Starting phenix.real_space_refine on Thu Aug 6 15:14:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byt_45044/08_2026/9byt_45044_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byt_45044/08_2026/9byt_45044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9byt_45044/08_2026/9byt_45044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byt_45044/08_2026/9byt_45044.map" model { file = "/net/cci-nas-00/data/ceres_data/9byt_45044/08_2026/9byt_45044_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byt_45044/08_2026/9byt_45044_neut.cif" } resolution = 3.52 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: 3.61, per 1000 atoms: 0.23 Number of scatterers: 16038 At special positions: 0 Unit cell: (94.581, 132.21, 132.21, 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: 1.26 Conformation dependent library (CDL) restraints added in 654.5 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: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.104A 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: 3.515A 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: 3.568A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.953A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.664A 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: 4.118A 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: 3.580A 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: 3.677A 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: 3.878A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A 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: 6.026A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.118A 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: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A 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: 3.566A 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: 6.360A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.427A 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: 6.605A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.394A 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: 6.478A 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: 7.185A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.660A 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: 6.383A 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: 6.063A 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: 4.050A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.516A 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: 6.749A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.11 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4852 1.34 - 1.46: 3027 1.46 - 1.58: 8326 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 4.82e+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 4.77e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.600 -0.060 1.25e-02 6.40e+03 2.31e+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 1.19e+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: 21523 2.09 - 4.18: 529 4.18 - 6.26: 64 6.26 - 8.35: 9 8.35 - 10.44: 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 110.54 116.62 -6.08 1.36e+00 5.41e-01 2.00e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.11 -4.40 1.15e+00 7.56e-01 1.46e+01 angle pdb=" N SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.23 -3.95 1.09e+00 8.42e-01 1.31e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.88 -4.38 1.23e+00 6.61e-01 1.27e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.72 -4.01 1.15e+00 7.56e-01 1.22e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.04: 9091 25.04 - 50.09: 653 50.09 - 75.13: 126 75.13 - 100.17: 26 100.17 - 125.21: 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 -98.19 125.21 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 -95.55 122.57 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 -134.24 12.24 0 2.50e+00 1.60e-01 2.40e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2132 0.093 - 0.185: 194 0.185 - 0.278: 29 0.278 - 0.371: 3 0.371 - 0.463: 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 2.05 0.46 2.00e-01 2.50e+01 5.36e+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 4.69e+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 0.34 2.00e-01 2.50e+01 2.97e+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 4.13e-02 2.73e+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 1.12e-02 2.19e+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 " -0.006 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 D 179 " -0.017 2.00e-02 2.50e+03 9.85e-03 1.94e+00 pdb=" CG TYR D 179 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR D 179 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 179 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR D 179 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 179 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR D 179 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 179 " -0.005 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 129 2.51 - 3.11: 11548 3.11 - 3.70: 27039 3.70 - 4.30: 41566 4.30 - 4.90: 65461 Nonbonded interactions: 145743 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.911 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 145738 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.620 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 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= 0.334 Angle : 0.787 10.439 22134 Z= 0.472 Chirality : 0.058 0.463 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.658 125.214 6202 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.28 % Allowed : 15.27 % Favored : 83.45 % 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: 0.47 (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 0.021 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 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 0.78749 / 0.47 (22134) hydrogen bonds : bond 0.15418 / 9.51 ( 871) hydrogen bonds : angle 6.51825 / 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 865 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 843 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.8483 (mt0) cc_final: 0.7267 (mt0) REVERT: A 157 LEU cc_start: 0.9043 (tp) cc_final: 0.8827 (tt) REVERT: A 158 ASN cc_start: 0.8905 (m-40) cc_final: 0.8612 (m-40) REVERT: A 179 LEU cc_start: 0.9247 (tp) cc_final: 0.8708 (tp) REVERT: A 194 LYS cc_start: 0.8983 (tttt) cc_final: 0.8756 (tttm) REVERT: A 588 GLN cc_start: 0.7707 (mm-40) cc_final: 0.7341 (mm-40) REVERT: A 598 MET cc_start: 0.7934 (mtm) cc_final: 0.7339 (mtp) REVERT: A 606 TYR cc_start: 0.7291 (m-80) cc_final: 0.7054 (m-80) REVERT: B 355 TYR cc_start: 0.7743 (m-80) cc_final: 0.7489 (m-80) REVERT: B 358 ILE cc_start: 0.9170 (mm) cc_final: 0.8931 (mm) REVERT: B 421 GLU cc_start: 0.7475 (tt0) cc_final: 0.7267 (tt0) REVERT: B 602 GLU cc_start: 0.6377 (pt0) cc_final: 0.6085 (pt0) REVERT: B 615 MET cc_start: 0.8772 (mmp) cc_final: 0.8473 (mmp) REVERT: C 250 VAL cc_start: 0.4562 (m) cc_final: 0.4325 (p) REVERT: D 178 PHE cc_start: 0.6980 (m-80) cc_final: 0.5802 (m-10) outliers start: 22 outliers final: 7 residues processed: 848 average time/residue: 0.1184 time to fit residues: 146.6703 Evaluate side-chains 552 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 545 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain D residue 59 LEU 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: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN A 304 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS A 645 GLN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.153892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.100321 restraints weight = 26961.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.104160 restraints weight = 11255.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.106552 restraints weight = 6576.