Starting phenix.real_space_refine on Sun Aug 24 01:05:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz6_45054/08_2025/9bz6_45054_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz6_45054/08_2025/9bz6_45054.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bz6_45054/08_2025/9bz6_45054_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz6_45054/08_2025/9bz6_45054_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bz6_45054/08_2025/9bz6_45054.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz6_45054/08_2025/9bz6_45054.map" } resolution = 3.87 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= -0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.39, per 1000 atoms: 0.21 Number of scatterers: 16038 At special positions: 0 Unit cell: (94.302, 137.904, 130.806, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 911.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.985A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.954A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.665A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.694A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.627A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.074A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.676A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.645A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.729A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.027A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.068A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.544A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.567A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.669A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.359A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.478A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.479A pdb=" N LEU A 656 " --> pdb=" O ARG A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.184A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.048A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 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: 3.16 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4683 1.33 - 1.46: 3123 1.46 - 1.58: 8399 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.061 1.25e-02 6.40e+03 2.37e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.579 -0.039 1.20e-02 6.94e+03 1.07e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.033 1.08e-02 8.57e+03 9.10e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.570 -0.032 1.17e-02 7.31e+03 7.72e+00 bond pdb=" CA ILE C 35 " pdb=" CB ILE C 35 " ideal model delta sigma weight residual 1.537 1.568 -0.031 1.21e-02 6.83e+03 6.66e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21579 2.09 - 4.19: 512 4.19 - 6.28: 36 6.28 - 8.37: 3 8.37 - 10.46: 4 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.61 -6.07 1.36e+00 5.41e-01 1.99e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.16 -4.45 1.15e+00 7.56e-01 1.50e+01 angle pdb=" N SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.21 -3.93 1.09e+00 8.42e-01 1.30e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.85 -4.35 1.23e+00 6.61e-01 1.25e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.48 3.71 1.06e+00 8.90e-01 1.22e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 9471 35.79 - 71.59: 336 71.59 - 107.38: 37 107.38 - 143.17: 3 143.17 - 178.96: 3 Dihedral angle restraints: 9850 sinusoidal: 4092 harmonic: 5758 Sorted by residual: dihedral pdb=" C2 TTP A 803 " pdb=" C1' TTP A 803 " pdb=" N1 TTP A 803 " pdb=" O4' TTP A 803 " ideal model delta sinusoidal sigma weight residual -58.32 120.65 -178.96 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 TTP B 801 " pdb=" C1' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " ideal model delta sinusoidal sigma weight residual 301.68 151.18 150.50 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" C5' TTP A 803 " pdb=" O5' TTP A 803 " pdb=" PA TTP A 803 " pdb=" O3A TTP A 803 " ideal model delta sinusoidal sigma weight residual 179.97 31.90 148.07 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 9847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2147 0.093 - 0.187: 181 0.187 - 0.280: 27 0.280 - 0.374: 3 0.374 - 0.467: 2 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.45e+00 chirality pdb=" CA TYR C 169 " pdb=" N TYR C 169 " pdb=" C TYR C 169 " pdb=" CB TYR C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " 0.017 2.00e-02 2.50e+03 1.10e-02 2.13e+00 pdb=" CG PHE D 92 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 169 " 0.017 2.00e-02 2.50e+03 9.80e-03 1.92e+00 pdb=" CG TYR C 169 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 169 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 169 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 169 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 169 " 0.008 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 130 2.51 - 3.11: 11571 3.11 - 3.70: 27063 3.70 - 4.30: 41557 4.30 - 4.90: 65468 Nonbonded interactions: 145789 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.013 3.040 ... (remaining 145784 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 16.470 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 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 : 0.006 0.061 16386 Z= 0.316 Angle : 0.740 10.463 22134 Z= 0.463 Chirality : 0.058 0.467 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.907 178.963 6154 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.34 % Allowed : 15.27 % Favored : 83.39 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.18), residues: 1932 helix: 0.59 (0.14), residues: 1151 sheet: 0.46 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 196 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE C 168 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.74027 (22134) hydrogen bonds : bond 0.15421 ( 871) hydrogen bonds : angle 6.51761 ( 2571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1091 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 1068 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.8399 (mt) cc_final: 0.7103 (mp) REVERT: A 76 ASP cc_start: 0.8141 (m-30) cc_final: 0.7769 (m-30) REVERT: A 172 LEU cc_start: 0.9016 (mp) cc_final: 0.8790 (mp) REVERT: A 188 ILE cc_start: 0.8484 (mt) cc_final: 0.8198 (mt) REVERT: A 258 ILE cc_start: 0.8967 (tp) cc_final: 0.8687 (tp) REVERT: A 267 ILE cc_start: 0.8497 (mp) cc_final: 0.7406 (mm) REVERT: A 345 LYS cc_start: 0.8631 (tttt) cc_final: 0.8418 (ttmm) REVERT: A 378 PHE cc_start: 0.8737 (p90) cc_final: 0.8535 (p90) REVERT: A 447 ASN cc_start: 0.7436 (m-40) cc_final: 0.6479 (m-40) REVERT: A 501 GLN cc_start: 0.8009 (tt0) cc_final: 0.7771 (tt0) REVERT: A 550 MET cc_start: 0.7374 (mtm) cc_final: 0.7104 (mtm) REVERT: A 597 ILE cc_start: 0.8819 (pt) cc_final: 0.8570 (pt) REVERT: A 618 LEU cc_start: 0.9315 (tp) cc_final: 0.9090 (tt) REVERT: A 624 PHE cc_start: 0.6889 (t80) cc_final: 0.6471 (t80) REVERT: A 630 TYR cc_start: 0.7985 (m-80) cc_final: 0.7422 (m-80) REVERT: B 11 GLN cc_start: 0.7869 (mt0) cc_final: 0.7568 (mt0) REVERT: B 27 ASP cc_start: 0.8050 (p0) cc_final: 0.7847 (p0) REVERT: B 157 LEU cc_start: 0.8567 (tp) cc_final: 0.8311 (tp) REVERT: B 172 LEU cc_start: 0.9171 (mp) cc_final: 0.8957 (mp) REVERT: B 177 ASP cc_start: 0.8070 (t0) cc_final: 0.7364 (t0) REVERT: B 204 SER cc_start: 0.8823 (m) cc_final: 0.8307 (t) REVERT: B 288 PHE cc_start: 0.8348 (t80) cc_final: 0.7495 (t80) REVERT: B 294 GLU cc_start: 0.6937 (mt-10) cc_final: 0.5187 (mt-10) REVERT: B 295 ASP cc_start: 0.7755 (t0) cc_final: 0.7390 (t0) REVERT: B 366 LYS cc_start: 0.8551 (ptpp) cc_final: 0.8316 (ptmt) REVERT: B 376 VAL cc_start: 0.9423 (t) cc_final: 0.9180 (m) REVERT: B 384 GLU cc_start: 0.8925 (pm20) cc_final: 0.8285 (pm20) REVERT: B 387 GLN cc_start: 0.7499 (mt0) cc_final: 0.7208 (mt0) REVERT: B 435 SER cc_start: 0.9153 (p) cc_final: 0.8911 (p) REVERT: B 480 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6877 (mt-10) REVERT: B 543 ILE cc_start: 0.8870 (mm) cc_final: 0.8653 (mm) REVERT: B 550 MET cc_start: 0.7979 (mtm) cc_final: 0.7718 (mtp) REVERT: B 597 ILE cc_start: 0.9119 (pt) cc_final: 0.8876 (pt) REVERT: C 24 GLN cc_start: 0.6658 (tp40) cc_final: 0.6407 (tp40) REVERT: C 112 LEU cc_start: 0.3589 (mt) cc_final: 0.3258 (mt) REVERT: C 118 ILE cc_start: 0.6611 (mt) cc_final: 0.6395 (mt) REVERT: C 163 LEU cc_start: 0.6487 (tt) cc_final: 0.6168 (tt) REVERT: D 80 HIS cc_start: 0.7053 (m-70) cc_final: 0.6700 (m170) REVERT: D 104 SER cc_start: 0.7255 (m) cc_final: 0.6974 (m) REVERT: D 119 ASN cc_start: 0.5381 (m-40) cc_final: 0.5118 (m-40) REVERT: D 125 VAL cc_start: 0.6417 (t) cc_final: 0.6130 (p) REVERT: D 131 LEU cc_start: 0.5783 (tp) cc_final: 0.5203 (tt) REVERT: D 195 LEU cc_start: 0.7591 (tt) cc_final: 0.7239 (tt) outliers start: 23 outliers final: 7 residues processed: 1072 average time/residue: 0.1424 time to fit residues: 222.3791 Evaluate side-chains 743 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 736 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.0670 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.6980 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 312 GLN A 370 ASN A 410 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 320 ASN B 329 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN B 676 HIS C 24 GLN C 28 GLN C 127 GLN C 234 GLN C 263 ASN D 28 GLN D 71 ASN D 80 HIS ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.131184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.096607 restraints weight = 36782.