9279 (m) cc_final: 0.8983 (p) REVERT: B 56 GLN cc_start: 0.7895 (tp40) cc_final: 0.7482 (mm-40) REVERT: B 74 TRP cc_start: 0.8199 (t-100) cc_final: 0.7991 (t-100) REVERT: B 128 ARG cc_start: 0.9037 (mmt90) cc_final: 0.8832 (mmt90) REVERT: B 146 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8921 (mm) REVERT: B 199 LEU cc_start: 0.9657 (mt) cc_final: 0.9395 (pp) REVERT: B 263 GLN cc_start: 0.8133 (tt0) cc_final: 0.7806 (mt0) REVERT: B 273 GLN cc_start: 0.7406 (tt0) cc_final: 0.6920 (tt0) REVERT: B 345 LYS cc_start: 0.9158 (mttt) cc_final: 0.8760 (mmtm) REVERT: B 348 LYS cc_start: 0.9634 (pttm) cc_final: 0.9384 (pttp) REVERT: B 351 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: C 37 MET cc_start: 0.9073 (tpt) cc_final: 0.8592 (tpp) REVERT: C 51 SER cc_start: 0.9336 (m) cc_final: 0.8980 (p) REVERT: C 56 GLN cc_start: 0.7875 (tp40) cc_final: 0.7447 (mm-40) REVERT: C 75 ARG cc_start: 0.9133 (ttm-80) cc_final: 0.8605 (mmm-85) REVERT: C 199 LEU cc_start: 0.9646 (mt) cc_final: 0.9336 (pp) REVERT: C 204 ASN cc_start: 0.8805 (m-40) cc_final: 0.8345 (p0) REVERT: C 273 GLN cc_start: 0.7341 (tt0) cc_final: 0.6958 (mt0) REVERT: C 274 LEU cc_start: 0.8967 (tp) cc_final: 0.8654 (tp) REVERT: C 348 LYS cc_start: 0.9647 (pttm) cc_final: 0.9373 (pttp) REVERT: D 74 TRP cc_start: 0.7755 (t60) cc_final: 0.7434 (t-100) REVERT: D 199 LEU cc_start: 0.9618 (mt) cc_final: 0.9349 (pp) REVERT: D 204 ASN cc_start: 0.9021 (m-40) cc_final: 0.8595 (p0) REVERT: D 263 GLN cc_start: 0.8209 (tt0) cc_final: 0.7865 (mt0) REVERT: D 273 GLN cc_start: 0.7263 (tt0) cc_final: 0.6870 (tt0) REVERT: D 348 LYS cc_start: 0.9668 (pttm) cc_final: 0.9367 (pttp) REVERT: D 351 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: E 36 LYS cc_start: 0.8794 (tttt) cc_final: 0.8475 (tptp) REVERT: E 56 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7589 (mm-40) REVERT: E 75 ARG cc_start: 0.9239 (ttm-80) cc_final: 0.8962 (mtp85) REVERT: E 196 GLU cc_start: 0.8471 (tt0) cc_final: 0.8255 (mt-10) REVERT: E 199 LEU cc_start: 0.9659 (mt) cc_final: 0.9415 (pp) REVERT: E 263 GLN cc_start: 0.8195 (tt0) cc_final: 0.7852 (mt0) REVERT: E 273 GLN cc_start: 0.7389 (tt0) cc_final: 0.6940 (tt0) REVERT: E 348 LYS cc_start: 0.9664 (pttm) cc_final: 0.9186 (pttp) REVERT: F 37 MET cc_start: 0.9048 (tpt) cc_final: 0.8561 (tpt) REVERT: F 111 TYR cc_start: 0.8303 (m-10) cc_final: 0.8006 (m-80) REVERT: F 128 ARG cc_start: 0.9060 (mmt90) cc_final: 0.8805 (mmt90) REVERT: F 233 TYR cc_start: 0.8857 (t80) cc_final: 0.8641 (t80) REVERT: F 255 ASP cc_start: 0.9351 (t0) cc_final: 0.9148 (t0) REVERT: F 263 GLN cc_start: 0.8187 (tt0) cc_final: 0.7814 (mt0) REVERT: F 273 GLN cc_start: 0.7442 (tt0) cc_final: 0.7007 (tt0) REVERT: F 348 LYS cc_start: 0.9644 (pttm) cc_final: 0.9286 (pttp) REVERT: G 36 LYS cc_start: 0.8798 (tttt) cc_final: 0.8479 (tptp) REVERT: G 56 GLN cc_start: 0.8053 (tp40) cc_final: 0.7570 (mm-40) REVERT: G 75 ARG cc_start: 0.9396 (mtp85) cc_final: 0.9171 (mmm-85) REVERT: G 128 ARG cc_start: 0.9022 (mmt90) cc_final: 0.8814 (mmt90) REVERT: G 196 GLU cc_start: 0.8326 (tt0) cc_final: 0.8019 (mt-10) REVERT: G 199 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9388 (pp) REVERT: G 204 ASN cc_start: 0.8847 (m-40) cc_final: 0.8422 (p0) REVERT: G 233 TYR cc_start: 0.9103 (t80) cc_final: 0.8810 (t80) REVERT: G 255 ASP cc_start: 0.9352 (t0) cc_final: 0.9146 (t0) REVERT: G 263 GLN cc_start: 0.8150 (tt0) cc_final: 0.7822 (mt0) REVERT: G 273 GLN cc_start: 0.7321 (tt0) cc_final: 0.6953 (tt0) outliers start: 63 outliers final: 39 residues processed: 709 average time/residue: 0.1113 time to fit residues: 117.0991 Evaluate side-chains 655 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 610 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 352 ASN Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 352 ASN Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 134 HIS Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 279 ASN Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 352 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 10 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 122 optimal weight: 0.0770 chunk 44 optimal weight: 2.9990 overall best weight: 1.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 ASN D 134 HIS E 134 HIS E 337 ASN E 352 ASN F 134 HIS G 279 ASN G 352 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.095979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.077549 restraints weight = 45649.538| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 4.55 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.6446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15421 Z= 0.159 Angle : 0.737 10.692 20923 Z= 0.360 Chirality : 0.043 0.199 2485 Planarity : 0.004 0.040 2478 Dihedral : 4.051 28.830 1967 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.39 % Allowed : 1.74 % Favored : 97.87 % Rotamer: Outliers : 4.60 % Allowed : 27.63 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.20), residues: 1785 helix: 1.81 (0.14), residues: 1330 sheet: -1.53 (0.55), residues: 84 loop : -0.07 (0.39), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 216 TYR 0.027 0.002 TYR F 83 PHE 0.018 0.001 PHE B 141 TRP 0.014 0.002 TRP F 104 HIS 0.014 0.002 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00358 (15407) covalent geometry : angle 0.73585 (20895) SS BOND : bond 0.00407 ( 14) SS BOND : angle 1.34020 ( 28) hydrogen bonds : bond 0.04127 ( 1073) hydrogen bonds : angle 4.56093 ( 3066) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 