Starting phenix.real_space_refine on Sun Aug 24 01:10:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byt_45044/08_2025/9byt_45044_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byt_45044/08_2025/9byt_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 { model { file = "/net/cci-nas-00/data/ceres_data/9byt_45044/08_2025/9byt_45044_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byt_45044/08_2025/9byt_45044_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9byt_45044/08_2025/9byt_45044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byt_45044/08_2025/9byt_45044.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.12, per 1000 atoms: 0.19 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: 1.25 Conformation dependent library (CDL) restraints added in 561.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.104A 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: 2.91 Time building geometry restraints manager: 1.56 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=" 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=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.038 1.20e-02 6.94e+03 1.01e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.032 1.08e-02 8.57e+03 8.86e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.569 -0.032 1.17e-02 7.31e+03 7.65e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.574 -0.033 1.25e-02 6.40e+03 7.18e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21572 2.09 - 4.18: 519 4.18 - 6.26: 37 6.26 - 8.35: 2 8.35 - 10.44: 4 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.62 -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 - 35.80: 9469 35.80 - 71.59: 338 71.59 - 107.39: 37 107.39 - 143.18: 3 143.18 - 178.98: 3 Dihedral angle restraints: 9850 sinusoidal: 4092 harmonic: 5758 Sorted by residual: dihedral pdb=" C2 TTP A 803 " pdb=" C1' TTP A 803 " pdb=" N1 TTP A 803 " pdb=" O4' TTP A 803 " ideal model delta sinusoidal sigma weight residual -58.32 120.66 -178.98 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 TTP B 801 " pdb=" C1' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " ideal model delta sinusoidal sigma weight residual 301.68 151.13 150.56 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" C5' TTP A 803 " pdb=" O5' TTP A 803 " pdb=" PA TTP A 803 " pdb=" O3A TTP A 803 " ideal model delta sinusoidal sigma weight residual 179.97 31.89 148.08 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 9847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2137 0.093 - 0.185: 189 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.930 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 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 0.060 16386 Z= 0.316 Angle : 0.740 10.439 22134 Z= 0.463 Chirality : 0.058 0.463 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.930 178.978 6154 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 aren 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 covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.74001 (22134) hydrogen bonds : bond 0.15418 ( 871) hydrogen bonds : angle 6.51825 ( 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 : 0.368 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: 0.1157 time to fit residues: 142.1737 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 : 0.524 ------------------------------------------------------------------------------- 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: 6.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 304 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** 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 D 132 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.152509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.098939 restraints weight = 27028.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.102745 restraints weight = 11348.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.105008 restraints weight = 6643.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.106455 restraints weight = 4768.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.107406 restraints weight = 3850.729| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16386 Z= 0.245 Angle : 0.677 10.641 22134 Z= 0.354 Chirality : 0.046 0.245 2360 Planarity : 0.004 0.047 2818 Dihedral : 11.591 176.301 2253 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.20 % Allowed : 18.47 % 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 aren not related in a simple way. whole: 1.37 (0.19), residues: 1932 helix: 1.32 (0.15), residues: 1142 sheet: -0.04 (0.41), residues: 142 loop : 0.60 (0.24), residues: 648 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 0.032 0.002 PHE C 168 TRP 0.011 0.002 TRP B 9 HIS 0.005 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00549 (16386) covalent geometry : angle 0.67660 (22134) hydrogen bonds : bond 0.04850 ( 871) hydrogen bonds : angle 5.02553 ( 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 650 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 578 time to evaluate : 0.414 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: A 65 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7708 (mt-10) REVERT: A 67 GLU cc_start: 0.8256 (pm20) cc_final: 0.8023 (pm20) REVERT: A 103 ASP cc_start: 0.8604 (m-30) cc_final: 0.8318 (m-30) REVERT: A 144 MET cc_start: 0.9052 (mtm) cc_final: 0.8404 (mtm) REVERT: A 147 GLN cc_start: 0.9205 (mt0) cc_final: 0.8696 (mt0) REVERT: A 148 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8199 (mt-10) REVERT: A 158 ASN cc_start: 0.9153 (m-40) cc_final: 0.8931 (m-40) REVERT: A 211 GLU cc_start: 0.8245 (mm-30) cc_final: 0.8000 (mm-30) REVERT: A 250 TYR cc_start: 0.9099 (m-80) cc_final: 0.8712 (m-80) REVERT: A 259 ASN cc_start: 0.8971 (m-40) cc_final: 0.8363 (m-40) REVERT: A 263 ASP cc_start: 0.8704 (m-30) cc_final: 0.8371 (m-30) REVERT: A 379 SER cc_start: 0.9362 (t) cc_final: 0.8900 (t) REVERT: A 381 LEU cc_start: 0.9450 (tp) cc_final: 0.9242 (tp) REVERT: A 384 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.7111 (pm20) REVERT: A 415 ASN cc_start: 0.9344 (t0) cc_final: 0.9054 (t0) REVERT: A 459 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.8990 (mttp) REVERT: A 583 SER cc_start: 0.9205 (OUTLIER) cc_final: 0.8752 (t) REVERT: A 628 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8370 (mm-30) REVERT: A 658 LEU cc_start: 0.9574 (mt) cc_final: 0.9329 (mp) REVERT: B 95 MET cc_start: 0.9017 (tpp) cc_final: 0.8779 (mmm) REVERT: B 109 ASN cc_start: 0.9259 (OUTLIER) cc_final: 0.8951 (m110) REVERT: B 172 LEU cc_start: 0.9508 (mp) cc_final: 0.9300 (mt) REVERT: B 263 ASP cc_start: 0.8810 (m-30) cc_final: 0.8552 (m-30) REVERT: B 274 ARG cc_start: 0.7955 (ttm110) cc_final: 0.7478 (ptp-170) REVERT: B 317 MET cc_start: 0.8816 (ptt) cc_final: 0.8591 (ptp) REVERT: B 355 TYR cc_start: 0.8496 (m-80) cc_final: 0.7772 (m-80) REVERT: B 358 ILE cc_start: 0.9617 (mm) cc_final: 0.9373 (mm) REVERT: B 384 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.7466 (pm20) REVERT: B 515 ASP cc_start: 0.8803 (m-30) cc_final: 0.8324 (m-30) REVERT: B 599 GLU cc_start: 0.8107 (pt0) cc_final: 0.7830 (pt0) REVERT: B 612 TYR cc_start: 0.8684 (m-80) cc_final: 0.8261 (m-80) REVERT: B 615 MET cc_start: 0.9542 (mmp) cc_final: 0.9219 (mmp) REVERT: C 21 PHE cc_start: 0.8999 (m-80) cc_final: 0.8699 (m-80) REVERT: C 154 PHE cc_start: 0.9040 (t80) cc_final: 0.8498 (t80) REVERT: C 162 TYR cc_start: 0.8907 (m-10) cc_final: 0.8230 (m-80) REVERT: C 189 GLU cc_start: 0.9115 (tp30) cc_final: 0.8833 (tp30) REVERT: C 193 LEU cc_start: 0.9186 (mt) cc_final: 0.8880 (mt) REVERT: C 196 ARG cc_start: 0.9206 (ptm-80) cc_final: 0.8876 (ptm-80) REVERT: C 241 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8860 (mp0) REVERT: C 243 THR cc_start: 0.8688 (p) cc_final: 0.8475 (t) REVERT: D 30 TRP cc_start: 0.7273 (p-90) cc_final: 0.6978 (p-90) REVERT: D 76 ILE cc_start: 0.7955 (tt) cc_final: 0.7722 (pt) REVERT: D 92 PHE cc_start: 0.6812 (t80) cc_final: 0.6450 (t80) REVERT: D 131 LEU cc_start: 0.8130 (tt) cc_final: 0.7539 (tp) REVERT: D 138 ILE cc_start: 0.9431 (mm) cc_final: 0.8840 (mm) REVERT: D 153 LEU cc_start: 0.6018 (tp) cc_final: 0.5680 (mm) REVERT: D 162 TYR cc_start: 0.7966 (t80) cc_final: 0.7559 (t80) REVERT: D 185 MET cc_start: 0.6013 (mmm) cc_final: 0.5649 (mmm) REVERT: D 197 ASP cc_start: 0.8729 (m-30) cc_final: 0.8459 (m-30) REVERT: D 233 ASN cc_start: 0.9182 (m-40) cc_final: 0.8893 (m110) REVERT: D 269 MET cc_start: 0.9117 (tmm) cc_final: 0.8608 (tmm) REVERT: D 287 LEU cc_start: 0.6406 (mt) cc_final: 0.6179 (mt) outliers start: 72 outliers final: 38 residues processed: 619 average time/residue: 0.1005 time to fit residues: 94.0753 Evaluate side-chains 554 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 511 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 277 THR 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 591 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU 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 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 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 100 VAL 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: 1.9990 chunk 131 optimal weight: 0.7980 chunk 164 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 159 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** D 25 ASN D 71 ASN D 128 ASN D 263 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.149910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.097468 restraints weight = 27606.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.101200 restraints weight = 11618.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.103514 restraints weight = 6758.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.104952 restraints weight = 4726.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.105762 restraints weight = 3776.785| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16386 Z= 0.206 Angle : 0.644 11.004 22134 Z= 0.337 Chirality : 0.045 0.325 2360 Planarity : 0.004 0.052 2818 Dihedral : 11.196 164.463 2249 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.20 % Allowed : 20.05 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.19), residues: 1932 helix: 1.26 (0.15), residues: 1151 sheet: -0.35 (0.40), residues: 148 loop : 0.51 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 261 TYR 0.033 0.002 TYR D 142 PHE 0.043 0.002 PHE D 172 TRP 0.013 0.002 TRP D 124 HIS 0.005 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00461 (16386) covalent geometry : angle 0.64390 (22134) hydrogen bonds : bond 0.04409 ( 871) hydrogen bonds : angle 4.95361 ( 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 622 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 550 time to evaluate : 0.481 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 65 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7669 (mt-10) REVERT: A 67 GLU cc_start: 0.8236 (pm20) cc_final: 0.8002 (pm20) REVERT: A 103 ASP cc_start: 0.8621 (m-30) cc_final: 0.8364 (m-30) REVERT: A 106 LEU cc_start: 0.9146 (tp) cc_final: 0.8922 (tp) REVERT: A 119 GLU cc_start: 0.8155 (mp0) cc_final: 0.7948 (mp0) REVERT: A 144 MET cc_start: 0.8956 (mtm) cc_final: 0.8372 (mtm) REVERT: A 147 GLN cc_start: 0.9203 (mt0) cc_final: 0.7497 (mt0) REVERT: A 148 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8285 (mt-10) REVERT: A 158 ASN cc_start: 0.9147 (m-40) cc_final: 0.8914 (m-40) REVERT: A 250 TYR cc_start: 0.9099 (m-80) cc_final: 0.8687 (m-80) REVERT: A 251 LEU cc_start: 0.9343 (tp) cc_final: 0.9025 (tp) REVERT: A 259 ASN cc_start: 0.9055 (m-40) cc_final: 0.8443 (m-40) REVERT: A 263 ASP cc_start: 0.8668 (m-30) cc_final: 0.8301 (m-30) REVERT: A 277 THR cc_start: 0.8490 (p) cc_final: 0.8179 (t) REVERT: A 379 SER cc_start: 0.9310 (t) cc_final: 0.8853 (t) REVERT: A 381 LEU cc_start: 0.9496 (tp) cc_final: 0.9251 (tp) REVERT: A 384 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.6874 (pm20) REVERT: A 415 ASN cc_start: 0.9358 (t0) cc_final: 0.9107 (t0) REVERT: A 459 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8969 (mttp) REVERT: A 583 SER cc_start: 0.9276 (m) cc_final: 0.8877 (t) REVERT: A 588 GLN cc_start: 0.9005 (mm-40) cc_final: 0.7843 (mm-40) REVERT: A 628 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8421 (mm-30) REVERT: A 683 TYR cc_start: 0.9185 (t80) cc_final: 0.8847 (t80) REVERT: B 111 LYS cc_start: 0.9388 (mmtp) cc_final: 0.8987 (mmtm) REVERT: B 152 SER cc_start: 0.9473 (p) cc_final: 0.9217 (p) REVERT: B 257 ASP cc_start: 0.8964 (m-30) cc_final: 0.8753 (m-30) REVERT: B 263 ASP cc_start: 0.8785 (m-30) cc_final: 0.8512 (m-30) REVERT: B 270 ASP cc_start: 0.8704 (t0) cc_final: 0.8466 (t0) REVERT: B 274 ARG cc_start: 0.8059 (ttm110) cc_final: 0.7429 (ptp-110) REVERT: B 317 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8447 (ptp) REVERT: B 355 TYR cc_start: 0.8449 (m-80) cc_final: 0.7772 (m-80) REVERT: B 359 MET cc_start: 0.9023 (ttp) cc_final: 0.8787 (tmm) REVERT: B 515 ASP cc_start: 0.8870 (m-30) cc_final: 0.8339 (m-30) REVERT: B 599 GLU cc_start: 0.8139 (pt0) cc_final: 0.7826 (pt0) REVERT: B 602 GLU cc_start: 0.7969 (pt0) cc_final: 0.7533 (pt0) REVERT: B 610 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8077 (ptmt) REVERT: B 615 MET cc_start: 0.9537 (mmp) cc_final: 0.9215 (mmp) REVERT: C 21 PHE cc_start: 0.9136 (m-80) cc_final: 0.8678 (m-80) REVERT: C 69 GLN cc_start: 0.8756 (tp40) cc_final: 0.8062 (tp40) REVERT: C 154 PHE cc_start: 0.9036 (t80) cc_final: 0.8577 (t80) REVERT: C 162 TYR cc_start: 0.8861 (m-10) cc_final: 0.8175 (m-80) REVERT: C 189 GLU cc_start: 0.9098 (tp30) cc_final: 0.8817 (tp30) REVERT: C 193 LEU cc_start: 0.9227 (mt) cc_final: 0.8999 (mt) REVERT: C 196 ARG cc_start: 0.9196 (ptm-80) cc_final: 0.8971 (ptm160) REVERT: C 213 TYR cc_start: 0.4137 (t80) cc_final: 0.3288 (t80) REVERT: C 244 GLU cc_start: 0.9578 (pt0) cc_final: 0.9221 (pp20) REVERT: C 245 ASP cc_start: 0.8304 (t0) cc_final: 0.8047 (t0) REVERT: C 259 PHE cc_start: 0.8320 (t80) cc_final: 0.8078 (t80) REVERT: C 270 ASN cc_start: 0.8098 (m-40) cc_final: 0.7707 (m-40) REVERT: D 30 TRP cc_start: 0.7095 (p-90) cc_final: 0.6862 (p-90) REVERT: D 132 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7945 (mm-40) REVERT: D 153 LEU cc_start: 0.6205 (tp) cc_final: 0.5605 (mm) REVERT: D 162 TYR cc_start: 0.7731 (t80) cc_final: 0.6982 (t80) REVERT: D 197 ASP cc_start: 0.8760 (m-30) cc_final: 0.8536 (m-30) REVERT: D 238 ASN cc_start: 0.6505 (t0) cc_final: 0.6047 (t0) REVERT: D 269 MET cc_start: 0.9149 (tmm) cc_final: 0.8848 (tmm) outliers start: 72 outliers final: 45 residues processed: 588 average time/residue: 0.0946 time to fit residues: 84.1424 Evaluate side-chains 