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.107924 restraints weight = 4645.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.108901 restraints weight = 3766.710| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (14 function evaluations) r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16386 Z= 0.215 Angle : 0.662 11.182 22134 Z= 0.348 Chirality : 0.045 0.283 2360 Planarity : 0.004 0.048 2818 Dihedral : 9.644 129.072 2301 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.90 % Allowed : 18.76 % Favored : 77.33 % 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: 1.37 (0.19), residues: 1932 helix: 1.36 (0.15), residues: 1130 sheet: -0.05 (0.41), residues: 142 loop : 0.57 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 235 TYR 0.021 0.002 TYR A 612 PHE 0.035 0.002 PHE C 168 TRP 0.011 0.002 TRP C 30 HIS 0.006 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.22 (16386) covalent geometry : angle 0.66205 / 0.35 (22134) hydrogen bonds : bond 0.04791 / 3.04 ( 871) hydrogen bonds : angle 5.01795 / 3.58 ( 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 646 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 579 time to evaluate : 0.431 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 103 ASP cc_start: 0.8576 (m-30) cc_final: 0.8275 (m-30) REVERT: A 144 MET cc_start: 0.9027 (mtm) cc_final: 0.8367 (mtm) REVERT: A 147 GLN cc_start: 0.9191 (mt0) cc_final: 0.7327 (mt0) REVERT: A 148 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8251 (mt-10) REVERT: A 157 LEU cc_start: 0.9266 (tp) cc_final: 0.9066 (tt) REVERT: A 158 ASN cc_start: 0.9124 (m-40) cc_final: 0.8765 (m-40) REVERT: A 179 LEU cc_start: 0.9388 (tp) cc_final: 0.8961 (tp) REVERT: A 250 TYR cc_start: 0.9091 (m-80) cc_final: 0.8709 (m-80) REVERT: A 251 LEU cc_start: 0.9320 (tp) cc_final: 0.8991 (tp) REVERT: A 259 ASN cc_start: 0.8945 (m-40) cc_final: 0.8359 (m-40) REVERT: A 263 ASP cc_start: 0.8698 (m-30) cc_final: 0.8377 (m-30) REVERT: A 355 TYR cc_start: 0.8791 (m-80) cc_final: 0.8559 (m-10) REVERT: A 379 SER cc_start: 0.9360 (t) cc_final: 0.8890 (t) REVERT: A 381 LEU cc_start: 0.9438 (tp) cc_final: 0.9233 (tp) REVERT: A 384 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.7238 (pm20) REVERT: A 415 ASN cc_start: 0.9328 (t0) cc_final: 0.9042 (t0) REVERT: A 436 LEU cc_start: 0.9410 (mt) cc_final: 0.9124 (mp) REVERT: A 459 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8967 (mttp) REVERT: A 583 SER cc_start: 0.9170 (OUTLIER) cc_final: 0.8714 (t) REVERT: A 588 GLN cc_start: 0.8975 (mm-40) cc_final: 0.7757 (mm-40) REVERT: A 628 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8440 (mm-30) REVERT: A 658 LEU cc_start: 0.9554 (mt) cc_final: 0.9330 (mp) REVERT: B 95 MET cc_start: 0.9009 (tpp) cc_final: 0.8778 (mmm) REVERT: B 101 TYR cc_start: 0.8927 (m-80) cc_final: 0.8664 (m-80) REVERT: B 109 ASN cc_start: 0.9252 (OUTLIER) cc_final: 0.8931 (m110) REVERT: B 172 LEU cc_start: 0.9497 (mp) cc_final: 0.9282 (mt) REVERT: B 213 ILE cc_start: 0.9024 (mp) cc_final: 0.8809 (mt) REVERT: B 263 ASP cc_start: 0.8819 (m-30) cc_final: 0.8542 (m-30) REVERT: B 274 ARG cc_start: 0.7935 (ttm110) cc_final: 0.7503 (ptp-170) REVERT: B 317 MET cc_start: 0.8766 (ptt) cc_final: 0.8538 (ptp) REVERT: B 355 TYR cc_start: 0.8505 (m-80) cc_final: 0.7723 (m-80) REVERT: B 358 ILE cc_start: 0.9620 (mm) cc_final: 0.9374 (mm) REVERT: B 396 ASP cc_start: 0.8975 (m-30) cc_final: 0.8712 (m-30) REVERT: B 515 ASP cc_start: 0.8819 (m-30) cc_final: 0.8356 (m-30) REVERT: B 599 GLU cc_start: 0.8071 (pt0) cc_final: 0.7819 (pt0) REVERT: B 615 MET cc_start: 0.9517 (mmp) cc_final: 0.9203 (mmp) REVERT: C 21 PHE cc_start: 0.8994 (m-80) cc_final: 0.8705 (m-80) REVERT: C 154 PHE cc_start: 0.9039 (t80) cc_final: 0.8602 (t80) REVERT: C 157 MET cc_start: 0.9310 (mtp) cc_final: 0.8855 (mtp) REVERT: C 162 TYR cc_start: 0.8886 (m-10) cc_final: 0.8212 (m-80) REVERT: C 189 GLU cc_start: 0.9118 (tp30) cc_final: 0.8830 (tp30) REVERT: C 193 LEU cc_start: 0.9185 (mt) cc_final: 0.8870 (mt) REVERT: C 196 ARG cc_start: 0.9247 (ptm-80) cc_final: 0.8926 (ptm-80) REVERT: C 243 THR cc_start: 0.8715 (p) cc_final: 0.8445 (t) REVERT: D 76 ILE cc_start: 0.7946 (tt) cc_final: 0.7714 (pt) REVERT: D 92 PHE cc_start: 0.6809 (t80) cc_final: 0.6460 (t80) REVERT: D 131 LEU cc_start: 0.8099 (tt) cc_final: 0.7598 (tp) REVERT: D 132 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7971 (mm110) REVERT: D 138 ILE cc_start: 0.9413 (mm) cc_final: 0.8783 (mm) REVERT: D 153 LEU cc_start: 0.5991 (tp) cc_final: 0.5698 (mm) REVERT: D 162 TYR cc_start: 0.7928 (t80) cc_final: 0.7499 (t80) REVERT: D 185 MET cc_start: 0.6039 (mmm) cc_final: 0.5680 (mmm) REVERT: D 197 ASP cc_start: 0.8724 (m-30) cc_final: 0.8458 (m-30) REVERT: D 233 ASN cc_start: 0.9175 (m-40) cc_final: 0.8871 (m110) REVERT: D 235 LEU cc_start: 0.9238 (mt) cc_final: 0.9006 (mt) REVERT: D 287 LEU cc_start: 0.6333 (mt) cc_final: 0.6108 (mt) outliers start: 67 outliers final: 35 residues processed: 617 average time/residue: 0.1025 time to fit residues: 96.5376 Evaluate side-chains 544 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 504 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 256 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 0.9980 chunk 131 optimal weight: 0.6980 chunk 164 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 150 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 158 optimal weight: 8.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN B 14 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN B 474 GLN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS C 192 ASN D 25 ASN D 71 ASN D 128 ASN D 263 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.152253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.099583 restraints weight = 27532.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.103418 restraints weight = 11400.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.105632 restraints weight = 6593.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.107171 restraints weight = 4695.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.108040 restraints weight = 3745.715| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (14 function evaluations) r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4313 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= 0.176 Angle : 0.625 11.064 22134 Z= 0.330 Chirality : 0.044 0.334 2360 Planarity : 0.004 0.053 2818 Dihedral : 9.191 129.641 2297 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.79 % Allowed : 20.63 % Favored : 75.58 % 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: 1.21 (0.19), residues: 1932 helix: 1.28 (0.15), residues: 1142 sheet: -0.27 (0.40), residues: 148 loop : 0.42 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 261 TYR 0.031 0.002 TYR D 142 PHE 0.039 0.002 PHE D 172 TRP 0.020 0.002 TRP D 30 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (16386) covalent geometry : angle 0.62533 / 0.33 (22134) hydrogen bonds : bond 0.04391 / 2.80 ( 871) hydrogen bonds : angle 4.93679 / 3.52 ( 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 625 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 560 time to evaluate : 0.663 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 67 GLU cc_start: 0.8215 (pm20) cc_final: 0.7983 (pm20) REVERT: A 103 ASP cc_start: 0.8582 (m-30) cc_final: 0.8319 (m-30) REVERT: A 106 LEU cc_start: 0.9159 (tp) cc_final: 0.8882 (tp) REVERT: A 119 GLU cc_start: 0.8144 (mp0) cc_final: 0.7932 (mp0) REVERT: A 144 MET cc_start: 0.8921 (mtm) cc_final: 0.8342 (mtm) REVERT: A 147 GLN cc_start: 0.9170 (mt0) cc_final: 0.7489 (mt0) REVERT: A 148 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8286 (mt-10) REVERT: A 158 ASN cc_start: 0.9117 (m-40) cc_final: 0.8896 (m-40) REVERT: A 250 TYR cc_start: 0.9113 (m-80) cc_final: 0.8724 (m-80) REVERT: A 259 