633 time to evaluate : 0.687 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: A 56 GLN cc_start: 0.7922 (tm-30) cc_final: 0.7470 (tp40) REVERT: A 75 ARG cc_start: 0.9232 (ttm-80) cc_final: 0.8994 (mmm-85) REVERT: A 128 ARG cc_start: 0.9094 (mmt90) cc_final: 0.8815 (mmt90) REVERT: A 199 LEU cc_start: 0.9588 (mt) cc_final: 0.9284 (pp) REVERT: A 216 ARG cc_start: 0.9195 (mmp80) cc_final: 0.8982 (tpp-160) REVERT: A 263 GLN cc_start: 0.8169 (tt0) cc_final: 0.7743 (mt0) REVERT: A 273 GLN cc_start: 0.7381 (tt0) cc_final: 0.7003 (tt0) REVERT: B 36 LYS cc_start: 0.8809 (tttt) cc_final: 0.8479 (tptp) REVERT: B 56 GLN cc_start: 0.7885 (tp40) cc_final: 0.7510 (mm-40) REVERT: B 75 ARG cc_start: 0.9334 (ttm-80) cc_final: 0.8548 (mmm-85) REVERT: B 83 TYR cc_start: 0.9250 (t80) cc_final: 0.9010 (t80) REVERT: B 128 ARG cc_start: 0.9061 (mmt90) cc_final: 0.8850 (mmt90) REVERT: B 146 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8907 (mm) REVERT: B 199 LEU cc_start: 0.9619 (mt) cc_final: 0.9353 (pp) REVERT: B 234 PHE cc_start: 0.9226 (t80) cc_final: 0.8848 (t80) REVERT: B 263 GLN cc_start: 0.8174 (tt0) cc_final: 0.7844 (mt0) REVERT: B 273 GLN cc_start: 0.7371 (tt0) cc_final: 0.6724 (tt0) REVERT: B 348 LYS cc_start: 0.9691 (pttm) cc_final: 0.9426 (pttp) REVERT: C 35 ASP cc_start: 0.8513 (m-30) cc_final: 0.7608 (m-30) REVERT: C 37 MET cc_start: 0.9082 (tpt) cc_final: 0.8563 (tpp) REVERT: C 51 SER cc_start: 0.9333 (m) cc_final: 0.8969 (p) REVERT: C 54 PHE cc_start: 0.8266 (t80) cc_final: 0.7912 (t80) REVERT: C 56 GLN cc_start: 0.7958 (tp40) cc_final: 0.7502 (mm-40) REVERT: C 75 ARG cc_start: 0.9189 (ttm-80) cc_final: 0.8610 (mmm-85) REVERT: C 83 TYR cc_start: 0.9165 (t80) cc_final: 0.8909 (t80) REVERT: C 199 LEU cc_start: 0.9586 (mt) cc_final: 0.9340 (pp) REVERT: C 204 ASN cc_start: 0.8822 (m-40) cc_final: 0.8405 (p0) REVERT: C 231 SER cc_start: 0.8966 (t) cc_final: 0.8473 (p) REVERT: C 234 PHE cc_start: 0.9224 (t80) cc_final: 0.8983 (t80) REVERT: C 273 GLN cc_start: 0.7375 (tt0) cc_final: 0.6930 (tt0) REVERT: C 274 LEU cc_start: 0.8994 (tp) cc_final: 0.8701 (tp) REVERT: C 277 LEU cc_start: 0.9325 (tp) cc_final: 0.9014 (tp) REVERT: D 35 ASP cc_start: 0.8513 (m-30) cc_final: 0.7725 (m-30) REVERT: D 51 SER cc_start: 0.9239 (m) cc_final: 0.9030 (p) REVERT: D 74 TRP cc_start: 0.7797 (t60) cc_final: 0.7425 (t-100) REVERT: D 83 TYR cc_start: 0.9188 (t80) cc_final: 0.8745 (t80) REVERT: D 204 ASN cc_start: 0.9006 (m-40) cc_final: 0.8607 (p0) REVERT: D 208 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8638 (mp) REVERT: D 234 PHE cc_start: 0.9262 (t80) cc_final: 0.8821 (t80) REVERT: D 263 GLN cc_start: 0.8250 (tt0) cc_final: 0.7885 (mt0) REVERT: D 273 GLN cc_start: 0.7316 (tt0) cc_final: 0.6630 (tt0) REVERT: D 340 GLU cc_start: 0.8156 (tp30) cc_final: 0.7948 (pm20) REVERT: D 348 LYS cc_start: 0.9661 (OUTLIER) cc_final: 0.9373 (pttp) REVERT: E 35 ASP cc_start: 0.8569 (m-30) cc_final: 0.8077 (m-30) REVERT: E 36 LYS cc_start: 0.8805 (tttt) cc_final: 0.8493 (tptp) REVERT: E 56 GLN cc_start: 0.8012 (tp40) cc_final: 0.7761 (mm-40) REVERT: E 75 ARG cc_start: 0.9245 (ttm-80) cc_final: 0.8982 (mtp85) REVERT: E 83 TYR cc_start: 0.9179 (t80) cc_final: 0.8964 (t80) REVERT: E 143 MET cc_start: 0.9073 (ptm) cc_final: 0.8671 (ptm) REVERT: E 199 LEU cc_start: 0.9640 (mt) cc_final: 0.9387 (pp) REVERT: E 263 GLN cc_start: 0.8246 (tt0) cc_final: 0.7895 (mt0) REVERT: E 273 GLN cc_start: 0.7376 (tt0) cc_final: 0.6951 (tt0) REVERT: E 351 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: F 37 MET cc_start: 0.9048 (tpt) cc_final: 0.8558 (tpt) REVERT: F 51 SER cc_start: 0.9318 (m) cc_final: 0.9118 (p) REVERT: F 128 ARG cc_start: 0.9080 (mmt90) cc_final: 0.8824 (mmt90) REVERT: F 208 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8547 (mp) REVERT: F 263 GLN cc_start: 0.8203 (tt0) cc_final: 0.7815 (mt0) REVERT: F 273 GLN cc_start: 0.7360 (tt0) cc_final: 0.6974 (tt0) REVERT: G 36 LYS cc_start: 0.8801 (tttt) cc_final: 0.8483 (tptp) REVERT: G 56 GLN cc_start: 0.8046 (tp40) cc_final: 0.7759 (mm-40) REVERT: G 74 TRP cc_start: 0.8508 (t60) cc_final: 0.8249 (t60) REVERT: G 128 ARG cc_start: 0.9064 (mmt90) cc_final: 0.8848 (mmt90) REVERT: G 233 TYR cc_start: 0.9125 (t80) cc_final: 0.8912 (t80) REVERT: G 255 ASP cc_start: 0.9407 (t0) cc_final: 0.9183 (t70) REVERT: G 263 GLN cc_start: 0.8150 (tt0) cc_final: 0.7827 (mt0) REVERT: G 273 GLN cc_start: 0.7330 (tt0) cc_final: 0.6956 (tt0) outliers start: 78 outliers final: 57 residues processed: 666 average time/residue: 0.1131 time to fit residues: 111.5779 Evaluate side-chains 627 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 565 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 104 TRP Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 134 HIS Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 104 TRP Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 351 GLU Chi-restraints excluded: chain E residue 352 ASN Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 134 HIS Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 352 ASN Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 352 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 72 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 HIS B 134 HIS D 273 GLN E 134 HIS F 134 HIS G 134 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.098095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.079940 restraints weight = 45176.490| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 4.66 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.6844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15421 Z= 0.149 Angle : 0.737 8.397 20923 Z= 0.359 Chirality : 0.042 0.188 2485 Planarity : 0.004 0.027 2478 Dihedral : 4.019 27.449 1967 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.39 % Allowed : 1.85 % Favored : 97.76 % Rotamer: Outliers : 4.55 % Allowed : 28.93 % Favored : 66.