Starting phenix.real_space_refine on Thu Aug 6 15:09:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzo_45072/08_2026/9bzo_45072_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzo_45072/08_2026/9bzo_45072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bzo_45072/08_2026/9bzo_45072_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzo_45072/08_2026/9bzo_45072_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bzo_45072/08_2026/9bzo_45072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzo_45072/08_2026/9bzo_45072.map" } resolution = 4.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 2.79, per 1000 atoms: 0.17 Number of scatterers: 16038 At special positions: 0 Unit cell: (94.302, 130.806, 130.806, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 709.0 milliseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 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: 3.984A 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: 4.851A 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: 3.628A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.018A 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: 4.073A 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: 3.879A 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: 3.730A 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: 3.632A 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: 4.067A 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: 3.881A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.514A 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: 3.668A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.359A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.478A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.454A 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: 6.717A 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: 5.661A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.229A 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: 4.048A 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: 7.905A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.548A 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: 7.593A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.03 Time building geometry restraints manager: 1.74 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: 4874 1.34 - 1.46: 3050 1.46 - 1.58: 8280 1.58 - 1.70: 26 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" O3B TTP B 801 " pdb=" PG TTP B 801 " ideal model delta sigma weight residual 1.748 1.610 0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" O3B TTP A 803 " pdb=" PG TTP A 803 " ideal model delta sigma weight residual 1.748 1.610 0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.060 1.25e-02 6.40e+03 2.34e+01 bond pdb=" O3A TTP A 803 " pdb=" PB TTP A 803 " ideal model delta sigma weight residual 1.675 1.606 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.17e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21523 2.09 - 4.18: 530 4.18 - 6.27: 64 6.27 - 8.36: 8 8.36 - 10.45: 9 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.64 -6.10 1.36e+00 5.41e-01 2.01e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.16 -4.45 1.15e+00 7.56e-01 1.50e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.83 -4.33 1.23e+00 6.61e-01 1.24e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.71 -4.00 1.15e+00 7.56e-01 1.21e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.56 3.63 1.06e+00 8.90e-01 1.17e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.05: 9088 25.05 - 50.10: 655 50.10 - 75.14: 127 75.14 - 100.19: 26 100.19 - 125.24: 2 Dihedral angle restraints: 9898 sinusoidal: 4140 harmonic: 5758 Sorted by residual: dihedral pdb=" O4' GDP A 802 " pdb=" C1' GDP A 802 " pdb=" N9 GDP A 802 " pdb=" C8 GDP A 802 " ideal model