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.100500 restraints weight = 17485.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.103093 restraints weight = 10421.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.104916 restraints weight = 7166.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.106173 restraints weight = 5395.195| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16386 Z= 0.174 Angle : 0.725 12.081 22134 Z= 0.378 Chirality : 0.046 0.263 2360 Planarity : 0.004 0.035 2818 Dihedral : 11.521 178.665 2253 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 4.14 % Allowed : 21.10 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.18), residues: 1932 helix: 1.16 (0.15), residues: 1136 sheet: 1.02 (0.47), residues: 96 loop : 0.31 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 243 TYR 0.052 0.002 TYR D 262 PHE 0.041 0.003 PHE C 168 TRP 0.025 0.002 TRP D 30 HIS 0.010 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00390 (16386) covalent geometry : angle 0.72518 (22134) hydrogen bonds : bond 0.05053 ( 871) hydrogen bonds : angle 5.37343 ( 2571) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 780 time to evaluate : 0.455 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: A 39 ASP cc_start: 0.8904 (m-30) cc_final: 0.8637 (m-30) REVERT: A 51 LEU cc_start: 0.9254 (tp) cc_final: 0.9002 (tp) REVERT: A 75 GLU cc_start: 0.8520 (tm-30) cc_final: 0.7445 (pp20) REVERT: A 76 ASP cc_start: 0.9136 (m-30) cc_final: 0.8369 (m-30) REVERT: A 172 LEU cc_start: 0.9429 (mp) cc_final: 0.9196 (mp) REVERT: A 202 ASN cc_start: 0.9550 (t0) cc_final: 0.8882 (t0) REVERT: A 221 LYS cc_start: 0.9314 (mmtp) cc_final: 0.8997 (mttp) REVERT: A 290 GLU cc_start: 0.9307 (tt0) cc_final: 0.8982 (tm-30) REVERT: A 322 MET cc_start: 0.8613 (mmt) cc_final: 0.8271 (mmm) REVERT: A 335 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8030 (mt-10) REVERT: A 378 PHE cc_start: 0.9260 (p90) cc_final: 0.8858 (p90) REVERT: A 384 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7390 (pm20) REVERT: A 386 LEU cc_start: 0.9241 (mt) cc_final: 0.9027 (mt) REVERT: A 447 ASN cc_start: 0.8386 (m-40) cc_final: 0.8101 (m-40) REVERT: A 561 LEU cc_start: 0.9159 (tp) cc_final: 0.8840 (tp) REVERT: A 597 ILE cc_start: 0.9313 (pt) cc_final: 0.9113 (pt) REVERT: A 618 LEU cc_start: 0.9526 (tp) cc_final: 0.9159 (tt) REVERT: A 639 ASP cc_start: 0.8455 (m-30) cc_final: 0.8073 (m-30) REVERT: A 662 MET cc_start: 0.8721 (ptp) cc_final: 0.8365 (ptp) REVERT: A 663 THR cc_start: 0.9456 (OUTLIER) cc_final: 0.9232 (t) REVERT: A 668 ASN cc_start: 0.9459 (m-40) cc_final: 0.9156 (m-40) REVERT: A 684 TYR cc_start: 0.7911 (OUTLIER) cc_final: 0.7365 (m-10) REVERT: B 15 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8330 (tp30) REVERT: B 87 LYS cc_start: 0.9260 (tptm) cc_final: 0.9025 (tppt) REVERT: B 172 LEU cc_start: 0.9377 (mp) cc_final: 0.9044 (mp) REVERT: B 181 ASP cc_start: 0.8815 (m-30) cc_final: 0.8562 (m-30) REVERT: B 211 GLU cc_start: 0.8517 (mm-30) cc_final: 0.7922 (mm-30) REVERT: B 288 PHE cc_start: 0.9278 (t80) cc_final: 0.8914 (t80) REVERT: B 290 GLU cc_start: 0.7986 (tp30) cc_final: 0.7781 (tp30) REVERT: B 350 ARG cc_start: 0.8517 (mtp85) cc_final: 0.7969 (mtp85) REVERT: B 355 TYR cc_start: 0.8227 (m-80) cc_final: 0.7684 (m-80) REVERT: B 361 GLN cc_start: 0.9007 (tt0) cc_final: 0.8451 (tt0) REVERT: B 378 PHE cc_start: 0.9315 (p90) cc_final: 0.9104 (p90) REVERT: B 399 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8203 (tp30) REVERT: B 415 ASN cc_start: 0.9450 (t0) cc_final: 0.9248 (t0) REVERT: B 425 ILE cc_start: 0.9440 (mt) cc_final: 0.9005 (mt) REVERT: B 493 MET cc_start: 0.9667 (tmm) cc_final: 0.9194 (tmm) REVERT: B 496 ASN cc_start: 0.9626 (t0) cc_final: 0.9412 (t0) REVERT: B 515 ASP cc_start: 0.9061 (m-30) cc_final: 0.8751 (m-30) REVERT: B 543 ILE cc_start: 0.9492 (mm) cc_final: 0.9168 (mm) REVERT: B 550 MET cc_start: 0.8001 (mtm) cc_final: 0.7749 (mtm) REVERT: B 558 TRP cc_start: 0.9496 (m100) cc_final: 0.8626 (m100) REVERT: B 588 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8932 (mm-40) REVERT: B 598 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.7982 (mtm) REVERT: B 599 GLU cc_start: 0.8510 (pt0) cc_final: 0.8274 (pt0) REVERT: B 604 ARG cc_start: 0.8408 (mmp80) cc_final: 0.8142 (mmt-90) REVERT: B 621 ASN cc_start: 0.9498 (p0) cc_final: 0.9294 (p0) REVERT: B 686 ARG cc_start: 0.8292 (mtp-110) cc_final: 0.7689 (mtp-110) REVERT: C 86 ARG cc_start: 0.8257 (mtt180) cc_final: 0.7830 (mpt180) REVERT: C 109 PHE cc_start: 0.8757 (m-80) cc_final: 0.8545 (m-80) REVERT: C 116 GLU cc_start: 0.9088 (pm20) cc_final: 0.8873 (pm20) REVERT: C 122 PHE cc_start: 0.8885 (m-80) cc_final: 0.8512 (m-80) REVERT: C 163 LEU cc_start: 0.9453 (tt) cc_final: 0.9107 (tt) REVERT: C 185 MET cc_start: 0.7920 (mmm) cc_final: 0.7489 (mmm) REVERT: C 237 GLU cc_start: 0.9518 (pt0) cc_final: 0.9135 (pp20) REVERT: C 255 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8357 (m-30) REVERT: C 268 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9232 (mt) REVERT: C 269 MET cc_start: 0.9505 (tmm) cc_final: 0.9222 (tmm) REVERT: C 271 LEU cc_start: 0.9341 (mt) cc_final: 0.9040 (mt) REVERT: D 18 THR cc_start: 0.9010 (p) cc_final: 0.8284 (m) REVERT: D 24 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8382 (mp10) REVERT: D 33 GLU cc_start: 0.9223 (mp0) cc_final: 0.8907 (pp20) REVERT: D 92 PHE cc_start: 0.8184 (t80) cc_final: 0.7843 (t80) REVERT: D 131 LEU cc_start: 0.7688 (tp) cc_final: 0.7329 (tt) REVERT: D 137 MET cc_start: 0.9194 (mtt) cc_final: 0.8942 (mtp) REVERT: D 178 PHE cc_start: 0.8932 (m-80) cc_final: 0.8581 (m-80) REVERT: D 184 LEU cc_start: 0.8630 (mt) cc_final: 0.8301 (mt) REVERT: D 231 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9171 (mm) REVERT: D 233 ASN cc_start: 0.9025 (m110) cc_final: 0.8808 (p0) REVERT: D 241 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8392 (mp0) REVERT: D 242 TYR cc_start: 0.8230 (t80) cc_final: 0.7718 (t80) REVERT: D 259 PHE cc_start: 0.8279 (t80) cc_final: 0.7411 (t80) REVERT: D 262 TYR cc_start: 0.9005 (t80) cc_final: 0.8769 (t80) outliers start: 71 outliers final: 31 residues processed: 807 average time/residue: 0.1094 time to fit residues: 132.2662 Evaluate side-chains 754 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 716 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 231 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 182 optimal weight: 0.6980 chunk 159 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN D 181 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.129187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.095562 restraints weight = 37051.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.099269 restraints weight = 17299.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.101644 restraints weight = 10237.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.103320 restraints weight = 7073.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104588 restraints weight = 5321.535| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16386 Z= 0.198 Angle : 0.701 12.966 22134 Z= 0.362 Chirality : 0.046 0.168 2360 Planarity : 0.004 0.038 2818 Dihedral : 11.385 176.791 2247 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.37 % Allowed : 22.96 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.19), residues: 1932 helix: 1.05 (0.15), residues: 1156 sheet: 0.06 (0.42), residues: 128 loop : 0.31 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 243 TYR 0.043 0.002 TYR D 262 PHE 0.052 0.002 PHE D 172 TRP 0.013 0.002 TRP D 30 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00439 (16386) covalent geometry : angle 0.70133 (22134) hydrogen bonds : bond 0.04501 ( 871) hydrogen bonds : angle 5.29912 ( 2571) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 752 time to evaluate : 0.632 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: A 8 LYS cc_start: 0.8894 (tttm) cc_final: 0.8636 (tppt) REVERT: A 12 LEU cc_start: 0.9413 (mt) cc_final: 0.9022 (mt) REVERT: A 39 ASP cc_start: 0.8981 (m-30) cc_final: 0.8775 (m-30) REVERT: A 76 ASP cc_start: 0.9128 (m-30) cc_final: 0.8598 (m-30) REVERT: A 150 GLN cc_start: 0.9092 (tp40) cc_final: 0.8649 (tp40) REVERT: A 163 ARG cc_start: 0.8005 (tpp80) cc_final: 0.7771 (mmm-85) REVERT: A 220 THR cc_start: 0.9406 (m) cc_final: 0.9064 (p) REVERT: A 221 LYS cc_start: 0.9350 (mmtp) cc_final: 0.9013 (mttp) REVERT: A 243 ARG cc_start: 0.8015 (ptm-80) cc_final: 0.7728 (ppt170) REVERT: A 252 ASN cc_start: 0.9249 (t0) cc_final: 0.9035 (t0) REVERT: A 259 ASN cc_start: 0.8929 (m-40) cc_final: 0.8724 (m110) REVERT: A 290 GLU cc_start: 0.9313 (tt0) cc_final: 0.8975 (tm-30) REVERT: A 335 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8031 (mt-10) REVERT: A 390 GLN cc_start: 0.8724 (mt0) cc_final: 0.8419 (mt0) REVERT: A 393 SER cc_start: 0.9653 (m) cc_final: 0.9408 (t) REVERT: A 444 ASP cc_start: 0.8582 (t0) cc_final: 0.7112 (t0) REVERT: A 446 ARG cc_start: 0.7455 (mtp85) cc_final: 0.6900 (mmm160) REVERT: A 447 ASN cc_start: 0.8495 (m-40) cc_final: 0.8187 (m-40) REVERT: A 459 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.8887 (mtmm) REVERT: A 493 MET cc_start: 0.9047 (tmm) cc_final: 0.8738 (tmm) REVERT: A 515 ASP cc_start: 0.9041 (m-30) cc_final: 0.8791 (m-30) REVERT: A 528 PHE cc_start: 0.8997 (m-80) cc_final: 0.8654 (m-80) REVERT: A 558 