543 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 493 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 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 439 VAL Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 565 VAL 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 216 VAL Chi-restraints excluded: chain B residue 223 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 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 610 LYS 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 147 LYS Chi-restraints excluded: chain C residue 161 VAL 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 C residue 318 ASP Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 34 GLU 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 282 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 185 optimal weight: 6.9990 chunk 191 optimal weight: 8.9990 chunk 159 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 93 optimal weight: 0.6980 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** 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 447 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN C 192 ASN C 234 GLN D 25 ASN D 85 GLN D 119 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.144460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.092793 restraints weight = 27833.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.096174 restraints weight = 11936.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.098380 restraints weight = 7058.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.099675 restraints weight = 4960.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.100597 restraints weight = 4011.705| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.5005 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= 0.372 Angle : 0.740 14.400 22134 Z= 0.383 Chirality : 0.048 0.382 2360 Planarity : 0.004 0.055 2818 Dihedral : 11.389 172.646 2249 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.95 % Allowed : 20.63 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.19), residues: 1932 helix: 1.06 (0.15), residues: 1151 sheet: -0.58 (0.48), residues: 118 loop : 0.36 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 235 TYR 0.034 0.002 TYR D 142 PHE 0.035 0.002 PHE D 172 TRP 0.013 0.002 TRP A 558 HIS 0.006 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00825 (16386) covalent geometry : angle 0.74048 (22134) hydrogen bonds : bond 0.04529 ( 871) hydrogen bonds : angle 5.08430 ( 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 567 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 482 time to evaluate : 0.372 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 65 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7821 (mt-10) REVERT: A 103 ASP cc_start: 0.8699 (m-30) cc_final: 0.8429 (m-30) REVERT: A 117 ARG cc_start: 0.8561 (mtp85) cc_final: 0.8244 (ttm-80) REVERT: A 119 GLU cc_start: 0.8287 (mp0) cc_final: 0.8029 (mp0) REVERT: A 144 MET cc_start: 0.9053 (mtm) cc_final: 0.8520 (mtm) REVERT: A 147 GLN cc_start: 0.9302 (mt0) cc_final: 0.8865 (mt0) REVERT: A 148 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8287 (mt-10) REVERT: A 209 LYS cc_start: 0.9114 (tttm) cc_final: 0.8474 (ttmm) REVERT: A 221 LYS cc_start: 0.9141 (mmmt) cc_final: 0.8791 (mmtp) REVERT: A 250 TYR cc_start: 0.9158 (m-80) cc_final: 0.8770 (m-80) REVERT: A 259 ASN cc_start: 0.9085 (m-40) cc_final: 0.8481 (m-40) REVERT: A 263 ASP cc_start: 0.8672 (m-30) cc_final: 0.8307 (m-30) REVERT: A 277 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8341 (t) REVERT: A 379 SER cc_start: 0.9341 (t) cc_final: 0.9038 (t) REVERT: A 381 LEU cc_start: 0.9564 (tp) cc_final: 0.9292 (tp) REVERT: A 384 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.6891 (pm20) REVERT: A 415 ASN cc_start: 0.9381 (t0) cc_final: 0.9142 (t0) REVERT: A 583 SER cc_start: 0.9384 (OUTLIER) cc_final: 0.9004 (t) REVERT: A 589 SER cc_start: 0.9370 (m) cc_final: 0.9083 (p) REVERT: A 628 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8479 (mm-30) REVERT: A 683 TYR cc_start: 0.9159 (t80) cc_final: 0.8932 (t80) REVERT: B 103 ASP cc_start: 0.8997 (m-30) cc_final: 0.8794 (m-30) REVERT: B 253 ILE cc_start: 0.9578 (tt) cc_final: 0.9260 (tt) REVERT: B 263 ASP cc_start: 0.8796 (m-30) cc_final: 0.8518 (m-30) REVERT: B 272 ASP cc_start: 0.8663 (p0) cc_final: 0.8420 (p0) REVERT: B 318 ASP cc_start: 0.8556 (t0) cc_final: 0.8244 (t0) REVERT: B 336 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.9044 (ttmm) REVERT: B 355 TYR cc_start: 0.8606 (m-80) cc_final: 0.7983 (m-80) REVERT: B 362 ASP cc_start: 0.8382 (m-30) cc_final: 0.8158 (m-30) REVERT: B 384 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.7337 (pm20) REVERT: B 515 ASP cc_start: 0.8880 (m-30) cc_final: 0.8359 (m-30) REVERT: B 586 TYR cc_start: 0.9085 (m-80) cc_final: 0.8829 (m-80) REVERT: B 599 GLU cc_start: 0.8226 (pt0) cc_final: 0.8001 (pt0) REVERT: B 602 GLU cc_start: 0.7962 (pt0) cc_final: 0.7296 (pt0) REVERT: B 610 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.7923 (ptmm) REVERT: B 612 TYR cc_start: 0.8724 (m-80) cc_final: 0.8147 (m-80) REVERT: B 615 MET cc_start: 0.9562 (mmp) cc_final: 0.9244 (mmp) REVERT: C 21 PHE cc_start: 0.9180 (m-80) cc_final: 0.8762 (m-80) REVERT: C 53 ASP cc_start: 0.8244 (t0) cc_final: 0.8043 (t0) REVERT: C 56 MET cc_start: 0.7067 (ptm) cc_final: 0.6351 (ttp) REVERT: C 122 PHE cc_start: 0.8747 (m-80) cc_final: 0.8529 (m-80) REVERT: C 124 TRP cc_start: 0.8714 (t60) cc_final: 0.8492 (t60) REVERT: C 137 MET cc_start: 0.8470 (mmm) cc_final: 0.8254 (mmm) REVERT: C 154 PHE cc_start: 0.9086 (t80) cc_final: 0.8631 (t80) REVERT: C 158 VAL cc_start: 0.9529 (t) cc_final: 0.8886 (t) REVERT: C 162 TYR cc_start: 0.8975 (m-10) cc_final: 0.8222 (m-80) REVERT: C 189 GLU cc_start: 0.9085 (tp30) cc_final: 0.8822 (tp30) REVERT: C 193 LEU cc_start: 0.9267 (mt) cc_final: 0.8991 (mt) REVERT: C 196 ARG cc_start: 0.9248 (ptm-80) cc_final: 0.8991 (ptm-80) REVERT: C 244 GLU cc_start: 0.9532 (pt0) cc_final: 0.9207 (pp20) REVERT: C 270 ASN cc_start: 0.8384 (m-40) cc_final: 0.8028 (m110) REVERT: D 30 TRP cc_start: 0.7347 (p-90) cc_final: 0.6788 (p-90) REVERT: D 197 ASP cc_start: 0.8874 (m-30) cc_final: 0.8633 (m-30) REVERT: D 261 ARG cc_start: 0.7977 (mtt180) cc_final: 0.7717 (mmt180) outliers start: 85 outliers final: 55 residues processed: 530 average time/residue: 0.1014 time to fit residues: 80.7363 Evaluate side-chains 516 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 455 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 306 ILE Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 403 ILE 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 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 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 260 ASP 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 161 VAL Chi-restraints excluded: chain C residue 262 TYR 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 C residue 318 ASP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 85 GLN 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 282 ILE Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 126 optimal weight: 0.0020 chunk 129 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 157 optimal weight: 10.0000 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 ASN A 645 GLN ** B 158 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 447 ASN B 645 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 85 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.150157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.099172 restraints weight = 27442.