ASN cc_start: 0.9042 (m-40) cc_final: 0.8434 (m-40) REVERT: A 263 ASP cc_start: 0.8649 (m-30) cc_final: 0.8296 (m-30) REVERT: A 277 THR cc_start: 0.8445 (p) cc_final: 0.8136 (t) REVERT: A 379 SER cc_start: 0.9293 (t) cc_final: 0.8827 (t) REVERT: A 381 LEU cc_start: 0.9483 (tp) cc_final: 0.9255 (tp) REVERT: A 384 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.7115 (pm20) REVERT: A 415 ASN cc_start: 0.9335 (t0) cc_final: 0.9099 (t0) REVERT: A 459 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8904 (mttp) REVERT: A 583 SER cc_start: 0.9238 (m) cc_final: 0.8825 (t) REVERT: A 588 GLN cc_start: 0.8921 (mm-40) cc_final: 0.7835 (mm-40) REVERT: A 628 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8417 (mm-30) REVERT: A 663 THR cc_start: 0.9103 (OUTLIER) cc_final: 0.8891 (t) REVERT: A 683 TYR cc_start: 0.9240 (t80) cc_final: 0.8883 (t80) REVERT: B 101 TYR cc_start: 0.9007 (m-80) cc_final: 0.8730 (m-80) REVERT: B 257 ASP cc_start: 0.8935 (m-30) cc_final: 0.8703 (m-30) REVERT: B 263 ASP cc_start: 0.8773 (m-30) cc_final: 0.8473 (m-30) REVERT: B 270 ASP cc_start: 0.8672 (t0) cc_final: 0.8346 (t0) REVERT: B 274 ARG cc_start: 0.7993 (ttm110) cc_final: 0.7639 (ptp90) REVERT: B 317 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8334 (ptp) REVERT: B 355 TYR cc_start: 0.8423 (m-80) cc_final: 0.7744 (m-80) REVERT: B 358 ILE cc_start: 0.9630 (mm) cc_final: 0.9373 (mm) REVERT: B 384 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.7399 (pm20) REVERT: B 515 ASP cc_start: 0.8829 (m-30) cc_final: 0.8301 (m-30) REVERT: B 599 GLU cc_start: 0.8110 (pt0) cc_final: 0.7831 (pt0) REVERT: B 602 GLU cc_start: 0.7919 (pt0) cc_final: 0.7500 (pt0) REVERT: B 610 LYS cc_start: 0.8282 (ptmm) cc_final: 0.7770 (ptmm) REVERT: B 615 MET cc_start: 0.9485 (mmp) cc_final: 0.9170 (mmp) REVERT: C 21 PHE cc_start: 0.9154 (m-80) cc_final: 0.8716 (m-80) REVERT: C 56 MET cc_start: 0.6900 (ptm) cc_final: 0.5945 (ttt) REVERT: C 93 MET cc_start: 0.8746 (mtt) cc_final: 0.8460 (mtt) REVERT: C 154 PHE cc_start: 0.9107 (t80) cc_final: 0.8738 (t80) REVERT: C 189 GLU cc_start: 0.9117 (tp30) cc_final: 0.8850 (tp30) REVERT: C 192 ASN cc_start: 0.8629 (m-40) cc_final: 0.8419 (m110) REVERT: C 193 LEU cc_start: 0.9227 (mt) cc_final: 0.9017 (mt) REVERT: C 196 ARG cc_start: 0.9212 (ptm-80) cc_final: 0.8983 (ptm160) REVERT: C 244 GLU cc_start: 0.9505 (pt0) cc_final: 0.9164 (pp20) REVERT: C 245 ASP cc_start: 0.8307 (t0) cc_final: 0.8046 (t0) REVERT: C 259 PHE cc_start: 0.8312 (t80) cc_final: 0.8104 (t80) REVERT: C 270 ASN cc_start: 0.8083 (m-40) cc_final: 0.7731 (m-40) REVERT: C 321 TYR cc_start: 0.9063 (m-80) cc_final: 0.6880 (t80) REVERT: D 132 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8133 (mm110) REVERT: D 153 LEU cc_start: 0.6485 (tp) cc_final: 0.5910 (mm) REVERT: D 162 TYR cc_start: 0.7770 (t80) cc_final: 0.7082 (t80) REVERT: D 195 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8678 (tt) REVERT: D 197 ASP cc_start: 0.8633 (m-30) cc_final: 0.8146 (m-30) REVERT: D 226 GLU cc_start: 0.9098 (pt0) cc_final: 0.8752 (pp20) REVERT: D 269 MET cc_start: 0.9112 (tmm) cc_final: 0.8831 (tmm) outliers start: 65 outliers final: 37 residues processed: 592 average time/residue: 0.1020 time to fit residues: 92.5707 Evaluate side-chains 547 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 503 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain D residue 25 ASN 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 132 GLN Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 127 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 185 optimal weight: 10.0000 chunk 191 optimal weight: 8.9990 chunk 159 optimal weight: 20.0000 chunk 182 optimal weight: 8.9990 chunk 93 optimal weight: 0.8980 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN A 320 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN D 119 ASN D 128 ASN D 132 GLN D 216 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.146502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.094606 restraints weight = 27734.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.098099 restraints weight = 11625.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.100180 restraints weight = 6915.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.101571 restraints weight = 5024.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.102374 restraints weight = 4045.801| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (11 function evaluations) r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 16386 Z= 0.341 Angle : 0.708 14.958 22134 Z= 0.368 Chirality : 0.047 0.382 2360 Planarity : 0.004 0.041 2818 Dihedral : 9.143 134.155 2297 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.60 % Allowed : 20.92 % Favored : 74.48 % 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: 1.07 (0.19), residues: 1932 helix: 1.15 (0.15), residues: 1149 sheet: -0.47 (0.41), residues: 148 loop : 0.42 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 235 TYR 0.032 0.002 TYR D 142 PHE 0.037 0.002 PHE C 277 TRP 0.013 0.002 TRP A 558 HIS 0.006 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00758 / 0.34 (16386) covalent geometry : angle 0.70803 / 0.37 (22134) hydrogen bonds : bond 0.04446 / 2.86 ( 871) hydrogen bonds : angle 5.04350 / 3.59 ( 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 574 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 495 time to evaluate : 0.522 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: A 67 GLU cc_start: 0.8218 (pm20) cc_final: 0.7944 (pm20) REVERT: A 103 ASP cc_start: 0.8693 (m-30) cc_final: 0.8432 (m-30) REVERT: A 117 ARG cc_start: 0.8533 (mtp85) cc_final: 0.8091 (ttm-80) REVERT: A 119 GLU cc_start: 0.8256 (mp0) cc_final: 0.8010 (mp0) REVERT: A 144 MET cc_start: 0.9012 (mtm) cc_final: 0.8472 (mtm) REVERT: A 147 GLN cc_start: 0.9272 (mt0) cc_final: 0.8810 (mt0) REVERT: A 148 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8275 (mt-10) REVERT: A 209 LYS cc_start: 0.9104 (tttm) cc_final: 0.8610 (ttmm) REVERT: A 250 TYR cc_start: 0.9147 (m-80) cc_final: 0.8763 (m-80) REVERT: A 259 ASN cc_start: 0.9084 (m-40) cc_final: 0.8487 (m-40) REVERT: A 263 ASP cc_start: 0.8694 (m-30) cc_final: 0.8341 (m-30) REVERT: A 277 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8274 (t) REVERT: A 379 SER cc_start: 0.9320 (t) cc_final: 0.8998 (t) REVERT: A 381 LEU cc_start: 0.9548 (tp) cc_final: 0.9276 (tp) REVERT: A 384 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.6910 (pm20) REVERT: A 415 ASN cc_start: 0.9389 (t0) cc_final: 0.9127 (t0) REVERT: A 583 SER cc_start: 0.9383 (OUTLIER) cc_final: 0.8993 (t) REVERT: A 589 SER cc_start: 0.9384 (m) cc_final: 0.9081 (p) REVERT: A 615 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8871 (mmm) REVERT: A 628 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8477 (mm-30) REVERT: A 683 TYR cc_start: 0.9147 (t80) cc_final: 0.8927 (t80) REVERT: B 111 LYS cc_start: 0.9425 (mmtp) cc_final: 0.9139 (mmtt) REVERT: B 253 ILE cc_start: 0.9580 (tt) cc_final: 0.9261 (tt) REVERT: B 257 ASP cc_start: 0.9014 (m-30) cc_final: 0.8798 (m-30) REVERT: B 263 ASP cc_start: 0.8795 (m-30) cc_final: 0.8512 (m-30) REVERT: B 272 ASP cc_start: 0.8617 (p0) cc_final: 0.8357 (p0) REVERT: B 317 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8733 (ptp) REVERT: B 336 LYS cc_start: 0.9421 (OUTLIER) cc_final: 0.9021 (ttmm) REVERT: B 355 TYR cc_start: 0.8579 (m-80) cc_final: 0.7926 (m-80) REVERT: B 362 ASP cc_start: 0.8353 (m-30) cc_final: 0.8109 (m-30) REVERT: B 384 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.7455 (pm20) REVERT: B 515 ASP cc_start: 0.8879 (m-30) cc_final: 0.8352 (m-30) REVERT: B 586 TYR cc_start: 0.9057 (m-80) cc_final: 0.8736 (m-80) REVERT: B 599 GLU cc_start: 0.8207 (pt0) cc_final: 0.8001 (pt0) REVERT: B 602 GLU cc_start: 0.7934 (pt0) cc_final: 0.7298 (pt0) REVERT: B 610 