TRP cc_start: 0.9333 (m100) cc_final: 0.8823 (m100) REVERT: A 590 SER cc_start: 0.9528 (t) cc_final: 0.9016 (p) REVERT: A 597 ILE cc_start: 0.9357 (pt) cc_final: 0.9124 (pt) REVERT: A 639 ASP cc_start: 0.8677 (m-30) cc_final: 0.8214 (m-30) REVERT: A 640 MET cc_start: 0.9462 (OUTLIER) cc_final: 0.8500 (tpp) REVERT: A 654 PHE cc_start: 0.9396 (t80) cc_final: 0.8874 (t80) REVERT: A 668 ASN cc_start: 0.9537 (m-40) cc_final: 0.9308 (m-40) REVERT: A 684 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.7357 (m-10) REVERT: B 99 LYS cc_start: 0.9182 (mmtt) cc_final: 0.8625 (mmmm) REVERT: B 150 GLN cc_start: 0.9176 (tp40) cc_final: 0.8962 (tp40) REVERT: B 172 LEU cc_start: 0.9450 (mp) cc_final: 0.9133 (mp) REVERT: B 235 ARG cc_start: 0.8841 (mtm110) cc_final: 0.8280 (mtm110) REVERT: B 288 PHE cc_start: 0.9284 (t80) cc_final: 0.9039 (t80) REVERT: B 344 GLU cc_start: 0.8874 (pt0) cc_final: 0.8569 (pp20) REVERT: B 355 TYR cc_start: 0.8440 (m-80) cc_final: 0.7748 (m-80) REVERT: B 361 GLN cc_start: 0.9132 (tt0) cc_final: 0.8884 (tt0) REVERT: B 374 SER cc_start: 0.9076 (t) cc_final: 0.8520 (p) REVERT: B 399 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8211 (tp30) REVERT: B 407 ILE cc_start: 0.8854 (mt) cc_final: 0.8653 (mt) REVERT: B 415 ASN cc_start: 0.9445 (t0) cc_final: 0.9176 (t0) REVERT: B 446 ARG cc_start: 0.7807 (ttm-80) cc_final: 0.7524 (mmm-85) REVERT: B 458 MET cc_start: 0.9336 (mmm) cc_final: 0.9069 (mmp) REVERT: B 493 MET cc_start: 0.9647 (tmm) cc_final: 0.9389 (tmm) REVERT: B 515 ASP cc_start: 0.9083 (m-30) cc_final: 0.8697 (m-30) REVERT: B 543 ILE cc_start: 0.9522 (mm) cc_final: 0.9175 (mm) REVERT: B 550 MET cc_start: 0.8263 (mtm) cc_final: 0.7878 (mtm) REVERT: B 558 TRP cc_start: 0.9618 (m100) cc_final: 0.8771 (m100) REVERT: B 588 GLN cc_start: 0.9344 (mm-40) cc_final: 0.8851 (mm-40) REVERT: B 599 GLU cc_start: 0.8531 (pt0) cc_final: 0.8290 (pt0) REVERT: B 610 LYS cc_start: 0.8845 (mtpp) cc_final: 0.8608 (mtpp) REVERT: B 686 ARG cc_start: 0.8317 (mtp-110) cc_final: 0.7625 (mtp85) REVERT: C 66 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8482 (t70) REVERT: C 86 ARG cc_start: 0.8468 (mtt180) cc_final: 0.8007 (mpt180) REVERT: C 95 MET cc_start: 0.8592 (tmm) cc_final: 0.8082 (tmm) REVERT: C 122 PHE cc_start: 0.8797 (m-80) cc_final: 0.8381 (m-80) REVERT: C 174 TYR cc_start: 0.8815 (OUTLIER) cc_final: 0.7466 (t80) REVERT: C 242 TYR cc_start: 0.9325 (t80) cc_final: 0.8867 (t80) REVERT: C 268 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9175 (mt) REVERT: C 269 MET cc_start: 0.9520 (tmm) cc_final: 0.9237 (tmm) REVERT: D 24 GLN cc_start: 0.8913 (mm-40) cc_final: 0.8428 (mp10) REVERT: D 74 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.7072 (tpt) REVERT: D 92 PHE cc_start: 0.8391 (t80) cc_final: 0.7912 (t80) REVERT: D 109 PHE cc_start: 0.8541 (m-80) cc_final: 0.8161 (m-80) REVERT: D 128 ASN cc_start: 0.9072 (t0) cc_final: 0.8660 (m-40) REVERT: D 137 MET cc_start: 0.9344 (mtt) cc_final: 0.9053 (mtp) REVERT: D 164 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7211 (mm-30) REVERT: D 178 PHE cc_start: 0.8813 (m-80) cc_final: 0.7774 (m-80) REVERT: D 184 LEU cc_start: 0.8783 (mt) cc_final: 0.8542 (mt) REVERT: D 198 GLU cc_start: 0.8976 (mm-30) cc_final: 0.7930 (mm-30) REVERT: D 224 LEU cc_start: 0.8784 (mm) cc_final: 0.8566 (mm) REVERT: D 259 PHE cc_start: 0.8449 (t80) cc_final: 0.7491 (t80) REVERT: D 265 ASN cc_start: 0.8943 (m110) cc_final: 0.8635 (m110) outliers start: 75 outliers final: 44 residues processed: 785 average time/residue: 0.1174 time to fit residues: 138.9067 Evaluate side-chains 728 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 677 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 309 LYS Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 287 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 185 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 438 HIS ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN D 25 ASN D 28 GLN D 233 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.118246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.085857 restraints weight = 38073.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.089203 restraints weight = 18093.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.091388 restraints weight = 10849.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.092927 restraints weight = 7497.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.093951 restraints weight = 5727.269| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.6218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 16386 Z= 0.334 Angle : 0.779 13.108 22134 Z= 0.407 Chirality : 0.048 0.291 2360 Planarity : 0.005 0.057 2818 Dihedral : 11.370 173.734 2244 Min Nonbonded Distance : 1.672 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 5.83 % Allowed : 25.23 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.18), residues: 1932 helix: 0.76 (0.15), residues: 1162 sheet: -0.40 (0.38), residues: 152 loop : -0.02 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 121 TYR 0.043 0.002 TYR D 142 PHE 0.048 0.003 PHE C 109 TRP 0.020 0.002 TRP C 44 HIS 0.007 0.002 HIS A 647 Details of bonding type rmsd covalent geometry : bond 0.00718 (16386) covalent geometry : angle 0.77906 (22134) hydrogen bonds : bond 0.04517 ( 871) hydrogen bonds : angle 5.50006 ( 2571) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 712 time to evaluate : 0.639 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: A 51 LEU cc_start: 0.9496 (tp) cc_final: 0.9207 (tp) REVERT: A 147 GLN cc_start: 0.9298 (mt0) cc_final: 0.8723 (mt0) REVERT: A 163 ARG cc_start: 0.8238 (tpp80) cc_final: 0.7974 (mmm-85) REVERT: A 166 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8626 (mm-30) REVERT: A 178 SER cc_start: 0.8655 (OUTLIER) cc_final: 0.8399 (t) REVERT: A 243 ARG cc_start: 0.8022 (ptm-80) cc_final: 0.7718 (ppt170) REVERT: A 251 LEU cc_start: 0.9503 (tp) cc_final: 0.9066 (tp) REVERT: A 252 ASN cc_start: 0.9391 (t0) cc_final: 0.9190 (t0) REVERT: A 290 GLU cc_start: 0.9319 (tt0) cc_final: 0.9059 (tm-30) REVERT: A 312 GLN cc_start: 0.8517 (mp10) cc_final: 0.8211 (mp10) REVERT: A 335 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8085 (mt-10) REVERT: A 384 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.7563 (pm20) REVERT: A 390 GLN cc_start: 0.8842 (mt0) cc_final: 0.8501 (mt0) REVERT: A 406 ASP cc_start: 0.8104 (m-30) cc_final: 0.7890 (m-30) REVERT: A 444 ASP cc_start: 0.8606 (t0) cc_final: 0.8003 (t0) REVERT: A 446 ARG cc_start: 0.7646 (mtp85) cc_final: 0.7190 (mmm160) REVERT: A 456 LYS cc_start: 0.9492 (ttmm) cc_final: 0.9180 (mtmm) REVERT: A 459 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.9085 (mtmm) REVERT: A 590 SER cc_start: 0.9494 (t) cc_final: 0.9237 (p) REVERT: A 597 ILE cc_start: 0.9322 (pt) cc_final: 0.9058 (pt) REVERT: A 618 LEU cc_start: 0.9500 (tp) cc_final: 0.9235 (tt) REVERT: A 639 ASP cc_start: 0.8814 (m-30) cc_final: 0.8205 (m-30) REVERT: A 640 MET cc_start: 0.9512 (OUTLIER) cc_final: 0.8612 (tpp) REVERT: A 645 GLN cc_start: 0.9457 (tp40) cc_final: 0.9180 (tp-100) REVERT: A 668 ASN cc_start: 0.9582 (m-40) cc_final: 0.9290 (m-40) REVERT: A 672 LEU cc_start: 0.9750 (mt) cc_final: 0.9478 (mm) REVERT: A 684 TYR cc_start: 0.8257 (OUTLIER) cc_final: 0.7653 (m-80) REVERT: B 71 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9344 (tp) REVERT: B 99 LYS cc_start: 0.9305 (mmtt) cc_final: 0.8776 (mmmm) REVERT: B 172 LEU cc_start: 0.9598 (mp) cc_final: 0.9365 (mp) REVERT: B 181 ASP cc_start: 0.8733 (m-30) cc_final: 0.8285 (m-30) REVERT: B 238 ASP cc_start: 0.7972 (t0) cc_final: 0.7582 (t0) REVERT: B 251 LEU cc_start: 0.9571 (tp) cc_final: 0.9360 (tp) REVERT: B 257 ASP cc_start: 0.8856 (m-30) cc_final: 0.8576 (m-30) REVERT: B 288 PHE cc_start: 0.9325 (t80) cc_final: 0.8987 (t80) REVERT: B 290 GLU cc_start: 0.8331 (tp30) cc_final: 0.8128 (tp30) REVERT: B 291 LEU cc_start: 0.9481 (mt) cc_final: 0.9240 (mp) REVERT: B 316 GLU cc_start: 0.9130 (tt0) cc_final: 0.8903 (pt0) REVERT: B 375 LYS cc_start: 0.9373 (mtpp) cc_final: 0.9099 (mtpp) REVERT: B 423 LYS cc_start: 0.9531 (mtmm) cc_final: 0.9084 (mmtp) REVERT: B 434 ASP cc_start: 0.8712 (m-30) cc_final: 0.8458 (m-30) REVERT: B 446 ARG cc_start: 0.7908 (ttm-80) cc_final: 0.7691 (mmm-85) REVERT: B 493 MET cc_start: 0.9617 (tmm) cc_final: 0.9308 (tmm) REVERT: B 515 ASP cc_start: 0.9104 (m-30) cc_final: 0.8830 (m-30) REVERT: B 543 ILE cc_start: 0.9590 (mm) cc_final: 0.9360 (mm) REVERT: B 550 MET cc_start: 0.8366 (mtm) cc_final: 0.8134 (mtm) REVERT: B 599 GLU cc_start: 0.8518 (pt0) cc_final: 0.8242 (pt0) REVERT: B 602 GLU cc_start: 0.8721 (pt0) cc_final: 0.8301 (pt0) REVERT: B 686 ARG cc_start: 0.8378 (mtp-110) cc_final: 0.8113 (mtp-110) REVERT: C 66 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8538 (t70) REVERT: C 86 ARG cc_start: 0.8686 (mtt180) cc_final: 0.8206 (mpt180) REVERT: C 92 PHE cc_start: 0.9155 (t80) cc_final: 0.8856 (t80) REVERT: C 95 MET cc_start: 0.8739 (tmm) cc_final: 0.8235 (tmm) REVERT: C 122 PHE cc_start: 0.8874 (m-80) cc_final: 0.8380 (m-80) REVERT: C 149 ASP cc_start: 0.8959 (t0) cc_final: 0.8722 (t0) REVERT: C 242 TYR cc_start: 0.9388 (t80) cc_final: 0.8865 (t80) REVERT: C 259 PHE cc_start: 0.8228 (t80) cc_final: 0.7206 (t80) REVERT: C 260 ILE cc_start: 0.8105 (pp) cc_final: 0.7810 (pp) REVERT: C 313 GLU cc_start: 0.9221 (tt0) cc_final: 0.8690 (tp30) REVERT: D 20 MET cc_start: 0.8722 (ttt) cc_final: 0.8407 (ptm) REVERT: D 24 GLN cc_start: 0.8927 (mm-40) cc_final: 0.8712 (mp10) REVERT: D 28 GLN cc_start: 0.9084 (mt0) cc_final: 0.8799 (tt0) REVERT: D 30 TRP cc_start: 0.8115 (p-90) cc_final: 0.7527 (p-90) REVERT: D 74 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7246 (tpt) REVERT: D 109 PHE cc_start: 0.8629 (m-80) cc_final: 0.8199 (m-80) REVERT: D 131 LEU cc_start: 0.7612 (tt) cc_final: 0.7247 (tp) REVERT: D 137 MET cc_start: 0.9502 (mtt) cc_final: 0.9249 (mtp) REVERT: D 164 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7391 (mm-30) REVERT: D 172 PHE cc_start: 0.9073 (m-80) cc_final: 0.8808 (m-80) REVERT: D 198 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8385 (mm-30) REVERT: D 224 LEU cc_start: 0.8806 (mm) cc_final: 0.8589 (mm) REVERT: D 235 LEU cc_start: 0.9157 (pp) cc_final: 0.8943 (pp) outliers start: 100 outliers final: 72 residues processed: 752 average time/residue: 0.1079 time to fit residues: 122.4866 Evaluate side-chains 735 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 655 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 287 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN C 24 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN D 210 GLN D 270 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.119416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.087570 restraints weight = 37072.