Starting phenix.real_space_refine on Thu Aug 6 15:07:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz6_45054/08_2026/9bz6_45054_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz6_45054/08_2026/9bz6_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_2026/9bz6_45054_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz6_45054/08_2026/9bz6_45054_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bz6_45054/08_2026/9bz6_45054.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz6_45054/08_2026/9bz6_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/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: 4.26, per 1000 atoms: 0.27 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: 1.34 Conformation dependent library (CDL) restraints added in 710.5 milliseconds 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: 0.46 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: 2.84 Time building geometry restraints manager: 1.84 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=" O3B TTP B 801 " pdb=" PG TTP B 801 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" O3B TTP A 803 " pdb=" PG TTP A 803 " ideal model delta sigma weight residual 1.748 1.610 0.138 2.00e-02 2.50e+03 4.78e+01 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=" O3A TTP A 803 " pdb=" PB TTP A 803 " ideal model delta sigma weight residual 1.675 1.606 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.608 0.067 2.00e-02 2.50e+03 1.14e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21528 2.09 - 4.19: 524 4.19 - 6.28: 63 6.28 - 8.37: 10 8.37 - 10.46: 9 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 - 25.04: 9092 25.04 - 50.07: 652 50.07 - 75.11: 126 75.11 - 100.15: 26 100.15 - 125.18: 2 Dihedral angle restraints: 9898 sinusoidal: 4140 harmonic: 5758 Sorted by residual: dihedral pdb=" O4' GDP A 802 " pdb=" C1' GDP A 802 " pdb=" N9 GDP A 802 " pdb=" C8 GDP A 802 " ideal model delta sinusoidal sigma weight residual 27.02 -98.16 125.18 1 2.00e+01 2.50e-03 3.78e+01 dihedral pdb=" O4' GDP B 804 " pdb=" C1' GDP B 804 " pdb=" N9 GDP B 804 " pdb=" C8 GDP B 804 " ideal model delta sinusoidal sigma weight residual 27.02 -95.62 122.65 1 2.00e+01 2.50e-03 3.69e+01 dihedral pdb=" C VAL C 125 " pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual -122.00 -134.36 12.36 0 2.50e+00 1.60e-01 2.44e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2142 0.093 - 0.187: 186 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.620 Find NCS groups from input model: 0.340 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 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 0.139 16386 Z= 0.335 Angle : 0.788 10.463 22134 Z= 0.472 Chirality : 0.058 0.467 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.634 125.184 6202 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 are 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/Z covalent geometry : bond 0.00597 / 0.33 (16386) covalent geometry : angle 0.78776 / 0.47 (22134) hydrogen bonds : bond 0.15421 / 9.51 ( 871) hydrogen bonds : angle 6.51761 / 4.65 ( 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 : 0.565 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: 0.8010 (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: 0.3588 (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: 0.5382 (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: 0.1369 time to fit residues: 216.3964 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 : 0.525 ------------------------------------------------------------------------------- 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: 2.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3735 r_free = 0.3735 target = 0.135056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.099614 restraints weight = 36492.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.103491 restraints weight = 17383.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.106191 restraints weight = 10626.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.108084 restraints weight = 7227.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.109447 restraints weight = 5430.819| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 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 = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16386 Z= 0.169 Angle : 0.711 11.643 22134 Z= 0.373 Chirality : 0.046 0.272 2360 Planarity : 0.004 0.036 2818 Dihedral : 10.002 127.390 2301 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.25 % Allowed : 21.04 % Favored : 74.71 % 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 are not related in a simple way. whole: 1.17 (0.18), residues: 1932 helix: 1.15 (0.15), residues: 1138 sheet: 1.02 (0.46), residues: 96 loop : 0.31 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 243 TYR 0.054 0.002 TYR D 262 PHE 0.039 0.003 PHE D 172 TRP 0.023 0.002 TRP D 30 HIS 0.010 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (16386) covalent geometry : angle 0.71092 / 0.37 (22134) hydrogen bonds : bond 0.04985 / 3.13 ( 871) hydrogen bonds : angle 5.35099 / 3.79 ( 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 863 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 790 time to evaluate : 0.611 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: A 39 ASP cc_start: 0.8906 (m-30) cc_final: 0.8647 (m-30) REVERT: A 51 LEU cc_start: 0.9251 (tp) cc_final: 0.9019 (tp) REVERT: A 75 GLU cc_start: 0.8516 (tm-30) cc_final: 0.7544 (pp20) REVERT: A 76 ASP cc_start: 0.9118 (m-30) cc_final: 0.8368 (m-30) REVERT: A 117 ARG cc_start: 0.8554 (mmm-85) cc_final: 0.8282 (mmm-85) REVERT: A 221 LYS cc_start: 0.9326 (mmtp) cc_final: 0.9035 (mttp) REVERT: A 290 GLU cc_start: 0.9311 (tt0) cc_final: 0.8982 (tm-30) REVERT: A 322 MET cc_start: 0.8615 (mmt) cc_final: 0.8290 (mmm) REVERT: A 335 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8056 (mt-10) REVERT: A 370 ASN cc_start: 0.9182 (m-40) cc_final: 0.8969 (m110) REVERT: A 375 LYS cc_start: 0.8473 (mttt) cc_final: 0.8272 (mmmm) REVERT: A 384 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7426 (pm20) REVERT: A 386 LEU cc_start: 0.9204 (mt) cc_final: 0.8980 (mt) REVERT: A 447 ASN cc_start: 0.8400 (m-40) cc_final: 0.8115 (m-40) REVERT: A 561 LEU cc_start: 0.9163 (tp) cc_final: 0.8847 (tp) REVERT: A 597 ILE cc_start: 0.9293 (pt) cc_final: 0.9067 (pt) REVERT: A 615 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.8907 (mmm) REVERT: A 618 LEU cc_start: 0.9510 (tp) cc_final: 0.9130 (tt) REVERT: A 639 ASP cc_start: 0.8467 (m-30) cc_final: 0.8067 (m-30) REVERT: A 662 MET cc_start: 0.8724 (ptp) cc_final: 0.8400 (ptp) REVERT: A 663 THR cc_start: 0.9463 (OUTLIER) cc_final: 0.9237 (t) REVERT: A 668 ASN cc_start: 0.9482 (m-40) cc_final: 0.9194 (m-40) REVERT: A 684 TYR cc_start: 0.7911 (OUTLIER) cc_final: 0.7393 (m-10) REVERT: B 15 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8370 (tp30) REVERT: B 87 LYS cc_start: 0.9235 (tptm) cc_final: 0.9015 (tppt) REVERT: B 172 LEU cc_start: 0.9375 (mp) cc_final: 0.9045 (mp) REVERT: B 211 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8078 (mm-30) REVERT: B 288 PHE cc_start: 0.9280 (t80) cc_final: 0.8896 (t80) REVERT: B 290 GLU cc_start: 0.7985 (tp30) cc_final: 0.7767 (tp30) REVERT: B 350 ARG cc_start: 0.8555 (mtp85) cc_final: 0.7901 (mtp85) REVERT: B 355 TYR cc_start: 0.8246 (m-80) cc_final: 0.7678 (m-80) REVERT: B 361 GLN cc_start: 0.9015 (tt0) cc_final: 0.8460 (tt0) REVERT: B 374 SER cc_start: 0.9064 (t) cc_final: 0.8768 (t) REVERT: B 378 PHE cc_start: 0.9310 (p90) cc_final: 0.9107 (p90) REVERT: B 399 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8652 (tp30) REVERT: B 425 ILE cc_start: 0.9444 (mt) cc_final: 0.9012 (mt) REVERT: B 458 MET cc_start: 0.9466 (mmm) cc_final: 0.9201 (mmp) REVERT: B 493 MET cc_start: 0.9670 (tmm) cc_final: 0.9223 (tmm) REVERT: B 496 ASN cc_start: 0.9616 (t0) cc_final: 0.9410 (t0) REVERT: B 515 ASP cc_start: 0.9080 (m-30) cc_final: 0.8733 (m-30) REVERT: B 543 ILE cc_start: 0.9495 (mm) cc_final: 0.9175 (mm) REVERT: B 550 MET cc_start: 0.8007 (mtm) cc_final: 0.7755 (mtm) REVERT: B 558 TRP cc_start: 0.9511 (m100) cc_final: 0.8649 (m100) REVERT: B 588 GLN cc_start: 0.9189 (mm-40) cc_final: 0.8949 (mm-40) REVERT: B 598 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7964 (mtm) REVERT: B 599 GLU cc_start: 0.8535 (pt0) cc_final: 0.8315 (pt0) REVERT: B 604 ARG cc_start: 0.8394 (mmp80) cc_final: 0.8131 (mmt-90) REVERT: B 621 ASN cc_start: 0.9495 (p0) cc_final: 0.9292 (p0) REVERT: B 632 MET cc_start: 0.8339 (mtp) cc_final: 0.5588 (mtp) REVERT: B 640 MET cc_start: 0.9186 (tpp) cc_final: 0.8913 (tpp) REVERT: B 686 ARG cc_start: 0.8313 (mtp-110) cc_final: 0.7688 (mtp-110) REVERT: C 86 ARG cc_start: 0.8275 (mtt180) cc_final: 0.7858 (mpt180) REVERT: C 109 PHE cc_start: 0.8829 (m-80) cc_final: 0.8615 (m-80) REVERT: C 116 GLU cc_start: 0.9083 (pm20) cc_final: 0.8867 (pm20) REVERT: C 118 ILE cc_start: 0.9806 (mt) cc_final: 0.9603 (mm) REVERT: C 122 PHE cc_start: 0.8872 (m-80) cc_final: 0.8543 (m-80) REVERT: C 163 LEU cc_start: 0.9458 (tt) cc_final: 0.9089 (tt) REVERT: C 185 MET cc_start: 0.7902 (mmm) cc_final: 0.7487 (mmm) REVERT: C 237 GLU cc_start: 0.9523 (pt0) cc_final: 0.9147 (pp20) REVERT: C 255 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8018 (m-30) REVERT: C 269 MET cc_start: 0.9482 (tmm) cc_final: 0.9203 (tmm) REVERT: C 271 LEU cc_start: 0.9324 (mt) cc_final: 0.9025 (mt) REVERT: D 18 THR cc_start: 0.9028 (p) cc_final: 0.8302 (m) REVERT: D 24 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8421 (mp10) REVERT: D 33 GLU cc_start: 0.9228 (mp0) cc_final: 0.8906 (pp20) REVERT: D 92 PHE cc_start: 0.8244 (t80) cc_final: 0.7916 (t80) REVERT: D 131 LEU cc_start: 0.7685 (tp) cc_final: 0.7337 (tt) REVERT: D 137 MET cc_start: 0.9212 (mtt) cc_final: 0.8969 (mtp) REVERT: D 178 PHE cc_start: 0.8969 (m-80) cc_final: 0.8594 (m-80) REVERT: D 184 LEU cc_start: 0.8604 (mt) cc_final: 0.8276 (mt) REVERT: D 231 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9185 (mm) REVERT: D 233 ASN cc_start: 0.9030 (m110) cc_final: 0.8816 (p0) REVERT: D 241 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8398 (mp0) REVERT: D 242 TYR cc_start: 0.8234 (t80) cc_final: 0.7740 (t80) REVERT: D 259 PHE cc_start: 0.8276 (t80) cc_final: 0.7423 (t80) REVERT: D 262 TYR cc_start: 0.8992 (t80) cc_final: 0.8765 (t80) outliers start: 73 outliers final: 31 residues processed: 818 average time/residue: 0.1274 time to fit residues: 157.5940 Evaluate side-chains 749 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 711 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 312 VAL 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 153 LEU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 239 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 182 optimal weight: 0.8980 chunk 159 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 150 optimal weight: 0.4980 chunk 63 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN C 263 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.131054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.097334 restraints weight = 36749.