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.102842 restraints weight = 11322.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.105113 restraints weight = 6490.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.106447 restraints weight = 4564.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.107376 restraints weight = 3668.296| |-----------------------------------------------------------------------------| 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 = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16386 Z= 0.147 Angle : 0.628 14.799 22134 Z= 0.327 Chirality : 0.043 0.383 2360 Planarity : 0.003 0.048 2818 Dihedral : 10.940 174.653 2248 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.44 % Allowed : 22.32 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.19), residues: 1932 helix: 1.18 (0.15), residues: 1137 sheet: -0.43 (0.41), residues: 148 loop : 0.37 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 235 TYR 0.037 0.002 TYR D 142 PHE 0.032 0.002 PHE C 168 TRP 0.011 0.001 TRP A 558 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00327 (16386) covalent geometry : angle 0.62754 (22134) hydrogen bonds : bond 0.04090 ( 871) hydrogen bonds : angle 4.90205 ( 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 589 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 530 time to evaluate : 0.503 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 103 ASP cc_start: 0.8682 (m-30) cc_final: 0.8416 (m-30) REVERT: A 106 LEU cc_start: 0.9093 (tp) cc_final: 0.8854 (tp) REVERT: A 144 MET cc_start: 0.8877 (mtm) cc_final: 0.8343 (mtm) REVERT: A 147 GLN cc_start: 0.9150 (mt0) cc_final: 0.8793 (mt0) REVERT: A 148 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8253 (mt-10) REVERT: A 209 LYS cc_start: 0.9003 (tttm) cc_final: 0.8410 (ttmm) REVERT: A 250 TYR cc_start: 0.9059 (m-80) cc_final: 0.8680 (m-80) REVERT: A 259 ASN cc_start: 0.9074 (m-40) cc_final: 0.8460 (m-40) REVERT: A 263 ASP cc_start: 0.8731 (m-30) cc_final: 0.8321 (m-30) REVERT: A 277 THR cc_start: 0.8388 (OUTLIER) cc_final: 0.8114 (t) REVERT: A 348 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8335 (ptp) REVERT: A 357 TYR cc_start: 0.9093 (m-10) cc_final: 0.8734 (m-10) REVERT: A 379 SER cc_start: 0.9293 (t) cc_final: 0.8824 (t) REVERT: A 384 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.6680 (pm20) REVERT: A 415 ASN cc_start: 0.9333 (t0) cc_final: 0.9093 (t0) REVERT: A 486 ASP cc_start: 0.8495 (t0) cc_final: 0.8221 (t0) REVERT: A 583 SER cc_start: 0.9334 (OUTLIER) cc_final: 0.8958 (t) REVERT: A 589 SER cc_start: 0.9379 (m) cc_final: 0.9041 (p) REVERT: A 628 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8421 (mm-30) REVERT: B 111 LYS cc_start: 0.9237 (mmtm) cc_final: 0.9018 (mmtt) REVERT: B 147 GLN cc_start: 0.8937 (mt0) cc_final: 0.8623 (mm110) REVERT: B 235 ARG cc_start: 0.8947 (ttm-80) cc_final: 0.8734 (ttm-80) REVERT: B 257 ASP cc_start: 0.8959 (m-30) cc_final: 0.8689 (m-30) REVERT: B 263 ASP cc_start: 0.8765 (m-30) cc_final: 0.8414 (m-30) REVERT: B 362 ASP cc_start: 0.8306 (m-30) cc_final: 0.8068 (m-30) REVERT: B 394 TYR cc_start: 0.9209 (m-80) cc_final: 0.8600 (m-80) REVERT: B 515 ASP cc_start: 0.8795 (m-30) cc_final: 0.8222 (m-30) REVERT: B 599 GLU cc_start: 0.8205 (pt0) cc_final: 0.7900 (pt0) REVERT: B 602 GLU cc_start: 0.8051 (pt0) cc_final: 0.7355 (pt0) REVERT: B 610 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8005 (ptmm) REVERT: B 612 TYR cc_start: 0.8622 (m-80) cc_final: 0.8244 (m-80) REVERT: B 615 MET cc_start: 0.9519 (mmp) cc_final: 0.9300 (mmp) REVERT: C 21 PHE cc_start: 0.9181 (m-80) cc_final: 0.8760 (m-80) REVERT: C 56 MET cc_start: 0.7009 (ptm) cc_final: 0.6306 (ttp) REVERT: C 93 MET cc_start: 0.8887 (mtt) cc_final: 0.8646 (mtt) REVERT: C 122 PHE cc_start: 0.8692 (m-80) cc_final: 0.8478 (m-80) REVERT: C 154 PHE cc_start: 0.9052 (t80) cc_final: 0.8768 (t80) REVERT: C 189 GLU cc_start: 0.9077 (tp30) cc_final: 0.8564 (tp30) REVERT: C 193 LEU cc_start: 0.9308 (mt) cc_final: 0.9022 (mt) REVERT: C 196 ARG cc_start: 0.9237 (ptm-80) cc_final: 0.8956 (ptt90) REVERT: C 244 GLU cc_start: 0.9544 (pt0) cc_final: 0.9200 (pp20) REVERT: C 259 PHE cc_start: 0.8297 (t80) cc_final: 0.8069 (t80) REVERT: C 270 ASN cc_start: 0.8375 (m-40) cc_final: 0.8068 (m110) REVERT: D 150 GLU cc_start: 0.5504 (OUTLIER) cc_final: 0.5264 (mm-30) REVERT: D 197 ASP cc_start: 0.8898 (m-30) cc_final: 0.8670 (m-30) REVERT: D 233 ASN cc_start: 0.9238 (m-40) cc_final: 0.9000 (p0) REVERT: D 265 ASN cc_start: 0.8256 (m-40) cc_final: 0.7893 (m-40) outliers start: 59 outliers final: 36 residues processed: 561 average time/residue: 0.0973 time to fit residues: 83.3902 Evaluate side-chains 534 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 492 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 168 VAL Chi-restraints excluded: chain A residue 216 VAL 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 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 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 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 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 587 VAL Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 610 LYS 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 161 VAL 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 85 GLN 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 282 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 2.9990 chunk 183 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 172 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 447 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** ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN D 80 HIS D 85 GLN ** D 132 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 = 0.3784 r_free = 0.3784 target = 0.146974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.095457 restraints weight = 27407.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.099007 restraints weight = 11721.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.101040 restraints weight = 6861.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.102455 restraints weight = 4977.