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.090862 restraints weight = 17975.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.092863 restraints weight = 10799.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.094511 restraints weight = 7757.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.095616 restraints weight = 5872.650| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.6570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16386 Z= 0.160 Angle : 0.734 13.692 22134 Z= 0.370 Chirality : 0.046 0.311 2360 Planarity : 0.004 0.044 2818 Dihedral : 10.850 176.688 2243 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.37 % Allowed : 28.90 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.19), residues: 1932 helix: 0.81 (0.15), residues: 1147 sheet: -0.39 (0.39), residues: 150 loop : 0.09 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 161 TYR 0.040 0.002 TYR D 142 PHE 0.039 0.002 PHE D 172 TRP 0.017 0.001 TRP D 124 HIS 0.014 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00368 (16386) covalent geometry : angle 0.73397 (22134) hydrogen bonds : bond 0.04276 ( 871) hydrogen bonds : angle 5.30951 ( 2571) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 732 time to evaluate : 0.495 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: A 51 LEU cc_start: 0.9295 (tp) cc_final: 0.9038 (tp) REVERT: A 139 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8661 (mt-10) REVERT: A 163 ARG cc_start: 0.8217 (tpp80) cc_final: 0.7886 (mmm-85) REVERT: A 178 SER cc_start: 0.8590 (OUTLIER) cc_final: 0.8338 (t) REVERT: A 220 THR cc_start: 0.9412 (m) cc_final: 0.9071 (p) REVERT: A 221 LYS cc_start: 0.9215 (mmtp) cc_final: 0.8872 (mttp) REVERT: A 243 ARG cc_start: 0.7978 (ptm-80) cc_final: 0.7685 (ppt170) REVERT: A 290 GLU cc_start: 0.9271 (tt0) cc_final: 0.8815 (tm-30) REVERT: A 335 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8196 (mt-10) REVERT: A 362 ASP cc_start: 0.8256 (m-30) cc_final: 0.7662 (m-30) REVERT: A 390 GLN cc_start: 0.8775 (mt0) cc_final: 0.8518 (mt0) REVERT: A 444 ASP cc_start: 0.8696 (t0) cc_final: 0.8090 (t0) REVERT: A 446 ARG cc_start: 0.7487 (mtp85) cc_final: 0.7102 (mmm160) REVERT: A 447 ASN cc_start: 0.8461 (m110) cc_final: 0.8257 (m-40) REVERT: A 456 LYS cc_start: 0.9481 (ttmm) cc_final: 0.9146 (mtmm) REVERT: A 459 LYS cc_start: 0.9352 (OUTLIER) cc_final: 0.8977 (mtmm) REVERT: A 493 MET cc_start: 0.9023 (tmm) cc_final: 0.8653 (tmm) REVERT: A 515 ASP cc_start: 0.9146 (m-30) cc_final: 0.8910 (m-30) REVERT: A 590 SER cc_start: 0.9595 (t) cc_final: 0.9144 (p) REVERT: A 595 MET cc_start: 0.8984 (mmm) cc_final: 0.8775 (mmm) REVERT: A 597 ILE cc_start: 0.9387 (pt) cc_final: 0.9123 (pt) REVERT: A 639 ASP cc_start: 0.8802 (m-30) cc_final: 0.8232 (m-30) REVERT: A 640 MET cc_start: 0.9524 (OUTLIER) cc_final: 0.8502 (tpp) REVERT: A 668 ASN cc_start: 0.9626 (m-40) cc_final: 0.9417 (m-40) REVERT: A 684 TYR cc_start: 0.8180 (OUTLIER) cc_final: 0.7460 (m-10) REVERT: B 31 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8656 (mp0) REVERT: B 60 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8796 (mp0) REVERT: B 167 LEU cc_start: 0.9347 (mt) cc_final: 0.9104 (mt) REVERT: B 172 LEU cc_start: 0.9517 (mp) cc_final: 0.9264 (mp) REVERT: B 181 ASP cc_start: 0.8657 (m-30) cc_final: 0.8161 (m-30) REVERT: B 192 LEU cc_start: 0.9525 (mp) cc_final: 0.9290 (mp) REVERT: B 238 ASP cc_start: 0.7958 (t0) cc_final: 0.7730 (t0) REVERT: B 257 ASP cc_start: 0.8964 (m-30) cc_final: 0.8703 (m-30) REVERT: B 290 GLU cc_start: 0.8347 (tp30) cc_final: 0.8097 (tp30) REVERT: B 375 LYS cc_start: 0.9344 (mtpp) cc_final: 0.9046 (mtpp) REVERT: B 423 LYS cc_start: 0.9549 (mtmm) cc_final: 0.9247 (mmtp) REVERT: B 446 ARG cc_start: 0.7765 (ttm-80) cc_final: 0.7508 (mmm-85) REVERT: B 458 MET cc_start: 0.9211 (mmm) cc_final: 0.8853 (mmp) REVERT: B 493 MET cc_start: 0.9602 (tmm) cc_final: 0.9296 (tmm) REVERT: B 515 ASP cc_start: 0.9081 (m-30) cc_final: 0.8705 (m-30) REVERT: B 543 ILE cc_start: 0.9539 (mm) cc_final: 0.9326 (mm) REVERT: B 599 GLU cc_start: 0.8430 (pt0) cc_final: 0.8114 (pt0) REVERT: B 602 GLU cc_start: 0.8807 (pt0) cc_final: 0.7670 (pt0) REVERT: B 604 ARG cc_start: 0.8478 (mmt-90) cc_final: 0.7605 (mmt-90) REVERT: B 610 LYS cc_start: 0.9040 (mtpp) cc_final: 0.8705 (mtpp) REVERT: B 686 ARG cc_start: 0.8456 (mtp-110) cc_final: 0.8224 (mtp-110) REVERT: C 55 TYR cc_start: 0.8993 (t80) cc_final: 0.8146 (t80) REVERT: C 66 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8598 (t70) REVERT: C 69 GLN cc_start: 0.8403 (tm-30) cc_final: 0.8165 (tm-30) REVERT: C 86 ARG cc_start: 0.8626 (mtt180) cc_final: 0.8231 (mpt180) REVERT: C 95 MET cc_start: 0.8657 (tmm) cc_final: 0.8188 (tmm) REVERT: C 96 MET cc_start: 0.8843 (mmm) cc_final: 0.8627 (mmm) REVERT: C 122 PHE cc_start: 0.8883 (m-80) cc_final: 0.8368 (m-80) REVERT: C 149 ASP cc_start: 0.8798 (t0) cc_final: 0.8593 (t0) REVERT: C 157 MET cc_start: 0.9663 (mpp) cc_final: 0.9445 (mpp) REVERT: C 174 TYR cc_start: 0.8924 (OUTLIER) cc_final: 0.7593 (t80) REVERT: C 242 TYR cc_start: 0.9341 (t80) cc_final: 0.8985 (t80) REVERT: C 259 PHE cc_start: 0.8181 (t80) cc_final: 0.7342 (t80) REVERT: C 260 ILE cc_start: 0.7955 (pp) cc_final: 0.7675 (pp) REVERT: C 269 MET cc_start: 0.9594 (tmm) cc_final: 0.9327 (tmm) REVERT: C 313 GLU cc_start: 0.9214 (tt0) cc_final: 0.8600 (tp30) REVERT: D 20 MET cc_start: 0.8798 (ttt) cc_final: 0.8572 (ptm) REVERT: D 30 TRP cc_start: 0.8007 (p-90) cc_final: 0.7565 (p-90) REVERT: D 46 TYR cc_start: 0.8904 (m-10) cc_final: 0.8039 (m-10) REVERT: D 74 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7372 (tpt) REVERT: D 92 PHE cc_start: 0.8501 (t80) cc_final: 0.8062 (t80) REVERT: D 109 PHE cc_start: 0.8609 (m-80) cc_final: 0.8169 (m-80) REVERT: D 137 MET cc_start: 0.9571 (mtt) cc_final: 0.9324 (mtp) REVERT: D 164 GLU cc_start: 0.8499 (mm-30) cc_final: 0.7529 (mm-30) REVERT: D 172 PHE cc_start: 0.9013 (m-80) cc_final: 0.8774 (m-80) REVERT: D 198 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8339 (mm-30) REVERT: D 259 PHE cc_start: 0.8675 (t80) cc_final: 0.7916 (t80) REVERT: D 263 ASN cc_start: 0.9126 (m-40) cc_final: 0.8817 (m-40) outliers start: 75 outliers final: 49 residues processed: 762 average time/residue: 0.1094 time to fit residues: 126.6911 Evaluate side-chains 744 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 686 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 287 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 27 optimal weight: 0.0010 chunk 136 optimal weight: 6.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN B 232 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN D 28 GLN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.121654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.089768 restraints weight = 37148.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.093071 restraints weight = 18028.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.095242 restraints weight = 10885.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.096780 restraints weight = 7629.