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.101050 restraints weight = 17079.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.103193 restraints weight = 10104.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.104934 restraints weight = 7209.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.106171 restraints weight = 5514.619| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (15 function evaluations) r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16386 Z= 0.172 Angle : 0.705 13.207 22134 Z= 0.362 Chirality : 0.045 0.171 2360 Planarity : 0.004 0.039 2818 Dihedral : 9.272 131.330 2295 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.79 % Allowed : 23.60 % Favored : 72.61 % 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 are not related in a simple way. whole: 0.95 (0.19), residues: 1932 helix: 0.98 (0.15), residues: 1156 sheet: 0.89 (0.46), residues: 98 loop : 0.19 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 243 TYR 0.044 0.002 TYR D 262 PHE 0.052 0.002 PHE C 168 TRP 0.014 0.002 TRP D 30 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (16386) covalent geometry : angle 0.70465 / 0.36 (22134) hydrogen bonds : bond 0.04527 / 2.87 ( 871) hydrogen bonds : angle 5.30748 / 3.78 ( 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 813 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 748 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8878 (tttm) cc_final: 0.8591 (tppt) REVERT: A 12 LEU cc_start: 0.9417 (mt) cc_final: 0.9006 (mt) REVERT: A 39 ASP cc_start: 0.8968 (m-30) cc_final: 0.8754 (m-30) REVERT: A 51 LEU cc_start: 0.9217 (tp) cc_final: 0.8977 (tp) REVERT: A 76 ASP cc_start: 0.9169 (m-30) cc_final: 0.8882 (m-30) REVERT: A 163 ARG cc_start: 0.7960 (tpp80) cc_final: 0.7719 (mmm-85) REVERT: A 178 SER cc_start: 0.8962 (OUTLIER) cc_final: 0.8095 (t) REVERT: A 220 THR cc_start: 0.9385 (m) cc_final: 0.9077 (p) REVERT: A 221 LYS cc_start: 0.9298 (mmtp) cc_final: 0.8966 (mttp) REVERT: A 243 ARG cc_start: 0.7998 (ptm-80) cc_final: 0.7723 (ppt170) REVERT: A 252 ASN cc_start: 0.9220 (t0) cc_final: 0.8985 (t0) REVERT: A 259 ASN cc_start: 0.8932 (m-40) cc_final: 0.8730 (m110) REVERT: A 290 GLU cc_start: 0.9317 (tt0) cc_final: 0.8974 (tm-30) REVERT: A 335 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8048 (mt-10) REVERT: A 390 GLN cc_start: 0.8674 (mt0) cc_final: 0.8246 (mt0) REVERT: A 393 SER cc_start: 0.9645 (m) cc_final: 0.9378 (t) REVERT: A 444 ASP cc_start: 0.8581 (t0) cc_final: 0.7220 (t0) REVERT: A 446 ARG cc_start: 0.7485 (mtp85) cc_final: 0.7066 (mmm160) REVERT: A 447 ASN cc_start: 0.8474 (m-40) cc_final: 0.8123 (m-40) REVERT: A 456 LYS cc_start: 0.8798 (mtmm) cc_final: 0.8553 (mtmm) REVERT: A 512 GLU cc_start: 0.8345 (pt0) cc_final: 0.8129 (pm20) REVERT: A 515 ASP cc_start: 0.9043 (m-30) cc_final: 0.8807 (m-30) REVERT: A 558 TRP cc_start: 0.9300 (m100) cc_final: 0.8844 (m100) REVERT: A 590 SER cc_start: 0.9611 (t) cc_final: 0.9032 (p) REVERT: A 597 ILE cc_start: 0.9334 (pt) cc_final: 0.9124 (pt) REVERT: A 639 ASP cc_start: 0.8663 (m-30) cc_final: 0.8246 (m-30) REVERT: A 640 MET cc_start: 0.9467 (OUTLIER) cc_final: 0.8505 (tpp) REVERT: A 645 GLN cc_start: 0.9310 (tp40) cc_final: 0.9074 (tp-100) REVERT: A 663 THR cc_start: 0.9526 (OUTLIER) cc_final: 0.9323 (t) REVERT: A 668 ASN cc_start: 0.9542 (m-40) cc_final: 0.9308 (m-40) REVERT: A 684 TYR cc_start: 0.7968 (OUTLIER) cc_final: 0.7321 (m-10) REVERT: B 99 LYS cc_start: 0.9183 (mmtt) cc_final: 0.8630 (mmmm) REVERT: B 150 GLN cc_start: 0.9139 (tp40) cc_final: 0.8855 (tp40) REVERT: B 152 SER cc_start: 0.9725 (p) cc_final: 0.9438 (p) REVERT: B 172 LEU cc_start: 0.9409 (mp) cc_final: 0.9082 (mp) REVERT: B 181 ASP cc_start: 0.8921 (m-30) cc_final: 0.8708 (m-30) REVERT: B 221 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8743 (mmtp) REVERT: B 235 ARG cc_start: 0.8807 (mtm110) cc_final: 0.8264 (mtm110) REVERT: B 274 ARG cc_start: 0.8679 (ttm-80) cc_final: 0.8422 (ttm-80) REVERT: B 288 PHE cc_start: 0.9253 (t80) cc_final: 0.8989 (t80) REVERT: B 316 GLU cc_start: 0.9110 (tt0) cc_final: 0.8800 (pt0) REVERT: B 344 GLU cc_start: 0.8874 (pt0) cc_final: 0.8569 (pp20) REVERT: B 350 ARG cc_start: 0.8712 (mtp85) cc_final: 0.7501 (mtp85) REVERT: B 355 TYR cc_start: 0.8429 (m-80) cc_final: 0.7773 (m-80) REVERT: B 361 GLN cc_start: 0.9100 (tt0) cc_final: 0.8843 (tt0) REVERT: B 374 SER cc_start: 0.9029 (t) cc_final: 0.8498 (p) REVERT: B 399 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8181 (tp30) REVERT: B 407 ILE cc_start: 0.8828 (mt) cc_final: 0.8603 (mt) REVERT: B 446 ARG cc_start: 0.7793 (ttm-80) cc_final: 0.7571 (mmm-85) REVERT: B 458 MET cc_start: 0.9341 (mmm) cc_final: 0.9090 (mmp) REVERT: B 493 MET cc_start: 0.9661 (tmm) cc_final: 0.9379 (tmm) REVERT: B 515 ASP cc_start: 0.9090 (m-30) cc_final: 0.8706 (m-30) REVERT: B 543 ILE cc_start: 0.9509 (mm) cc_final: 0.9162 (mm) REVERT: B 550 MET cc_start: 0.8251 (mtm) cc_final: 0.7840 (mtm) REVERT: B 558 TRP cc_start: 0.9584 (m100) cc_final: 0.8685 (m100) REVERT: B 588 GLN cc_start: 0.9339 (mm-40) cc_final: 0.8783 (mm-40) REVERT: B 598 MET cc_start: 0.8439 (mtm) cc_final: 0.8013 (mtm) REVERT: B 599 GLU cc_start: 0.8496 (pt0) cc_final: 0.8240 (pt0) REVERT: B 604 ARG cc_start: 0.8585 (mmp80) cc_final: 0.8148 (mmt-90) REVERT: B 610 LYS cc_start: 0.8809 (mtpp) cc_final: 0.8553 (mtpp) REVERT: B 686 ARG cc_start: 0.8323 (mtp-110) cc_final: 0.7713 (mtp-110) REVERT: C 66 ASP cc_start: 0.8902 (OUTLIER) cc_final: 0.8479 (t70) REVERT: C 86 ARG cc_start: 0.8415 (mtt180) cc_final: 0.7992 (mpt180) REVERT: C 95 MET cc_start: 0.8573 (tmm) cc_final: 0.8096 (tmm) REVERT: C 112 LEU cc_start: 0.8121 (mt) cc_final: 0.7596 (pp) REVERT: C 118 ILE cc_start: 0.9725 (mt) cc_final: 0.9461 (mt) REVERT: C 122 PHE cc_start: 0.8801 (m-80) cc_final: 0.8360 (m-80) REVERT: C 137 MET cc_start: 0.9075 (tpp) cc_final: 0.8785 (tpp) REVERT: C 179 TYR cc_start: 0.8737 (t80) cc_final: 0.8529 (t80) REVERT: C 201 HIS cc_start: 0.8834 (m-70) cc_final: 0.8473 (m-70) REVERT: C 212 ILE cc_start: 0.9169 (mt) cc_final: 0.8882 (tp) REVERT: C 269 MET cc_start: 0.9547 (tmm) cc_final: 0.9295 (tmm) REVERT: D 18 THR cc_start: 0.9011 (p) cc_final: 0.8651 (m) REVERT: D 24 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8403 (mp10) REVERT: D 74 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.7112 (tpt) REVERT: D 92 PHE cc_start: 0.8368 (t80) cc_final: 0.7809 (t80) REVERT: D 109 PHE cc_start: 0.8536 (m-80) cc_final: 0.8140 (m-80) REVERT: D 137 MET cc_start: 0.9339 (mtt) cc_final: 0.9028 (mtp) REVERT: D 178 PHE cc_start: 0.8807 (m-80) cc_final: 0.7989 (m-80) REVERT: D 184 LEU cc_start: 0.8825 (mt) cc_final: 0.8554 (mt) REVERT: D 231 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9177 (mm) REVERT: D 259 PHE cc_start: 0.8440 (t80) cc_final: 0.7484 (t80) REVERT: D 265 ASN cc_start: 0.8852 (m110) cc_final: 0.8545 (m110) outliers start: 65 outliers final: 39 residues processed: 779 average time/residue: 0.1254 time to fit residues: 148.8909 Evaluate side-chains 740 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 693 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 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 437 THR 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 663 THR 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 108 THR Chi-restraints excluded: chain B residue 155 THR 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 221 LYS 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 66 ASP Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 309 LYS Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 231 LEU 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: 5.9990 chunk 157 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 185 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 182 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 GLN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN C 127 GLN ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 GLN ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN D 28 GLN D 181 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 = 0.3578 r_free = 0.3578 target = 0.119840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.086225 restraints weight = 38284.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.089649 restraints weight = 18477.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.091877 restraints weight = 11218.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.093499 restraints weight = 7866.