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.20), residues: 1785 helix: 1.75 (0.14), residues: 1330 sheet: None (None), residues: 0 loop : -0.25 (0.33), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 216 TYR 0.026 0.002 TYR G 83 PHE 0.020 0.001 PHE E 234 TRP 0.025 0.002 TRP B 74 HIS 0.005 0.001 HIS F 134 Details of bonding type rmsd covalent geometry : bond 0.00336 (15407) covalent geometry : angle 0.73584 (20895) SS BOND : bond 0.00328 ( 14) SS BOND : angle 1.24581 ( 28) hydrogen bonds : bond 0.03987 ( 1073) hydrogen bonds : angle 4.54336 ( 3066) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 611 time to evaluate : 0.619 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: A 56 GLN cc_start: 0.7941 (tm-30) cc_final: 0.7469 (tp40) REVERT: A 128 ARG cc_start: 0.9108 (mmt90) cc_final: 0.8835 (mmt90) REVERT: A 199 LEU cc_start: 0.9562 (mt) cc_final: 0.9279 (pp) REVERT: A 216 ARG cc_start: 0.9220 (mmp80) cc_final: 0.8881 (mmp80) REVERT: A 273 GLN cc_start: 0.7359 (tt0) cc_final: 0.6968 (tt0) REVERT: B 56 GLN cc_start: 0.7831 (tp40) cc_final: 0.7424 (mm-40) REVERT: B 74 TRP cc_start: 0.8173 (t-100) cc_final: 0.7917 (t-100) REVERT: B 75 ARG cc_start: 0.9324 (ttm-80) cc_final: 0.9108 (mmm-85) REVERT: B 128 ARG cc_start: 0.9053 (mmt90) cc_final: 0.8839 (mmt90) REVERT: B 146 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8887 (mm) REVERT: B 199 LEU cc_start: 0.9599 (mt) cc_final: 0.9356 (pp) REVERT: B 208 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8579 (mp) REVERT: B 234 PHE cc_start: 0.9191 (t80) cc_final: 0.8674 (t80) REVERT: B 263 GLN cc_start: 0.8147 (tt0) cc_final: 0.7835 (mt0) REVERT: B 273 GLN cc_start: 0.7363 (tt0) cc_final: 0.6723 (tt0) REVERT: B 348 LYS cc_start: 0.9713 (OUTLIER) cc_final: 0.9447 (pttp) REVERT: C 51 SER cc_start: 0.9297 (m) cc_final: 0.8932 (p) REVERT: C 56 GLN cc_start: 0.7870 (tp40) cc_final: 0.7468 (mm-40) REVERT: C 75 ARG cc_start: 0.9193 (ttm-80) cc_final: 0.8659 (mmm-85) REVERT: C 199 LEU cc_start: 0.9575 (mt) cc_final: 0.9335 (pp) REVERT: C 204 ASN cc_start: 0.8806 (m-40) cc_final: 0.8344 (p0) REVERT: C 231 SER cc_start: 0.8890 (t) cc_final: 0.8412 (p) REVERT: C 234 PHE cc_start: 0.9209 (t80) cc_final: 0.8925 (t80) REVERT: C 273 GLN cc_start: 0.7382 (tt0) cc_final: 0.6928 (tt0) REVERT: C 274 LEU cc_start: 0.8957 (tp) cc_final: 0.8641 (tp) REVERT: C 277 LEU cc_start: 0.9285 (tp) cc_final: 0.8942 (tp) REVERT: C 348 LYS cc_start: 0.9630 (pttm) cc_final: 0.9416 (pttp) REVERT: D 74 TRP cc_start: 0.7770 (t60) cc_final: 0.7399 (t-100) REVERT: D 104 TRP cc_start: 0.7462 (OUTLIER) cc_final: 0.7221 (m100) REVERT: D 199 LEU cc_start: 0.9558 (mt) cc_final: 0.9272 (pp) REVERT: D 204 ASN cc_start: 0.8979 (m-40) cc_final: 0.8605 (p0) REVERT: D 208 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8617 (mp) REVERT: D 234 PHE cc_start: 0.9257 (t80) cc_final: 0.8789 (t80) REVERT: D 247 ILE cc_start: 0.9575 (pt) cc_final: 0.9188 (mt) REVERT: D 263 GLN cc_start: 0.8247 (tt0) cc_final: 0.7894 (mt0) REVERT: D 273 GLN cc_start: 0.7397 (tt0) cc_final: 0.6553 (tt0) REVERT: D 348 LYS cc_start: 0.9676 (OUTLIER) cc_final: 0.9426 (pttt) REVERT: E 56 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7756 (mm-40) REVERT: E 139 LEU cc_start: 0.9552 (mt) cc_final: 0.9348 (mm) REVERT: E 143 MET cc_start: 0.9033 (ptm) cc_final: 0.8613 (ptm) REVERT: E 199 LEU cc_start: 0.9639 (mt) cc_final: 0.9386 (pp) REVERT: E 208 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8808 (mp) REVERT: E 263 GLN cc_start: 0.8223 (tt0) cc_final: 0.7868 (mt0) REVERT: E 273 GLN cc_start: 0.7386 (tt0) cc_final: 0.7101 (tt0) REVERT: E 348 LYS cc_start: 0.9702 (pttm) cc_final: 0.9457 (pttp) REVERT: E 351 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: F 37 MET cc_start: 0.9033 (tpt) cc_final: 0.8511 (tpt) REVERT: F 45 LEU cc_start: 0.9388 (tp) cc_final: 0.9187 (tp) REVERT: F 83 TYR cc_start: 0.9216 (t80) cc_final: 0.8964 (t80) REVERT: F 128 ARG cc_start: 0.9060 (mmt90) cc_final: 0.8835 (mmt90) REVERT: F 199 LEU cc_start: 0.9566 (mt) cc_final: 0.9287 (pp) REVERT: F 216 ARG cc_start: 0.8907 (mmp80) cc_final: 0.8609 (tpp80) REVERT: F 234 PHE cc_start: 0.9240 (t80) cc_final: 0.9001 (t80) REVERT: F 263 GLN cc_start: 0.8182 (tt0) cc_final: 0.7793 (mt0) REVERT: F 273 GLN cc_start: 0.7371 (tt0) cc_final: 0.6874 (mt0) REVERT: G 56 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7755 (mm-40) REVERT: G 75 ARG cc_start: 0.9433 (mtp85) cc_final: 0.8452 (mmm-85) REVERT: G 128 ARG cc_start: 0.9043 (mmt90) cc_final: 0.8799 (mmt90) REVERT: G 199 LEU cc_start: 0.9554 (mt) cc_final: 0.9294 (pp) REVERT: G 233 TYR cc_start: 0.9082 (t80) cc_final: 0.8872 (t80) REVERT: G 273 GLN cc_start: 0.7325 (tt0) cc_final: 0.6977 (tt0) outliers start: 77 outliers final: 51 residues processed: 649 average time/residue: 0.1126 time to fit residues: 109.4926 Evaluate side-chains 630 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 569 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 348 LYS Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 104 TRP Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 104 TRP Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 