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.097702 restraints weight = 5817.285| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.6956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16386 Z= 0.155 Angle : 0.753 13.760 22134 Z= 0.379 Chirality : 0.048 0.414 2360 Planarity : 0.004 0.052 2818 Dihedral : 10.345 171.608 2243 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.79 % Allowed : 31.35 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.18), residues: 1932 helix: 0.73 (0.15), residues: 1147 sheet: -0.51 (0.39), residues: 150 loop : -0.01 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 164 TYR 0.036 0.002 TYR B 574 PHE 0.036 0.002 PHE D 172 TRP 0.020 0.001 TRP D 124 HIS 0.016 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00358 (16386) covalent geometry : angle 0.75306 (22134) hydrogen bonds : bond 0.04255 ( 871) hydrogen bonds : angle 5.37842 ( 2571) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 723 time to evaluate : 0.484 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: A 123 SER cc_start: 0.9601 (OUTLIER) cc_final: 0.9121 (p) REVERT: A 128 PHE cc_start: 0.9454 (t80) cc_final: 0.9247 (t80) REVERT: A 139 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8639 (mt-10) REVERT: A 163 ARG cc_start: 0.8299 (tpp80) cc_final: 0.7877 (mmm-85) REVERT: A 194 LYS cc_start: 0.9634 (ttpp) cc_final: 0.9281 (ttpp) REVERT: A 214 LYS cc_start: 0.8361 (mmtm) cc_final: 0.8159 (mmtt) REVERT: A 220 THR cc_start: 0.9429 (m) cc_final: 0.8997 (p) REVERT: A 221 LYS cc_start: 0.9148 (mmtp) cc_final: 0.8819 (mttp) REVERT: A 232 ASN cc_start: 0.9379 (m110) cc_final: 0.8991 (m110) REVERT: A 243 ARG cc_start: 0.7866 (ptm-80) cc_final: 0.7601 (ppt170) REVERT: A 266 LYS cc_start: 0.9135 (mtmm) cc_final: 0.8924 (mtmm) REVERT: A 290 GLU cc_start: 0.9241 (tt0) cc_final: 0.8824 (tm-30) REVERT: A 335 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8178 (mt-10) REVERT: A 362 ASP cc_start: 0.8200 (m-30) cc_final: 0.7799 (m-30) REVERT: A 390 GLN cc_start: 0.8880 (mt0) cc_final: 0.8383 (mt0) REVERT: A 406 ASP cc_start: 0.7949 (m-30) cc_final: 0.7604 (t0) REVERT: A 444 ASP cc_start: 0.8685 (t0) cc_final: 0.8178 (t0) REVERT: A 446 ARG cc_start: 0.7419 (mtp85) cc_final: 0.7070 (mmm160) REVERT: A 459 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.9022 (mtmm) REVERT: A 493 MET cc_start: 0.9050 (tmm) cc_final: 0.8632 (tmm) REVERT: A 515 ASP cc_start: 0.9062 (m-30) cc_final: 0.8831 (m-30) REVERT: A 590 SER cc_start: 0.9563 (t) cc_final: 0.9170 (p) REVERT: A 597 ILE cc_start: 0.9371 (pt) cc_final: 0.9081 (pt) REVERT: A 599 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8522 (pt0) REVERT: A 602 GLU cc_start: 0.8041 (pt0) cc_final: 0.7515 (pt0) REVERT: A 604 ARG cc_start: 0.8955 (mmm-85) cc_final: 0.8580 (mmm-85) REVERT: A 618 LEU cc_start: 0.9461 (tp) cc_final: 0.9200 (tt) REVERT: A 639 ASP cc_start: 0.8791 (m-30) cc_final: 0.8194 (m-30) REVERT: A 640 MET cc_start: 0.9547 (OUTLIER) cc_final: 0.8516 (tpp) REVERT: A 645 GLN cc_start: 0.9382 (tp40) cc_final: 0.8981 (tp-100) REVERT: A 668 ASN cc_start: 0.9680 (m-40) cc_final: 0.9472 (m-40) REVERT: A 684 TYR cc_start: 0.8121 (OUTLIER) cc_final: 0.7443 (m-10) REVERT: B 15 GLU cc_start: 0.8758 (tp30) cc_final: 0.8498 (tp30) REVERT: B 31 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8658 (mp0) REVERT: B 60 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8832 (mp0) REVERT: B 128 PHE cc_start: 0.9751 (t80) cc_final: 0.9324 (t80) REVERT: B 167 LEU cc_start: 0.9316 (mt) cc_final: 0.9113 (mt) REVERT: B 172 LEU cc_start: 0.9530 (mp) cc_final: 0.9285 (mp) REVERT: B 181 ASP cc_start: 0.8624 (m-30) cc_final: 0.8079 (m-30) REVERT: B 202 ASN cc_start: 0.9418 (t0) cc_final: 0.9179 (t0) REVERT: B 236 TYR cc_start: 0.9499 (t80) cc_final: 0.9185 (t80) REVERT: B 238 ASP cc_start: 0.8007 (t0) cc_final: 0.7621 (t0) REVERT: B 290 GLU cc_start: 0.8386 (tp30) cc_final: 0.7977 (tp30) REVERT: B 308 LYS cc_start: 0.9498 (mtpp) cc_final: 0.9123 (mtmm) REVERT: B 375 LYS cc_start: 0.9275 (mtpp) cc_final: 0.8942 (mtpp) REVERT: B 423 LYS cc_start: 0.9595 (mtmm) cc_final: 0.9269 (mmtp) REVERT: B 434 ASP cc_start: 0.8686 (m-30) cc_final: 0.8418 (m-30) REVERT: B 446 ARG cc_start: 0.7710 (ttm-80) cc_final: 0.7437 (mmm-85) REVERT: B 458 MET cc_start: 0.9078 (mmm) cc_final: 0.8783 (mmp) REVERT: B 493 MET cc_start: 0.9519 (tmm) cc_final: 0.9203 (tmm) REVERT: B 515 ASP cc_start: 0.9057 (m-30) cc_final: 0.8697 (m-30) REVERT: B 599 GLU cc_start: 0.8405 (pt0) cc_final: 0.8127 (pt0) REVERT: B 602 GLU cc_start: 0.8764 (pt0) cc_final: 0.8315 (pt0) REVERT: B 610 LYS cc_start: 0.8955 (mtpp) cc_final: 0.8590 (mtpp) REVERT: B 631 ASP cc_start: 0.9158 (m-30) cc_final: 0.8803 (m-30) REVERT: B 686 ARG cc_start: 0.8497 (mtp-110) cc_final: 0.8265 (mtp85) REVERT: C 20 MET cc_start: 0.9561 (ptp) cc_final: 0.9295 (pmm) REVERT: C 23 ASN cc_start: 0.9580 (t0) cc_final: 0.9349 (m-40) REVERT: C 66 ASP cc_start: 0.8933 (OUTLIER) cc_final: 0.8659 (t70) REVERT: C 86 ARG cc_start: 0.8663 (mtt180) cc_final: 0.8295 (mpt180) REVERT: C 92 PHE cc_start: 0.8715 (t80) cc_final: 0.8486 (t80) REVERT: C 122 PHE cc_start: 0.8914 (m-80) cc_final: 0.8475 (m-80) REVERT: C 143 LYS cc_start: 0.9042 (tptt) cc_final: 0.8667 (tptp) REVERT: C 157 MET cc_start: 0.9657 (mpp) cc_final: 0.9445 (mpp) REVERT: C 174 TYR cc_start: 0.8874 (OUTLIER) cc_final: 0.7666 (t80) REVERT: C 178 PHE cc_start: 0.8747 (t80) cc_final: 0.8346 (t80) REVERT: C 208 LEU cc_start: 0.9471 (mt) cc_final: 0.9195 (pp) REVERT: C 242 TYR cc_start: 0.9358 (t80) cc_final: 0.8904 (t80) REVERT: C 244 GLU cc_start: 0.9360 (OUTLIER) cc_final: 0.9012 (pp20) REVERT: C 259 PHE cc_start: 0.8140 (t80) cc_final: 0.7127 (t80) REVERT: C 260 ILE cc_start: 0.8178 (pp) cc_final: 0.7905 (pp) REVERT: C 269 MET cc_start: 0.9631 (tmm) cc_final: 0.9393 (tmm) REVERT: C 313 GLU cc_start: 0.9198 (tt0) cc_final: 0.8691 (tp30) REVERT: C 320 PHE cc_start: 0.9180 (m-80) cc_final: 0.8902 (m-10) REVERT: D 18 THR cc_start: 0.9053 (p) cc_final: 0.8812 (m) REVERT: D 20 MET cc_start: 0.8820 (ttt) cc_final: 0.8479 (ppp) REVERT: D 30 TRP cc_start: 0.8175 (p-90) cc_final: 0.7804 (p-90) REVERT: D 74 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7433 (tpt) REVERT: D 109 PHE cc_start: 0.8637 (m-80) cc_final: 0.8196 (m-80) REVERT: D 128 ASN cc_start: 0.9004 (t0) cc_final: 0.8708 (t0) REVERT: D 137 MET cc_start: 0.9587 (mtt) cc_final: 0.9310 (mtp) REVERT: D 164 GLU cc_start: 0.8505 (mm-30) cc_final: 0.7525 (mm-30) REVERT: D 172 PHE cc_start: 0.8963 (m-80) cc_final: 0.8686 (m-80) REVERT: D 178 PHE cc_start: 0.9200 (m-80) cc_final: 0.8556 (t80) REVERT: D 198 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8348 (mm-30) REVERT: D 242 TYR cc_start: 0.8936 (t80) cc_final: 0.8572 (t80) REVERT: D 259 PHE cc_start: 0.8715 (t80) cc_final: 0.7961 (t80) REVERT: D 263 ASN cc_start: 0.8993 (m-40) cc_final: 0.8586 (m-40) REVERT: D 265 ASN cc_start: 0.8704 (m110) cc_final: 0.8485 (m110) outliers start: 65 outliers final: 38 residues processed: 750 average time/residue: 0.1096 time to fit residues: 125.1295 Evaluate side-chains 712 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 664 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 186 optimal weight: 0.0040 chunk 140 optimal weight: 20.0000 chunk 115 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 156 optimal weight: 0.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.120822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.088260 restraints weight = 36889.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.091633 restraints weight = 17380.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.093862 restraints weight = 10445.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.095439 restraints weight = 7268.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.096512 restraints weight = 5532.802| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.7258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16386 Z= 0.159 Angle : 0.779 16.438 22134 Z= 0.387 Chirality : 0.047 0.391 2360 Planarity : 0.004 0.053 2818 Dihedral : 10.254 174.025 2243 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.61 % Allowed : 33.22 % Favored : 63.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.18), residues: 1932 helix: 0.72 (0.15), residues: 1146 sheet: -0.67 (0.37), residues: 160 loop : 0.02 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 686 TYR 0.053 0.002 TYR D 142 PHE 0.033 0.002 PHE C 172 TRP 0.023 0.001 TRP D 124 HIS 0.026 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00361 (16386) covalent geometry : angle 0.77921 (22134) hydrogen bonds : bond 0.04254 ( 871) hydrogen bonds : angle 5.38031 ( 2571) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 702 time to evaluate : 0.524 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 51 LEU cc_start: 0.9060 (tp) cc_final: 0.8658 (mp) REVERT: A 56 ASP cc_start: 0.9240 (m-30) cc_final: 0.8922 (m-30) REVERT: A 123 SER cc_start: 0.9572 (OUTLIER) cc_final: 0.9116 (p) REVERT: A 128 PHE cc_start: 0.9465 (t80) cc_final: 0.8910 (t80) REVERT: A 139 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8642 (mt-10) REVERT: A 158 ASN cc_start: 0.9396 (m-40) cc_final: 0.9038 (m-40) REVERT: A 163 ARG cc_start: 0.8331 (tpp80) cc_final: 0.8107 (mmm-85) REVERT: A 194 LYS cc_start: 0.9605 (ttpp) cc_final: 0.9244 (ttpp) REVERT: A 221 LYS cc_start: 0.9130 (mmtp) cc_final: 0.8790 (mttp) REVERT: A 232 ASN cc_start: 0.9531 (m110) cc_final: 0.9073 (m110) REVERT: A 243 ARG cc_start: 0.7840 (ptm-80) cc_final: 0.7533 (ppt170) REVERT: A 266 LYS cc_start: 0.9113 (mtmm) cc_final: 0.8828 (mtmm) REVERT: A 290 GLU cc_start: 0.9282 (tt0) cc_final: 0.8802 (tm-30) REVERT: A 335 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8240 (mt-10) REVERT: A 362 ASP cc_start: 0.8307 (m-30) cc_final: 0.8005 (m-30) REVERT: A 381 LEU cc_start: 0.9439 (tp) cc_final: 0.9067 (tp) REVERT: A 390 GLN cc_start: 0.8958 (mt0) cc_final: 0.8464 (mt0) REVERT: A 396 ASP cc_start: 0.8838 (p0) cc_final: 0.8522 (p0) REVERT: A 406 ASP cc_start: 0.8017 (m-30) cc_final: 0.7645 (t0) REVERT: A 444 ASP cc_start: 0.8750 (t0) cc_final: 0.7379 (t0) REVERT: A 446 ARG cc_start: 0.7499 (mtp85) cc_final: 0.7218 (mmm160) REVERT: A 456 LYS cc_start: 0.9523 (tppp) cc_final: 0.9205 (mtmm) REVERT: A 459 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8905 (mtmm) REVERT: A 493 MET cc_start: 0.9004 (tmm) cc_final: 0.8539 (tmm) REVERT: A 498 TYR cc_start: 0.8542 (m-80) cc_final: 0.8214 (m-10) REVERT: A 515 ASP cc_start: 0.9071 (m-30) cc_final: 0.8805 (m-30) REVERT: A 597 ILE cc_start: 0.9294 (pt) cc_final: 0.8956 (pt) REVERT: A 599 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8239 (pt0) REVERT: A 602 GLU cc_start: 0.8190 (pt0) cc_final: 0.7834 (pt0) REVERT: A 604 ARG cc_start: 0.9063 (mmm-85) cc_final: 0.8793 (mmm-85) REVERT: A 639 ASP cc_start: 0.8678 (m-30) cc_final: 0.8126 (m-30) REVERT: A 640 MET cc_start: 0.9530 (OUTLIER) cc_final: 0.8532 (tpp) REVERT: A 645 GLN cc_start: 0.9397 (tp40) cc_final: 0.8962 (tp-100) REVERT: A 668 ASN cc_start: 0.9720 (m-40) cc_final: 0.9496 (m-40) REVERT: A 684 TYR cc_start: 0.8069 (OUTLIER) cc_final: 0.7340 (m-10) REVERT: B 31 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8684 (mp0) REVERT: B 82 LYS cc_start: 0.9600 (mmmm) cc_final: 0.9301 (mmtm) REVERT: B 128 PHE cc_start: 0.9750 (t80) cc_final: 0.9294 (t80) REVERT: B 172 LEU cc_start: 0.9487 (mp) cc_final: 0.9266 (mp) REVERT: B 181 ASP cc_start: 0.8580 (m-30) cc_final: 0.8039 (m-30) REVERT: B 202 ASN cc_start: 0.9472 (t0) cc_final: 0.9099 (t0) REVERT: B 232 ASN cc_start: 0.9160 (t0) cc_final: 0.8903 (t0) REVERT: B 235 ARG cc_start: 0.8987 (mtm110) cc_final: 0.8643 (ttp-110) REVERT: B 236 TYR cc_start: 0.9467 (t80) cc_final: 0.9244 (t80) REVERT: B 261 PHE cc_start: 0.9494 (t80) cc_final: 0.9138 (t80) REVERT: B 290 GLU cc_start: 0.8441 (tp30) cc_final: 0.8072 (tp30) REVERT: B 308 LYS cc_start: 0.9513 (mtpp) cc_final: 0.9252 (mtmm) REVERT: B 375 LYS cc_start: 0.9260 (mtpp) cc_final: 0.8915 (mtpp) REVERT: B 423 LYS cc_start: 0.9597 (mtmm) cc_final: 0.9173 (mtpp) REVERT: B 434 ASP cc_start: 0.8769 (m-30) cc_final: 0.8480 (m-30) REVERT: B 446 ARG cc_start: 0.7768 (ttm-80) cc_final: 0.6882 (mmm-85) REVERT: B 458 MET cc_start: 0.9018 (mmm) cc_final: 0.8723 (mmp) REVERT: B 493 MET cc_start: 0.9526 (tmm) cc_final: 0.9216 (tmm) REVERT: B 515 ASP cc_start: 0.9090 (m-30) cc_final: 0.8703 (m-30) REVERT: B 599 GLU cc_start: 0.8422 (pt0) cc_final: 0.8064 (pt0) REVERT: B 602 GLU cc_start: 0.8939 (pt0) cc_final: 0.8422 (pt0) REVERT: B 610 LYS cc_start: 0.8976 (mtpp) cc_final: 0.8670 (mtpp) REVERT: B 631 ASP cc_start: 0.9199 (m-30) cc_final: 0.8934 (m-30) REVERT: B 632 MET cc_start: 0.8401 (mmm) cc_final: 0.7920 (mmm) REVERT: B 686 ARG cc_start: 0.8529 (mtp-110) cc_final: 0.8219 (mtp85) REVERT: C 23 ASN cc_start: 0.9611 (t0) cc_final: 0.9345 (m-40) REVERT: C 55 TYR cc_start: 0.9018 (t80) cc_final: 0.8167 (t80) REVERT: C 66 ASP cc_start: 0.9001 (OUTLIER) cc_final: 0.8684 (t70) REVERT: C 86 ARG cc_start: 0.8678 (mtt180) cc_final: 0.8290 (mpt180) REVERT: C 92 PHE cc_start: 0.8555 (t80) cc_final: 0.8162 (t80) REVERT: C 137 MET cc_start: 0.9470 (tpp) cc_final: 0.9127 (tpt) REVERT: C 143 LYS cc_start: 0.9065 (tptt) cc_final: 0.8662 (tptp) REVERT: C 174 TYR cc_start: 0.8992 (OUTLIER) cc_final: 0.7827 (t80) REVERT: C 178 PHE cc_start: 0.8699 (t80) cc_final: 0.8470 (t80) REVERT: C 189 GLU cc_start: 0.9213 (pm20) cc_final: 0.8928 (pm20) REVERT: C 242 TYR cc_start: 0.9436 (t80) cc_final: 0.8939 (t80) REVERT: C 244 GLU cc_start: 0.9368 (OUTLIER) cc_final: 0.8939 (pp20) REVERT: C 245 ASP cc_start: 0.9196 (t0) cc_final: 0.8865 (t0) REVERT: C 259 PHE cc_start: 0.8198 (t80) cc_final: 0.7282 (t80) REVERT: C 260 ILE cc_start: 0.8238 (pp) cc_final: 0.7980 (pp) REVERT: C 313 GLU cc_start: 0.9202 (tt0) cc_final: 0.8668 (tp30) REVERT: D 18 THR cc_start: 0.9082 (p) cc_final: 0.8750 (m) REVERT: D 20 MET cc_start: 0.8913 (ttt) cc_final: 0.8531 (ppp) REVERT: D 30 TRP cc_start: 0.8134 (p-90) cc_final: 0.7695 (p-90) REVERT: D 40 ASP cc_start: 0.8811 (m-30) cc_final: 0.8534 (m-30) REVERT: D 74 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7689 (tpt) REVERT: D 109 PHE cc_start: 0.8703 (m-80) cc_final: 0.8279 (m-80) REVERT: D 120 GLU cc_start: 0.9254 (tm-30) cc_final: 0.9002 (tm-30) REVERT: D 123 GLU cc_start: 0.9079 (mp0) cc_final: 0.7955 (tp30) REVERT: D 137 MET cc_start: 0.9618 (mtt) cc_final: 0.9350 (mtp) REVERT: D 164 GLU cc_start: 0.8519 (mm-30) cc_final: 0.7570 (mm-30) REVERT: D 172 PHE cc_start: 0.8963 (m-80) cc_final: 0.8656 (m-80) REVERT: D 178 PHE cc_start: 0.9205 (m-80) cc_final: 0.8613 (t80) REVERT: D 198 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8401 (mm-30) REVERT: D 233 ASN cc_start: 0.9075 (OUTLIER) cc_final: 0.8838 (p0) REVERT: D 259 PHE cc_start: 0.8743 (t80) cc_final: 0.8110 (t80) REVERT: D 263 ASN cc_start: 0.8839 (m-40) cc_final: 0.8589 (m-40) outliers start: 62 outliers final: 41 residues processed: 732 average time/residue: 0.1216 time to fit residues: 135.8591 Evaluate side-chains 725 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 674 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 233 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 HIS A 650 GLN ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.122538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.090984 restraints weight = 37037.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.094335 restraints weight = 17985.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.096563 restraints weight = 10800.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.098010 restraints weight = 7512.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.099052 restraints weight = 5787.326| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.7514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16386 Z= 0.157 Angle : 0.817 16.464 22134 Z= 0.403 Chirality : 0.049 0.382 2360 Planarity : 0.004 0.052 2818 Dihedral : 10.175 171.667 2243 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.44 % Allowed : 33.86 % Favored : 62.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.18), residues: 1932 helix: 0.68 (0.15), residues: 1141 sheet: -0.73 (0.37), residues: 160 loop : -0.03 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 686 TYR 0.062 0.002 TYR D 142 PHE 0.034 0.002 PHE D 172 TRP 0.025 0.002 TRP D 124 HIS 0.022 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00359 (16386) covalent geometry : angle 0.81749 (22134) hydrogen bonds : bond 0.04253 ( 871) hydrogen bonds : angle 5.43492 ( 2571) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 711 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: A 9 TRP cc_start: 0.9146 (p90) cc_final: 0.8911 (p90) REVERT: A 51 LEU cc_start: 0.8956 (tp) cc_final: 0.8672 (mp) REVERT: A 56 ASP cc_start: 0.9151 (m-30) cc_final: 0.8817 (m-30) REVERT: A 123 SER cc_start: 0.9582 (OUTLIER) cc_final: 0.9118 (p) REVERT: A 128 PHE cc_start: 0.9459 (t80) cc_final: 0.8937 (t80) REVERT: A 139 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8612 (mt-10) REVERT: A 161 ARG cc_start: 0.8595 (ptm160) cc_final: 0.8336 (ptm160) REVERT: A 194 LYS cc_start: 0.9627 (ttpp) cc_final: 0.9387 (ttpp) REVERT: A 221 LYS cc_start: 0.9090 (mmtp) cc_final: 0.8802 (mttp) REVERT: A 232 ASN cc_start: 0.9485 (m110) cc_final: 0.9076 (m110) REVERT: A 243 ARG cc_start: 0.7743 (ptm-80) cc_final: 0.7516 (ppt170) REVERT: A 266 LYS cc_start: 0.9120 (mtmm) cc_final: 0.8733 (mtmm) REVERT: A 290 GLU cc_start: 0.9214 (tt0) cc_final: 0.8818 (tm-30) REVERT: A 335 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8202 (mt-10) REVERT: A 362 ASP cc_start: 0.8163 (m-30) cc_final: 0.7944 (m-30) REVERT: A 381 LEU cc_start: 0.9442 (tp) cc_final: 0.9104 (tp) REVERT: A 390 GLN cc_start: 0.8903 (mt0) cc_final: 0.8431 (mt0) REVERT: A 406 ASP cc_start: 0.8019 (m-30) cc_final: 0.7788 (t0) REVERT: A 444 ASP cc_start: 0.8714 (t0) cc_final: 0.7270 (t0) REVERT: A 446 ARG cc_start: 0.7440 (mtp85) cc_final: 0.7133 (mmm160) REVERT: A 456 LYS cc_start: 0.9452 (tppp) cc_final: 0.9155 (mtmm) REVERT: A 459 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8659 (mttp) REVERT: A 493 MET cc_start: 0.9056 (tmm) cc_final: 0.8583 (tmm) REVERT: A 498 TYR cc_start: 0.8595 (m-80) cc_final: 0.8362 (m-10) REVERT: A 516 GLN cc_start: 0.9176 (mt0) cc_final: 0.8976 (mt0) REVERT: A 597 ILE cc_start: 0.9119 (pt) cc_final: 0.8864 (pt) REVERT: A 599 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8017 (pt0) REVERT: A 602 GLU cc_start: 0.7840 (pt0) cc_final: 0.7512 (pt0) REVERT: A 604 ARG cc_start: 0.8955 (mmm-85) cc_final: 0.8701 (mmm-85) REVERT: A 632 MET cc_start: 0.8515 (mtp) cc_final: 0.8268 (mtp) REVERT: A 639 ASP cc_start: 0.8630 (m-30) cc_final: 0.8080 (m-30) REVERT: A 640 MET cc_start: 0.9416 (OUTLIER) cc_final: 0.8952 (tpp) REVERT: A 645 GLN cc_start: 0.9413 (tp40) cc_final: 0.9027 (tp-100) REVERT: A 684 TYR cc_start: 0.8095 (OUTLIER) cc_final: 0.7436 (m-10) REVERT: B 31 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8639 (mt-10) REVERT: B 82 LYS cc_start: 0.9533 (mmmm) cc_final: 0.9108 (mmtm) REVERT: B 128 PHE cc_start: 0.9735 (t80) cc_final: 0.9315 (t80) REVERT: B 172 LEU cc_start: 0.9456 (mp) cc_final: 0.9209 (mp) REVERT: B 181 ASP cc_start: 0.8651 (m-30) cc_final: 0.8114 (m-30) REVERT: B 232 ASN cc_start: 0.9111 (t0) cc_final: 0.8748 (t0) REVERT: B 235 ARG cc_start: 0.9001 (mtm110) cc_final: 0.8642 (ttp-110) REVERT: B 236 TYR cc_start: 0.9422 (t80) cc_final: 0.8973 (t80) REVERT: B 263 ASP cc_start: 0.8964 (m-30) cc_final: 0.8530 (m-30) REVERT: B 290 GLU cc_start: 0.8417 (tp30) cc_final: 0.8061 (tp30) REVERT: B 308 LYS cc_start: 0.9452 (mtpp) cc_final: 0.9092 (ptpp) REVERT: B 375 LYS cc_start: 0.9299 (mtpp) cc_final: 0.8931 (mtpp) REVERT: B 423 LYS cc_start: 0.9564 (mtmm) cc_final: 0.9175 (mtpp) REVERT: B 425 ILE cc_start: 0.9230 (pt) cc_final: 0.8956 (pt) REVERT: B 446 ARG cc_start: 0.7640 (ttm-80) cc_final: 0.7203 (mmm-85) REVERT: B 458 MET cc_start: 0.8965 (mmm) cc_final: 0.8734 (mmp) REVERT: B 493 MET cc_start: 0.9379 (tmm) cc_final: 0.9028 (tmm) REVERT: B 515 ASP cc_start: 0.8996 (m-30) cc_final: 0.8695 (m-30) REVERT: B 599 GLU cc_start: 0.8369 (pt0) cc_final: 0.8028 (pt0) REVERT: B 602 GLU cc_start: 0.8832 (pt0) cc_final: 0.8317 (pt0) REVERT: B 610 LYS cc_start: 0.8950 (mtpp) cc_final: 0.8595 (mtpp) REVERT: B 631 ASP cc_start: 0.9164 (m-30) cc_final: 0.8909 (m-30) REVERT: B 686 ARG cc_start: 0.8431 (mtp-110) cc_final: 0.8187 (mtp85) REVERT: C 23 ASN cc_start: 0.9581 (t0) cc_final: 0.9324 (m-40) REVERT: C 66 ASP cc_start: 0.8969 (OUTLIER) cc_final: 0.8589 (t70) REVERT: C 86 ARG cc_start: 0.8696 (mtt180) cc_final: 0.8307 (mpt180) REVERT: C 122 PHE cc_start: 0.8816 (m-80) cc_final: 0.8447 (m-80) REVERT: C 137 MET cc_start: 0.9431 (tpp) cc_final: 0.9079 (tpt) REVERT: C 143 LYS cc_start: 0.9024 (tptt) cc_final: 0.8567 (tptp) REVERT: C 157 MET cc_start: 0.9603 (mpp) cc_final: 0.9376 (mpp) REVERT: C 174 TYR cc_start: 0.9046 (OUTLIER) cc_final: 0.7934 (t80) REVERT: C 208 LEU cc_start: 0.9486 (mt) cc_final: 0.9201 (pp) REVERT: C 237 GLU cc_start: 0.9516 (pt0) cc_final: 0.9110 (pp20) REVERT: C 242 TYR cc_start: 0.9373 (t80) cc_final: 0.8897 (t80) REVERT: C 244 GLU cc_start: 0.9359 (OUTLIER) cc_final: 0.8938 (pp20) REVERT: C 245 ASP cc_start: 0.9121 (t0) cc_final: 0.8784 (t0) REVERT: C 313 GLU cc_start: 0.9149 (tt0) cc_final: 0.8679 (tp30) REVERT: C 314 PRO cc_start: 0.9360 (Cg_exo) cc_final: 0.8874 (Cg_endo) REVERT: D 30 TRP cc_start: 0.8208 (p-90) cc_final: 0.7795 (p-90) REVERT: D 40 ASP cc_start: 0.8771 (m-30) cc_final: 0.8414 (m-30) REVERT: D 74 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.8028 (tpt) REVERT: D 109 PHE cc_start: 0.8667 (m-80) cc_final: 0.8241 (m-80) REVERT: D 123 GLU cc_start: 0.9055 (mp0) cc_final: 0.8084 (tp30) REVERT: D 137 MET cc_start: 0.9589 (mtt) cc_final: 0.9327 (mtp) REVERT: D 164 GLU cc_start: 0.8476 (mm-30) cc_final: 0.7433 (mm-30) REVERT: D 172 PHE cc_start: 0.8873 (m-80) cc_final: 0.8511 (m-80) REVERT: D 178 PHE cc_start: 0.9164 (m-80) cc_final: 0.8631 (t80) REVERT: D 198 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8608 (mm-30) REVERT: D 259 PHE cc_start: 0.8735 (t80) cc_final: 0.8098 (t80) REVERT: D 263 ASN cc_start: 0.8998 (m110) cc_final: 0.8517 (m110) outliers start: 59 outliers final: 44 residues processed: 733 average time/residue: 0.1095 time to fit residues: 122.3608 Evaluate side-chains 714 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 661 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 HIS ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 132 GLN D 136 GLN D 216 GLN D 233 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.121170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.089812 restraints weight = 36922.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.092995 restraints weight = 18083.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.095106 restraints weight = 11225.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.096588 restraints weight = 7776.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.097638 restraints weight = 5960.062| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.7712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16386 Z= 0.180 Angle : 0.840 16.061 22134 Z= 0.421 Chirality : 0.050 0.352 2360 Planarity : 0.004 0.054 2818 Dihedral : 10.220 171.292 2243 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.55 % Allowed : 34.73 % Favored : 61.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.19), residues: 1932 helix: 0.62 (0.15), residues: 1145 sheet: -0.78 (0.38), residues: 160 loop : 0.04 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 225 TYR 0.056 0.002 TYR D 142 PHE 0.037 0.002 PHE C 172 TRP 0.027 0.002 TRP D 124 HIS 0.028 0.002 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00413 (16386) covalent geometry : angle 0.84047 (22134) hydrogen bonds : bond 0.04315 ( 871) hydrogen bonds : angle 5.50605 ( 2571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 676 time to evaluate : 0.740 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: A 51 LEU cc_start: 0.9015 (tp) cc_final: 0.8644 (mp) REVERT: A 123 SER cc_start: 0.9593 (OUTLIER) cc_final: 0.9123 (p) REVERT: A 139 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8781 (mt-10) REVERT: A 194 LYS cc_start: 0.9622 (ttpp) cc_final: 0.9406 (ttpp) REVERT: A 221 LYS cc_start: 0.9141 (mmtp) cc_final: 0.8802 (mttp) REVERT: A 232 ASN cc_start: 0.9562 (m110) cc_final: 0.9120 (m-40) REVERT: A 243 ARG cc_start: 0.7749 (ptm-80) cc_final: 0.7515 (ppt170) REVERT: A 290 GLU cc_start: 0.9164 (tt0) cc_final: 0.8822 (tm-30) REVERT: A 335 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8176 (mt-10) REVERT: A 381 LEU cc_start: 0.9486 (tp) cc_final: 0.9144 (tp) REVERT: A 384 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.7505 (pm20) REVERT: A 390 GLN cc_start: 0.8884 (mt0) cc_final: 0.8437 (mt0) REVERT: A 396 ASP cc_start: 0.8472 (p0) cc_final: 0.8105 (p0) REVERT: A 406 ASP cc_start: 0.8054 (m-30) cc_final: 0.7851 (t0) REVERT: A 459 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8637 (mttp) REVERT: A 493 MET cc_start: 0.9034 (tmm) cc_final: 0.8528 (tmm) REVERT: A 498 TYR cc_start: 0.8577 (m-80) cc_final: 0.8327 (m-10) REVERT: A 505 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8160 (mt-10) REVERT: A 515 ASP cc_start: 0.8983 (m-30) cc_final: 0.8731 (m-30) REVERT: A 597 ILE cc_start: 0.9095 (pt) cc_final: 0.8841 (pt) REVERT: A 599 GLU cc_start: 0.8573 (mt-10) cc_final: 0.7928 (pt0) REVERT: A 602 GLU cc_start: 0.7862 (pt0) cc_final: 0.6972 (pt0) REVERT: A 604 ARG cc_start: 0.8986 (mmm-85) cc_final: 0.8561 (mmm-85) REVERT: A 639 ASP cc_start: 0.8616 (m-30) cc_final: 0.8098 (m-30) REVERT: A 645 GLN cc_start: 0.9426 (tp40) cc_final: 0.9021 (tp-100) REVERT: A 684 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7703 (m-10) REVERT: B 82 LYS cc_start: 0.9539 (mmmm) cc_final: 0.9148 (mmtm) REVERT: B 117 ARG cc_start: 0.8937 (mmm160) cc_final: 0.8249 (mmt180) REVERT: B 128 PHE cc_start: 0.9749 (t80) cc_final: 0.9322 (t80) REVERT: B 172 LEU cc_start: 0.9452 (mp) cc_final: 0.9204 (mp) REVERT: B 181 ASP cc_start: 0.8561 (m-30) cc_final: 0.7956 (m-30) REVERT: B 232 ASN cc_start: 0.9162 (t0) cc_final: 0.8822 (t0) REVERT: B 235 ARG cc_start: 0.9030 (mtm110) cc_final: 0.8649 (ttp-110) REVERT: B 236 TYR cc_start: 0.9424 (t80) cc_final: 0.9009 (t80) REVERT: B 263 ASP cc_start: 0.8960 (m-30) cc_final: 0.8541 (m-30) REVERT: B 290 GLU cc_start: 0.8471 (tp30) cc_final: 0.8075 (tp30) REVERT: B 308 LYS cc_start: 0.9451 (mtpp) cc_final: 0.9069 (ptpp) REVERT: B 375 LYS cc_start: 0.9332 (mtpp) cc_final: 0.8986 (mtpp) REVERT: B 423 LYS cc_start: 0.9577 (mtmm) cc_final: 0.9205 (mtpp) REVERT: B 425 ILE cc_start: 0.9216 (pt) cc_final: 0.8763 (pt) REVERT: B 434 ASP cc_start: 0.8728 (m-30) cc_final: 0.8512 (m-30) REVERT: B 446 ARG cc_start: 0.7544 (ttm-80) cc_final: 0.6939 (mmm-85) REVERT: B 458 MET cc_start: 0.9051 (mmm) cc_final: 0.8820 (mmp) REVERT: B 515 ASP cc_start: 0.8987 (m-30) cc_final: 0.8725 (m-30) REVERT: B 599 GLU cc_start: 0.8400 (pt0) cc_final: 0.8058 (pt0) REVERT: B 602 GLU cc_start: 0.8784 (pt0) cc_final: 0.8190 (pt0) REVERT: B 610 LYS cc_start: 0.8927 (mtpp) cc_final: 0.8600 (mtpp) REVERT: B 631 ASP cc_start: 0.9157 (m-30) cc_final: 0.8939 (m-30) REVERT: B 686 ARG cc_start: 0.8369 (mtp-110) cc_final: 0.8108 (mtp85) REVERT: C 20 MET cc_start: 0.9526 (ptp) cc_final: 0.9183 (pmm) REVERT: C 21 PHE cc_start: 0.9431 (m-80) cc_final: 0.8995 (t80) REVERT: C 23 ASN cc_start: 0.9582 (t0) cc_final: 0.9365 (m-40) REVERT: C 55 TYR cc_start: 0.8996 (t80) cc_final: 0.8116 (t80) REVERT: C 86 ARG cc_start: 0.8723 (mtt180) cc_final: 0.8293 (mpt180) REVERT: C 96 MET cc_start: 0.8952 (mmm) cc_final: 0.8446 (mmm) REVERT: C 143 LYS cc_start: 0.9027 (tptt) cc_final: 0.8589 (tptp) REVERT: C 174 TYR cc_start: 0.9048 (OUTLIER) cc_final: 0.7977 (t80) REVERT: C 178 PHE cc_start: 0.8661 (t80) cc_final: 0.8277 (t80) REVERT: C 242 TYR cc_start: 0.9362 (t80) cc_final: 0.8878 (t80) REVERT: C 244 GLU cc_start: 0.9341 (OUTLIER) cc_final: 0.8925 (pp20) REVERT: C 245 ASP cc_start: 0.9104 (t0) cc_final: 0.8769 (t0) REVERT: C 313 GLU cc_start: 0.9167 (tt0) cc_final: 0.8888 (tt0) REVERT: D 20 MET cc_start: 0.8747 (ppp) cc_final: 0.8079 (ppp) REVERT: D 24 GLN cc_start: 0.8832 (mm-40) cc_final: 0.8213 (mp10) REVERT: D 30 TRP cc_start: 0.8239 (p-90) cc_final: 0.7777 (p-90) REVERT: D 40 ASP cc_start: 0.8812 (m-30) cc_final: 0.8500 (m-30) REVERT: D 74 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8189 (tpt) REVERT: D 109 PHE cc_start: 0.8705 (m-80) cc_final: 0.8288 (m-80) REVERT: D 123 GLU cc_start: 0.9113 (mp0) cc_final: 0.8832 (pp20) REVERT: D 137 MET cc_start: 0.9589 (mtt) cc_final: 0.9320 (mtp) REVERT: D 164 GLU cc_start: 0.8407 (mm-30) cc_final: 0.7365 (mm-30) REVERT: D 172 PHE cc_start: 0.8874 (m-80) cc_final: 0.8490 (m-80) REVERT: D 178 PHE cc_start: 0.9196 (m-80) cc_final: 0.8649 (t80) REVERT: D 198 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8588 (mm-30) REVERT: D 227 PHE cc_start: 0.8960 (t80) cc_final: 0.8493 (t80) REVERT: D 230 ASP cc_start: 0.9337 (t0) cc_final: 0.8616 (m-30) REVERT: D 233 ASN cc_start: 0.9029 (m110) cc_final: 0.8745 (p0) REVERT: D 259 PHE cc_start: 0.8734 (t80) cc_final: 0.8074 (t80) REVERT: D 263 ASN cc_start: 0.8904 (m110) cc_final: 0.8472 (m110) REVERT: D 273 PHE cc_start: 0.5678 (m-10) cc_final: 0.5436 (m-10) outliers start: 61 outliers final: 44 residues processed: 701 average time/residue: 0.1100 time to fit residues: 116.6335 Evaluate side-chains 708 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 657 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 189 optimal weight: 0.0980 chunk 181 optimal weight: 0.9980 chunk 165 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 HIS A 650 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 HIS ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.125180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.093052 restraints weight = 36877.