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.094557 restraints weight = 6048.669| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (9 function evaluations) r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.6141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 16386 Z= 0.305 Angle : 0.755 12.519 22134 Z= 0.397 Chirality : 0.048 0.189 2360 Planarity : 0.004 0.043 2818 Dihedral : 9.272 138.936 2292 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 5.65 % Allowed : 24.65 % Favored : 69.70 % 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 are not related in a simple way. whole: 0.60 (0.18), residues: 1932 helix: 0.79 (0.15), residues: 1161 sheet: -0.31 (0.39), residues: 148 loop : 0.07 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 686 TYR 0.045 0.002 TYR D 142 PHE 0.044 0.003 PHE C 109 TRP 0.026 0.002 TRP D 30 HIS 0.007 0.002 HIS A 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.31 (16386) covalent geometry : angle 0.75467 / 0.40 (22134) hydrogen bonds : bond 0.04489 / 2.88 ( 871) hydrogen bonds : angle 5.44654 / 3.86 ( 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 814 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 717 time to evaluate : 0.575 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 51 LEU cc_start: 0.9439 (tp) cc_final: 0.9089 (tp) REVERT: A 95 MET cc_start: 0.9042 (mmm) cc_final: 0.8757 (tpp) REVERT: A 150 GLN cc_start: 0.9045 (tp-100) cc_final: 0.8820 (tp-100) REVERT: A 163 ARG cc_start: 0.8226 (tpp80) cc_final: 0.7984 (mmm-85) REVERT: A 166 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8701 (mm-30) REVERT: A 178 SER cc_start: 0.8728 (OUTLIER) cc_final: 0.8310 (t) REVERT: A 194 LYS cc_start: 0.9596 (ttpp) cc_final: 0.9340 (ttpp) REVERT: A 220 THR cc_start: 0.9407 (m) cc_final: 0.9107 (p) REVERT: A 221 LYS cc_start: 0.9346 (mmtp) cc_final: 0.8994 (mttp) REVERT: A 243 ARG cc_start: 0.8022 (ptm-80) cc_final: 0.7745 (ppt170) REVERT: A 250 TYR cc_start: 0.9029 (m-80) cc_final: 0.8524 (m-80) REVERT: A 251 LEU cc_start: 0.9489 (tp) cc_final: 0.9128 (tp) REVERT: A 252 ASN cc_start: 0.9370 (t0) cc_final: 0.9169 (t0) REVERT: A 290 GLU cc_start: 0.9317 (tt0) cc_final: 0.9049 (tm-30) REVERT: A 335 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8114 (mt-10) REVERT: A 384 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.7749 (pm20) REVERT: A 390 GLN cc_start: 0.8827 (mt0) cc_final: 0.8356 (mt0) REVERT: A 444 ASP cc_start: 0.8618 (t0) cc_final: 0.8027 (t0) REVERT: A 446 ARG cc_start: 0.7586 (mtp85) cc_final: 0.7155 (mmm160) REVERT: A 459 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.8971 (mttp) REVERT: A 515 ASP cc_start: 0.9105 (m-30) cc_final: 0.8900 (m-30) REVERT: A 590 SER cc_start: 0.9517 (t) cc_final: 0.9203 (p) REVERT: A 597 ILE cc_start: 0.9336 (pt) cc_final: 0.9075 (pt) REVERT: A 618 LEU cc_start: 0.9490 (tp) cc_final: 0.9229 (tt) REVERT: A 639 ASP cc_start: 0.8807 (m-30) cc_final: 0.8220 (m-30) REVERT: A 640 MET cc_start: 0.9485 (OUTLIER) cc_final: 0.8625 (tpp) REVERT: A 645 GLN cc_start: 0.9497 (tp40) cc_final: 0.9199 (tp-100) REVERT: A 668 ASN cc_start: 0.9579 (m-40) cc_final: 0.9317 (m-40) REVERT: A 683 TYR cc_start: 0.8947 (t80) cc_final: 0.8566 (t80) REVERT: A 684 TYR cc_start: 0.8228 (OUTLIER) cc_final: 0.7519 (m-10) REVERT: B 99 LYS cc_start: 0.9298 (mmtt) cc_final: 0.8779 (mmmm) REVERT: B 172 LEU cc_start: 0.9567 (mp) cc_final: 0.9296 (mp) REVERT: B 202 ASN cc_start: 0.9399 (t0) cc_final: 0.9015 (t0) REVERT: B 238 ASP cc_start: 0.8016 (t0) cc_final: 0.7729 (t0) REVERT: B 257 ASP cc_start: 0.8898 (m-30) cc_final: 0.8608 (m-30) REVERT: B 288 PHE cc_start: 0.9270 (t80) cc_final: 0.8892 (t80) REVERT: B 290 GLU cc_start: 0.8375 (tp30) cc_final: 0.8168 (tp30) REVERT: B 308 LYS cc_start: 0.9500 (mtpp) cc_final: 0.9136 (mtmm) REVERT: B 344 GLU cc_start: 0.8829 (pt0) cc_final: 0.8469 (pp20) REVERT: B 352 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8103 (mm-30) REVERT: B 375 LYS cc_start: 0.9373 (mtpp) cc_final: 0.9124 (mtpp) REVERT: B 423 LYS cc_start: 0.9522 (mtmm) cc_final: 0.9162 (mmtp) REVERT: B 434 ASP cc_start: 0.8728 (m-30) cc_final: 0.8445 (m-30) REVERT: B 446 ARG cc_start: 0.7808 (ttm-80) cc_final: 0.7554 (mmm-85) REVERT: B 458 MET cc_start: 0.9357 (mmm) cc_final: 0.9077 (mmp) REVERT: B 493 MET cc_start: 0.9624 (tmm) cc_final: 0.9281 (tmm) REVERT: B 515 ASP cc_start: 0.9100 (m-30) cc_final: 0.8792 (m-30) REVERT: B 543 ILE cc_start: 0.9590 (mm) cc_final: 0.9364 (mm) REVERT: B 599 GLU cc_start: 0.8498 (pt0) cc_final: 0.8244 (pt0) REVERT: B 602 GLU cc_start: 0.8740 (pt0) cc_final: 0.7891 (pt0) REVERT: B 604 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7815 (mmt-90) REVERT: B 610 LYS cc_start: 0.8916 (mtpp) cc_final: 0.8527 (mtpp) REVERT: B 631 ASP cc_start: 0.8842 (t0) cc_final: 0.8491 (t0) REVERT: B 657 PHE cc_start: 0.8945 (m-80) cc_final: 0.8667 (m-80) REVERT: B 686 ARG cc_start: 0.8351 (mtp-110) cc_final: 0.7609 (mtp85) REVERT: C 66 ASP cc_start: 0.8992 (OUTLIER) cc_final: 0.8574 (t70) REVERT: C 86 ARG cc_start: 0.8639 (mtt180) cc_final: 0.8159 (mpt180) REVERT: C 95 MET cc_start: 0.8714 (tmm) cc_final: 0.8259 (tmm) REVERT: C 118 ILE cc_start: 0.9737 (mt) cc_final: 0.9419 (mt) REVERT: C 122 PHE cc_start: 0.8895 (m-80) cc_final: 0.8418 (m-80) REVERT: C 174 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.7550 (t80) REVERT: C 179 TYR cc_start: 0.8843 (t80) cc_final: 0.8537 (t80) REVERT: C 242 TYR cc_start: 0.9531 (t80) cc_final: 0.9030 (t80) REVERT: C 259 PHE cc_start: 0.8317 (t80) cc_final: 0.7408 (t80) REVERT: C 260 ILE cc_start: 0.8055 (pp) cc_final: 0.7625 (pp) REVERT: C 269 MET cc_start: 0.9686 (tmm) cc_final: 0.9445 (tmm) REVERT: D 18 THR cc_start: 0.9073 (p) cc_final: 0.8586 (m) REVERT: D 20 MET cc_start: 0.8804 (ttt) cc_final: 0.8472 (ptm) REVERT: D 24 GLN cc_start: 0.8915 (mm-40) cc_final: 0.8686 (mp10) REVERT: D 28 GLN cc_start: 0.9100 (mt0) cc_final: 0.8792 (tt0) REVERT: D 74 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7258 (tpt) REVERT: D 109 PHE cc_start: 0.8585 (m-80) cc_final: 0.8177 (m-80) REVERT: D 129 LYS cc_start: 0.9501 (mmmt) cc_final: 0.9231 (tptp) REVERT: D 131 LEU cc_start: 0.7669 (tt) cc_final: 0.7433 (tp) REVERT: D 137 MET cc_start: 0.9472 (mtt) cc_final: 0.9212 (mtp) REVERT: D 172 PHE cc_start: 0.9068 (m-80) cc_final: 0.8851 (m-80) REVERT: D 236 TYR cc_start: 0.9157 (t80) cc_final: 0.8573 (t80) REVERT: D 259 PHE cc_start: 0.8716 (t80) cc_final: 0.7938 (t80) outliers start: 97 outliers final: 65 residues processed: 761 average time/residue: 0.1290 time to fit residues: 148.7489 Evaluate side-chains 732 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 658 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 141 VAL 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 224 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 349 LEU 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 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 640 MET Chi-restraints excluded: chain A residue 663 THR 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 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 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 604 ARG Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 662 MET 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 174 TYR Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 312 VAL 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 89 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 168 optimal weight: 8.9990 chunk 157 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 GLN ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN C 216 GLN ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3579 r_free = 0.3579 target = 0.121145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.087698 restraints weight = 37346.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.091212 restraints weight = 17738.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.093530 restraints weight = 10713.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.095206 restraints weight = 7408.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.096400 restraints weight = 5614.544| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 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 = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (15 function evaluations) r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.6523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16386 Z= 0.152 Angle : 0.733 13.734 22134 Z= 0.374 Chirality : 0.046 0.289 2360 Planarity : 0.004 0.047 2818 Dihedral : 8.840 136.310 2292 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.37 % Allowed : 29.02 % Favored : 66.61 % 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 are not related in a simple way. whole: 0.64 (0.19), residues: 1932 helix: 0.84 (0.15), residues: 1148 sheet: -0.47 (0.38), residues: 160 loop : 0.16 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 164 TYR 0.058 0.002 TYR D 142 PHE 0.042 0.002 PHE D 172 TRP 0.033 0.002 TRP D 30 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (16386) covalent geometry : angle 0.73286 / 0.37 (22134) hydrogen bonds : bond 0.04271 / 2.73 ( 871) hydrogen bonds : angle 5.27125 / 3.75 ( 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 801 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 726 time to evaluate : 0.627 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: A 51 LEU cc_start: 0.9304 (tp) cc_final: 0.9031 (tp) REVERT: A 56 ASP cc_start: 0.9221 (m-30) cc_final: 0.8941 (m-30) REVERT: A 95 MET cc_start: 0.9030 (mmm) cc_final: 0.8801 (tpp) REVERT: A 123 SER cc_start: 0.9621 (OUTLIER) cc_final: 0.9173 (p) REVERT: A 150 GLN cc_start: 0.9145 (tp40) cc_final: 0.8723 (tp40) REVERT: A 163 ARG cc_start: 0.8286 (tpp80) cc_final: 0.7944 (mmm-85) REVERT: A 178 SER cc_start: 0.8652 (OUTLIER) cc_final: 0.8342 (t) REVERT: A 190 MET cc_start: 0.9132 (mtp) cc_final: 0.8917 (mtp) REVERT: A 191 GLN cc_start: 0.8493 (mm-40) cc_final: 0.7994 (mt0) REVERT: A 194 LYS cc_start: 0.9573 (ttpp) cc_final: 0.9335 (ttpp) REVERT: A 220 THR cc_start: 0.9351 (m) cc_final: 0.8920 (p) REVERT: A 221 LYS cc_start: 0.9221 (mmtp) cc_final: 0.8806 (mttp) REVERT: A 232 ASN cc_start: 0.9266 (m-40) cc_final: 0.8970 (m110) REVERT: A 243 ARG cc_start: 0.7996 (ptm-80) cc_final: 0.7638 (ppt170) REVERT: A 290 GLU cc_start: 0.9341 (tt0) cc_final: 0.8851 (tm-30) REVERT: A 301 PHE cc_start: 0.9251 (m-10) cc_final: 0.8945 (m-10) REVERT: A 312 GLN cc_start: 0.8475 (mp10) cc_final: 0.8144 (pm20) REVERT: A 335 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8244 (mt-10) REVERT: A 362 ASP cc_start: 0.8321 (m-30) cc_final: 0.7723 (m-30) REVERT: A 384 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.7427 (pm20) REVERT: A 390 GLN cc_start: 0.8834 (mt0) cc_final: 0.8565 (mt0) REVERT: A 406 ASP cc_start: 0.8203 (m-30) cc_final: 0.7771 (t0) REVERT: A 444 ASP cc_start: 0.8736 (t0) cc_final: 0.8117 (t0) REVERT: A 446 ARG cc_start: 0.7448 (mtp85) cc_final: 0.7041 (mmm160) REVERT: A 447 ASN cc_start: 0.8553 (m110) cc_final: 0.7120 (m110) REVERT: A 456 LYS cc_start: 0.9506 (ttmm) cc_final: 0.9174 (mtmm) REVERT: A 459 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8935 (mtmm) REVERT: A 493 MET cc_start: 0.8998 (tmm) cc_final: 0.8633 (tmm) REVERT: A 515 ASP cc_start: 0.9160 (m-30) cc_final: 0.8937 (m-30) REVERT: A 590 SER cc_start: 0.9544 (t) cc_final: 0.9049 (p) REVERT: A 597 ILE cc_start: 0.9413 (pt) cc_final: 0.9131 (pt) REVERT: A 598 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8402 (tpp) REVERT: A 599 GLU cc_start: 0.8855 (mt-10) cc_final: 0.7924 (pt0) REVERT: A 639 ASP cc_start: 0.8840 (m-30) cc_final: 0.8209 (m-30) REVERT: A 640 MET cc_start: 0.9546 (OUTLIER) cc_final: 0.8595 (tpp) REVERT: A 645 GLN cc_start: 0.9368 (tp40) cc_final: 0.9038 (tp-100) REVERT: A 684 TYR cc_start: 0.7989 (OUTLIER) cc_final: 0.7300 (m-10) REVERT: B 15 GLU cc_start: 0.8880 (tp30) cc_final: 0.8601 (tp30) REVERT: B 31 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8668 (mp0) REVERT: B 60 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8894 (mp0) REVERT: B 99 LYS cc_start: 0.9256 (mmtt) cc_final: 0.8707 (mmmm) REVERT: B 112 LYS cc_start: 0.9441 (mmmt) cc_final: 0.9206 (mmmt) REVERT: B 172 LEU cc_start: 0.9458 (mp) cc_final: 0.9177 (mp) REVERT: B 238 ASP cc_start: 0.7944 (t0) cc_final: 0.7684 (t0) REVERT: B 257 ASP cc_start: 0.9020 (m-30) cc_final: 0.8768 (m-30) REVERT: B 290 GLU cc_start: 0.8457 (tp30) cc_final: 0.8156 (tp30) REVERT: B 344 GLU cc_start: 0.8872 (pt0) cc_final: 0.8662 (pt0) REVERT: B 352 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8125 (mm-30) REVERT: B 375 LYS cc_start: 0.9303 (mtpp) cc_final: 0.9026 (mtpp) REVERT: B 423 LYS cc_start: 0.9520 (mtmm) cc_final: 0.9064 (mmtp) REVERT: B 434 ASP cc_start: 0.8868 (m-30) cc_final: 0.8500 (m-30) REVERT: B 446 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7623 (mmm-85) REVERT: B 447 ASN cc_start: 0.8702 (m-40) cc_final: 0.8346 (t0) REVERT: B 458 MET cc_start: 0.9201 (mmm) cc_final: 0.8841 (mmp) REVERT: B 480 GLU cc_start: 0.8433 (mp0) cc_final: 0.7742 (mp0) REVERT: B 493 MET cc_start: 0.9639 (tmm) cc_final: 0.9307 (tmm) REVERT: B 515 ASP cc_start: 0.9100 (m-30) cc_final: 0.8708 (m-30) REVERT: B 543 ILE cc_start: 0.9511 (mm) cc_final: 0.9301 (mm) REVERT: B 599 GLU cc_start: 0.8446 (pt0) cc_final: 0.8031 (pt0) REVERT: B 602 GLU cc_start: 0.8906 (pt0) cc_final: 0.8541 (pt0) REVERT: B 604 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8205 (mmp80) REVERT: B 610 LYS cc_start: 0.8915 (mtpp) cc_final: 0.8666 (mtpp) REVERT: B 631 ASP cc_start: 0.8880 (t0) cc_final: 0.8487 (t0) REVERT: B 632 MET cc_start: 0.8477 (mmm) cc_final: 0.7507 (mmm) REVERT: B 686 ARG cc_start: 0.8497 (mtp-110) cc_final: 0.8064 (mtp-110) REVERT: C 21 PHE cc_start: 0.9329 (m-80) cc_final: 0.8921 (t80) REVERT: C 55 TYR cc_start: 0.9028 (t80) cc_final: 0.8288 (t80) REVERT: C 66 ASP cc_start: 0.8938 (OUTLIER) cc_final: 0.8580 (t70) REVERT: C 69 GLN cc_start: 0.8430 (tm-30) cc_final: 0.8185 (tm-30) REVERT: C 86 ARG cc_start: 0.8618 (mtt180) cc_final: 0.8207 (mpt180) REVERT: C 96 MET cc_start: 0.8790 (mmm) cc_final: 0.8502 (mmm) REVERT: C 118 ILE cc_start: 0.9739 (mt) cc_final: 0.9520 (mt) REVERT: C 122 PHE cc_start: 0.8932 (m-80) cc_final: 0.8420 (m-80) REVERT: C 149 ASP cc_start: 0.8483 (t0) cc_final: 0.8281 (t0) REVERT: C 174 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.7437 (t80) REVERT: C 178 PHE cc_start: 0.8810 (t80) cc_final: 0.8575 (t80) REVERT: C 179 TYR cc_start: 0.8786 (t80) cc_final: 0.8526 (t80) REVERT: C 237 GLU cc_start: 0.9533 (pt0) cc_final: 0.9149 (pp20) REVERT: C 242 TYR cc_start: 0.9523 (t80) cc_final: 0.8997 (t80) REVERT: C 269 MET cc_start: 0.9678 (tmm) cc_final: 0.9428 (tmm) REVERT: D 18 THR cc_start: 0.9034 (p) cc_final: 0.8656 (m) REVERT: D 28 GLN cc_start: 0.9050 (mt0) cc_final: 0.8800 (tt0) REVERT: D 74 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7507 (tpt) REVERT: D 109 PHE cc_start: 0.8605 (m-80) cc_final: 0.8183 (m-80) REVERT: D 137 MET cc_start: 0.9580 (mtt) cc_final: 0.9311 (mtp) REVERT: D 164 GLU cc_start: 0.8598 (mm-30) cc_final: 0.7605 (mm-30) REVERT: D 172 PHE cc_start: 0.9121 (m-80) cc_final: 0.8818 (m-80) REVERT: D 178 PHE cc_start: 0.9290 (m-80) cc_final: 0.8769 (t80) REVERT: D 198 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8472 (mm-30) REVERT: D 231 LEU cc_start: 0.9564 (mm) cc_final: 0.9188 (mm) REVERT: D 259 PHE cc_start: 0.8628 (t80) cc_final: 0.7885 (t80) REVERT: D 263 ASN cc_start: 0.9115 (m-40) cc_final: 0.8827 (m-40) outliers start: 75 outliers final: 40 residues processed: 756 average time/residue: 0.1118 time to fit residues: 129.6637 Evaluate side-chains 744 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 691 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 341 LYS 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 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 598 MET 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 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 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 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 604 ARG Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 620 SER 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 174 TYR Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 226 GLU 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 145 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 72 optimal weight: 0.0040 chunk 172 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 136 optimal weight: 7.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN C 216 GLN C 263 ASN D 181 GLN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.121941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.089428 restraints weight = 36867.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.092961 restraints weight = 17314.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.095054 restraints weight = 10261.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.096840 restraints weight = 7241.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.097854 restraints weight = 5390.359| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.096 | | 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) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.6826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16386 Z= 0.151 Angle : 0.748 13.736 22134 Z= 0.380 Chirality : 0.047 0.323 2360 Planarity : 0.004 0.049 2818 Dihedral : 8.633 136.783 2291 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.08 % Allowed : 31.29 % Favored : 64.63 % 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 are not related in a simple way. whole: 0.45 (0.18), residues: 1932 helix: 0.73 (0.15), residues: 1150 sheet: -0.47 (0.38), residues: 160 loop : -0.06 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 686 TYR 0.048 0.002 TYR D 142 PHE 0.039 0.002 PHE C 172 TRP 0.034 0.002 TRP D 30 HIS 0.016 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (16386) covalent geometry : angle 0.74835 / 0.38 (22134) hydrogen bonds : bond 0.04191 / 2.68 ( 871) hydrogen bonds : angle 5.29490 / 3.75 ( 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 780 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 710 time to evaluate : 0.510 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: 0.9293 (tp) cc_final: 0.9093 (tp) REVERT: A 95 MET cc_start: 0.9040 (mmm) cc_final: 0.8832 (tpp) REVERT: A 123 SER cc_start: 0.9584 (OUTLIER) cc_final: 0.9113 (p) REVERT: A 128 PHE cc_start: 0.9393 (t80) cc_final: 0.9150 (t80) REVERT: A 190 MET cc_start: 0.9168 (mtp) cc_final: 0.8935 (mtp) REVERT: A 194 LYS cc_start: 0.9584 (ttpp) cc_final: 0.9310 (ttpp) REVERT: A 221 LYS cc_start: 0.9206 (mmtp) cc_final: 0.8819 (mttp) REVERT: A 232 ASN cc_start: 0.9323 (m-40) cc_final: 0.9071 (m-40) REVERT: A 243 ARG cc_start: 0.7917 (ptm-80) cc_final: 0.7597 (ppt170) REVERT: A 251 LEU cc_start: 0.9459 (tp) cc_final: 0.9016 (tp) REVERT: A 290 GLU cc_start: 0.9332 (tt0) cc_final: 0.8851 (tm-30) REVERT: A 335 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8195 (mt-10) REVERT: A 359 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8293 (ttp) REVERT: A 362 ASP cc_start: 0.8288 (m-30) cc_final: 0.7896 (m-30) REVERT: A 390 GLN cc_start: 0.8863 (mt0) cc_final: 0.8378 (mt0) REVERT: A 406 ASP cc_start: 0.8031 (m-30) cc_final: 0.7618 (t0) REVERT: A 444 ASP cc_start: 0.8724 (t0) cc_final: 0.8210 (t0) REVERT: A 446 ARG cc_start: 0.7457 (mtp85) cc_final: 0.7048 (mmm160) REVERT: A 456 LYS cc_start: 0.9494 (ttmm) cc_final: 0.9142 (mtmm) REVERT: A 459 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.8890 (mtmm) REVERT: A 493 MET cc_start: 0.8988 (tmm) cc_final: 0.8572 (tmm) REVERT: A 498 TYR cc_start: 0.8883 (m-80) cc_final: 0.8496 (m-80) REVERT: A 515 ASP cc_start: 0.9147 (m-30) cc_final: 0.8920 (m-30) REVERT: A 590 SER cc_start: 0.9585 (t) cc_final: 0.9066 (p) REVERT: A 597 ILE cc_start: 0.9361 (pt) cc_final: 0.9100 (pt) REVERT: A 599 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8326 (pt0) REVERT: A 602 GLU cc_start: 0.8184 (pt0) cc_final: 0.7714 (pt0) REVERT: A 604 ARG cc_start: 0.9002 (mmm-85) cc_final: 0.8783 (mtp85) REVERT: A 639 ASP cc_start: 0.8734 (m-30) cc_final: 0.8143 (m-30) REVERT: A 640 MET cc_start: 0.9509 (OUTLIER) cc_final: 0.9015 (tpp) REVERT: A 645 GLN cc_start: 0.9286 (tp40) cc_final: 0.8966 (tp-100) REVERT: A 663 THR cc_start: 0.9134 (OUTLIER) cc_final: 0.8910 (t) REVERT: A 684 TYR cc_start: 0.8065 (OUTLIER) cc_final: 0.7415 (m-10) REVERT: B 15 GLU cc_start: 0.8932 (tp30) cc_final: 0.8624 (tp30) REVERT: B 31 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8644 (mt-10) REVERT: B 99 LYS cc_start: 