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.7818 (ptmm) REVERT: B 612 TYR cc_start: 0.8674 (m-80) cc_final: 0.7905 (m-80) REVERT: B 615 MET cc_start: 0.9556 (mmp) cc_final: 0.9246 (mmp) REVERT: C 21 PHE cc_start: 0.9186 (m-80) cc_final: 0.8765 (m-80) REVERT: C 56 MET cc_start: 0.7045 (ptm) cc_final: 0.6356 (ttp) REVERT: C 122 PHE cc_start: 0.8772 (m-80) cc_final: 0.8563 (m-80) REVERT: C 124 TRP cc_start: 0.8739 (t60) cc_final: 0.8496 (t60) REVERT: C 137 MET cc_start: 0.8398 (mmm) cc_final: 0.8151 (mmm) REVERT: C 158 VAL cc_start: 0.9519 (t) cc_final: 0.9135 (t) REVERT: C 162 TYR cc_start: 0.8831 (m-80) cc_final: 0.7726 (m-80) REVERT: C 189 GLU cc_start: 0.9092 (tp30) cc_final: 0.8805 (tp30) REVERT: C 192 ASN cc_start: 0.8667 (m-40) cc_final: 0.8355 (m-40) REVERT: C 193 LEU cc_start: 0.9272 (mt) cc_final: 0.8970 (mt) REVERT: C 196 ARG cc_start: 0.9240 (ptm-80) cc_final: 0.8951 (ptt90) REVERT: C 270 ASN cc_start: 0.8332 (m-40) cc_final: 0.7940 (m110) REVERT: D 30 TRP cc_start: 0.6983 (p-90) cc_final: 0.6038 (p-90) REVERT: D 69 GLN cc_start: 0.8292 (tp40) cc_final: 0.8054 (pt0) REVERT: D 132 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8063 (mm110) REVERT: D 197 ASP cc_start: 0.8660 (m-30) cc_final: 0.8413 (m-30) REVERT: D 265 ASN cc_start: 0.8211 (m-40) cc_final: 0.7905 (m-40) outliers start: 79 outliers final: 48 residues processed: 538 average time/residue: 0.1052 time to fit residues: 86.8589 Evaluate side-chains 514 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 457 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 615 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 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP 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 132 GLN Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 318 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN B 645 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 128 ASN ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.148862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.097284 restraints weight = 27471.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.100942 restraints weight = 11551.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.103071 restraints weight = 6762.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.104435 restraints weight = 4855.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.105376 restraints weight = 3942.891| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16386 Z= 0.172 Angle : 0.627 14.487 22134 Z= 0.329 Chirality : 0.044 0.404 2360 Planarity : 0.003 0.052 2818 Dihedral : 8.806 134.106 2296 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.02 % Allowed : 22.32 % Favored : 73.66 % 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: 1.06 (0.19), residues: 1932 helix: 1.16 (0.15), residues: 1134 sheet: -0.45 (0.41), residues: 148 loop : 0.38 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 235 TYR 0.040 0.002 TYR D 142 PHE 0.041 0.002 PHE C 154 TRP 0.012 0.001 TRP D 44 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (16386) covalent geometry : angle 0.62681 / 0.33 (22134) hydrogen bonds : bond 0.04105 / 2.62 ( 871) hydrogen bonds : angle 4.92154 / 3.52 ( 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 572 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 503 time to evaluate : 0.595 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 103 ASP cc_start: 0.8631 (m-30) cc_final: 0.8352 (m-30) REVERT: A 106 LEU cc_start: 0.9111 (tp) cc_final: 0.8870 (tp) REVERT: A 144 MET cc_start: 0.8876 (mtm) cc_final: 0.8343 (mtm) REVERT: A 147 GLN cc_start: 0.9190 (mt0) cc_final: 0.8883 (mt0) REVERT: A 148 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8263 (mt-10) REVERT: A 209 LYS cc_start: 0.9030 (tttm) cc_final: 0.8441 (ttmm) REVERT: A 250 TYR cc_start: 0.9080 (m-80) cc_final: 0.8714 (m-80) REVERT: A 259 ASN cc_start: 0.9086 (m-40) cc_final: 0.8476 (m-40) REVERT: A 263 ASP cc_start: 0.8720 (m-30) cc_final: 0.8359 (m-30) REVERT: A 277 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8125 (t) REVERT: A 350 ARG cc_start: 0.9244 (mtp85) cc_final: 0.8231 (mtp85) REVERT: A 379 SER cc_start: 0.9291 (t) cc_final: 0.8895 (t) REVERT: A 384 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.6705 (pm20) REVERT: A 583 SER cc_start: 0.9350 (OUTLIER) cc_final: 0.8982 (t) REVERT: A 589 SER cc_start: 0.9370 (m) cc_final: 0.9026 (p) REVERT: A 628 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8495 (mm-30) REVERT: A 683 TYR cc_start: 0.9197 (t80) cc_final: 0.8929 (t80) REVERT: B 257 ASP cc_start: 0.8956 (m-30) cc_final: 0.8680 (m-30) REVERT: B 263 ASP cc_start: 0.8757 (m-30) cc_final: 0.8412 (m-30) REVERT: B 317 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8499 (ptp) REVERT: B 359 MET cc_start: 0.9047 (ttp) cc_final: 0.8843 (tmm) REVERT: B 362 ASP cc_start: 0.8325 (m-30) cc_final: 0.8024 (m-30) REVERT: B 384 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.7326 (pm20) REVERT: B 394 TYR cc_start: 0.9197 (m-80) cc_final: 0.8657 (m-80) REVERT: B 515 ASP cc_start: 0.8784 (m-30) cc_final: 0.8218 (m-30) REVERT: B 595 MET cc_start: 0.9022 (mmm) cc_final: 0.8387 (mmm) REVERT: B 599 GLU cc_start: 0.8201 (pt0) cc_final: 0.7904 (pt0) REVERT: B 610 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.7812 (ptmm) REVERT: B 612 TYR cc_start: 0.8611 (m-80) cc_final: 0.7982 (m-80) REVERT: B 615 MET cc_start: 0.9529 (mmp) cc_final: 0.9289 (mmp) REVERT: C 21 PHE cc_start: 0.9197 (m-80) cc_final: 0.8791 (m-80) REVERT: C 56 MET cc_start: 0.6793 (ptm) cc_final: 0.6099 (ttp) REVERT: C 107 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7581 (p0) REVERT: C 122 PHE cc_start: 0.8685 (m-80) cc_final: 0.8474 (m-80) REVERT: C 137 MET cc_start: 0.8573 (mmm) cc_final: 0.8310 (mmm) REVERT: C 154 PHE cc_start: 0.9182 (t80) cc_final: 0.8849 (t80) REVERT: C 158 VAL cc_start: 0.9585 (t) cc_final: 0.9251 (t) REVERT: C 162 TYR cc_start: 0.8816 (m-80) cc_final: 0.7877 (m-80) REVERT: C 189 GLU cc_start: 0.9100 (tp30) cc_final: 0.8770 (tp30) REVERT: C 193 LEU cc_start: 0.9329 (mt) cc_final: 0.9042 (mt) REVERT: C 196 ARG cc_start: 0.9235 (ptm-80) cc_final: 0.8915 (ptt90) REVERT: C 259 PHE cc_start: 0.8299 (t80) cc_final: 0.8059 (t80) REVERT: D 30 TRP cc_start: 0.6875 (p-90) cc_final: 0.6408 (p-90) REVERT: D 132 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8057 (mm-40) REVERT: D 150 GLU cc_start: 0.5465 (OUTLIER) cc_final: 0.5175 (mm-30) REVERT: D 162 TYR cc_start: 0.7566 (t80) cc_final: 0.6964 (t80) REVERT: D 231 LEU cc_start: 0.9002 (tp) cc_final: 0.8776 (pp) REVERT: D 265 ASN cc_start: 0.8208 (m-40) cc_final: 0.7831 (m-40) REVERT: D 287 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6451 (mt) outliers start: 69 outliers final: 39 residues processed: 539 average time/residue: 0.1001 time to fit residues: 82.6622 Evaluate side-chains 511 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 462 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 287 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 1.9990 chunk 183 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 172 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 132 GLN ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.145770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.095361 restraints weight = 27583.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.098856 restraints weight = 11656.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.100911 restraints weight = 6737.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.102378 restraints weight = 4798.