351 GLU Chi-restraints excluded: chain E residue 352 ASN Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 104 TRP Chi-restraints excluded: chain F residue 134 HIS Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 134 HIS Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 352 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 118 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 173 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 174 optimal weight: 0.0870 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 HIS B 134 HIS ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS E 134 HIS F 134 HIS G 134 HIS G 352 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.097475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.078819 restraints weight = 45261.392| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 4.67 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.7139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15421 Z= 0.154 Angle : 0.739 7.884 20923 Z= 0.363 Chirality : 0.042 0.169 2485 Planarity : 0.004 0.051 2478 Dihedral : 3.995 27.085 1967 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.39 % Allowed : 1.62 % Favored : 97.98 % Rotamer: Outliers : 5.02 % Allowed : 30.99 % Favored : 63.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.20), residues: 1785 helix: 1.70 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -0.29 (0.34), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 216 TYR 0.033 0.001 TYR G 83 PHE 0.016 0.001 PHE G 116 TRP 0.014 0.002 TRP A 104 HIS 0.007 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00348 (15407) covalent geometry : angle 0.73827 (20895) SS BOND : bond 0.00378 ( 14) SS BOND : angle 1.27719 ( 28) hydrogen bonds : bond 0.03840 ( 1073) hydrogen bonds : angle 4.61160 ( 3066) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 580 time to evaluate : 0.600 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: A 45 LEU cc_start: 0.9414 (tp) cc_final: 0.9208 (tp) REVERT: A 56 GLN cc_start: 0.7904 (tm-30) cc_final: 0.7409 (tp40) REVERT: A 128 ARG cc_start: 0.9098 (mmt90) cc_final: 0.8838 (mmt90) REVERT: A 199 LEU cc_start: 0.9552 (mt) cc_final: 0.9277 (pp) REVERT: A 216 ARG cc_start: 0.9238 (mmp80) cc_final: 0.8919 (mmp80) REVERT: A 263 GLN cc_start: 0.8129 (tt0) cc_final: 0.7847 (mt0) REVERT: A 273 GLN cc_start: 0.7225 (tt0) cc_final: 0.6877 (tt0) REVERT: B 56 GLN cc_start: 0.7796 (tp40) cc_final: 0.7414 (mm-40) REVERT: B 75 ARG cc_start: 0.9323 (ttm-80) cc_final: 0.9110 (mmm-85) REVERT: B 199 LEU cc_start: 0.9567 (mt) cc_final: 0.9295 (pp) REVERT: B 208 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8560 (mp) REVERT: B 234 PHE cc_start: 0.9187 (t80) cc_final: 0.8883 (t80) REVERT: B 263 GLN cc_start: 0.8152 (tt0) cc_final: 0.7837 (mt0) REVERT: B 348 LYS cc_start: 0.9729 (OUTLIER) cc_final: 0.9452 (pttp) REVERT: C 51 SER cc_start: 0.9334 (m) cc_final: 0.8992 (p) REVERT: C 54 PHE cc_start: 0.8189 (t80) cc_final: 0.7662 (t80) REVERT: C 56 GLN cc_start: 0.7916 (tp40) cc_final: 0.7571 (mm-40) REVERT: C 75 ARG cc_start: 0.9176 (ttm-80) cc_final: 0.8687 (mmm-85) REVERT: C 199 LEU cc_start: 0.9541 (mt) cc_final: 0.9313 (pp) REVERT: C 231 SER cc_start: 0.8892 (t) cc_final: 0.8405 (p) REVERT: C 234 PHE cc_start: 0.9167 (t80) cc_final: 0.8922 (t80) REVERT: C 263 GLN cc_start: 0.8418 (tt0) cc_final: 0.8092 (mt0) REVERT: C 273 GLN cc_start: 0.7346 (tt0) cc_final: 0.6928 (tt0) REVERT: C 274 LEU cc_start: 0.9007 (tp) cc_final: 0.8703 (tp) REVERT: C 344 TYR cc_start: 0.7008 (t80) cc_final: 0.6608 (t80) REVERT: C 348 LYS cc_start: 0.9693 (pttm) cc_final: 0.9361 (ptpp) REVERT: D 35 ASP cc_start: 0.8500 (m-30) cc_final: 0.8029 (t0) REVERT: D 74 TRP cc_start: 0.7724 (t60) cc_final: 0.7387 (t-100) REVERT: D 199 LEU cc_start: 0.9538 (mt) cc_final: 0.9269 (pp) REVERT: D 204 ASN cc_start: 0.9016 (m-40) cc_final: 0.8628 (p0) REVERT: D 208 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8577 (mp) REVERT: D 234 PHE cc_start: 0.9242 (t80) cc_final: 0.8769 (t80) REVERT: D 247 ILE cc_start: 0.9562 (pt) cc_final: 0.9177 (mt) REVERT: D 263 GLN cc_start: 0.8261 (tt0) cc_final: 0.7927 (mt0) REVERT: D 273 GLN cc_start: 0.7452 (tt0) cc_final: 0.6581 (mt0) REVERT: D 348 LYS cc_start: 0.9676 (OUTLIER) cc_final: 0.9422 (pttt) REVERT: E 36 LYS cc_start: 0.8694 (tttt) cc_final: 0.8327 (tptp) REVERT: E 51 SER cc_start: 0.9227 (m) cc_final: 0.9024 (p) REVERT: E 56 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7773 (mm-40) REVERT: E 139 LEU cc_start: 0.9551 (mt) cc_final: 0.9346 (mm) REVERT: E 143 MET cc_start: 0.9031 (ptm) cc_final: 0.8625 (ptm) REVERT: E 199 LEU cc_start: 0.9636 (mt) cc_final: 0.9388 (pp) REVERT: E 208 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8790 (mp) REVERT: E 263 GLN cc_start: 0.8198 (tt0) cc_final: 0.7840 (mt0) REVERT: E 273 GLN cc_start: 0.7442 (tt0) cc_final: 0.7102 (tt0) REVERT: E 348 LYS cc_start: 0.9701 (OUTLIER) cc_final: 0.9467 (pttp) REVERT: F 128 ARG cc_start: 0.9098 (mmt90) cc_final: 0.8863 (mmt90) REVERT: F 199 LEU cc_start: 0.9563 (mt) cc_final: 0.9277 (pp) REVERT: F 216 ARG cc_start: 0.9117 (mmp80) cc_final: 0.8569 (tpp80) REVERT: F 234 PHE cc_start: 0.9230 (t80) cc_final: 0.8937 (t80) REVERT: F 263 GLN cc_start: 0.8158 (tt0) cc_final: 0.7817 (mt0) REVERT: G 35 ASP cc_start: 0.8549 (m-30) cc_final: 0.8065 (t0) REVERT: G 54 PHE cc_start: 0.8311 (t80) cc_final: 0.7892 (t80) REVERT: G 56 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7766 (mm-40) REVERT: G 75 ARG cc_start: 0.9433 (mtp85) cc_final: 0.8480 (mmm-85) REVERT: G 128 ARG cc_start: 0.9038 (mmt90) cc_final: 0.8798 (mmt90) REVERT: G 199 LEU cc_start: 0.9558 (mt) cc_final: 0.9284 (pp) REVERT: G 233 TYR cc_start: 0.9053 (t80) cc_final: 0.8756 (t80) REVERT: G 263 GLN cc_start: 0.8111 (tt0) cc_final: 0.7828 (mt0) REVERT: G 273 GLN cc_start: 0.7357 (tt0) cc_final: 0.6994 (tt0) outliers start: 85 outliers final: 60 residues processed: 622 average time/residue: 0.1183 time to fit residues: 109.1444 Evaluate side-chains 615 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 547 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 348 LYS Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 104 TRP Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 134 HIS Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 104 TRP Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 348 LYS Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 104 TRP Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 352 ASN Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 104 TRP Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 351 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 176 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 165 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 130 optimal weight: 0.4980 chunk 52 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 134 HIS B 134 HIS ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.099178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.080167 restraints weight = 45659.164| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 4.75 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.7505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15421 Z= 0.144 Angle : 0.756 10.952 20923 Z= 0.368 Chirality : 0.042 0.175 2485 Planarity : 0.003 0.048 2478 Dihedral : 3.979 25.708 1967 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.39 % Allowed : 1.85 % Favored : 97.76 % Rotamer: Outliers : 4.19 % Allowed : 32.53 % Favored : 63.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.20), residues: 1785 helix: 1.62 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -0.33 (0.34), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 216 TYR 0.026 0.001 TYR G 83 PHE 0.015 0.001 PHE B 109 TRP 0.017 0.002 TRP B 74 HIS 0.008 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00322 (15407) covalent geometry : angle 0.75507 (20895) SS BOND : bond 0.00280 ( 14) SS BOND : angle 1.12820 ( 28) hydrogen bonds : bond 0.03845 ( 1073) hydrogen bonds : angle 4.63266 ( 3066) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 591 time to evaluate : 0.607 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: A 128 ARG cc_start: 0.9065 (mmt90) cc_final: 0.8808 (mmt90) REVERT: A 196 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8071 (mt-10) REVERT: A 199 LEU cc_start: 0.9570 (mt) cc_final: 0.9290 (pp) REVERT: A 204 ASN cc_start: 0.8839 (m-40) cc_final: 0.8338 (p0) REVERT: A 216 ARG cc_start: 0.9230 (mmp80) cc_final: 0.8988 (mmp80) REVERT: A 263 GLN cc_start: 0.8107 (tt0) cc_final: 0.7876 (mt0) REVERT: A 273 GLN cc_start: 0.7154 (tt0) cc_final: 0.6953 (tt0) REVERT: B 35 ASP cc_start: 0.8569 (m-30) cc_final: 0.8118 (t0) REVERT: B 36 LYS cc_start: 0.8784 (tttt) cc_final: 0.8470 (tptp) REVERT: B 56 GLN cc_start: 0.7583 (tp40) cc_final: 0.7204 (mm-40) REVERT: B 104 TRP cc_start: 0.7481 (OUTLIER) cc_final: 0.7223 (m100) REVERT: B 199 LEU cc_start: 0.9577 (mt) cc_final: 0.9319 (pp) REVERT: B 208 LEU cc_start: 0.8911 (mt) cc_final: 0.8514 (mp) REVERT: B 234 PHE cc_start: 0.9157 (t80) cc_final: 0.8672 (t80) REVERT: B 263 GLN cc_start: 0.8123 (tt0) cc_final: 0.7825 (mt0) REVERT: B 273 GLN cc_start: 0.7398 (tt0) cc_final: 0.6695 (tt0) REVERT: B 348 LYS cc_start: 0.9722 (OUTLIER) cc_final: 0.9451 (pttp) REVERT: C 45 LEU cc_start: 0.8892 (tp) cc_final: 0.8652 (tt) REVERT: C 54 PHE cc_start: 0.8093 (t80) cc_final: 0.7684 (t80) REVERT: C 75 ARG cc_start: 0.9119 (ttm-80) cc_final: 0.8707 (mmm-85) REVERT: C 199 LEU cc_start: 0.9504 (mt) cc_final: 0.9240 (pp) REVERT: C 204 ASN cc_start: 0.8856 (m-40) cc_final: 0.8378 (p0) REVERT: C 231 SER cc_start: 0.8892 (t) cc_final: 0.8419 (p) REVERT: C 234 PHE cc_start: 0.9115 (t80) cc_final: 0.8880 (t80) REVERT: C 263 GLN cc_start: 0.8369 (tt0) cc_final: 0.8068 (mt0) REVERT: C 273 GLN cc_start: 0.7337 (tt0) cc_final: 0.6965 (tt0) REVERT: C 274 LEU cc_start: 0.8937 (tp) cc_final: 0.8553 (tp) REVERT: C 348 LYS cc_start: 0.9710 (pttm) cc_final: 0.9357 (ptpp) REVERT: D 74 TRP cc_start: 0.7649 (t60) cc_final: 0.7324 (t-100) REVERT: D 104 TRP cc_start: 0.7516 (OUTLIER) cc_final: 0.7302 (m100) REVERT: D 196 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8010 (mt-10) REVERT: D 199 LEU cc_start: 0.9541 (mt) cc_final: 0.9250 (pp) REVERT: D 204 ASN cc_start: 0.9102 (m-40) cc_final: 0.8678 (p0) REVERT: D 216 ARG cc_start: 0.9121 (mmt-90) cc_final: 0.8876 (mmp80) REVERT: D 234 PHE cc_start: 0.9179 (t80) cc_final: 0.8771 (t80) REVERT: D 273 GLN cc_start: 0.7451 (tt0) cc_final: 0.6549 (mt0) REVERT: D 348 LYS cc_start: 0.9693 (OUTLIER) cc_final: 0.9445 (pttt) REVERT: E 36 LYS cc_start: 0.8631 (tttt) cc_final: 0.8264 (tptp) REVERT: E 54 PHE cc_start: 0.8085 (t80) cc_final: 0.7881 (t80) REVERT: E 56 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7732 (mm110) REVERT: E 75 ARG cc_start: 0.9220 (ttm-80) cc_final: 0.9000 (ttm-80) REVERT: E 139 LEU cc_start: 0.9552 (mt) cc_final: 0.9337 (mm) REVERT: E 143 MET cc_start: 0.9019 (ptm) cc_final: 0.8633 (ptm) REVERT: E 199 LEU cc_start: 