0.9253 (mmtt) cc_final: 0.8708 (mmmm) REVERT: B 112 LYS cc_start: 0.9451 (mmmt) cc_final: 0.9243 (mmmt) REVERT: B 154 PRO cc_start: 0.9329 (Cg_exo) cc_final: 0.9119 (Cg_endo) REVERT: B 172 LEU cc_start: 0.9425 (mp) cc_final: 0.9169 (mp) REVERT: B 238 ASP cc_start: 0.8026 (t0) cc_final: 0.7607 (t0) REVERT: B 257 ASP cc_start: 0.9029 (m-30) cc_final: 0.8775 (m-30) REVERT: B 290 GLU cc_start: 0.8500 (tp30) cc_final: 0.8143 (tp30) REVERT: B 344 GLU cc_start: 0.8878 (pt0) cc_final: 0.8664 (pt0) REVERT: B 352 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8051 (mm-30) REVERT: B 375 LYS cc_start: 0.9256 (mtpp) cc_final: 0.8940 (mtpp) REVERT: B 423 LYS cc_start: 0.9596 (mtmm) cc_final: 0.9269 (mmtp) REVERT: B 434 ASP cc_start: 0.8827 (m-30) cc_final: 0.8411 (m-30) REVERT: B 446 ARG cc_start: 0.7879 (ttm-80) cc_final: 0.7530 (mmm-85) REVERT: B 447 ASN cc_start: 0.8642 (m-40) cc_final: 0.7227 (m-40) REVERT: B 458 MET cc_start: 0.9108 (mmm) cc_final: 0.8769 (mmp) REVERT: B 493 MET cc_start: 0.9568 (tmm) cc_final: 0.9214 (tmm) REVERT: B 515 ASP cc_start: 0.9064 (m-30) cc_final: 0.8696 (m-30) REVERT: B 599 GLU cc_start: 0.8403 (pt0) cc_final: 0.8011 (pt0) REVERT: B 602 GLU cc_start: 0.8936 (pt0) cc_final: 0.8496 (pt0) REVERT: B 604 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8276 (mmp80) REVERT: B 610 LYS cc_start: 0.8993 (mtpp) cc_final: 0.8608 (mtpp) REVERT: B 631 ASP cc_start: 0.8854 (t0) cc_final: 0.8464 (t0) REVERT: B 686 ARG cc_start: 0.8465 (mtp-110) cc_final: 0.8241 (mtp85) REVERT: C 21 PHE cc_start: 0.9388 (m-80) cc_final: 0.9151 (m-80) REVERT: C 66 ASP cc_start: 0.8966 (OUTLIER) cc_final: 0.8646 (t70) REVERT: C 86 ARG cc_start: 0.8651 (mtt180) cc_final: 0.8241 (mpt180) REVERT: C 174 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.7449 (t80) REVERT: C 179 TYR cc_start: 0.8724 (t80) cc_final: 0.8489 (t80) REVERT: C 237 GLU cc_start: 0.9529 (pt0) cc_final: 0.9134 (pp20) REVERT: C 242 TYR cc_start: 0.9503 (t80) cc_final: 0.8970 (t80) REVERT: C 268 LEU cc_start: 0.9005 (tp) cc_final: 0.8188 (tp) REVERT: C 269 MET cc_start: 0.9664 (tmm) cc_final: 0.9402 (tmm) REVERT: C 320 PHE cc_start: 0.9128 (m-80) cc_final: 0.8717 (m-80) REVERT: D 18 THR cc_start: 0.8997 (p) cc_final: 0.8551 (m) REVERT: D 20 MET cc_start: 0.8898 (ptm) cc_final: 0.8171 (ppp) REVERT: D 24 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8325 (mp10) REVERT: D 28 GLN cc_start: 0.9052 (mt0) cc_final: 0.8604 (tt0) REVERT: D 40 ASP cc_start: 0.8681 (m-30) cc_final: 0.7906 (t0) REVERT: D 47 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7404 (mt) REVERT: D 74 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7614 (tpt) REVERT: D 109 PHE cc_start: 0.8599 (m-80) cc_final: 0.8155 (m-80) REVERT: D 130 TYR cc_start: 0.8725 (m-10) cc_final: 0.8435 (m-10) REVERT: D 137 MET cc_start: 0.9615 (mtt) cc_final: 0.9326 (mtp) REVERT: D 164 GLU cc_start: 0.8499 (mm-30) cc_final: 0.7552 (mm-30) REVERT: D 172 PHE cc_start: 0.8991 (m-80) cc_final: 0.8722 (m-80) REVERT: D 178 PHE cc_start: 0.9239 (m-80) cc_final: 0.8610 (t80) REVERT: D 198 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8373 (mm-30) REVERT: D 231 LEU cc_start: 0.9526 (mm) cc_final: 0.9204 (mm) REVERT: D 259 PHE cc_start: 0.8679 (t80) cc_final: 0.8011 (t80) REVERT: D 263 ASN cc_start: 0.8898 (m110) cc_final: 0.8698 (m110) REVERT: D 265 ASN cc_start: 0.8631 (m110) cc_final: 0.8393 (m110) outliers start: 70 outliers final: 46 residues processed: 739 average time/residue: 0.1040 time to fit residues: 117.9231 Evaluate side-chains 748 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 690 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP 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 289 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET 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 552 ILE 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 632 MET Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR 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 71 LEU 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 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 546 LEU Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 620 SER 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 162 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 263 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 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 Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 127 GLN C 216 GLN C 238 ASN ** C 263 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 = 0.3533 r_free = 0.3533 target = 0.117813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.086271 restraints weight = 37441.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.089412 restraints weight = 18326.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.091451 restraints weight = 11094.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.092918 restraints weight = 7846.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.093917 restraints weight = 6011.922| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.7113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 16386 Z= 0.221 Angle : 0.787 16.330 22134 Z= 0.404 Chirality : 0.048 0.210 2360 Planarity : 0.004 0.054 2818 Dihedral : 8.745 139.469 2291 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.20 % Allowed : 32.52 % Favored : 63.29 % 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 are not related in a simple way. whole: 0.41 (0.19), residues: 1932 helix: 0.67 (0.15), residues: 1138 sheet: -0.51 (0.39), residues: 150 loop : -0.01 (0.24), residues: 644 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 0.042 0.002 PHE B 261 TRP 0.035 0.002 TRP D 30 HIS 0.018 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.22 (16386) covalent geometry : angle 0.78651 / 0.40 (22134) hydrogen bonds : bond 0.04292 / 2.77 ( 871) hydrogen bonds : angle 5.44892 / 3.87 ( 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 749 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 677 time to evaluate : 0.635 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: A 15 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8406 (mm-30) REVERT: A 95 MET cc_start: 0.8900 (mmm) cc_final: 0.8601 (tpp) REVERT: A 123 SER cc_start: 0.9624 (OUTLIER) cc_final: 0.9152 (p) REVERT: A 186 ILE cc_start: 0.9554 (mp) cc_final: 0.9345 (mp) REVERT: A 190 MET cc_start: 0.9204 (mtp) cc_final: 0.8987 (mtp) REVERT: A 194 LYS cc_start: 0.9631 (ttpp) cc_final: 0.9357 (ttpp) REVERT: A 220 THR cc_start: 0.9410 (m) cc_final: 0.9107 (p) REVERT: A 221 LYS cc_start: 0.9283 (mmtp) cc_final: 0.9004 (mmtp) REVERT: A 232 ASN cc_start: 0.9298 (m-40) cc_final: 0.9066 (m110) REVERT: A 243 ARG cc_start: 0.7852 (ptm-80) cc_final: 0.7558 (ppt170) REVERT: A 290 GLU cc_start: 0.9224 (tt0) cc_final: 0.8864 (tm-30) REVERT: A 335 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8093 (mt-10) REVERT: A 359 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8415 (ttp) REVERT: A 362 ASP cc_start: 0.8224 (m-30) cc_final: 0.7778 (m-30) REVERT: A 384 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.7520 (pm20) REVERT: A 390 GLN cc_start: 0.8897 (mt0) cc_final: 0.8440 (mt0) REVERT: A 406 ASP cc_start: 0.7937 (m-30) cc_final: 0.7685 (t0) REVERT: A 444 ASP cc_start: 0.8684 (t0) cc_final: 0.8081 (t0) REVERT: A 446 ARG cc_start: 0.7488 (mtp85) cc_final: 0.7130 (mmm160) REVERT: A 456 LYS cc_start: 0.9458 (ttmm) cc_final: 0.9155 (mtmm) REVERT: A 459 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.9019 (mtmm) REVERT: A 493 MET cc_start: 0.9037 (tmm) cc_final: 0.8560 (tmm) REVERT: A 498 TYR cc_start: 0.8915 (m-80) cc_final: 0.8657 (m-80) REVERT: A 590 SER cc_start: 0.9551 (t) cc_final: 0.9230 (p) REVERT: A 597 ILE cc_start: 0.9399 (pt) cc_final: 0.9143 (pt) REVERT: A 599 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8432 (pt0) REVERT: A 602 GLU cc_start: 0.8000 (pt0) cc_final: 0.7711 (pt0) REVERT: A 604 ARG cc_start: 0.8977 (mmm-85) cc_final: 0.8769 (mtp85) REVERT: A 639 ASP cc_start: 0.8718 (m-30) cc_final: 0.8166 (m-30) REVERT: A 640 MET cc_start: 0.9433 (OUTLIER) cc_final: 0.8688 (tpp) REVERT: A 683 TYR cc_start: 0.8896 (t80) cc_final: 0.8507 (t80) REVERT: A 684 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7504 (m-10) REVERT: B 82 LYS cc_start: 0.9584 (mmmm) cc_final: 0.9295 (mmtt) REVERT: B 99 LYS cc_start: 0.9306 (mmtt) cc_final: 0.8767 (mmmm) REVERT: B 112 LYS cc_start: 0.9483 (mmmt) cc_final: 0.9244 (mmmt) REVERT: B 128 PHE cc_start: 0.9720 (t80) cc_final: 0.9268 (t80) REVERT: B 172 LEU cc_start: 0.9567 (mp) cc_final: 0.9317 (mp) REVERT: B 213 ILE cc_start: 0.9344 (mp) cc_final: 0.9083 (mt) REVERT: B 235 ARG cc_start: 0.9006 (mtm110) cc_final: 0.8728 (ttp-110) REVERT: B 238 ASP cc_start: 0.8053 (t0) cc_final: 0.7640 (t0) REVERT: B 257 ASP cc_start: 0.8821 (m-30) cc_final: 0.8526 (m-30) REVERT: B 263 ASP cc_start: 0.8988 (m-30) cc_final: 0.8529 (m-30) REVERT: B 290 GLU cc_start: 0.8375 (tp30) cc_final: 0.7994 (tp30) REVERT: B 308 LYS cc_start: 0.9481 (mtpp) cc_final: 0.9109 (mtmm) REVERT: B 344 GLU cc_start: 0.8763 (pt0) cc_final: 0.8562 (pt0) REVERT: B 352 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8040 (mm-30) REVERT: B 375 LYS cc_start: 0.9332 (mtpp) cc_final: 0.8994 (mtpp) REVERT: B 423 LYS cc_start: 0.9579 (mtmm) cc_final: 0.9250 (mtpp) REVERT: B 434 ASP cc_start: 0.8710 (m-30) cc_final: 0.8307 (m-30) REVERT: B 446 ARG cc_start: 0.7821 (ttm-80) cc_final: 0.7370 (mmm-85) REVERT: B 447 ASN cc_start: 0.8074 (m-40) cc_final: 0.7804 (m-40) REVERT: B 493 MET cc_start: 0.9547 (tmm) cc_final: 0.9045 (tmm) REVERT: B 515 ASP cc_start: 0.9023 (m-30) cc_final: 0.8760 (m-30) REVERT: B 599 GLU cc_start: 0.8442 (pt0) cc_final: 0.8194 (pt0) REVERT: B 602 GLU cc_start: 0.8740 (pt0) cc_final: 0.8403 (pt0) REVERT: B 610 LYS cc_start: 0.8955 (mtpp) cc_final: 0.8574 (mtpp) REVERT: B 631 ASP cc_start: 0.8817 (t0) cc_final: 0.8485 (t0) REVERT: B 686 ARG cc_start: 0.8378 (mtp-110) cc_final: 0.8114 (mtp85) REVERT: C 23 ASN cc_start: 0.9572 (t0) cc_final: 0.9349 (m110) REVERT: C 66 ASP