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.103266 restraints weight = 3813.794| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 16386 Z= 0.282 Angle : 0.684 13.724 22134 Z= 0.357 Chirality : 0.046 0.378 2360 Planarity : 0.004 0.054 2818 Dihedral : 8.738 135.514 2296 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.72 % Allowed : 22.79 % Favored : 72.49 % 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: 1.02 (0.19), residues: 1932 helix: 1.11 (0.15), residues: 1150 sheet: -0.62 (0.41), residues: 148 loop : 0.45 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 235 TYR 0.047 0.002 TYR D 142 PHE 0.035 0.002 PHE C 154 TRP 0.020 0.002 TRP D 44 HIS 0.005 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.28 (16386) covalent geometry : angle 0.68401 / 0.36 (22134) hydrogen bonds : bond 0.04214 / 2.66 ( 871) hydrogen bonds : angle 5.01821 / 3.60 ( 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 550 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 469 time to evaluate : 0.573 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: A 76 ASP cc_start: 0.8743 (m-30) cc_final: 0.8358 (m-30) REVERT: A 103 ASP cc_start: 0.8715 (m-30) cc_final: 0.8439 (m-30) REVERT: A 106 LEU cc_start: 0.9156 (tp) cc_final: 0.8842 (tp) REVERT: A 144 MET cc_start: 0.8971 (mtm) cc_final: 0.8455 (mtm) REVERT: A 147 GLN cc_start: 0.9207 (mt0) cc_final: 0.8827 (mt0) REVERT: A 148 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8243 (mt-10) REVERT: A 209 LYS cc_start: 0.9062 (tttm) cc_final: 0.8468 (ttmm) REVERT: A 250 TYR cc_start: 0.9130 (m-80) cc_final: 0.8749 (m-80) REVERT: A 259 ASN cc_start: 0.9135 (m-40) cc_final: 0.8526 (m-40) REVERT: A 263 ASP cc_start: 0.8683 (m-30) cc_final: 0.8360 (m-30) REVERT: A 277 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8256 (t) REVERT: A 379 SER cc_start: 0.9293 (t) cc_final: 0.8902 (t) REVERT: A 384 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.6827 (pm20) REVERT: A 453 ARG cc_start: 0.9274 (OUTLIER) cc_final: 0.8504 (ttt-90) REVERT: A 486 ASP cc_start: 0.8500 (t0) cc_final: 0.8230 (t0) REVERT: A 589 SER cc_start: 0.9319 (m) cc_final: 0.9082 (p) REVERT: A 628 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8512 (mm-30) REVERT: A 683 TYR cc_start: 0.9161 (t80) cc_final: 0.8901 (t80) REVERT: A 686 ARG cc_start: 0.8349 (ttm-80) cc_final: 0.7740 (mmt-90) REVERT: B 103 ASP cc_start: 0.8993 (m-30) cc_final: 0.8776 (m-30) REVERT: B 108 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8207 (p) REVERT: B 111 LYS cc_start: 0.9192 (mmtm) cc_final: 0.8977 (mmtt) REVERT: B 150 GLN cc_start: 0.9178 (tp-100) cc_final: 0.8959 (tp-100) REVERT: B 253 ILE cc_start: 0.9553 (tt) cc_final: 0.9228 (tt) REVERT: B 257 ASP cc_start: 0.8993 (m-30) cc_final: 0.8743 (m-30) REVERT: B 263 ASP cc_start: 0.8769 (m-30) cc_final: 0.8422 (m-30) REVERT: B 274 ARG cc_start: 0.8290 (ttm110) cc_final: 0.7346 (ptp-110) REVERT: B 317 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8730 (ptp) REVERT: B 336 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.9109 (ttmm) REVERT: B 355 TYR cc_start: 0.8580 (m-80) cc_final: 0.7972 (m-80) REVERT: B 362 ASP cc_start: 0.8353 (m-30) cc_final: 0.8050 (m-30) REVERT: B 384 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.7244 (pm20) REVERT: B 515 ASP cc_start: 0.8824 (m-30) cc_final: 0.8297 (m-30) REVERT: B 586 TYR cc_start: 0.8950 (m-80) cc_final: 0.8547 (m-80) REVERT: B 595 MET cc_start: 0.9069 (mmm) cc_final: 0.8394 (mmm) REVERT: B 599 GLU cc_start: 0.8275 (pt0) cc_final: 0.8035 (pt0) REVERT: B 602 GLU cc_start: 0.7905 (pt0) cc_final: 0.7286 (pt0) REVERT: B 610 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.7887 (ptmm) REVERT: B 612 TYR cc_start: 0.8679 (m-80) cc_final: 0.7918 (m-80) REVERT: B 615 MET cc_start: 0.9541 (mmp) cc_final: 0.9264 (mmp) REVERT: C 21 PHE cc_start: 0.9251 (m-80) cc_final: 0.8858 (m-80) REVERT: C 35 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7615 (tp) REVERT: C 56 MET cc_start: 0.6909 (ptm) cc_final: 0.5815 (ttm) REVERT: C 121 VAL cc_start: 0.8090 (p) cc_final: 0.7575 (p) REVERT: C 122 PHE cc_start: 0.8759 (m-80) cc_final: 0.8500 (m-80) REVERT: C 129 LYS cc_start: 0.9158 (tptt) cc_final: 0.8893 (tmtt) REVERT: C 189 GLU cc_start: 0.9094 (tp30) cc_final: 0.8764 (tp30) REVERT: C 193 LEU cc_start: 0.9378 (mt) cc_final: 0.9114 (mt) REVERT: C 196 ARG cc_start: 0.9252 (ptm-80) cc_final: 0.8960 (ptt90) REVERT: C 259 PHE cc_start: 0.8342 (t80) cc_final: 0.8032 (t80) REVERT: D 24 GLN cc_start: 0.9117 (tp40) cc_final: 0.8588 (tp40) REVERT: D 25 ASN cc_start: 0.9211 (t0) cc_final: 0.8994 (t0) REVERT: D 28 GLN cc_start: 0.8221 (mm-40) cc_final: 0.6953 (mm110) REVERT: D 30 TRP cc_start: 0.7085 (p-90) cc_final: 0.6081 (p-90) REVERT: D 132 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8138 (mm110) REVERT: D 137 MET cc_start: 0.8951 (mpp) cc_final: 0.8490 (mtt) REVERT: D 174 TYR cc_start: 0.7248 (t80) cc_final: 0.6990 (t80) REVERT: D 233 ASN cc_start: 0.9199 (m-40) cc_final: 0.8951 (m-40) REVERT: D 236 TYR cc_start: 0.8358 (t80) cc_final: 0.8120 (t80) REVERT: D 238 ASN cc_start: 0.7198 (t0) cc_final: 0.6938 (t0) REVERT: D 265 ASN cc_start: 0.8167 (m-40) cc_final: 0.7927 (m-40) REVERT: D 287 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.6541 (mt) outliers start: 81 outliers final: 51 residues processed: 514 average time/residue: 0.1066 time to fit residues: 83.3159 Evaluate side-chains 505 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 443 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 348 MET 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 413 SER Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER 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 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 287 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 186 optimal weight: 20.0000 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN D 23 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.149072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.098996 restraints weight = 27121.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.102525 restraints weight = 11377.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.104649 restraints weight = 6514.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.106049 restraints weight = 4561.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.106947 restraints weight = 3644.674| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.5558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16386 Z= 0.160 Angle : 0.646 14.155 22134 Z= 0.335 Chirality : 0.044 0.362 2360 Planarity : 0.004 0.074 2818 Dihedral : 8.302 134.644 2294 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.90 % Allowed : 23.25 % Favored : 72.84 % 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: 1.00 (0.19), residues: 1932 helix: 1.12 (0.15), residues: 1144 sheet: -0.68 (0.41), residues: 148 loop : 0.41 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 196 TYR 0.034 0.001 TYR D 142 PHE 0.040 0.002 PHE C 154 TRP 0.021 0.002 TRP D 44 HIS 0.005 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (16386) covalent geometry : angle 0.64577 / 0.33 (22134) hydrogen bonds : bond 0.04050 / 2.59 ( 871) hydrogen bonds : angle 4.97075 / 3.57 ( 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 551 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 484 time to evaluate : 0.568 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: A 103 ASP cc_start: 0.8703 (m-30) cc_final: 0.8410 (m-30) REVERT: A 106 LEU cc_start: 0.9141 (tp) cc_final: 0.8813 (tp) REVERT: A 144 MET cc_start: 0.8859 (mtm) cc_final: 0.8310 (mtm) REVERT: A 148 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8231 (mt-10) REVERT: A 209 LYS cc_start: 0.9003 (tttm) cc_final: 0.8404 (ttmm) REVERT: A 250 TYR cc_start: 0.9085 (m-80) cc_final: 0.8694 (m-80) REVERT: A 259 ASN cc_start: 0.9070 (m-40) cc_final: 0.8410 (m-40) REVERT: A 263 ASP cc_start: 0.8743 (m-30) cc_final: 0.8332 (m-30) REVERT: A 277 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8100 (t) REVERT: A 350 ARG cc_start: 0.9204 (mtp85) cc_final: 0.8152 (mtp85) REVERT: A 379 SER