delta sinusoidal sigma weight residual 27.02 -98.22 125.24 1 2.00e+01 2.50e-03 3.78e+01 dihedral pdb=" O4' GDP B 804 " pdb=" C1' GDP B 804 " pdb=" N9 GDP B 804 " pdb=" C8 GDP B 804 " ideal model delta sinusoidal sigma weight residual 27.02 -95.60 122.62 1 2.00e+01 2.50e-03 3.69e+01 dihedral pdb=" C VAL C 125 " pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual -122.00 -134.27 12.27 0 2.50e+00 1.60e-01 2.41e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2138 0.093 - 0.185: 187 0.185 - 0.277: 30 0.277 - 0.370: 3 0.370 - 0.462: 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 5.35e+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 4.55e+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 2.96e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+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 1.11e-02 2.17e+00 pdb=" CG PHE D 92 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 177 " -0.017 2.00e-02 2.50e+03 9.87e-03 1.95e+00 pdb=" CG TYR C 177 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR C 177 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR C 177 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C 177 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 177 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 177 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 177 " -0.010 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 129 2.51 - 3.11: 11552 3.11 - 3.70: 27036 3.70 - 4.30: 41525 4.30 - 4.90: 65391 Nonbonded interactions: 145633 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.991 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.013 3.040 ... (remaining 145628 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.750 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5938 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 0.138 16386 Z= 0.334 Angle : 0.788 10.446 22134 Z= 0.471 Chirality : 0.058 0.462 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.681 125.240 6202 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.34 % Allowed : 15.33 % Favored : 83.33 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.18), residues: 1932 helix: 0.59 (0.14), residues: 1151 sheet: 0.46 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 196 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.33 (16386) covalent geometry : angle 0.78766 / 0.47 (22134) hydrogen bonds : bond 0.15421 / 9.51 ( 871) hydrogen bonds : angle 6.51764 / 4.65 ( 2571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 974 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 951 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.7829 (tp) cc_final: 0.7603 (tp) REVERT: A 71 LEU cc_start: 0.9357 (mt) cc_final: 0.9124 (mm) REVERT: A 95 MET cc_start: 0.8236 (tpp) cc_final: 0.7826 (mmm) REVERT: A 129 PHE cc_start: 0.7705 (m-10) cc_final: 0.7339 (m-10) REVERT: A 143 LEU cc_start: 0.8767 (tp) cc_final: 0.8530 (tp) REVERT: A 147 GLN cc_start: 0.8533 (mt0) cc_final: 0.8326 (mt0) REVERT: A 149 TYR cc_start: 0.7936 (t80) cc_final: 0.7589 (t80) REVERT: A 162 LYS cc_start: 0.7852 (ttpt) cc_final: 0.7282 (ttmm) REVERT: A 171 PHE cc_start: 0.8422 (m-80) cc_final: 0.8056 (m-80) REVERT: A 191 GLN cc_start: 0.8352 (mm-40) cc_final: 0.7552 (mt0) REVERT: A 199 VAL cc_start: 0.9238 (t) cc_final: 0.9018 (t) REVERT: A 226 VAL cc_start: 0.9057 (t) cc_final: 0.8748 (t) REVERT: A 267 ILE cc_start: 0.8851 (mp) cc_final: 0.8568 (tp) REVERT: A 278 LEU cc_start: 0.8842 (tp) cc_final: 0.8316 (tp) REVERT: A 287 LYS cc_start: 0.9090 (tptt) cc_final: 0.8764 (mmmm) REVERT: A 291 LEU cc_start: 0.8938 (mt) cc_final: 0.8687 (mt) REVERT: A 300 VAL cc_start: 0.7976 (m) cc_final: 0.7705 (m) REVERT: A 322 MET cc_start: 0.6879 (mmp) cc_final: 0.6193 (mmm) REVERT: A 349 LEU cc_start: 0.8582 (mt) cc_final: 0.8085 (mt) REVERT: A 373 ILE