cc_start: 0.8986 (OUTLIER) cc_final: 0.8670 (t70) REVERT: C 86 ARG cc_start: 0.8746 (mtt180) cc_final: 0.8301 (mpt180) REVERT: C 137 MET cc_start: 0.9319 (tpp) cc_final: 0.8879 (tpt) REVERT: C 147 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7793 (ptmt) REVERT: C 174 TYR cc_start: 0.8828 (OUTLIER) cc_final: 0.7707 (t80) REVERT: C 178 PHE cc_start: 0.8738 (t80) cc_final: 0.8525 (t80) REVERT: C 242 TYR cc_start: 0.9416 (t80) cc_final: 0.8914 (t80) REVERT: C 269 MET cc_start: 0.9623 (tmm) cc_final: 0.9391 (tmm) REVERT: D 20 MET cc_start: 0.9016 (ptm) cc_final: 0.8504 (ppp) REVERT: D 24 GLN cc_start: 0.9069 (mm-40) cc_final: 0.8652 (mm-40) REVERT: D 28 GLN cc_start: 0.9015 (mt0) cc_final: 0.8763 (tt0) REVERT: D 74 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7682 (tpt) REVERT: D 109 PHE cc_start: 0.8668 (m-80) cc_final: 0.8216 (m-80) REVERT: D 131 LEU cc_start: 0.8164 (tt) cc_final: 0.7854 (tp) REVERT: D 137 MET cc_start: 0.9592 (mtt) cc_final: 0.9323 (mtp) REVERT: D 153 LEU cc_start: 0.6673 (tt) cc_final: 0.6343 (tt) REVERT: D 164 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7395 (mm-30) REVERT: D 172 PHE cc_start: 0.8887 (m-80) cc_final: 0.8557 (m-80) REVERT: D 178 PHE cc_start: 0.9314 (m-80) cc_final: 0.8508 (t80) REVERT: D 198 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8300 (mm-30) REVERT: D 231 LEU cc_start: 0.9533 (mm) cc_final: 0.9248 (mm) REVERT: D 233 ASN cc_start: 0.9083 (m110) cc_final: 0.8784 (p0) REVERT: D 273 PHE cc_start: 0.6045 (m-10) cc_final: 0.5838 (m-10) outliers start: 72 outliers final: 49 residues processed: 707 average time/residue: 0.1236 time to fit residues: 133.9026 Evaluate side-chains 705 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 646 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR 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 359 MET 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 632 MET Chi-restraints excluded: chain A residue 640 MET 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 143 LEU Chi-restraints excluded: chain B residue 155 THR 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 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 546 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 147 LYS 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 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 59 LEU Chi-restraints excluded: chain D residue 74 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 134 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.122631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.090702 restraints weight = 37304.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.093987 restraints weight = 18240.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.096169 restraints weight = 11048.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.097647 restraints weight = 7695.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.098706 restraints weight = 5915.584| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.7367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16386 Z= 0.158 Angle : 0.799 15.627 22134 Z= 0.402 Chirality : 0.048 0.224 2360 Planarity : 0.004 0.055 2818 Dihedral : 8.599 137.388 2291 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.61 % Allowed : 32.75 % Favored : 63.64 % 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 are not related in a simple way. whole: 0.33 (0.19), residues: 1932 helix: 0.61 (0.15), residues: 1128 sheet: -0.63 (0.38), residues: 160 loop : -0.01 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 686 TYR 0.051 0.002 TYR D 142 PHE 0.041 0.002 PHE C 172 TRP 0.039 0.002 TRP D 30 HIS 0.025 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (16386) covalent geometry : angle 0.79887 / 0.40 (22134) hydrogen bonds : bond 0.04305 / 2.75 ( 871) hydrogen bonds : angle 5.42783 / 3.86 ( 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 744 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 682 time to evaluate : 0.637 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 12 LEU cc_start: 0.9478 (mp) cc_final: 0.9103 (mp) REVERT: A 15 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8441 (mm-30) REVERT: A 51 LEU cc_start: 0.9105 (tp) cc_final: 0.8721 (mp) REVERT: A 56 ASP cc_start: 0.9212 (m-30) cc_final: 0.8867 (m-30) REVERT: A 123 SER cc_start: 0.9603 (OUTLIER) cc_final: 0.9084 (p) REVERT: A 128 PHE cc_start: 0.9411 (t80) cc_final: 0.8893 (t80) REVERT: A 190 MET cc_start: 0.9194 (mtp) cc_final: 0.8975 (mtp) REVERT: A 194 LYS cc_start: 0.9588 (ttpp) cc_final: 0.9268 (ttpp) REVERT: A 232 ASN cc_start: 0.9403 (m-40) cc_final: 0.9070 (m110) REVERT: A 243 ARG cc_start: 0.7695 (ptm-80) cc_final: 0.7439 (ppt170) REVERT: A 290 GLU cc_start: 0.9253 (tt0) cc_final: 0.8763 (tm-30) REVERT: A 335 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8135 (mt-10) REVERT: A 359 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8316 (ttp) REVERT: A 362 ASP cc_start: 0.8246 (m-30) cc_final: 0.8015 (m-30) REVERT: A 381 LEU cc_start: 0.9475 (tp) cc_final: 0.9141 (tp) REVERT: A 390 GLN cc_start: 0.8925 (mt0) cc_final: 0.8474 (mt0) REVERT: A 406 ASP cc_start: 0.8053 (m-30) cc_final: 0.7756 (t0) REVERT: A 444 ASP cc_start: 0.8747 (t0) cc_final: 0.8122 (t0) REVERT: A 446 ARG cc_start: 0.7474 (mtp85) cc_final: 0.7098 (mmm160) REVERT: A 456 LYS cc_start: 0.9468 (ttmm) cc_final: 0.9130 (mtmm) REVERT: A 459 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.8978 (mtmm) REVERT: A 493 MET cc_start: 0.9023 (tmm) cc_final: 0.8549 (tmm) REVERT: A 498 TYR cc_start: 0.8894 (m-80) cc_final: 0.8590 (m-80) REVERT: A 515 ASP cc_start: 0.9104 (m-30) cc_final: 0.8858 (m-30) REVERT: A 590 SER cc_start: 0.9595 (t) cc_final: 0.9127 (p) REVERT: A 597 ILE cc_start: 0.9274 (pt) cc_final: 0.8987 (pt) REVERT: A 599 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8125 (pt0) REVERT: A 602 GLU cc_start: 0.7980 (pt0) cc_final: 0.7074 (pt0) REVERT: A 604 ARG cc_start: 0.8991 (mmm-85) cc_final: 0.8747 (mmm-85) REVERT: A 639 ASP cc_start: 0.8676 (m-30) cc_final: 0.8119 (m-30) REVERT: A 640 MET cc_start: 0.9416 (OUTLIER) cc_final: 0.8713 (tmm) REVERT: A 645 GLN cc_start: 0.9306 (tp40) cc_final: 0.8878 (tp-100) REVERT: A 684 TYR cc_start: 0.8159 (OUTLIER) cc_final: 0.7458 (m-10) REVERT: B 15 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8798 (mt-10) REVERT: B 82 LYS cc_start: 0.9562 (mmmm) cc_final: 0.9123 (mmtm) REVERT: B 99 LYS cc_start: 0.9280 (mmtt) cc_final: 0.8761 (mmmm) REVERT: B 112 LYS cc_start: 0.9458 (mmmt) cc_final: 0.9216 (mmmt) REVERT: B 128 PHE cc_start: 0.9715 (t80) cc_final: 0.9249 (t80) REVERT: B 172 LEU cc_start: 0.9491 (mp) cc_final: 0.9246 (mp) REVERT: B 211 GLU cc_start: 0.8664 (mm-30) cc_final: 0.7641 (mm-30) REVERT: B 235 ARG cc_start: 0.8975 (mtm110) cc_final: 0.8747 (ttp-110) REVERT: B 238 ASP cc_start: 0.8119 (t0) cc_final: 0.7821 (t0) REVERT: B 263 ASP cc_start: 0.8987 (m-30) cc_final: 0.8549 (m-30) REVERT: B 290 GLU cc_start: 0.8471 (tp30) cc_final: 0.8091 (tp30) REVERT: B 308 LYS cc_start: 0.9489 (mtpp) cc_final: 0.9080 (mtmm) REVERT: B 352 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8016 (mm-30) REVERT: B 375 LYS cc_start: 0.9276 (mtpp) cc_final: 0.8931 (mtpp) REVERT: B 423 LYS cc_start: 0.9593 (mtmm) cc_final: 0.9245 (mtpp) REVERT: B 434 ASP cc_start: 0.8721 (m-30) cc_final: 0.8305 (m-30) REVERT: B 446 ARG cc_start: 0.7663 (ttm-80) cc_final: 0.7302 (mmm-85) REVERT: B 447 ASN cc_start: 0.8039 (m-40) cc_final: 0.7799 (m-40) REVERT: B 458 MET cc_start: 0.9077 (mmm) cc_final: 0.8727 (mmp) REVERT: B 493 MET cc_start: 0.9547 (tmm) cc_final: 0.9232 (tmm) REVERT: B 515 ASP cc_start: 0.9019 (m-30) cc_final: 0.8721 (m-30) REVERT: B 599 GLU cc_start: 0.8387 (pt0) cc_final: 0.7989 (pt0) REVERT: B 610 LYS cc_start: 0.8995 (mtpp) cc_final: 0.8627 (mtpp) REVERT: B 631 ASP cc_start: 0.8818 (t0) cc_final: 0.8453 (t0) REVERT: B 686 ARG cc_start: 0.8433 (mtp-110) cc_final: 0.8176 (mtp85) REVERT: C 20 MET cc_start: 0.9535 (pmm) cc_final: 0.9243 (pmm) REVERT: C 21 PHE cc_start: 0.9559 (m-80) cc_final: 0.9208 (t80) REVERT: C 23 ASN cc_start: 0.9535 (t0) cc_final: 0.9328 (m-40) REVERT: C 55 TYR cc_start: 0.8965 (t80) cc_final: 0.8129 (t80) REVERT: C 66 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8665 (t70) REVERT: C 86 ARG cc_start: 0.8712 (mtt180) cc_final: 0.8286 (mpt180) REVERT: C 147 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7789 (ptmt) REVERT: C 174 TYR cc_start: 0.8905 (OUTLIER) cc_final: 0.7743 (t80) REVERT: C 208 LEU cc_start: 0.9439 (mt) cc_final: 0.9235 (pp) REVERT: C 242 TYR cc_start: 0.9429 (t80) cc_final: 0.8964 (t80) REVERT: C 259 PHE cc_start: 0.8558 (t80) cc_final: 0.7718 (t80) REVERT: C 269 MET cc_start: 0.9610 (tmm) cc_final: 0.9372 (tmm) REVERT: C 320 PHE cc_start: 0.9122 (m-80) cc_final: 0.8836 (m-80) REVERT: D 20 MET cc_start: 0.9062 (ptm) cc_final: 0.8708 (ppp) REVERT: D 24 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8727 (mm-40) REVERT: D 28 GLN cc_start: 0.8982 (mt0) cc_final: 0.8764 (tt0) REVERT: D 74 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7923 (tpt) REVERT: D 109 PHE cc_start: 0.8686 (m-80) cc_final: 0.8247 (m-80) REVERT: D 137 MET cc_start: 0.9587 (mtt) cc_final: 0.9318 (mtp) REVERT: D 164 GLU cc_start: 0.8501 (mm-30) cc_final: 0.7484 (mm-30) REVERT: D 172 PHE cc_start: 0.8860 (m-80) cc_final: 0.8454 (m-80) REVERT: D 178 PHE cc_start: 0.9257 (m-80) cc_final: 0.8512 (t80) REVERT: D 198 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8500 (mm-30) REVERT: D 227 PHE cc_start: 0.9212 (t80) cc_final: 0.8984 (t80) REVERT: D 230 ASP cc_start: 0.9362 (t0) cc_final: 0.8803 (m-30) REVERT: D 231 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9299 (mm) REVERT: D 259 PHE cc_start: 0.8835 (t80) cc_final: 0.8224 (t80) REVERT: D 261 ARG cc_start: 0.7923 (mtm-85) cc_final: 0.7620 (mtm-85) REVERT: D 265 ASN cc_start: 0.8429 (m110) cc_final: 0.7842 (m110) outliers start: 62 outliers final: 47 residues processed: 703 average time/residue: 0.1177 time to fit residues: 126.2662 Evaluate side-chains 711 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 654 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 69 LEU Chi-restraints excluded: chain A residue 122 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 289 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET 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 632 MET Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 143 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 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 546 LEU 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 679 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 147 LYS 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 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 59 LEU Chi-restraints excluded: chain D residue 74 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 231 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 469 HIS ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.122339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.090760 restraints weight = 36969.