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.103262 restraints weight = 3981.428| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 16386 Z= 0.267 Angle : 0.689 14.022 22134 Z= 0.359 Chirality : 0.046 0.375 2360 Planarity : 0.004 0.052 2818 Dihedral : 10.777 163.506 2248 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.37 % Allowed : 22.73 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.19), residues: 1932 helix: 1.11 (0.15), residues: 1145 sheet: -0.58 (0.41), residues: 148 loop : 0.38 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 235 TYR 0.046 0.002 TYR D 142 PHE 0.027 0.002 PHE D 172 TRP 0.033 0.002 TRP D 30 HIS 0.004 0.001 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00599 (16386) covalent geometry : angle 0.68930 (22134) hydrogen bonds : bond 0.04141 ( 871) hydrogen bonds : angle 5.02216 ( 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 561 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 486 time to evaluate : 0.442 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: 0.8238 (pm20) cc_final: 0.7949 (pm20) REVERT: A 103 ASP cc_start: 0.8731 (m-30) cc_final: 0.8454 (m-30) REVERT: A 106 LEU cc_start: 0.9147 (tp) cc_final: 0.8893 (tp) REVERT: A 144 MET cc_start: 0.8975 (mtm) cc_final: 0.8434 (mtm) REVERT: A 147 GLN cc_start: 0.9204 (mt0) cc_final: 0.8800 (mt0) REVERT: A 148 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8214 (mt-10) REVERT: A 209 LYS cc_start: 0.9024 (tttm) cc_final: 0.8409 (ttmm) REVERT: A 250 TYR cc_start: 0.9133 (m-80) cc_final: 0.8738 (m-80) REVERT: A 259 ASN cc_start: 0.9130 (m-40) cc_final: 0.8546 (m-40) REVERT: A 263 ASP cc_start: 0.8748 (m-30) cc_final: 0.8339 (m-30) REVERT: A 277 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8247 (t) REVERT: A 379 SER cc_start: 0.9277 (t) cc_final: 0.8898 (t) REVERT: A 384 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.6835 (pm20) REVERT: A 453 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.8463 (ttt-90) REVERT: A 589 SER cc_start: 0.9369 (m) cc_final: 0.9080 (p) REVERT: A 628 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8462 (mm-30) REVERT: A 686 ARG cc_start: 0.8352 (ttm-80) cc_final: 0.7741 (mmt-90) REVERT: B 108 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8357 (p) REVERT: B 253 ILE cc_start: 0.9552 (tt) cc_final: 0.9231 (tt) REVERT: B 257 ASP cc_start: 0.9044 (m-30) cc_final: 0.8770 (m-30) REVERT: B 263 ASP cc_start: 0.8790 (m-30) cc_final: 0.8454 (m-30) REVERT: B 274 ARG cc_start: 0.8283 (ttm110) cc_final: 0.7454 (ptp-110) REVERT: B 318 ASP cc_start: 0.8494 (t0) cc_final: 0.8197 (t0) REVERT: B 336 LYS cc_start: 0.9430 (OUTLIER) cc_final: 0.9104 (ttmm) REVERT: B 355 TYR cc_start: 0.8564 (m-80) cc_final: 0.7996 (m-80) REVERT: B 362 ASP cc_start: 0.8347 (m-30) cc_final: 0.8059 (m-30) REVERT: B 515 ASP cc_start: 0.8842 (m-30) cc_final: 0.8262 (m-30) REVERT: B 586 TYR cc_start: 0.8959 (m-80) cc_final: 0.8694 (m-80) REVERT: B 595 MET cc_start: 0.9075 (mmm) cc_final: 0.8394 (mmm) REVERT: B 602 GLU cc_start: 0.7919 (pt0) cc_final: 0.7218 (pt0) REVERT: B 615 MET cc_start: 0.9541 (mmp) cc_final: 0.9279 (mmp) REVERT: C 21 PHE cc_start: 0.9245 (m-80) cc_final: 0.8893 (m-80) REVERT: C 35 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7580 (tp) REVERT: C 56 MET cc_start: 0.6874 (ptm) cc_final: 0.6255 (ttp) REVERT: C 122 PHE cc_start: 0.8764 (m-80) cc_final: 0.8532 (m-80) REVERT: C 189 GLU cc_start: 0.8941 (tp30) cc_final: 0.8633 (tp30) REVERT: C 193 LEU cc_start: 0.9416 (mt) cc_final: 0.9096 (mt) REVERT: C 196 ARG cc_start: 0.9241 (ptm-80) cc_final: 0.8940 (ptt90) REVERT: C 244 GLU cc_start: 0.9510 (pt0) cc_final: 0.9192 (pp20) REVERT: D 44 TRP cc_start: 0.8273 (t-100) cc_final: 0.7910 (t-100) REVERT: D 150 GLU cc_start: 0.5392 (OUTLIER) cc_final: 0.5071 (mm-30) REVERT: D 197 ASP cc_start: 0.8882 (m-30) cc_final: 0.8400 (m-30) REVERT: D 226 GLU cc_start: 0.8830 (pp20) cc_final: 0.8590 (pp20) REVERT: D 227 PHE cc_start: 0.9179 (t80) cc_final: 0.8827 (t80) REVERT: D 233 ASN cc_start: 0.9275 (m-40) cc_final: 0.8975 (m110) REVERT: D 265 ASN cc_start: 0.8187 (m-40) cc_final: 0.7962 (m-40) outliers start: 75 outliers final: 52 residues processed: 530 average time/residue: 0.1018 time to fit residues: 81.7675 Evaluate side-chains 515 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 456 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 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 349 LEU 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 431 LEU 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 336 LYS 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 589 SER 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 161 VAL 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 C residue 318 ASP Chi-restraints excluded: chain D residue 85 GLN 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 150 GLU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 105 optimal weight: 4.9990 chunk 56 optimal weight: 0.2980 chunk 186 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** B 158 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 447 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 85 GLN D 132 GLN D 270 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.150342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.099623 restraints weight = 27231.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.103250 restraints weight = 11463.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.105335 restraints weight = 6564.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.106824 restraints weight = 4658.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107727 restraints weight = 3697.887| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 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 = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16386 Z= 0.158 Angle : 0.663 13.753 22134 Z= 0.345 Chirality : 0.045 0.382 2360 Planarity : 0.004 0.051 2818 Dihedral : 10.072 155.588 2246 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.44 % Allowed : 23.83 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.19), residues: 1932 helix: 1.05 (0.15), residues: 1145 sheet: -0.59 (0.40), residues: 148 loop : 0.41 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 235 TYR 0.038 0.002 TYR D 142 PHE 0.042 0.002 PHE C 154 TRP 0.024 0.002 TRP D 30 HIS 0.006 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00357 (16386) covalent geometry : angle 0.66327 (22134) hydrogen bonds : bond 0.03981 ( 871) hydrogen bonds : angle 4.99983 ( 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 558 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 499 time to evaluate : 0.399 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: A 67 GLU cc_start: 0.8170 (pm20) cc_final: 0.7945 (pm20) REVERT: A 103 ASP cc_start: 0.8691 (m-30) cc_final: 0.8434 (m-30) REVERT: A 106 LEU cc_start: 0.9134 (tp) cc_final: 0.8837 (tp) REVERT: A 144 MET cc_start: 0.8849 (mtm) cc_final: 0.8299 (mtm) REVERT: A 147 GLN cc_start: 0.9090 (mt0) cc_final: 0.8850 (mt0) REVERT: A 148 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8214 (mt-10) REVERT: A 209 LYS cc_start: 0.9063 (tttm) cc_final: 0.8490 (ttmm) REVERT: A 250 TYR cc_start: 0.9084 (m-80) cc_final: 0.8716 (m-80) REVERT: A 259 ASN cc_start: 0.9077 (m-40) cc_final: 0.8439 (m-40) REVERT: A 263 ASP cc_start: 0.8756 (m-30) cc_final: 0.8323 (m-30) REVERT: A 277 THR cc_start: 0.8380 (p) cc_final: 0.8094 (t) REVERT: A 350 ARG cc_start: 0.9234 (mtp85) cc_final: 0.8176 (mtp85) REVERT: A 379 SER cc_start: 0.9234 (t) cc_final: 0.8844 (t) REVERT: A 384 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.6636 (pm20) REVERT: A 583 SER cc_start: 0.9347 (OUTLIER) cc_final: 0.9025 (t) REVERT: A 589 SER cc_start: 0.9330 (m) cc_final: 0.9009 (p) REVERT: A 604 ARG cc_start: 0.8549 (mmp80) cc_final: 0.8163 (mmt-90) REVERT: A 628 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8454 (mm-30) REVERT: A 686 ARG cc_start: 0.8315 (ttm-80) cc_final: 0.7796 (mmt-90) REVERT: B 51 LEU cc_start: 0.9468 (tt) cc_final: 0.9254 (mt) REVERT: B 65 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7929 (mm-30) REVERT: B 108 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8456 (p) REVERT: B 257 ASP cc_start: 0.9002 (m-30) cc_final: 0.8692 (m-30) REVERT: B 263 ASP cc_start: 0.8736 (m-30) cc_final: 0.8375 (m-30) REVERT: B 274 ARG cc_start: 0.8221 (ttm110) cc_final: 0.7470 (ptp-110) REVERT: B 318 ASP cc_start: 0.8492 (t0) cc_final: 0.8221 (t0) REVERT: B 336 LYS cc_start: 0.9416 (OUTLIER) cc_final: 0.9071 (ttmm) REVERT: B 355 TYR cc_start: 0.8380 (m-80) cc_final: 0.7796 (m-80) REVERT: B 362 ASP cc_start: 0.8293 (m-30) cc_final: 0.8025 (m-30) REVERT: B 384 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.7272 (pm20) REVERT: B 394 TYR cc_start: 0.9242 (m-80) cc_final: 0.8457 (m-80) REVERT: B 515 ASP cc_start: 0.8794 (m-30) cc_final: 0.8238 (m-30) REVERT: B 595 MET cc_start: 0.9033 (mmm) cc_final: 0.8356 (mmm) REVERT: B 602 GLU cc_start: 0.7945 (pt0) cc_final: 0.7304 (pt0) REVERT: B 603 GLU cc_start: 0.7139 (tp30) cc_final: 0.6789 (tp30) REVERT: B 615 MET cc_start: 0.9500 (mmp) cc_final: 0.9276 (mmp) REVERT: B 628 GLU cc_start: 0.8545 (mt-10) cc_final: 0.7822 (mm-30) REVERT: C 21 PHE cc_start: 0.9260 (m-80) cc_final: 0.8889 (m-80) REVERT: C 56 MET cc_start: 0.6847 (ptm) cc_final: 0.5720 (ttm) REVERT: C 95 MET cc_start: 0.8937 (tmm) cc_final: 0.8732 (tmm) REVERT: C 122 PHE cc_start: 0.8773 (m-80) cc_final: 0.8540 (m-80) REVERT: C 189 GLU cc_start: 0.8959 (tp30) cc_final: 0.8638 (tp30) REVERT: C 193 LEU cc_start: 0.9396 (mt) cc_final: 0.9085 (mt) REVERT: C 196 ARG cc_start: 0.9226 (ptm-80) cc_final: 0.8940 (ptt90) REVERT: C 244 GLU cc_start: 0.9490 (pt0) cc_final: 0.9153 (pp20) REVERT: D 233 ASN cc_start: 0.9238 (m-40) cc_final: 0.8952 (m110) outliers start: 59 outliers final: 45 residues processed: 532 average time/residue: 0.0975 time to fit residues: 78.8891 Evaluate side-chains 523 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 473 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 279 SER Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU 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 232 ASN 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 440 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 589 SER 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 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 271 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 85 GLN 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 282 ILE Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 19 optimal weight: 0.0770 chunk 134 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 158 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 151 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 588 GLN ** 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 447 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** D 85 GLN ** 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 = 0.3825 r_free = 0.3825 target = 0.150391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.100020 restraints weight = 27451.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.103600 restraints weight = 11387.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.105654 restraints weight = 6552.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.107147 restraints weight = 4661.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.107970 restraints weight = 3719.612| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 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 = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.5758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16386 Z= 0.169 Angle : 0.670 13.190 22134 Z= 0.350 Chirality : 0.045 0.386 2360 Planarity : 0.004 0.054 2818 Dihedral : 9.651 146.668 2246 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.44 % Allowed : 24.83 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.19), residues: 1932 helix: 1.05 (0.15), residues: 1142 sheet: -0.70 (0.41), residues: 152 loop : 0.43 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 235 TYR 0.033 0.002 TYR D 142 PHE 0.053 0.002 PHE C 154 TRP 0.022 0.002 TRP D 30 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00384 (16386) covalent geometry : angle 0.67027 (22134) hydrogen bonds : bond 0.04008 ( 871) hydrogen bonds : angle 5.00581 ( 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 556 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 497 time to evaluate : 0.498 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 67 GLU cc_start: 0.8216 (pm20) cc_final: 0.8004 (pm20) REVERT: A 103 ASP cc_start: 0.8697 (m-30) cc_final: 0.8436 (m-30) REVERT: A 106 LEU cc_start: 0.9132 (tp) cc_final: 0.8836 (tp) REVERT: A 144 MET cc_start: 0.8859 (mtm) cc_final: 0.8307 (mtm) REVERT: A 148 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8152 (mt-10) REVERT: A 209 LYS cc_start: 0.9070 (tttm) cc_final: 0.8581 (ttmm) REVERT: A 250 TYR cc_start: 0.9092 (m-80) cc_final: 0.8798 (m-80) REVERT: A 259 ASN cc_start: 0.9053 (m-40) cc_final: 0.8393 (m-40) REVERT: A 263 ASP cc_start: 0.8746 (m-30) cc_final: 0.8318 (m-30) REVERT: A 277 THR cc_start: 0.8355 (p) cc_final: 0.8073 (t) REVERT: A 357 TYR cc_start: 0.9064 (m-10) cc_final: 0.8680 (m-10) REVERT: A 384 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.6681 (pm20) REVERT: A 453 ARG cc_start: 0.9228 (OUTLIER) cc_final: 0.8829 (ttt90) REVERT: A 493 MET cc_start: 0.9126 (tmm) cc_final: 0.8884 (tmm) REVERT: A 583 SER cc_start: 0.9327 (OUTLIER) cc_final: 0.9024 (t) REVERT: A 589 SER cc_start: 0.9351 (m) cc_final: 0.9059 (p) REVERT: B 51 LEU cc_start: 0.9466 (tt) cc_final: 0.9257 (mt) REVERT: B 65 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7896 (mm-30) REVERT: B 257 ASP cc_start: 0.8999 (m-30) cc_final: 0.8663 (m-30) REVERT: B 263 ASP cc_start: 0.8742 (m-30) cc_final: 0.8359 (m-30) REVERT: B 274 ARG cc_start: 0.8231 (ttm110) cc_final: 0.7495 (ptp-110) REVERT: B 318 ASP cc_start: 0.8508 (t0) cc_final: 0.8293 (t70) REVERT: B 336 LYS cc_start: 0.9422 (OUTLIER) cc_final: 0.9080 (ttmm) REVERT: B 355 TYR cc_start: 0.8403 (m-80) cc_final: 0.7833 (m-80) REVERT: B 362 ASP cc_start: 0.8309 (m-30) cc_final: 0.8035 (m-30) REVERT: B 384 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.7078 (pm20) REVERT: B 394 TYR cc_start: 0.9254 (m-80) cc_final: 0.8389 (m-80) REVERT: B 447 ASN cc_start: 0.8609 (m110) cc_final: 0.8077 (m-40) REVERT: B 515 ASP cc_start: 0.8818 (m-30) cc_final: 0.8251 (m-30) REVERT: B 586 TYR cc_start: 0.8817 (m-80) cc_final: 0.8412 (m-80) REVERT: B 595 MET cc_start: 0.9018 (mmm) cc_final: 0.8330 (mmm) REVERT: B 602 GLU cc_start: 0.7862 (pt0) cc_final: 0.7600 (pt0) REVERT: B 603 GLU cc_start: 0.7106 (tp30) cc_final: 0.6777 (tp30) REVERT: B 615 MET cc_start: 0.9500 (mmp) cc_final: 0.9266 (mmp) REVERT: B 628 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8023 (mm-30) REVERT: C 17 PHE cc_start: 0.8987 (p90) cc_final: 0.8549 (p90) REVERT: C 20 MET cc_start: 0.9029 (ptp) cc_final: 0.8756 (pmm) REVERT: C 21 PHE cc_start: 0.9250 (m-80) cc_final: 0.8667 (m-80) REVERT: C 56 MET cc_start: 0.6832 (ptm) cc_final: 0.6485 (ttp) REVERT: C 95 MET cc_start: 0.8865 (tmm) cc_final: 0.8426 (tmm) REVERT: C 96 MET cc_start: 0.7692 (mmt) cc_final: 0.7383 (mmm) REVERT: C 122 PHE cc_start: 0.8814 (m-80) cc_final: 0.8560 (m-80) REVERT: C 189 GLU cc_start: 0.8992 (tp30) cc_final: 0.8685 (tp30) REVERT: C 193 LEU cc_start: 0.9414 (mt) cc_final: 0.9139 (mt) REVERT: C 196 ARG cc_start: 0.9228 (ptm-80) cc_final: 0.9000 (ptt90) REVERT: D 24 GLN