0.9637 (mt) cc_final: 0.9402 (pp) REVERT: E 263 GLN cc_start: 0.8139 (tt0) cc_final: 0.7776 (mt0) REVERT: E 273 GLN cc_start: 0.7440 (tt0) cc_final: 0.7015 (tt0) REVERT: E 348 LYS cc_start: 0.9705 (pttm) cc_final: 0.9474 (pttp) REVERT: F 128 ARG cc_start: 0.9072 (mmt90) cc_final: 0.8831 (mmt90) REVERT: F 199 LEU cc_start: 0.9553 (mt) cc_final: 0.9288 (pp) REVERT: F 216 ARG cc_start: 0.9123 (mmp80) cc_final: 0.8668 (tpp80) REVERT: F 234 PHE cc_start: 0.9189 (t80) cc_final: 0.8837 (t80) REVERT: F 263 GLN cc_start: 0.8167 (tt0) cc_final: 0.7859 (mt0) REVERT: F 273 GLN cc_start: 0.7354 (tt0) cc_final: 0.6918 (mt0) REVERT: G 35 ASP cc_start: 0.8687 (m-30) cc_final: 0.8293 (t0) REVERT: G 36 LYS cc_start: 0.8718 (tttt) cc_final: 0.8409 (tptp) REVERT: G 56 GLN cc_start: 0.7946 (tp40) cc_final: 0.7672 (mm110) REVERT: G 128 ARG cc_start: 0.9045 (mmt90) cc_final: 0.8835 (mmt90) REVERT: G 199 LEU cc_start: 0.9571 (mt) cc_final: 0.9339 (pp) REVERT: G 233 TYR cc_start: 0.8960 (t80) cc_final: 0.8718 (t80) REVERT: G 263 GLN cc_start: 0.8119 (tt0) cc_final: 0.7847 (mt0) REVERT: G 273 GLN cc_start: 0.7298 (tt0) cc_final: 0.6984 (tt0) outliers start: 71 outliers final: 42 residues processed: 628 average time/residue: 0.1121 time to fit residues: 104.6619 Evaluate side-chains 594 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 547 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 348 LYS Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 104 TRP Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 134 HIS Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 104 TRP Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 351 GLU Chi-restraints excluded: chain F residue 104 TRP Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 352 ASN Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 134 HIS Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 351 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 54 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 chunk 174 optimal weight: 0.3980 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 179 optimal weight: 0.5980 chunk 62 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.099798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.081189 restraints weight = 44563.722| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 4.68 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.7850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15421 Z= 0.152 Angle : 0.812 18.852 20923 Z= 0.391 Chirality : 0.043 0.233 2485 Planarity : 0.003 0.024 2478 Dihedral : 3.986 26.289 1967 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.39 % Allowed : 2.02 % Favored : 97.59 % Rotamer: Outliers : 3.42 % Allowed : 33.29 % Favored : 63.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.20), residues: 1785 helix: 1.54 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -0.32 (0.33), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 216 TYR 0.022 0.001 TYR G 83 PHE 0.027 0.001 PHE A 234 TRP 0.052 0.003 TRP A 104 HIS 0.015 0.001 HIS D 134 Details of bonding type rmsd covalent geometry : bond 0.00350 (15407) covalent geometry : angle 0.81098 (20895) SS BOND : bond 0.00291 ( 14) SS BOND : angle 1.14652 ( 28) hydrogen bonds : bond 0.03948 ( 1073) hydrogen bonds : angle 4.68556 ( 3066) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 582 time to evaluate : 0.598 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: A 104 TRP cc_start: 0.8679 (m100) cc_final: 0.8414 (m100) REVERT: A 109 PHE cc_start: 0.9219 (t80) cc_final: 0.8985 (t80) REVERT: A 128 ARG cc_start: 0.9062 (mmt90) cc_final: 0.8808 (mmt90) REVERT: A 152 ARG cc_start: 0.8898 (mtm180) cc_final: 0.8660 (ttp80) REVERT: A 196 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8126 (mt-10) REVERT: A 199 LEU cc_start: 0.9544 (mt) cc_final: 0.9275 (pp) REVERT: A 204 ASN cc_start: 0.8791 (m-40) cc_final: 0.8269 (p0) REVERT: A 263 GLN cc_start: 0.8113 (tt0) cc_final: 0.7899 (mt0) REVERT: A 273 GLN cc_start: 0.7223 (tt0) cc_final: 0.6847 (tt0) REVERT: A 348 LYS cc_start: 0.9687 (pttm) cc_final: 0.9378 (ptpp) REVERT: B 36 LYS cc_start: 0.8844 (tttt) cc_final: 0.8547 (tptp) REVERT: B 56 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.6998 (mm-40) REVERT: B 196 GLU cc_start: 0.8301 (tt0) cc_final: 0.8069 (mt-10) REVERT: B 199 LEU cc_start: 0.9544 (mt) cc_final: 0.9304 (pp) REVERT: B 234 PHE cc_start: 0.9110 (t80) cc_final: 0.8748 (t80) REVERT: B 263 GLN cc_start: 0.8105 (tt0) cc_final: 0.7878 (mt0) REVERT: B 273 GLN cc_start: 0.7333 (tt0) cc_final: 0.6431 (tt0) REVERT: B 348 LYS cc_start: 0.9714 (OUTLIER) cc_final: 0.9435 (pttp) REVERT: C 35 ASP cc_start: 0.8448 (m-30) cc_final: 0.8042 (t0) REVERT: C 36 LYS cc_start: 0.8750 (tttt) cc_final: 0.8425 (tptp) REVERT: C 51 SER cc_start: 0.9330 (m) cc_final: 0.9129 (m) REVERT: C 54 PHE cc_start: 0.8042 (t80) cc_final: 0.7661 (t80) REVERT: C 75 ARG cc_start: 0.9114 (ttm-80) cc_final: 0.8739 (mmm-85) REVERT: C 199 LEU cc_start: 0.9477 (mt) cc_final: 0.9230 (pp) REVERT: C 204 ASN cc_start: 0.8813 (m-40) cc_final: 0.8312 (p0) REVERT: C 231 SER cc_start: 0.8899 (t) cc_final: 0.8415 (p) REVERT: C 234 PHE cc_start: 0.9115 (t80) cc_final: 0.8763 (t80) REVERT: C 263 GLN cc_start: 0.8330 (tt0) cc_final: 0.8049 (mt0) REVERT: C 273 GLN cc_start: 0.7330 (tt0) cc_final: 0.6900 (tt0) REVERT: C 274 LEU cc_start: 0.8913 (tp) cc_final: 0.8613 (tp) REVERT: C 277 LEU cc_start: 0.9214 (tp) cc_final: 0.8868 (tp) REVERT: D 36 LYS cc_start: 0.8857 (tttt) cc_final: 0.8570 (tptp) REVERT: D 74 