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.094018 restraints weight = 18153.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.096211 restraints weight = 11242.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.097727 restraints weight = 7775.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.098789 restraints weight = 5877.269| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.7620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16386 Z= 0.159 Angle : 0.830 14.879 22134 Z= 0.416 Chirality : 0.049 0.249 2360 Planarity : 0.004 0.058 2818 Dihedral : 8.525 137.953 2291 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.61 % Allowed : 33.39 % Favored : 63.00 % 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 are not related in a simple way. whole: 0.28 (0.19), residues: 1932 helix: 0.58 (0.15), residues: 1129 sheet: -0.69 (0.39), residues: 160 loop : -0.03 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 686 TYR 0.049 0.001 TYR D 142 PHE 0.045 0.002 PHE C 172 TRP 0.042 0.002 TRP D 30 HIS 0.029 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (16386) covalent geometry : angle 0.83028 / 0.42 (22134) hydrogen bonds : bond 0.04364 / 2.79 ( 871) hydrogen bonds : angle 5.47194 / 3.89 ( 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 742 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 680 time to evaluate : 0.623 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: A 12 LEU cc_start: 0.9529 (mp) cc_final: 0.9312 (mp) REVERT: A 15 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8439 (mm-30) REVERT: A 51 LEU cc_start: 0.9027 (tp) cc_final: 0.8671 (mp) REVERT: A 56 ASP cc_start: 0.9176 (m-30) cc_final: 0.8840 (m-30) REVERT: A 123 SER cc_start: 0.9580 (OUTLIER) cc_final: 0.9094 (p) REVERT: A 158 ASN cc_start: 0.9500 (m-40) cc_final: 0.9205 (m-40) REVERT: A 190 MET cc_start: 0.9216 (mtp) cc_final: 0.8969 (mtp) REVERT: A 194 LYS cc_start: 0.9588 (ttpp) cc_final: 0.9274 (ttpp) REVERT: A 220 THR cc_start: 0.9397 (m) cc_final: 0.9100 (p) REVERT: A 232 ASN cc_start: 0.9450 (m-40) cc_final: 0.9075 (m110) REVERT: A 243 ARG cc_start: 0.7716 (ptm-80) cc_final: 0.7460 (ppt170) REVERT: A 290 GLU cc_start: 0.9252 (tt0) cc_final: 0.8798 (tm-30) REVERT: A 335 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8204 (mt-10) REVERT: A 359 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8280 (ttp) REVERT: A 381 LEU cc_start: 0.9438 (tp) cc_final: 0.9086 (tp) REVERT: A 390 GLN cc_start: 0.8943 (mt0) cc_final: 0.8492 (mt0) REVERT: A 406 ASP cc_start: 0.8086 (m-30) cc_final: 0.7830 (t0) REVERT: A 444 ASP cc_start: 0.8690 (t0) cc_final: 0.8097 (t0) REVERT: A 446 ARG cc_start: 0.7498 (mtp85) cc_final: 0.7107 (mmm160) REVERT: A 456 LYS cc_start: 0.9482 (ttmm) cc_final: 0.9133 (mtmm) REVERT: A 459 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.9016 (mtmm) REVERT: A 493 MET cc_start: 0.9020 (tmm) cc_final: 0.8550 (tmm) REVERT: A 498 TYR cc_start: 0.8904 (m-80) cc_final: 0.8601 (m-80) REVERT: A 515 ASP cc_start: 0.9054 (m-30) cc_final: 0.8802 (m-30) REVERT: A 590 SER cc_start: 0.9599 (t) cc_final: 0.9149 (p) REVERT: A 597 ILE cc_start: 0.9143 (pt) cc_final: 0.8814 (pt) REVERT: A 599 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8197 (pt0) REVERT: A 602 GLU cc_start: 0.7866 (pt0) cc_final: 0.7152 (pt0) REVERT: A 604 ARG cc_start: 0.8981 (mmm-85) cc_final: 0.8721 (mmm-85) REVERT: A 615 MET cc_start: 0.9371 (OUTLIER) cc_final: 0.9074 (mmm) REVERT: A 618 LEU cc_start: 0.9400 (tp) cc_final: 0.9178 (tt) REVERT: A 639 ASP cc_start: 0.8569 (m-30) cc_final: 0.8180 (m-30) REVERT: A 640 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.8641 (tmm) REVERT: A 645 GLN cc_start: 0.9368 (tp40) cc_final: 0.8968 (tp-100) REVERT: A 662 MET cc_start: 0.8548 (pmm) cc_final: 0.8322 (pmm) REVERT: A 684 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.7528 (m-10) REVERT: B 15 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8737 (mt-10) REVERT: B 82 LYS cc_start: 0.9538 (mmmm) cc_final: 0.9134 (mmtm) REVERT: B 99 LYS cc_start: 0.9282 (mmtt) cc_final: 0.8758 (mmmm) REVERT: B 100 PHE cc_start: 0.9426 (t80) cc_final: 0.9206 (t80) REVERT: B 112 LYS cc_start: 0.9433 (mmmt) cc_final: 0.9190 (mmmt) REVERT: B 128 PHE cc_start: 0.9717 (t80) cc_final: 0.9246 (t80) REVERT: B 172 LEU cc_start: 0.9408 (mp) cc_final: 0.9171 (mp) REVERT: B 184 ARG cc_start: 0.9528 (tpp-160) cc_final: 0.9089 (tpp80) REVERT: B 211 GLU cc_start: 0.8546 (mm-30) cc_final: 0.7593 (mm-30) REVERT: B 213 ILE cc_start: 0.9330 (mp) cc_final: 0.9032 (mt) REVERT: B 263 ASP cc_start: 0.8968 (m-30) cc_final: 0.8518 (m-30) REVERT: B 290 GLU cc_start: 0.8448 (tp30) cc_final: 0.8005 (tp30) REVERT: B 308 LYS cc_start: 0.9471 (mtpp) cc_final: 0.9065 (mtmm) REVERT: B 352 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8095 (mm-30) REVERT: B 375 LYS cc_start: 0.9252 (mtpp) cc_final: 0.8902 (mtpp) REVERT: B 423 LYS cc_start: 0.9586 (mtmm) cc_final: 0.9245 (mtpp) REVERT: B 434 ASP cc_start: 0.8795 (m-30) cc_final: 0.8365 (m-30) REVERT: B 446 ARG cc_start: 0.7645 (ttm-80) cc_final: 0.7272 (mmm-85) REVERT: B 447 ASN cc_start: 0.8025 (m-40) cc_final: 0.7803 (m-40) REVERT: B 458 MET cc_start: 0.9037 (mmm) cc_final: 0.8721 (mmp) REVERT: B 493 MET cc_start: 0.9543 (tmm) cc_final: 0.9213 (tmm) REVERT: B 515 ASP cc_start: 0.8991 (m-30) cc_final: 0.8687 (m-30) REVERT: B 599 GLU cc_start: 0.8361 (pt0) cc_final: 0.8014 (pt0) REVERT: B 602 GLU cc_start: 0.8935 (pt0) cc_final: 0.8205 (pt0) REVERT: B 610 LYS cc_start: 0.9017 (mtpp) cc_final: 0.8651 (mtpp) REVERT: B 686 ARG cc_start: 0.8448 (mtp-110) cc_final: 0.8123 (mtp85) REVERT: C 20 MET cc_start: 0.9553 (pmm) cc_final: 0.9222 (pmm) REVERT: C 21 PHE cc_start: 0.9554 (m-80) cc_final: 0.9217 (t80) REVERT: C 23 ASN cc_start: 0.9564 (t0) cc_final: 0.9338 (m110) REVERT: C 66 ASP cc_start: 0.9006 (OUTLIER) cc_final: 0.8765 (t70) REVERT: C 86 ARG cc_start: 0.8774 (mtt180) cc_final: 0.8365 (mpt180) REVERT: C 96 MET cc_start: 0.8859 (mmm) cc_final: 0.8319 (mmm) REVERT: C 147 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7916 (ptmt) REVERT: C 174 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.7832 (t80) REVERT: C 178 PHE cc_start: 0.8711 (t80) cc_final: 0.8286 (t80) REVERT: C 242 TYR cc_start: 0.9445 (t80) cc_final: 0.8972 (t80) REVERT: C 259 PHE cc_start: 0.8578 (t80) cc_final: 0.7745 (t80) REVERT: C 266 LYS cc_start: 0.9630 (mmmt) cc_final: 0.9426 (tppt) REVERT: D 20 MET cc_start: 0.9072 (ptm) cc_final: 0.8285 (ppp) REVERT: D 23 ASN cc_start: 0.9436 (m110) cc_final: 0.9048 (p0) REVERT: D 24 GLN cc_start: 0.9100 (mm-40) cc_final: 0.8359 (mp10) REVERT: D 79 GLU cc_start: 0.8937 (tt0) cc_final: 0.8559 (pt0) REVERT: D 109 PHE cc_start: 0.8698 (m-80) cc_final: 0.8235 (m-80) REVERT: D 137 MET cc_start: 0.9610 (mtt) cc_final: 0.9337 (mtp) REVERT: D 172 PHE cc_start: 0.8847 (m-80) cc_final: 0.8449 (m-80) REVERT: D 178 PHE cc_start: 0.9261 (m-80) cc_final: 0.8491 (t80) REVERT: D 227 PHE cc_start: 0.9171 (t80) cc_final: 0.8927 (t80) REVERT: D 230 ASP cc_start: 0.9327 (t0) cc_final: 0.8714 (m-30) REVERT: D 231 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9152 (mm) REVERT: D 233 ASN cc_start: 0.9085 (m110) cc_final: 0.8748 (p0) REVERT: D 259 PHE cc_start: 0.8850 (t80) cc_final: 0.8252 (t80) REVERT: D 261 ARG cc_start: 0.7884 (mtm-85) cc_final: 0.7603 (mtm-85) REVERT: D 265 ASN cc_start: 0.8362 (m110) cc_final: 0.7985 (m-40) outliers start: 62 outliers final: 46 residues processed: 704 average time/residue: 0.1210 time to fit residues: 130.1349 Evaluate side-chains 722 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 666 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 289 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET 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 584 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 143 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 381 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 546 LEU 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 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 66 ASP Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 166 PHE 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 D residue 25 ASN 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 129 LYS 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 231 LEU 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 71 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 0.0030 chunk 189 optimal weight: 8.9990 chunk 181 optimal weight: 8.9990 chunk 165 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 54 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 HIS ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 HIS ** D 265 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 = 0.3624 r_free = 0.3624 target = 0.123798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.092325 restraints weight = 37077.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.095771 restraints weight = 18241.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.097976 restraints weight = 11026.