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096569 restraints weight = 17531.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.098896 restraints weight = 10420.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.100492 restraints weight = 7146.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.101574 restraints weight = 5422.060| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.7918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16386 Z= 0.163 Angle : 0.865 18.412 22134 Z= 0.429 Chirality : 0.050 0.244 2360 Planarity : 0.004 0.053 2818 Dihedral : 10.049 170.852 2243 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.15 % Allowed : 34.85 % Favored : 62.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.18), residues: 1932 helix: 0.57 (0.15), residues: 1138 sheet: -0.81 (0.38), residues: 160 loop : -0.04 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 225 TYR 0.055 0.002 TYR D 142 PHE 0.043 0.002 PHE B 74 TRP 0.025 0.001 TRP D 124 HIS 0.030 0.002 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00375 (16386) covalent geometry : angle 0.86478 (22134) hydrogen bonds : bond 0.04344 ( 871) hydrogen bonds : angle 5.47956 ( 2571) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 682 time to evaluate : 0.496 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: A 123 SER cc_start: 0.9562 (OUTLIER) cc_final: 0.9100 (p) REVERT: A 139 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8616 (mt-10) REVERT: A 161 ARG cc_start: 0.8430 (ptm160) cc_final: 0.8201 (ptp-170) REVERT: A 194 LYS cc_start: 0.9570 (ttpp) cc_final: 0.9141 (ttpp) REVERT: A 220 THR cc_start: 0.9390 (m) cc_final: 0.8935 (p) REVERT: A 232 ASN cc_start: 0.9615 (m110) cc_final: 0.9114 (m110) REVERT: A 290 GLU cc_start: 0.9238 (tt0) cc_final: 0.8806 (tm-30) REVERT: A 335 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8235 (mt-10) REVERT: A 381 LEU cc_start: 0.9491 (tp) cc_final: 0.9135 (tp) REVERT: A 384 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.7416 (pm20) REVERT: A 390 GLN cc_start: 0.8946 (mt0) cc_final: 0.8485 (mt0) REVERT: A 406 ASP cc_start: 0.8093 (m-30) cc_final: 0.7818 (t0) REVERT: A 420 MET cc_start: 0.8934 (mmm) cc_final: 0.8654 (mmm) REVERT: A 459 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8526 (mttp) REVERT: A 493 MET cc_start: 0.8987 (tmm) cc_final: 0.8499 (tmm) REVERT: A 505 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8271 (mt-10) REVERT: A 515 ASP cc_start: 0.8984 (m-30) cc_final: 0.8459 (m-30) REVERT: A 597 ILE cc_start: 0.9012 (pt) cc_final: 0.8697 (pt) REVERT: A 599 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8114 (pt0) REVERT: A 602 GLU cc_start: 0.8046 (pt0) cc_final: 0.7690 (pt0) REVERT: A 604 ARG cc_start: 0.9000 (mmm-85) cc_final: 0.8742 (mmm-85) REVERT: A 618 LEU cc_start: 0.9193 (tp) cc_final: 0.8908 (tp) REVERT: A 636 LYS cc_start: 0.9165 (mmmt) cc_final: 0.8953 (mmmm) REVERT: A 639 ASP cc_start: 0.8578 (m-30) cc_final: 0.8174 (m-30) REVERT: A 645 GLN cc_start: 0.9377 (tp40) cc_final: 0.8980 (tp-100) REVERT: A 684 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.7624 (m-10) REVERT: B 15 GLU cc_start: 0.8822 (tp30) cc_final: 0.8520 (tp30) REVERT: B 82 LYS cc_start: 0.9521 (mmmm) cc_final: 0.9139 (mmtm) REVERT: B 107 LYS cc_start: 0.9449 (mmmm) cc_final: 0.9051 (mmmm) REVERT: B 116 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8312 (mt-10) REVERT: B 128 PHE cc_start: 0.9764 (t80) cc_final: 0.9333 (t80) REVERT: B 172 LEU cc_start: 0.9336 (mp) cc_final: 0.9103 (mp) REVERT: B 181 ASP cc_start: 0.8562 (m-30) cc_final: 0.7974 (m-30) REVERT: B 211 GLU cc_start: 0.8522 (mm-30) cc_final: 0.7583 (mm-30) REVERT: B 214 LYS cc_start: 0.9237 (ttpp) cc_final: 0.8956 (ttpp) REVERT: B 263 ASP cc_start: 0.8976 (m-30) cc_final: 0.8524 (m-30) REVERT: B 290 GLU cc_start: 0.8569 (tp30) cc_final: 0.8104 (tp30) REVERT: B 308 LYS cc_start: 0.9495 (mtpp) cc_final: 0.9088 (ptpp) REVERT: B 375 LYS cc_start: 0.9275 (mtpp) cc_final: 0.8916 (mtpp) REVERT: B 423 LYS cc_start: 0.9581 (mtmm) cc_final: 0.9195 (mtpp) REVERT: B 434 ASP cc_start: 0.8778 (m-30) cc_final: 0.8547 (m-30) REVERT: B 446 ARG cc_start: 0.7560 (ttm-80) cc_final: 0.6873 (mmm-85) REVERT: B 458 MET cc_start: 0.8979 (mmm) cc_final: 0.8738 (mmp) REVERT: B 474 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8361 (mt0) REVERT: B 515 ASP cc_start: 0.9044 (m-30) cc_final: 0.8727 (m-30) REVERT: B 599 GLU cc_start: 0.8381 (pt0) cc_final: 0.7992 (pt0) REVERT: B 602 GLU cc_start: 0.9003 (pt0) cc_final: 0.8415 (pt0) REVERT: B 610 LYS cc_start: 0.8944 (mtpp) cc_final: 0.8605 (mtpp) REVERT: B 686 ARG cc_start: 0.8431 (mtp-110) cc_final: 0.7986 (mtp85) REVERT: C 20 MET cc_start: 0.9545 (ptp) cc_final: 0.9326 (pmm) REVERT: C 21 PHE cc_start: 0.9441 (m-80) cc_final: 0.8981 (t80) REVERT: C 23 ASN cc_start: 0.9604 (t0) cc_final: 0.9371 (m-40) REVERT: C 55 TYR cc_start: 0.9061 (t80) cc_final: 0.8290 (t80) REVERT: C 86 ARG cc_start: 0.8704 (mtt180) cc_final: 0.8259 (mpt180) REVERT: C 93 MET cc_start: 0.9357 (ttt) cc_final: 0.9066 (tmt) REVERT: C 96 MET cc_start: 0.8908 (mmm) cc_final: 0.8340 (mmm) REVERT: C 122 PHE cc_start: 0.8875 (m-80) cc_final: 0.8504 (m-80) REVERT: C 137 MET cc_start: 0.9394 (tpp) cc_final: 0.9030 (tpp) REVERT: C 143 LYS cc_start: 0.8952 (tptt) cc_final: 0.8516 (tptp) REVERT: C 174 TYR cc_start: 0.9092 (OUTLIER) cc_final: 0.8043 (t80) REVERT: C 178 PHE cc_start: 0.8689 (t80) cc_final: 0.8267 (t80) REVERT: C 237 GLU cc_start: 0.9504 (pt0) cc_final: 0.9155 (pp20) REVERT: C 242 TYR cc_start: 0.9434 (t80) cc_final: 0.8871 (t80) REVERT: C 244 GLU cc_start: 0.9354 (OUTLIER) cc_final: 0.9023 (pp20) REVERT: C 313 GLU cc_start: 0.9182 (tt0) cc_final: 0.8556 (tp30) REVERT: D 20 MET cc_start: 0.8906 (ppp) cc_final: 0.8309 (ppp) REVERT: D 24 GLN cc_start: 0.8916 (mm-40) cc_final: 0.8478 (mp10) REVERT: D 30 TRP cc_start: 0.8197 (p-90) cc_final: 0.7794 (p-90) REVERT: D 40 ASP cc_start: 0.8892 (m-30) cc_final: 0.8580 (m-30) REVERT: D 46 TYR cc_start: 0.8988 (m-80) cc_final: 0.8091 (m-10) REVERT: D 79 GLU cc_start: 0.8971 (tt0) cc_final: 0.8545 (pt0) REVERT: D 109 PHE cc_start: 0.8698 (m-80) cc_final: 0.8285 (m-80) REVERT: D 123 GLU cc_start: 0.9175 (mp0) cc_final: 0.8597 (pt0) REVERT: D 130 TYR cc_start: 0.8730 (m-10) cc_final: 0.8383 (m-10) REVERT: D 137 MET cc_start: 0.9599 (mtt) cc_final: 0.9348 (mtp) REVERT: D 153 LEU cc_start: 0.6427 (tt) cc_final: 0.6213 (tt) REVERT: D 164 GLU cc_start: 0.8604 (mm-30) cc_final: 0.7535 (mm-30) REVERT: D 172 PHE cc_start: 0.8894 (m-80) cc_final: 0.8499 (m-80) REVERT: D 178 PHE cc_start: 0.9208 (m-80) cc_final: 0.8780 (t80) REVERT: D 198 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8592 (mm-30) REVERT: D 259 PHE cc_start: 0.8732 (t80) cc_final: 0.8084 (t80) REVERT: D 263 ASN cc_start: 0.8925 (m110) cc_final: 0.8440 (m110) outliers start: 54 outliers final: 42 residues processed: 705 average time/residue: 0.1054 time to fit residues: 112.2555 Evaluate side-chains 707 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 658 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 28 optimal weight: 0.0870 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 HIS ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN C 38 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN ** D 238 ASN ** 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 = 0.3615 r_free = 0.3615 target = 0.124819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.092423 restraints weight = 36880.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.095895 restraints weight = 17732.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.098197 restraints weight = 10745.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.099830 restraints weight = 7432.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.100964 restraints weight = 5642.611| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.8091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 16386 Z= 0.171 Angle : 0.875 14.977 22134 Z= 0.438 Chirality : 0.051 0.242 2360 Planarity : 0.004 0.053 2818 Dihedral : 9.968 175.341 2243 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.86 % Allowed : 36.01 % Favored : 61.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.19), residues: 1932 helix: 0.58 (0.15), residues: 1138 sheet: -0.77 (0.39), residues: 160 loop : -0.05 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 686 TYR 0.054 0.002 TYR D 142 PHE 0.055 0.002 PHE B 261 TRP 0.024 0.002 TRP D 124 HIS 0.029 0.002 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00395 (16386) covalent geometry : angle 0.87515 (22134) hydrogen bonds : bond 0.04397 ( 871) hydrogen bonds : angle 5.48264 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3214.66 seconds wall clock time: 56 minutes 28.02 seconds (3388.02 seconds total)