TRP cc_start: 0.7608 (t60) cc_final: 0.7246 (t-100) REVERT: D 152 ARG cc_start: 0.8868 (mtm180) cc_final: 0.8606 (ttp80) REVERT: D 199 LEU cc_start: 0.9512 (mt) cc_final: 0.9255 (pp) REVERT: D 204 ASN cc_start: 0.9062 (m-40) cc_final: 0.8632 (p0) REVERT: D 231 SER cc_start: 0.8978 (t) cc_final: 0.8506 (p) REVERT: D 234 PHE cc_start: 0.9162 (t80) cc_final: 0.8758 (t80) REVERT: D 247 ILE cc_start: 0.9521 (pt) cc_final: 0.9102 (mt) REVERT: D 263 GLN cc_start: 0.8125 (tt0) cc_final: 0.7903 (mt0) REVERT: D 273 GLN cc_start: 0.7506 (tt0) cc_final: 0.6594 (tt0) REVERT: D 348 LYS cc_start: 0.9676 (OUTLIER) cc_final: 0.9399 (pttt) REVERT: E 36 LYS cc_start: 0.8635 (tttt) cc_final: 0.8255 (tptp) REVERT: E 75 ARG cc_start: 0.9219 (ttm-80) cc_final: 0.8903 (ttm-80) REVERT: E 139 LEU cc_start: 0.9548 (mt) cc_final: 0.9324 (mt) REVERT: E 143 MET cc_start: 0.8999 (ptm) cc_final: 0.8599 (ptm) REVERT: E 199 LEU cc_start: 0.9617 (mt) cc_final: 0.9379 (pp) REVERT: E 263 GLN cc_start: 0.8143 (tt0) cc_final: 0.7806 (mt0) REVERT: E 273 GLN cc_start: 0.7383 (tt0) cc_final: 0.7102 (tt0) REVERT: E 348 LYS cc_start: 0.9694 (pttm) cc_final: 0.9452 (pttp) REVERT: F 83 TYR cc_start: 0.9130 (t80) cc_final: 0.8902 (t80) REVERT: F 128 ARG cc_start: 0.9059 (mmt90) cc_final: 0.8821 (mmt90) REVERT: F 199 LEU cc_start: 0.9524 (mt) cc_final: 0.9287 (pp) REVERT: F 234 PHE cc_start: 0.9236 (t80) cc_final: 0.8971 (t80) REVERT: F 263 GLN cc_start: 0.8184 (tt0) cc_final: 0.7899 (mt0) REVERT: F 273 GLN cc_start: 0.7323 (tt0) cc_final: 0.6836 (mt0) REVERT: G 35 ASP cc_start: 0.8662 (m-30) cc_final: 0.8348 (t0) REVERT: G 36 LYS cc_start: 0.8748 (tttt) cc_final: 0.8445 (tptp) REVERT: G 56 GLN cc_start: 0.7879 (tp40) cc_final: 0.7582 (mm110) REVERT: G 128 ARG cc_start: 0.9052 (mmt90) cc_final: 0.8819 (mmt90) REVERT: G 199 LEU cc_start: 0.9549 (mt) cc_final: 0.9306 (pp) REVERT: G 263 GLN cc_start: 0.8118 (tt0) cc_final: 0.7852 (mt0) REVERT: G 273 GLN cc_start: 0.7301 (tt0) cc_final: 0.7005 (tt0) REVERT: G 292 TYR cc_start: 0.8941 (t80) cc_final: 0.8696 (t80) outliers start: 58 outliers final: 45 residues processed: 611 average time/residue: 0.1048 time to fit residues: 95.9757 Evaluate side-chains 593 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 545 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 348 LYS Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 104 TRP Chi-restraints excluded: chain D residue 134 HIS Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain E residue 104 TRP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 351 GLU Chi-restraints excluded: chain F residue 104 TRP Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 352 ASN Chi-restraints excluded: chain G residue 104 TRP Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 134 HIS Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 351 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 87 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 181 optimal weight: 0.5980 chunk 140 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.099274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.080852 restraints weight = 45030.607| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 4.78 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.8015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15421 Z= 0.164 Angle : 0.855 18.555 20923 Z= 0.411 Chirality : 0.044 0.259 2485 Planarity : 0.004 0.038 2478 Dihedral : 4.024 26.102 1967 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.39 % Allowed : 2.02 % Favored : 97.59 % Rotamer: Outliers : 2.89 % Allowed : 34.71 % Favored : 62.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.20), residues: 1785 helix: 1.53 (0.14), residues: 1330 sheet: None (None), residues: 0 loop : -0.28 (0.32), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 152 TYR 0.020 0.001 TYR G 150 PHE 0.021 0.001 PHE C 109 TRP 0.050 0.003 TRP A 104 HIS 0.011 0.001 HIS D 134 Details of bonding type rmsd covalent geometry : bond 0.00386 (15407) covalent geometry : angle 0.85443 (20895) SS BOND : bond 0.00340 ( 14) SS BOND : angle 1.25245 ( 28) hydrogen bonds : bond 0.03995 ( 1073) hydrogen bonds : angle 4.77568 ( 3066) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 548 time to evaluate : 0.534 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: A 104 TRP cc_start: 0.8691 (m100) cc_final: 0.8441 (m100) REVERT: A 128 ARG cc_start: 0.9080 (mmt90) cc_final: 0.8827 (mmt90) REVERT: A 152 ARG cc_start: 0.8860 (mtm180) cc_final: 0.8650 (ttp80) REVERT: A 199 LEU cc_start: 0.9519 (mt) cc_final: 0.9260 (pp) REVERT: A 204 ASN cc_start: 0.8784 (m-40) cc_final: 0.8254 (p0) REVERT: A 216 ARG cc_start: 0.9043 (mmp80) cc_final: 0.8715 (mmp80) REVERT: A 263 GLN cc_start: 0.8167 (tt0) cc_final: 0.7933 (mt0) REVERT: A 348 LYS cc_start: 0.9699 (pttm) cc_final: 0.9364 (ptpp) REVERT: B 36 LYS cc_start: 0.8881 (tttt) cc_final: 0.8592 (tptp) REVERT: B 56 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.7097 (mm-40) REVERT: B 75 ARG cc_start: 0.9376 (mmm-85) cc_final: 0.8640 (mmm-85) REVERT: B 152 ARG cc_start: 0.8906 (mtm180) cc_final: 0.8629 (ttp80) REVERT: B 199 LEU cc_start: 0.9490 (mt) cc_final: 0.9242 (pp) REVERT: B 215 CYS cc_start: 0.9250 (m) cc_final: 0.8708 (t) REVERT: B 234 PHE cc_start: 0.9125 (t80) cc_final: 0.8580 (t80) REVERT: B 263 GLN cc_start: 0.8120 (tt0) cc_final: 0.7878 (mt0) REVERT: B 348 LYS cc_start: 0.9718 (OUTLIER) cc_final: 0.9439 (pttp) REVERT: C 35 ASP cc_start: 0.8523 (m-30) cc_final: 0.8140 (t0) REVERT: C 36 LYS cc_start: 