cc_start: 0.9238 (t) cc_final: 0.8793 (t) REVERT: A 384 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.6709 (pm20) REVERT: A 486 ASP cc_start: 0.8510 (t0) cc_final: 0.8229 (t0) REVERT: A 583 SER cc_start: 0.9348 (OUTLIER) cc_final: 0.8996 (t) REVERT: A 589 SER cc_start: 0.9346 (m) cc_final: 0.9007 (p) REVERT: A 686 ARG cc_start: 0.8321 (ttm-80) cc_final: 0.7761 (mmt-90) REVERT: B 257 ASP cc_start: 0.8966 (m-30) cc_final: 0.8669 (m-30) REVERT: B 263 ASP cc_start: 0.8749 (m-30) cc_final: 0.8362 (m-30) REVERT: B 274 ARG cc_start: 0.8293 (ttm110) cc_final: 0.7396 (ptp-110) REVERT: B 317 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8400 (ptp) REVERT: B 336 LYS cc_start: 0.9420 (OUTLIER) cc_final: 0.9088 (ttmm) REVERT: B 355 TYR cc_start: 0.8395 (m-80) cc_final: 0.7796 (m-80) REVERT: B 359 MET cc_start: 0.9045 (ttp) cc_final: 0.8831 (tmm) REVERT: B 362 ASP cc_start: 0.8323 (m-30) cc_final: 0.8053 (m-30) REVERT: B 384 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.7252 (pm20) REVERT: B 394 TYR cc_start: 0.9253 (m-80) cc_final: 0.8533 (m-80) REVERT: B 515 ASP cc_start: 0.8803 (m-30) cc_final: 0.8244 (m-30) REVERT: B 571 TYR cc_start: 0.8823 (t80) cc_final: 0.7809 (t80) REVERT: B 586 TYR cc_start: 0.8872 (m-80) cc_final: 0.8637 (m-80) REVERT: B 595 MET cc_start: 0.9044 (mmm) cc_final: 0.8368 (mmm) REVERT: B 599 GLU cc_start: 0.8282 (pt0) cc_final: 0.7999 (pt0) REVERT: B 602 GLU cc_start: 0.7941 (pt0) cc_final: 0.7216 (pt0) REVERT: B 610 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.7868 (ptmm) REVERT: B 612 TYR cc_start: 0.8591 (m-80) cc_final: 0.7892 (m-80) REVERT: B 615 MET cc_start: 0.9511 (mmp) cc_final: 0.9281 (mmp) REVERT: C 21 PHE cc_start: 0.9266 (m-80) cc_final: 0.8877 (m-80) REVERT: C 56 MET cc_start: 0.6667 (ptm) cc_final: 0.5678 (ttm) REVERT: C 95 MET cc_start: 0.8902 (tmm) cc_final: 0.8693 (tmm) REVERT: C 110 MET cc_start: 0.8338 (mpp) cc_final: 0.8132 (mpp) REVERT: C 121 VAL cc_start: 0.8088 (p) cc_final: 0.7524 (p) REVERT: C 122 PHE cc_start: 0.8778 (m-80) cc_final: 0.8518 (m-80) REVERT: C 129 LYS cc_start: 0.9174 (tptt) cc_final: 0.8914 (tmtt) REVERT: C 154 PHE cc_start: 0.9222 (t80) cc_final: 0.8975 (t80) REVERT: C 189 GLU cc_start: 0.9109 (tp30) cc_final: 0.8770 (tp30) REVERT: C 193 LEU cc_start: 0.9356 (mt) cc_final: 0.9111 (mt) REVERT: C 196 ARG cc_start: 0.9271 (ptm-80) cc_final: 0.8987 (ptt90) REVERT: C 241 GLU cc_start: 0.9336 (pt0) cc_final: 0.9081 (pt0) REVERT: C 259 PHE cc_start: 0.8392 (t80) cc_final: 0.8182 (t80) REVERT: C 271 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8534 (mm) REVERT: D 24 GLN cc_start: 0.9186 (tp40) cc_final: 0.8882 (tp40) REVERT: D 30 TRP cc_start: 0.7096 (p-90) cc_final: 0.6157 (p-90) REVERT: D 44 TRP cc_start: 0.8304 (t-100) cc_final: 0.7860 (t-100) REVERT: D 132 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.8015 (mm110) REVERT: D 236 TYR cc_start: 0.8299 (t80) cc_final: 0.7977 (t80) REVERT: D 287 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6567 (mt) outliers start: 67 outliers final: 43 residues processed: 520 average time/residue: 0.1069 time to fit residues: 84.8594 Evaluate side-chains 511 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 458 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 287 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 158 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 151 optimal weight: 20.0000 chunk 81 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 ASN A 320 ASN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.151397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.101632 restraints weight = 27373.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.105243 restraints weight = 11280.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.107338 restraints weight = 6445.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.108820 restraints weight = 4550.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.109513 restraints weight = 3613.175| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16386 Z= 0.147 Angle : 0.647 12.958 22134 Z= 0.336 Chirality : 0.044 0.346 2360 Planarity : 0.004 0.090 2818 Dihedral : 7.939 134.854 2294 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.38 % Allowed : 24.42 % Favored : 72.20 % 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: 1.04 (0.19), residues: 1932 helix: 1.17 (0.15), residues: 1147 sheet: -0.70 (0.41), residues: 148 loop : 0.39 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 196 TYR 0.029 0.001 TYR D 142 PHE 0.041 0.002 PHE C 154 TRP 0.015 0.001 TRP D 44 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (16386) covalent geometry : angle 0.64748 / 0.34 (22134) hydrogen bonds : bond 0.03905 / 2.50 ( 871) hydrogen bonds : angle 4.93916 / 3.55 ( 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 553 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 495 time to evaluate : 0.518 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 103 ASP cc_start: 0.8710 (m-30) cc_final: 0.8496 (m-30) REVERT: A 106 LEU cc_start: 0.9116 (tp) cc_final: 0.8796 (tp) REVERT: A 144 MET cc_start: 0.8782 (mtm) cc_final: 0.8214 (mtm) REVERT: A 148 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8243 (mt-10) REVERT: A 209 LYS cc_start: 0.9030 (tttm) cc_final: 0.8518 (ttmm) REVERT: A 250 TYR cc_start: 0.9094 (m-80) cc_final: 0.8748 (m-80) REVERT: A 259 ASN cc_start: 0.9034 (m-40) cc_final: 0.8445 (m-40) REVERT: A 263 ASP cc_start: 0.8734 (m-30) cc_final: 0.8406 (m-30) REVERT: A 277 THR cc_start: 0.8296 (p) cc_final: 0.8039 (t) REVERT: A 357 TYR cc_start: 0.9017 (m-10) cc_final: 0.8655 (m-10) REVERT: A 379 SER cc_start: 0.9240 (t) cc_final: 0.8836 (t) REVERT: A 384 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.6581 (pm20) REVERT: A 486 ASP cc_start: 0.8434 (t0) cc_final: 0.8230 (t0) REVERT: A 493 MET cc_start: 0.9130 (tmm) cc_final: 0.8902 (tmm) REVERT: A 583 SER cc_start: 0.9284 (OUTLIER) cc_final: 0.9014 (t) REVERT: A 589 SER cc_start: 0.9393 (m) cc_final: 0.9070 (p) REVERT: A 683 TYR cc_start: 0.9227 (t80) cc_final: 0.8922 (t80) REVERT: A 686 ARG cc_start: 0.8319 (ttm-80) cc_final: 0.7768 (mmt-90) REVERT: B 108 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8409 (p) REVERT: B 257 ASP cc_start: 0.8964 (m-30) cc_final: 0.8662 (m-30) REVERT: B 263 ASP cc_start: 0.8735 (m-30) cc_final: 0.8354 (m-30) REVERT: B 274 ARG cc_start: 0.8302 (ttm110) cc_final: 0.7395 (ptp-110) REVERT: B 317 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8331 (ptp) REVERT: B 355 TYR cc_start: 0.8360 (m-80) cc_final: 0.7861 (m-80) REVERT: B 359 MET cc_start: 0.9057 (ttp) cc_final: 0.8850 (tmm) REVERT: B 362 ASP cc_start: 0.8275 (m-30) cc_final: 0.8003 (m-30) REVERT: B 384 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.7082 (pm20) REVERT: B 394 TYR cc_start: 0.9254 (m-80) cc_final: 0.8448 (m-80) REVERT: B 515 ASP cc_start: 0.8769 (m-30) cc_final: 0.8213 (m-30) REVERT: B 595 MET cc_start: 0.9012 (mmm) cc_final: 0.8317 (mmm) REVERT: B 599 GLU cc_start: 0.8251 (pt0) cc_final: 0.7959 (pt0) REVERT: B 602 GLU cc_start: 0.7983 (pt0) cc_final: 0.7201 (pt0) REVERT: B 610 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.7847 (ptmm) REVERT: B 612 TYR cc_start: 0.8523 (m-80) cc_final: 0.7816 (m-80) REVERT: B 615 MET cc_start: 0.9499 (mmp) cc_final: 0.9273 (mmp) REVERT: C 17 PHE cc_start: 0.8602 (p90) cc_final: 0.8291 (p90) REVERT: C 20 MET cc_start: 0.9001 (ptp) cc_final: 0.8772 (pmm) REVERT: C 21 PHE cc_start: 0.9303 (m-80) cc_final: 0.8669 (m-80) REVERT: C 56 MET cc_start: 0.6772 (ptm) cc_final: 0.5748 (ttm) REVERT: C 95 MET cc_start: 0.8805 (tmm) cc_final: 0.8538 (tmm) REVERT: C 121 VAL cc_start: 0.8031 (p) cc_final: 0.7460 (p) REVERT: C 122 PHE cc_start: 0.8782 (m-80) cc_final: 0.8546 (m-80) REVERT: C 129 LYS cc_start: 0.9163 (tptt) cc_final: 0.8939 (tmtt) REVERT: C 162 TYR cc_start: 0.8943 (m-80) cc_final: 0.7784 (m-80) REVERT: C 189 GLU cc_start: 0.9119 (tp30) cc_final: 0.8797 (tp30) REVERT: C 192 ASN cc_start: 0.8675 (m-40) cc_final: 0.8422 (m-40) REVERT: C 193 LEU cc_start: 0.9395 (mt) cc_final: 0.9179 (mt) REVERT: C 196 ARG cc_start: 0.9234 (ptm-80) cc_final: 0.8992 (ptt90) REVERT: C 241 GLU cc_start: 0.9328 (pt0) cc_final: 0.9098 (pt0) REVERT: C 259 PHE cc_start: 0.8500 (t80) cc_final: 0.8203 (t80) REVERT: D 24 GLN cc_start: 0.9123 (tp40) cc_final: 0.8706 (tp40) REVERT: D 132 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8037 (mm-40) REVERT: D 157 MET cc_start: 0.2067 (ptt) cc_final: 0.1835 (ptt) REVERT: D 236 TYR cc_start: 0.8200 (t80) cc_final: 0.7847 (t80) REVERT: D 245 ASP cc_start: 0.7851 (t0) cc_final: 0.7430 (m-30) REVERT: D 287 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6633 (mt) outliers start: 58 outliers final: 42 residues processed: 522 average time/residue: 0.1028 time to fit residues: 82.4196 Evaluate side-chains 518 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 468 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 348 MET 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 413 SER Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE 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 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 287 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 0.2980 chunk 133 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 16 optimal weight: 0.3980 chunk 114 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.152664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.102800 restraints weight = 27276.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.106454 restraints weight = 11426.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.108575 restraints weight = 6513.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.110110 restraints weight = 4603.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.110975 restraints weight = 3652.263| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.5912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16386 Z= 0.145 Angle : 0.671 12.627 22134 Z= 0.349 Chirality : 0.045 0.361 2360 Planarity : 0.004 0.085 2818 Dihedral : 7.783 134.988 2292 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.09 % Allowed : 25.29 % Favored : 71.62 % 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: 0.99 (0.19), residues: 1932 helix: 1.14 (0.15), residues: 1141 sheet: -0.57 (0.43), residues: 140 loop : 0.30 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 196 TYR 0.026 0.001 TYR D 142 PHE 0.036 0.002 PHE C 172 TRP 0.019 0.001 TRP D 44 HIS 0.004 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (16386) covalent geometry : angle 0.67123 / 0.35 (22134) hydrogen bonds : bond 0.03918 / 2.53 ( 871) hydrogen bonds : angle 4.94705 / 3.57 ( 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 538 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 485 time to evaluate : 0.579 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 103 ASP cc_start: 0.8711 (m-30) cc_final: 0.8501 (m-30) REVERT: A 106 LEU cc_start: 0.9102 (tp) cc_final: 0.8730 (tp) REVERT: A 144 MET cc_start: 0.8746 (mtm) cc_final: 0.8194 (mtm) REVERT: A 148 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8123 (mt-10) REVERT: A 164 ARG cc_start: 0.8310 (ptt90) cc_final: 0.7957 (ptt-90) REVERT: A 209 LYS cc_start: 0.8993 (tttm) cc_final: 0.8487 (ttmm) REVERT: A 250 TYR cc_start: 0.9092 (m-80) cc_final: 0.8724 (m-80) REVERT: A 259 ASN cc_start: 0.9015 (m-40) cc_final: 0.8421 (m-40) REVERT: A 263 ASP cc_start: 0.8691 (m-30) cc_final: 0.8360 (m-30) REVERT: A 277 THR cc_start: 0.8260 (p) cc_final: 0.8016 (t) REVERT: A 357 TYR cc_start: 0.9035 (m-10) cc_final: 0.8667 (m-10) REVERT: A 379 SER cc_start: 0.9237 (t) cc_final: 0.8801 (t) REVERT: A 384 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.6590 (pm20) REVERT: A 486 ASP cc_start: 0.8436 (t0) cc_final: 0.8218 (t0) REVERT: A 493 MET cc_start: 0.9126 (tmm) cc_final: 0.8889 (tmm) REVERT: A 583 SER cc_start: 0.9270 (OUTLIER) cc_final: 0.8999 (t) REVERT: A 586 TYR cc_start: 0.8809 (m-10) cc_final: 0.8338 (m-80) REVERT: A 588 GLN cc_start: 0.9333 (tp40) cc_final: 0.9127 (tp40) REVERT: A 589 SER cc_start: 0.9374 (m) cc_final: 0.9041 (p) REVERT: A 598 MET cc_start: 0.8570 (mtm) cc_final: 0.8217 (mtm) REVERT: A 683 TYR cc_start: 0.9216 (t80) cc_final: 0.8916 (t80) REVERT: A 686 ARG cc_start: 0.8311 (ttm-80) cc_final: 0.8108 (mmm-85) REVERT: B 108 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8487 (p) REVERT: B 257 ASP cc_start: 0.8752 (m-30) cc_final: 0.8495 (m-30) REVERT: B 263 ASP cc_start: 0.8733 (m-30) cc_final: 0.8330 (m-30) REVERT: B 274 ARG cc_start: 0.8201 (ttm110) cc_final: 0.7371 (ptp-110) REVERT: B 317 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8275 (ptp) REVERT: B 355 TYR cc_start: 0.8349 (m-80) cc_final: 0.7889 (m-80) REVERT: B 362 ASP cc_start: 0.8231 (m-30) cc_final: 0.7955 (m-30) REVERT: B 384 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.7018 (pm20) REVERT: B 394 TYR cc_start: 0.9252 (m-80) cc_final: 0.8350 (m-80) REVERT: B 447 ASN cc_start: 0.8492 (OUTLIER) cc_final: 0.7961 (m-40) REVERT: B 515 ASP cc_start: 0.8756 (m-30) cc_final: 0.8210 (m-30) REVERT: B 586 TYR cc_start: 0.8744 (m-80) cc_final: 0.8260 (m-80) REVERT: B 595 MET cc_start: 0.8974 (mmm) cc_final: 0.8275 (mmm) REVERT: B 602 GLU cc_start: 0.7908 (pt0) cc_final: 0.7642 (pt0) REVERT: B 610 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.7822 (ptmm) REVERT: B 612 TYR cc_start: 0.8495 (m-80) cc_final: 0.7785 (m-80) REVERT: B 628 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8252 (mm-30) REVERT: C 17 PHE cc_start: 0.8546 (p90) cc_final: 0.8216 (p90) REVERT: C 20 MET cc_start: 0.8985 (ptp) cc_final: 0.8748 (pmm) REVERT: C 21 PHE cc_start: 0.9310 (m-80) cc_final: 0.8649 (m-80) REVERT: C 56 MET cc_start: 0.6831 (ptm) cc_final: 0.6331 (ttp) REVERT: C 95 MET cc_start: 0.8742 (tmm) cc_final: 0.8475 (tmm) REVERT: C 121 VAL cc_start: 0.8019 (p) cc_final: 0.7742 (p) REVERT: C 122 PHE cc_start: 0.8797 (m-80) cc_final: 0.8558 (m-80) REVERT: C 129 LYS cc_start: 0.9161 (tptt) cc_final: 0.8955 (tmtt) REVERT: C 162 TYR cc_start: 0.8973 (m-80) cc_final: 0.8633 (m-80) REVERT: C 189 GLU cc_start: 0.9056 (tp30) cc_final: 0.8733 (tp30) REVERT: C 192 ASN cc_start: 0.8691 (m-40) cc_final: 0.8435 (m-40) REVERT: C 193 LEU cc_start: 0.9399 (mt) cc_final: 0.9180 (mt) REVERT: C 196 ARG cc_start: 0.9214 (ptm-80) cc_final: 0.8982 (ptt90) REVERT: C 241 GLU cc_start: 0.9318 (pt0) cc_final: 0.8948 (pt0) REVERT: C 244 GLU cc_start: 0.9445 (pt0) cc_final: 0.9145 (pp20) REVERT: C 259 PHE cc_start: 0.8507 (t80) cc_final: 0.8227 (t80) REVERT: D 30 TRP cc_start: 0.7250 (p-90) cc_final: 0.6419 (p-90) REVERT: D 44 TRP cc_start: 0.8220 (t-100) cc_final: 0.7870 (t-100) REVERT: D 56 MET cc_start: 0.7810 (ptp) cc_final: 0.7514 (mmp) REVERT: D 132 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7932 (mm110) REVERT: D 154 PHE cc_start: 0.7878 (t80) cc_final: 0.7513 (t80) REVERT: D 233 ASN cc_start: 0.9116 (m-40) cc_final: 0.8808 (m110) REVERT: D 236 TYR cc_start: 0.8182 (t80) cc_final: 0.7838 (t80) outliers start: 53 outliers final: 37 residues processed: 508 average time/residue: 0.0982 time to fit residues: 76.8805 Evaluate side-chains 513 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 468 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 348 MET 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 413 SER Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE 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 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 447 ASN Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 0.0030 chunk 62 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 189 optimal weight: 8.9990 chunk 181 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 54 optimal weight: 0.0170 chunk 132 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.5628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.153401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.103974 restraints weight = 27262.