cc_start: 0.8841 (tp40) cc_final: 0.8609 (tp40) REVERT: D 44 TRP cc_start: 0.8290 (t-100) cc_final: 0.7939 (t-100) REVERT: D 56 MET cc_start: 0.7951 (ptp) cc_final: 0.7553 (mmp) REVERT: D 233 ASN cc_start: 0.9291 (m-40) cc_final: 0.8885 (m110) outliers start: 59 outliers final: 44 residues processed: 526 average time/residue: 0.1034 time to fit residues: 82.3197 Evaluate side-chains 528 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 479 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 267 ILE 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 349 LEU 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 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 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 440 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 589 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 147 LYS 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 141 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 86 optimal weight: 0.0050 chunk 49 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.152648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.102001 restraints weight = 27290.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.105701 restraints weight = 11509.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.107838 restraints weight = 6603.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.109285 restraints weight = 4651.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.110266 restraints weight = 3726.834| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 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 = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.6000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16386 Z= 0.143 Angle : 0.680 13.401 22134 Z= 0.354 Chirality : 0.045 0.389 2360 Planarity : 0.004 0.046 2818 Dihedral : 9.260 135.067 2246 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.51 % Allowed : 26.17 % Favored : 71.33 % 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 aren not related in a simple way. whole: 0.99 (0.19), residues: 1932 helix: 1.18 (0.15), residues: 1116 sheet: -0.49 (0.42), residues: 140 loop : 0.24 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 686 TYR 0.019 0.001 TYR D 142 PHE 0.041 0.002 PHE C 259 TRP 0.017 0.002 TRP D 30 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00322 (16386) covalent geometry : angle 0.67983 (22134) hydrogen bonds : bond 0.03980 ( 871) hydrogen bonds : angle 4.93720 ( 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 562 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 519 time to evaluate : 0.610 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 67 GLU cc_start: 0.8244 (pm20) cc_final: 0.7502 (pm20) REVERT: A 103 ASP cc_start: 0.8710 (m-30) cc_final: 0.8499 (m-30) REVERT: A 106 LEU cc_start: 0.9103 (tp) cc_final: 0.8784 (tp) REVERT: A 144 MET cc_start: 0.8739 (mtm) cc_final: 0.8167 (mtm) REVERT: A 148 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8194 (mt-10) REVERT: A 209 LYS cc_start: 0.9026 (tttm) cc_final: 0.8562 (ttmm) REVERT: A 250 TYR cc_start: 0.9038 (m-80) cc_final: 0.8821 (m-80) REVERT: A 259 ASN cc_start: 0.9053 (m-40) cc_final: 0.8480 (m-40) REVERT: A 263 ASP cc_start: 0.8728 (m-30) cc_final: 0.8504 (m-30) REVERT: A 277 THR cc_start: 0.8263 (p) cc_final: 0.8011 (t) REVERT: A 350 ARG cc_start: 0.9208 (mtp85) cc_final: 0.8152 (mtp85) REVERT: A 357 TYR cc_start: 0.9026 (m-10) cc_final: 0.8569 (m-10) REVERT: A 384 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.6637 (pm20) REVERT: A 486 ASP cc_start: 0.8410 (t0) cc_final: 0.8195 (t0) REVERT: A 493 MET cc_start: 0.9098 (tmm) cc_final: 0.8853 (tmm) REVERT: A 583 SER cc_start: 0.9287 (OUTLIER) cc_final: 0.9007 (t) REVERT: A 586 TYR cc_start: 0.8798 (m-10) cc_final: 0.8359 (m-10) REVERT: A 589 SER cc_start: 0.9337 (m) cc_final: 0.9068 (p) REVERT: A 683 TYR cc_start: 0.9172 (t80) cc_final: 0.8831 (t80) REVERT: B 65 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7820 (mm-30) REVERT: B 147 GLN cc_start: 0.8835 (mt0) cc_final: 0.8599 (mm110) REVERT: B 263 ASP cc_start: 0.8711 (m-30) cc_final: 0.8326 (m-30) REVERT: B 274 ARG cc_start: 0.8231 (ttm110) cc_final: 0.7515 (ptp-110) REVERT: B 318 ASP cc_start: 0.8466 (t0) cc_final: 0.8256 (t70) REVERT: B 362 ASP cc_start: 0.8228 (m-30) cc_final: 0.7968 (m-30) REVERT: B 384 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.7131 (pm20) REVERT: B 394 TYR cc_start: 0.9231 (m-80) cc_final: 0.8296 (m-80) REVERT: B 447 ASN cc_start: 0.8328 (m110) cc_final: 0.7722 (m110) REVERT: B 515 ASP cc_start: 0.8764 (m-30) cc_final: 0.8208 (m-30) REVERT: B 586 TYR cc_start: 0.8651 (m-80) cc_final: 0.8339 (m-80) REVERT: B 595 MET cc_start: 0.8995 (mmm) cc_final: 0.8310 (mmm) REVERT: B 599 GLU cc_start: 0.8206 (pt0) cc_final: 0.7884 (pt0) REVERT: B 602 GLU cc_start: 0.7904 (pt0) cc_final: 0.7553 (pt0) REVERT: B 603 GLU cc_start: 0.7066 (tp30) cc_final: 0.6755 (tp30) REVERT: B 628 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8177 (mm-30) REVERT: C 17 PHE cc_start: 0.8984 (p90) cc_final: 0.8496 (p90) REVERT: C 20 MET cc_start: 0.8983 (ptp) cc_final: 0.8688 (pmm) REVERT: C 21 PHE cc_start: 0.9274 (m-80) cc_final: 0.8669 (m-80) REVERT: C 56 MET cc_start: 0.6777 (ptm) cc_final: 0.6082 (ttp) REVERT: C 95 MET cc_start: 0.8789 (tmm) cc_final: 0.8372 (tmm) REVERT: C 96 MET cc_start: 0.7723 (mmt) cc_final: 0.7446 (mmm) REVERT: C 121 VAL cc_start: 0.8166 (p) cc_final: 0.7693 (p) REVERT: C 122 PHE cc_start: 0.8730 (m-80) cc_final: 0.8518 (m-80) REVERT: C 124 TRP cc_start: 0.8623 (t60) cc_final: 0.8156 (t60) REVERT: C 189 GLU cc_start: 0.9011 (tp30) cc_final: 0.8769 (tp30) REVERT: C 193 LEU cc_start: 0.9413 (mt) cc_final: 0.9152 (mt) REVERT: C 196 ARG cc_start: 0.9189 (ptm-80) cc_final: 0.8970 (ptt90) REVERT: D 24 GLN cc_start: 0.8893 (tp40) cc_final: 0.8580 (tp40) REVERT: D 44 TRP cc_start: 0.8325 (t-100) cc_final: 0.7969 (t-100) REVERT: D 56 MET cc_start: 0.7992 (ptp) cc_final: 0.7662 (mmp) REVERT: D 74 MET cc_start: 0.6351 (tpt) cc_final: 0.5447 (ttp) REVERT: D 233 ASN cc_start: 0.9234 (m-40) cc_final: 0.8867 (m110) REVERT: D 236 TYR cc_start: 0.8010 (t80) cc_final: 0.7324 (t80) REVERT: D 269 MET cc_start: 0.9003 (tmm) cc_final: 0.8728 (tmm) outliers start: 43 outliers final: 36 residues processed: 540 average time/residue: 0.1014 time to fit residues: 83.5406 Evaluate side-chains 530 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 491 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 341 LYS Chi-restraints excluded: chain A residue 349 LEU 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 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 145 ILE Chi-restraints excluded: chain B residue 216 VAL 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 589 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 107 ASN Chi-restraints excluded: chain C residue 117 THR 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 161 VAL Chi-restraints excluded: chain D residue 200 ILE 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: 3.9990 chunk 62 optimal weight: 5.9990 chunk 33 optimal weight: 0.0870 chunk 35 optimal weight: 1.9990 chunk 189 optimal weight: 9.9990 chunk 181 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 132 optimal weight: 0.0570 chunk 50 optimal weight: 0.1980 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN 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 = 0.154566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.105180 restraints weight = 27270.