0.8812 (tttt) cc_final: 0.8472 (tptp) REVERT: C 51 SER cc_start: 0.9294 (m) cc_final: 0.8927 (p) REVERT: C 54 PHE cc_start: 0.8163 (t80) cc_final: 0.7902 (t80) REVERT: C 75 ARG cc_start: 0.9160 (ttm-80) cc_final: 0.8724 (mmm-85) REVERT: C 81 ASP cc_start: 0.8965 (m-30) cc_final: 0.8699 (m-30) REVERT: C 104 TRP cc_start: 0.8848 (m100) cc_final: 0.8605 (m100) REVERT: C 199 LEU cc_start: 0.9458 (mt) cc_final: 0.9229 (pp) REVERT: C 204 ASN cc_start: 0.8825 (m-40) cc_final: 0.8315 (p0) REVERT: C 231 SER cc_start: 0.8923 (t) cc_final: 0.8446 (p) REVERT: C 234 PHE cc_start: 0.9107 (t80) cc_final: 0.8761 (t80) REVERT: C 263 GLN cc_start: 0.8379 (tt0) cc_final: 0.8091 (mt0) REVERT: C 273 GLN cc_start: 0.7317 (tt0) cc_final: 0.6840 (tt0) REVERT: C 274 LEU cc_start: 0.8934 (tp) cc_final: 0.8640 (tp) REVERT: C 277 LEU cc_start: 0.9172 (tp) cc_final: 0.8839 (tp) REVERT: D 36 LYS cc_start: 0.8904 (tttt) cc_final: 0.8613 (tptp) REVERT: D 74 TRP cc_start: 0.7591 (t60) cc_final: 0.7235 (t-100) REVERT: D 152 ARG cc_start: 0.8822 (mtm180) cc_final: 0.8515 (ttp80) REVERT: D 199 LEU cc_start: 0.9457 (mt) cc_final: 0.9213 (pp) REVERT: D 204 ASN cc_start: 0.8997 (m-40) cc_final: 0.8566 (p0) REVERT: D 215 CYS cc_start: 0.9252 (m) cc_final: 0.8872 (t) REVERT: D 231 SER cc_start: 0.8989 (t) cc_final: 0.8516 (p) REVERT: D 234 PHE cc_start: 0.9180 (t80) cc_final: 0.8738 (t80) REVERT: D 247 ILE cc_start: 0.9524 (pt) cc_final: 0.9099 (mt) REVERT: D 263 GLN cc_start: 0.8161 (tt0) cc_final: 0.7957 (mt0) REVERT: D 273 GLN cc_start: 0.7517 (tt0) cc_final: 0.6571 (tt0) REVERT: D 348 LYS cc_start: 0.9692 (OUTLIER) cc_final: 0.9390 (pttt) REVERT: E 36 LYS cc_start: 0.8642 (tttt) cc_final: 0.8286 (tptp) REVERT: E 75 ARG cc_start: 0.9269 (ttm-80) cc_final: 0.8537 (mmm-85) REVERT: E 139 LEU cc_start: 0.9561 (mt) cc_final: 0.9330 (mt) REVERT: E 143 MET cc_start: 0.9005 (ptm) cc_final: 0.8599 (ptm) REVERT: E 199 LEU cc_start: 0.9597 (mt) cc_final: 0.9352 (pp) REVERT: E 263 GLN cc_start: 0.8174 (tt0) cc_final: 0.7820 (mt0) REVERT: E 273 GLN cc_start: 0.7345 (tt0) cc_final: 0.7086 (tt0) REVERT: E 348 LYS cc_start: 0.9706 (OUTLIER) cc_final: 0.9458 (pttp) REVERT: F 35 ASP cc_start: 0.8817 (m-30) cc_final: 0.8440 (m-30) REVERT: F 36 LYS cc_start: 0.8776 (tttt) cc_final: 0.8421 (tptp) REVERT: F 81 ASP cc_start: 0.8912 (m-30) cc_final: 0.8645 (m-30) REVERT: F 128 ARG cc_start: 0.9089 (mmt90) cc_final: 0.8849 (mmt90) REVERT: F 199 LEU cc_start: 0.9505 (mt) cc_final: 0.9256 (pp) REVERT: F 215 CYS cc_start: 0.9271 (m) cc_final: 0.8978 (t) REVERT: F 234 PHE cc_start: 0.9238 (t80) cc_final: 0.8953 (t80) REVERT: F 263 GLN cc_start: 0.8217 (tt0) cc_final: 0.7868 (mt0) REVERT: F 348 LYS cc_start: 0.9666 (pttm) cc_final: 0.9300 (ptpp) REVERT: G 36 LYS cc_start: 0.8795 (tttt) cc_final: 0.8500 (tptp) REVERT: G 56 GLN cc_start: 0.7974 (tp40) cc_final: 0.7646 (mm-40) REVERT: G 75 ARG cc_start: 0.9367 (mtp85) cc_final: 0.8470 (mmm-85) REVERT: G 128 ARG cc_start: 0.9065 (mmt90) cc_final: 0.8836 (mmt90) REVERT: G 199 LEU cc_start: 0.9547 (mt) cc_final: 0.9290 (pp) REVERT: G 215 CYS cc_start: 0.9366 (m) cc_final: 0.9000 (t) REVERT: G 263 GLN cc_start: 0.8165 (tt0) cc_final: 0.7874 (mt0) REVERT: G 273 GLN cc_start: 0.7344 (tt0) cc_final: 0.6983 (tt0) REVERT: G 348 LYS cc_start: 0.9678 (pttm) cc_final: 0.9263 (ptpp) outliers start: 49 outliers final: 43 residues processed: 572 average time/residue: 0.1151 time to fit residues: 97.4072 Evaluate side-chains 574 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 527 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 348 LYS Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 104 TRP Chi-restraints excluded: chain D residue 134 HIS Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain E residue 104 TRP Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 348 LYS Chi-restraints excluded: chain E residue 351 GLU Chi-restraints excluded: chain F residue 104 TRP Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 352 ASN Chi-restraints excluded: chain G residue 104 TRP Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 134 HIS Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 351 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 126 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.100354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.081253 restraints weight = 45041.717| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 4.78 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.8196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15421 Z= 0.158 Angle : 0.866 18.082 20923 Z= 0.416 Chirality : 0.044 0.206 2485 Planarity : 0.004 0.088 2478 Dihedral : 4.035 25.961 1967 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.39 % Allowed : 1.96 % Favored : 97.65 % Rotamer: Outliers : 3.01 % Allowed : 34.59 % Favored : 62.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.20), residues: 1785 helix: 1.44 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -0.24 (0.33), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 152 TYR 0.021 0.001 TYR G 150 PHE 0.020 0.001 PHE G 234 TRP 0.048 0.003 TRP A 104 HIS 0.006 0.001 HIS D 134 Details of bonding type rmsd covalent geometry : bond 0.00364 (15407) covalent geometry : angle 0.86556 (20895) SS BOND : bond 0.00305 ( 14) SS BOND : angle 1.16319 ( 28) hydrogen bonds : bond 0.04004 ( 1073) hydrogen bonds : angle 4.75372 ( 3066) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3037.47 seconds wall clock time: 53 minutes 20.25 seconds (3200.25 seconds total)