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107592 restraints weight = 11311.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.109740 restraints weight = 6445.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.111212 restraints weight = 4524.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.112086 restraints weight = 3625.977| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.6080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16386 Z= 0.143 Angle : 0.685 12.564 22134 Z= 0.357 Chirality : 0.046 0.365 2360 Planarity : 0.004 0.045 2818 Dihedral : 7.661 135.166 2292 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.03 % Allowed : 25.41 % Favored : 71.56 % 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: 0.97 (0.19), residues: 1932 helix: 1.11 (0.15), residues: 1138 sheet: -0.58 (0.43), residues: 140 loop : 0.30 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 235 TYR 0.029 0.001 TYR A 571 PHE 0.040 0.002 PHE C 172 TRP 0.017 0.001 TRP D 44 HIS 0.004 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (16386) covalent geometry : angle 0.68466 / 0.36 (22134) hydrogen bonds : bond 0.03903 / 2.52 ( 871) hydrogen bonds : angle 4.96059 / 3.57 ( 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 547 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 495 time to evaluate : 0.552 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: A 67 GLU cc_start: 0.8452 (pm20) cc_final: 0.7728 (pm20) REVERT: A 103 ASP cc_start: 0.8724 (m-30) cc_final: 0.8516 (m-30) REVERT: A 106 LEU cc_start: 0.9074 (tp) cc_final: 0.8729 (tp) REVERT: A 144 MET cc_start: 0.8740 (mtm) cc_final: 0.8190 (mtm) REVERT: A 148 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8092 (mt-10) REVERT: A 164 ARG cc_start: 0.8266 (ptt90) cc_final: 0.7918 (ptt-90) REVERT: A 209 LYS cc_start: 0.8999 (tttm) cc_final: 0.8513 (ttmm) REVERT: A 228 LYS cc_start: 0.8990 (ttmm) cc_final: 0.8478 (mttp) REVERT: A 250 TYR cc_start: 0.9093 (m-80) cc_final: 0.8742 (m-80) REVERT: A 259 ASN cc_start: 0.9014 (m-40) cc_final: 0.8421 (m-40) REVERT: A 263 ASP cc_start: 0.8681 (m-30) cc_final: 0.8368 (m-30) REVERT: A 277 THR cc_start: 0.8214 (p) cc_final: 0.7979 (t) REVERT: A 357 TYR cc_start: 0.9038 (m-10) cc_final: 0.8683 (m-10) REVERT: A 379 SER cc_start: 0.9229 (t) cc_final: 0.8790 (t) REVERT: A 384 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.6607 (pm20) REVERT: A 486 ASP cc_start: 0.8410 (t0) cc_final: 0.8196 (t0) REVERT: A 493 MET cc_start: 0.9113 (tmm) cc_final: 0.8875 (tmm) REVERT: A 530 LYS cc_start: 0.8607 (pttm) cc_final: 0.8272 (pttm) REVERT: A 583 SER cc_start: 0.9267 (OUTLIER) cc_final: 0.8939 (t) REVERT: A 586 TYR cc_start: 0.8725 (m-10) cc_final: 0.8295 (m-80) REVERT: A 598 MET cc_start: 0.8496 (mtm) cc_final: 0.8158 (mtm) REVERT: A 683 TYR cc_start: 0.9208 (t80) cc_final: 0.8918 (t80) REVERT: B 108 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8387 (p) REVERT: B 263 ASP cc_start: 0.8716 (m-30) cc_final: 0.8311 (m-30) REVERT: B 274 ARG cc_start: 0.8197 (ttm110) cc_final: 0.7350 (ptp-110) REVERT: B 317 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8158 (ptp) REVERT: B 362 ASP cc_start: 0.8227 (m-30) cc_final: 0.7970 (m-30) REVERT: B 384 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.7060 (pm20) REVERT: B 394 TYR cc_start: 0.9245 (m-80) cc_final: 0.8267 (m-80) REVERT: B 515 ASP cc_start: 0.8754 (m-30) cc_final: 0.8196 (m-30) REVERT: B 586 TYR cc_start: 0.8687 (m-80) cc_final: 0.8310 (m-80) REVERT: B 595 MET cc_start: 0.8977 (mmm) cc_final: 0.8262 (mmm) REVERT: B 599 GLU cc_start: 0.8270 (pt0) cc_final: 0.7863 (pt0) REVERT: B 602 GLU cc_start: 0.7935 (pt0) cc_final: 0.7653 (pt0) REVERT: B 610 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.7827 (ptmm) REVERT: B 612 TYR cc_start: 0.8454 (m-80) cc_final: 0.7740 (m-80) REVERT: B 628 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8220 (mm-30) REVERT: C 17 PHE cc_start: 0.8528 (p90) cc_final: 0.8205 (p90) REVERT: C 20 MET cc_start: 0.8948 (ptp) cc_final: 0.8695 (pmm) REVERT: C 21 PHE cc_start: 0.9312 (m-80) cc_final: 0.8667 (m-80) REVERT: C 56 MET cc_start: 0.6797 (ptm) cc_final: 0.6060 (ttp) REVERT: C 95 MET cc_start: 0.8772 (tmm) cc_final: 0.8388 (tmm) REVERT: C 96 MET cc_start: 0.7632 (mmt) cc_final: 0.7376 (mmm) REVERT: C 121 VAL cc_start: 0.7964 (p) cc_final: 0.7668 (p) REVERT: C 122 PHE cc_start: 0.8730 (m-80) cc_final: 0.8493 (m-80) REVERT: C 124 TRP cc_start: 0.8682 (t60) cc_final: 0.8238 (t60) REVERT: C 162 TYR cc_start: 0.8902 (m-80) cc_final: 0.8599 (m-80) REVERT: C 189 GLU cc_start: 0.9077 (tp30) cc_final: 0.8757 (tp30) REVERT: C 193 LEU cc_start: 0.9408 (mt) cc_final: 0.9203 (mt) REVERT: C 244 GLU cc_start: 0.9434 (pt0) cc_final: 0.9126 (pp20) REVERT: C 259 PHE cc_start: 0.8520 (t80) cc_final: 0.8258 (t80) REVERT: C 281 ASP cc_start: 0.7708 (p0) cc_final: 0.7296 (t0) REVERT: D 30 TRP cc_start: 0.7444 (p-90) cc_final: 0.6412 (p-90) REVERT: D 44 TRP cc_start: 0.8223 (t-100) cc_final: 0.7861 (t-100) REVERT: D 56 MET cc_start: 0.7836 (ptp) cc_final: 0.7555 (mmp) REVERT: D 74 MET cc_start: 0.6086 (tpt) cc_final: 0.4281 (ttp) REVERT: D 132 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7888 (mm110) REVERT: D 154 PHE cc_start: 0.7675 (t80) cc_final: 0.7442 (t80) REVERT: D 233 ASN cc_start: 0.9096 (m-40) cc_final: 0.8776 (m110) REVERT: D 236 TYR cc_start: 0.8063 (t80) cc_final: 0.7674 (t80) outliers start: 52 outliers final: 38 residues processed: 519 average time/residue: 0.1037 time to fit residues: 82.5825 Evaluate side-chains 508 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 463 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 348 MET 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 413 SER Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE 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 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 286 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: 0.0980 chunk 48 optimal weight: 0.6980 chunk 39 optimal weight: 0.0040 chunk 25 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 chunk 125 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 418 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.154568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.105545 restraints weight = 27074.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.109080 restraints weight = 11643.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.111249 restraints weight = 6725.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112673 restraints weight = 4749.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.113444 restraints weight = 3802.184| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.6246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16386 Z= 0.140 Angle : 0.699 14.181 22134 Z= 0.363 Chirality : 0.046 0.346 2360 Planarity : 0.003 0.046 2818 Dihedral : 7.563 135.274 2292 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.45 % Allowed : 26.69 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.19), residues: 1932 helix: 1.07 (0.15), residues: 1146 sheet: -0.57 (0.43), residues: 140 loop : 0.33 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 235 TYR 0.025 0.001 TYR A 571 PHE 0.039 0.002 PHE C 172 TRP 0.016 0.001 TRP D 44 HIS 0.003 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (16386) covalent geometry : angle 0.69907 / 0.36 (22134) hydrogen bonds : bond 0.03924 / 2.52 ( 871) hydrogen bonds : angle 5.00235 / 3.62 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2951.74 seconds wall clock time: 51 minutes 48.85 seconds (3108.85 seconds total)