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.108879 restraints weight = 11301.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.111150 restraints weight = 6416.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.112503 restraints weight = 4454.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.113437 restraints weight = 3560.478| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 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 = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.6261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16386 Z= 0.137 Angle : 0.705 14.348 22134 Z= 0.363 Chirality : 0.045 0.394 2360 Planarity : 0.004 0.044 2818 Dihedral : 9.070 135.125 2244 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.27 % Allowed : 27.10 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.19), residues: 1932 helix: 1.14 (0.15), residues: 1116 sheet: -0.51 (0.43), residues: 140 loop : 0.24 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 235 TYR 0.027 0.001 TYR D 262 PHE 0.049 0.002 PHE C 259 TRP 0.016 0.001 TRP D 30 HIS 0.008 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00303 (16386) covalent geometry : angle 0.70550 (22134) hydrogen bonds : bond 0.03954 ( 871) hydrogen bonds : angle 4.97885 ( 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 564 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 525 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: A 106 LEU cc_start: 0.9061 (tp) cc_final: 0.8729 (tp) REVERT: A 144 MET cc_start: 0.8684 (mtm) cc_final: 0.8135 (mtm) REVERT: A 148 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8101 (mt-10) REVERT: A 209 LYS cc_start: 0.9042 (tttm) cc_final: 0.8708 (ttmm) REVERT: A 228 LYS cc_start: 0.8946 (ttmm) cc_final: 0.8476 (mttp) REVERT: A 259 ASN cc_start: 0.9023 (m-40) cc_final: 0.8384 (m-40) REVERT: A 263 ASP cc_start: 0.8601 (m-30) cc_final: 0.8327 (m-30) REVERT: A 277 THR cc_start: 0.8213 (p) cc_final: 0.7979 (t) REVERT: A 357 TYR cc_start: 0.9047 (m-10) cc_final: 0.8618 (m-10) REVERT: A 384 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.6556 (pm20) REVERT: A 453 ARG cc_start: 0.9208 (OUTLIER) cc_final: 0.8919 (ttt90) REVERT: A 493 MET cc_start: 0.9096 (tmm) cc_final: 0.8850 (tmm) REVERT: A 583 SER cc_start: 0.9234 (OUTLIER) cc_final: 0.8874 (t) REVERT: A 586 TYR cc_start: 0.8672 (m-10) cc_final: 0.8360 (m-10) REVERT: A 589 SER cc_start: 0.9225 (m) cc_final: 0.9008 (p) REVERT: A 683 TYR cc_start: 0.9161 (t80) cc_final: 0.8808 (t80) REVERT: B 116 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8310 (mt-10) REVERT: B 263 ASP cc_start: 0.8684 (m-30) cc_final: 0.8284 (m-30) REVERT: B 274 ARG cc_start: 0.8222 (ttm110) cc_final: 0.7524 (ptp-110) REVERT: B 318 ASP cc_start: 0.8433 (t0) cc_final: 0.8225 (t70) REVERT: B 362 ASP cc_start: 0.8244 (m-30) cc_final: 0.7996 (m-30) REVERT: B 384 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.7011 (pm20) REVERT: B 515 ASP cc_start: 0.8718 (m-30) cc_final: 0.8154 (m-30) REVERT: B 586 TYR cc_start: 0.8606 (m-80) cc_final: 0.8363 (m-80) REVERT: B 595 MET cc_start: 0.8972 (mmm) cc_final: 0.8266 (mmm) REVERT: B 599 GLU cc_start: 0.8227 (pt0) cc_final: 0.7859 (pt0) REVERT: B 602 GLU cc_start: 0.7867 (pt0) cc_final: 0.7563 (pt0) REVERT: B 603 GLU cc_start: 0.7061 (tp30) cc_final: 0.6775 (tp30) REVERT: B 628 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8176 (mm-30) REVERT: C 17 PHE cc_start: 0.8944 (p90) cc_final: 0.8469 (p90) REVERT: C 21 PHE cc_start: 0.9296 (m-80) cc_final: 0.8771 (m-80) REVERT: C 56 MET cc_start: 0.6623 (ptm) cc_final: 0.6105 (ttp) REVERT: C 95 MET cc_start: 0.8756 (tmm) cc_final: 0.8363 (tmm) REVERT: C 121 VAL cc_start: 0.8064 (p) cc_final: 0.7725 (p) REVERT: C 122 PHE cc_start: 0.8753 (m-80) cc_final: 0.8551 (m-80) REVERT: C 124 TRP cc_start: 0.8679 (t60) cc_final: 0.8209 (t60) REVERT: C 189 GLU cc_start: 0.8946 (tp30) cc_final: 0.8657 (tp30) REVERT: C 193 LEU cc_start: 0.9391 (mt) cc_final: 0.9174 (mt) REVERT: C 196 ARG cc_start: 0.9169 (ptm-80) cc_final: 0.8969 (ptt90) REVERT: D 24 GLN cc_start: 0.8875 (tp40) cc_final: 0.8513 (tp40) REVERT: D 44 TRP cc_start: 0.8268 (t-100) cc_final: 0.7922 (t-100) REVERT: D 56 MET cc_start: 0.7958 (ptp) cc_final: 0.7629 (mmp) REVERT: D 119 ASN cc_start: 0.9065 (m110) cc_final: 0.8417 (p0) REVERT: D 226 GLU cc_start: 0.8441 (pp20) cc_final: 0.8151 (mp0) REVERT: D 233 ASN cc_start: 0.9226 (m-40) cc_final: 0.8807 (m110) REVERT: D 236 TYR cc_start: 0.7982 (t80) cc_final: 0.6999 (t80) REVERT: D 265 ASN cc_start: 0.8183 (m-40) cc_final: 0.7940 (m-40) REVERT: D 269 MET cc_start: 0.8973 (tmm) cc_final: 0.8684 (tmm) outliers start: 39 outliers final: 26 residues processed: 543 average time/residue: 0.0987 time to fit residues: 81.4445 Evaluate side-chains 514 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 484 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 349 LEU 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 453 ARG Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE 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 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 435 SER Chi-restraints excluded: chain B residue 587 VAL 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 280 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 200 ILE 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: 3.9990 chunk 1 optimal weight: 0.0470 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 148 optimal weight: 20.0000 chunk 125 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 645 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** 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 = 0.3856 r_free = 0.3856 target = 0.152846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.103344 restraints weight = 27226.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.106832 restraints weight = 11680.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.109015 restraints weight = 6807.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.110354 restraints weight = 4808.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.111240 restraints weight = 3864.801| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 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 = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.6397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16386 Z= 0.157 Angle : 0.714 14.436 22134 Z= 0.370 Chirality : 0.046 0.386 2360 Planarity : 0.004 0.045 2818 Dihedral : 9.068 135.724 2243 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.21 % Allowed : 27.86 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.19), residues: 1932 helix: 1.12 (0.15), residues: 1121 sheet: -0.61 (0.44), residues: 140 loop : 0.17 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 235 TYR 0.029 0.001 TYR D 262 PHE 0.050 0.002 PHE C 259 TRP 0.015 0.002 TRP D 30 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00357 (16386) covalent geometry : angle 0.71430 (22134) hydrogen bonds : bond 0.03920 ( 871) hydrogen bonds : angle 5.01259 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2822.42 seconds wall clock time: 49 minutes 34.03 seconds (2974.03 seconds total)