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.099493 restraints weight = 7642.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.100534 restraints weight = 5798.554| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.7879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 16386 Z= 0.157 Angle : 0.851 14.443 22134 Z= 0.424 Chirality : 0.049 0.245 2360 Planarity : 0.004 0.056 2818 Dihedral : 8.314 137.972 2291 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.09 % Allowed : 34.32 % Favored : 62.59 % 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 are not related in a simple way. whole: 0.22 (0.19), residues: 1932 helix: 0.56 (0.15), residues: 1128 sheet: -0.72 (0.39), residues: 160 loop : -0.11 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 164 TYR 0.049 0.002 TYR D 142 PHE 0.048 0.002 PHE C 172 TRP 0.041 0.002 TRP D 30 HIS 0.030 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (16386) covalent geometry : angle 0.85113 / 0.42 (22134) hydrogen bonds : bond 0.04390 / 2.80 ( 871) hydrogen bonds : angle 5.48351 / 3.90 ( 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 747 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 694 time to evaluate : 0.453 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: A 12 LEU cc_start: 0.9508 (mp) cc_final: 0.9307 (mp) REVERT: A 56 ASP cc_start: 0.9156 (m-30) cc_final: 0.8818 (m-30) REVERT: A 194 LYS cc_start: 0.9587 (ttpp) cc_final: 0.9271 (ttpp) REVERT: A 220 THR cc_start: 0.9393 (m) cc_final: 0.9097 (p) REVERT: A 232 ASN cc_start: 0.9464 (m-40) cc_final: 0.9101 (m110) REVERT: A 243 ARG cc_start: 0.7769 (ptm-80) cc_final: 0.7509 (ppt170) REVERT: A 290 GLU cc_start: 0.9249 (tt0) cc_final: 0.8804 (tm-30) REVERT: A 335 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8169 (mt-10) REVERT: A 359 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8241 (ttp) REVERT: A 381 LEU cc_start: 0.9450 (tp) cc_final: 0.9108 (tp) REVERT: A 384 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.7495 (pm20) REVERT: A 390 GLN cc_start: 0.8956 (mt0) cc_final: 0.8509 (mt0) REVERT: A 394 TYR cc_start: 0.9134 (m-80) cc_final: 0.8847 (m-80) REVERT: A 406 ASP cc_start: 0.8090 (m-30) cc_final: 0.7842 (t0) REVERT: A 418 ASN cc_start: 0.9373 (m-40) cc_final: 0.8941 (m110) REVERT: A 420 MET cc_start: 0.8873 (mmm) cc_final: 0.8664 (mmm) REVERT: A 456 LYS cc_start: 0.9472 (ttmm) cc_final: 0.9111 (mtmm) REVERT: A 459 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.8789 (mtmm) REVERT: A 493 MET cc_start: 0.9030 (tmm) cc_final: 0.8565 (tmm) REVERT: A 590 SER cc_start: 0.9601 (t) cc_final: 0.9127 (p) REVERT: A 597 ILE cc_start: 0.9052 (pt) cc_final: 0.8724 (pt) REVERT: A 599 GLU cc_start: 0.8557 (mt-10) cc_final: 0.7968 (pt0) REVERT: A 602 GLU cc_start: 0.7800 (pt0) cc_final: 0.6858 (pt0) REVERT: A 604 ARG cc_start: 0.8945 (mmm-85) cc_final: 0.8618 (mmm-85) REVERT: A 615 MET cc_start: 0.9355 (OUTLIER) cc_final: 0.9074 (mmm) REVERT: A 618 LEU cc_start: 0.9375 (tp) cc_final: 0.9159 (tt) REVERT: A 639 ASP cc_start: 0.8591 (m-30) cc_final: 0.8196 (m-30) REVERT: A 640 MET cc_start: 0.9278 (OUTLIER) cc_final: 0.8570 (tmm) REVERT: A 645 GLN cc_start: 0.9362 (tp40) cc_final: 0.7823 (tp-100) REVERT: A 650 GLN cc_start: 0.8808 (mt0) cc_final: 0.7974 (mt0) REVERT: A 662 MET cc_start: 0.8542 (pmm) cc_final: 0.8314 (pmm) REVERT: A 680 LYS cc_start: 0.8885 (mttt) cc_final: 0.7943 (mttt) REVERT: A 684 TYR cc_start: 0.8230 (OUTLIER) cc_final: 0.7688 (m-10) REVERT: B 15 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8742 (mt-10) REVERT: B 82 LYS cc_start: 0.9493 (mmmm) cc_final: 0.9129 (mmtp) REVERT: B 88 LYS cc_start: 0.9052 (mmmm) cc_final: 0.8779 (mmmm) REVERT: B 99 LYS cc_start: 0.9234 (mmtt) cc_final: 0.8738 (mmmm) REVERT: B 100 PHE cc_start: 0.9409 (t80) cc_final: 0.9198 (t80) REVERT: B 112 LYS cc_start: 0.9415 (mmmt) cc_final: 0.9175 (mmmt) REVERT: B 128 PHE cc_start: 0.9720 (t80) cc_final: 0.9258 (t80) REVERT: B 172 LEU cc_start: 0.9371 (mp) cc_final: 0.9142 (mp) REVERT: B 211 GLU cc_start: 0.8513 (mm-30) cc_final: 0.7620 (mm-30) REVERT: B 216 VAL cc_start: 0.8450 (OUTLIER) cc_final: 0.8130 (m) REVERT: B 236 TYR cc_start: 0.9355 (t80) cc_final: 0.9058 (t80) REVERT: B 263 ASP cc_start: 0.8915 (m-30) cc_final: 0.8448 (m-30) REVERT: B 290 GLU cc_start: 0.8434 (tp30) cc_final: 0.7965 (tp30) REVERT: B 308 LYS cc_start: 0.9485 (mtpp) cc_final: 0.9205 (mtmm) REVERT: B 322 MET cc_start: 0.9315 (tpp) cc_final: 0.8707 (mpp) REVERT: B 352 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8058 (mm-30) REVERT: B 375 LYS cc_start: 0.9239 (mtpp) cc_final: 0.8886 (mtpp) REVERT: B 423 LYS cc_start: 0.9579 (mtmm) cc_final: 0.9066 (mtpp) REVERT: B 434 ASP cc_start: 0.8765 (m-30) cc_final: 0.8323 (m-30) REVERT: B 458 MET cc_start: 0.8978 (mmm) cc_final: 0.8656 (mmp) REVERT: B 493 MET cc_start: 0.9533 (tmm) cc_final: 0.9214 (tmm) REVERT: B 515 ASP cc_start: 0.8981 (m-30) cc_final: 0.8667 (m-30) REVERT: B 599 GLU cc_start: 0.8347 (pt0) cc_final: 0.8017 (pt0) REVERT: B 602 GLU cc_start: 0.8952 (pt0) cc_final: 0.8287 (pt0) REVERT: B 610 LYS cc_start: 0.9033 (mtpp) cc_final: 0.8670 (mtpp) REVERT: B 686 ARG cc_start: 0.8420 (mtp-110) cc_final: 0.8197 (mtp85) REVERT: C 20 MET cc_start: 0.9544 (pmm) cc_final: 0.9239 (pmm) REVERT: C 21 PHE cc_start: 0.9549 (m-80) cc_final: 0.9181 (t80) REVERT: C 23 ASN cc_start: 0.9579 (t0) cc_final: 0.9320 (m110) REVERT: C 55 TYR cc_start: 0.9036 (t80) cc_final: 0.8292 (t80) REVERT: C 66 ASP cc_start: 0.8979 (OUTLIER) cc_final: 0.8735 (t70) REVERT: C 86 ARG cc_start: 0.8817 (mtt180) cc_final: 0.8392 (mpt180) REVERT: C 93 MET cc_start: 0.9345 (ttt) cc_final: 0.9114 (tmt) REVERT: C 96 MET cc_start: 0.9007 (mmm) cc_final: 0.8394 (mmm) REVERT: C 122 PHE cc_start: 0.8795 (m-80) cc_final: 0.8317 (m-80) REVERT: C 137 MET cc_start: 0.9282 (tpp) cc_final: 0.8854 (tpp) REVERT: C 147 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8015 (ptmt) REVERT: C 154 PHE cc_start: 0.9336 (t80) cc_final: 0.9114 (t80) REVERT: C 174 TYR cc_start: 0.8971 (OUTLIER) cc_final: 0.7963 (t80) REVERT: C 178 PHE cc_start: 0.8701 (t80) cc_final: 0.8417 (t80) REVERT: C 179 TYR cc_start: 0.8960 (t80) cc_final: 0.8725 (t80) REVERT: C 242 TYR cc_start: 0.9464 (t80) cc_final: 0.8881 (t80) REVERT: C 255 ASP cc_start: 0.9131 (m-30) cc_final: 0.8676 (m-30) REVERT: C 259 PHE cc_start: 0.8582 (t80) cc_final: 0.7758 (t80) REVERT: D 20 MET cc_start: 0.9103 (ptm) cc_final: 0.8385 (ppp) REVERT: D 23 ASN cc_start: 0.9436 (m110) cc_final: 0.9057 (p0) REVERT: D 24 GLN cc_start: 0.9129 (mm-40) cc_final: 0.8325 (mp10) REVERT: D 79 GLU cc_start: 0.8864 (tt0) cc_final: 0.8433 (pt0) REVERT: D 109 PHE cc_start: 0.8708 (m-80) cc_final: 0.8267 (m-80) REVERT: D 123 GLU cc_start: 0.9197 (mp0) cc_final: 0.8789 (mp0) REVERT: D 129 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8603 (tptp) REVERT: D 137 MET cc_start: 0.9614 (mtt) cc_final: 0.9349 (mtp) REVERT: D 172 PHE cc_start: 0.8824 (m-80) cc_final: 0.8432 (m-80) REVERT: D 227 PHE cc_start: 0.9099 (t80) cc_final: 0.8858 (t80) REVERT: D 230 ASP cc_start: 0.9291 (t0) cc_final: 0.8663 (m-30) REVERT: D 231 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9145 (mm) REVERT: D 233 ASN cc_start: 0.9099 (m110) cc_final: 0.8775 (p0) REVERT: D 259 PHE cc_start: 0.8798 (t80) cc_final: 0.8263 (t80) REVERT: D 261 ARG cc_start: 0.7799 (mtm-85) cc_final: 0.7539 (mtm-85) REVERT: D 265 ASN cc_start: 0.8217 (m110) cc_final: 0.7630 (m110) outliers start: 53 outliers final: 39 residues processed: 715 average time/residue: 0.1004 time to fit residues: 109.2786 Evaluate side-chains 711 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 660 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 122 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 359 MET 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 584 ILE 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 143 LEU Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 220 THR 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 546 LEU 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 679 ILE Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 147 LYS 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 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 129 LYS 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 231 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 125 optimal weight: 0.0970 chunk 28 optimal weight: 0.0770 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 GLN B 150 GLN B 191 GLN ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 265 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.124978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.093574 restraints weight = 37118.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.096939 restraints weight = 18179.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.099148 restraints weight = 11041.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.100648 restraints weight = 7657.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.101731 restraints weight = 5863.184| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.8020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 16386 Z= 0.165 Angle : 0.882 14.682 22134 Z= 0.441 Chirality : 0.049 0.225 2360 Planarity : 0.004 0.054 2818 Dihedral : 8.209 138.120 2291 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.09 % Allowed : 35.31 % Favored : 61.60 % 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 are not related in a simple way. whole: 0.20 (0.19), residues: 1932 helix: 0.57 (0.15), residues: 1127 sheet: -0.74 (0.39), residues: 160 loop : -0.17 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 225 TYR 0.050 0.002 TYR D 142 PHE 0.048 0.002 PHE C 172 TRP 0.039 0.002 TRP D 30 HIS 0.030 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (16386) covalent geometry : angle 0.88201 / 0.44 (22134) hydrogen bonds : bond 0.04413 / 2.81 ( 871) hydrogen bonds : angle 5.52102 / 3.93 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3444.85 seconds wall clock time: 60 minutes 24.62 seconds (3624.62 seconds total)