cc_start: 0.9336 (mt) cc_final: 0.9128 (mt) REVERT: A 377 LYS cc_start: 0.8334 (mttt) cc_final: 0.7416 (mtmm) REVERT: A 385 VAL cc_start: 0.8338 (t) cc_final: 0.8115 (t) REVERT: A 407 ILE cc_start: 0.8376 (mt) cc_final: 0.7958 (mt) REVERT: A 431 LEU cc_start: 0.9208 (mt) cc_final: 0.8872 (mt) REVERT: A 435 SER cc_start: 0.9237 (p) cc_final: 0.8138 (p) REVERT: A 436 LEU cc_start: 0.9337 (mt) cc_final: 0.8685 (mt) REVERT: A 493 MET cc_start: 0.8014 (tmm) cc_final: 0.7699 (tmm) REVERT: A 515 ASP cc_start: 0.7742 (m-30) cc_final: 0.7440 (m-30) REVERT: A 547 PHE cc_start: 0.7693 (m-80) cc_final: 0.7104 (m-10) REVERT: A 561 LEU cc_start: 0.9084 (tp) cc_final: 0.8797 (tp) REVERT: A 630 TYR cc_start: 0.7064 (m-80) cc_final: 0.6411 (m-10) REVERT: A 634 MET cc_start: 0.8595 (mmp) cc_final: 0.8293 (mmm) REVERT: A 641 ILE cc_start: 0.8969 (mm) cc_final: 0.8759 (mm) REVERT: A 648 ILE cc_start: 0.8283 (mm) cc_final: 0.8040 (mm) REVERT: A 650 GLN cc_start: 0.7404 (mt0) cc_final: 0.7093 (mt0) REVERT: A 653 SER cc_start: 0.9117 (OUTLIER) cc_final: 0.8897 (p) REVERT: A 664 THR cc_start: 0.8780 (p) cc_final: 0.8558 (p) REVERT: B 18 ILE cc_start: 0.8623 (mt) cc_final: 0.8414 (mp) REVERT: B 21 ASP cc_start: 0.7903 (m-30) cc_final: 0.7620 (m-30) REVERT: B 81 PHE cc_start: 0.7397 (m-80) cc_final: 0.7186 (m-80) REVERT: B 99 LYS cc_start: 0.9215 (mmtt) cc_final: 0.8767 (mmmt) REVERT: B 109 ASN cc_start: 0.8797 (m-40) cc_final: 0.8077 (m-40) REVERT: B 122 ILE cc_start: 0.9114 (mt) cc_final: 0.8772 (mt) REVERT: B 179 LEU cc_start: 0.8301 (tp) cc_final: 0.8045 (tp) REVERT: B 186 ILE cc_start: 0.9327 (mt) cc_final: 0.9079 (mt) REVERT: B 187 ASP cc_start: 0.7738 (t70) cc_final: 0.7221 (t0) REVERT: B 191 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8067 (mm-40) REVERT: B 192 LEU cc_start: 0.9001 (mt) cc_final: 0.8672 (mt) REVERT: B 204 SER cc_start: 0.8623 (m) cc_final: 0.8003 (m) REVERT: B 206 LEU cc_start: 0.9174 (mt) cc_final: 0.8667 (mt) REVERT: B 250 TYR cc_start: 0.7617 (m-80) cc_final: 0.7397 (m-80) REVERT: B 264 THR cc_start: 0.8002 (p) cc_final: 0.7345 (p) REVERT: B 265 LYS cc_start: 0.8508 (mmtt) cc_final: 0.8233 (mmmt) REVERT: B 286 ASP cc_start: 0.5894 (OUTLIER) cc_final: 0.5630 (m-30) REVERT: B 291 LEU cc_start: 0.9109 (mt) cc_final: 0.8877 (mt) REVERT: B 300 VAL cc_start: 0.8796 (m) cc_final: 0.8583 (m) REVERT: B 322 MET cc_start: 0.7844 (mmm) cc_final: 0.6034 (mmm) REVERT: B 337 ILE cc_start: 0.8650 (pt) cc_final: 0.8215 (mp) REVERT: B 343 LEU cc_start: 0.8274 (mt) cc_final: 0.7996 (mt) REVERT: B 359 MET cc_start: 0.8120 (ttt) cc_final: 0.7716 (ttt) REVERT: B 364 VAL cc_start: 0.8175 (t) cc_final: 0.7943 (t) REVERT: B 373 ILE cc_start: 0.9172 (mt) cc_final: 0.8142 (mt) REVERT: B 410 ASN cc_start: 0.8395 (m110) cc_final: 0.8154 (m110) REVERT: B 430 LYS cc_start: 0.8042 (mttt) cc_final: 0.7257 (mtpp) REVERT: B 431 LEU cc_start: 0.9080 (mt) cc_final: 0.8560 (mt) REVERT: B 508 LYS cc_start: 0.8646 (tttt) cc_final: 0.8367 (ttpt) REVERT: B 575 ARG cc_start: 0.8151 (mtm110) cc_final: 0.7804 (mtm-85) REVERT: B 586 TYR cc_start: 0.6732 (m-80) cc_final: 0.6393 (m-10) REVERT: B 612 TYR cc_start: 0.6928 (m-80) cc_final: 0.6575 (m-80) REVERT: B 656 LEU cc_start: 0.8166 (mt) cc_final: 0.7937 (mt) REVERT: B 683 TYR cc_start: 0.7618 (t80) cc_final: 0.7350 (t80) REVERT: C 17 PHE cc_start: 0.5346 (p90) cc_final: 0.4535 (p90) REVERT: C 67 THR cc_start: 0.6972 (m) cc_final: 0.6648 (m) REVERT: C 100 VAL cc_start: 0.3793 (t) cc_final: 0.2958 (t) REVERT: C 108 ILE cc_start: 0.7782 (mt) cc_final: 0.7083 (mm) REVERT: C 118 ILE cc_start: 0.6148 (mt) cc_final: 0.5522 (mp) REVERT: C 163 LEU cc_start: 0.7081 (tt) cc_final: 0.6225 (tt) REVERT: C 174 TYR cc_start: 0.3126 (OUTLIER) cc_final: 0.2879 (t80) REVERT: C 212 ILE cc_start: 0.8024 (mt) cc_final: 0.7135 (mt) REVERT: D 130 TYR cc_start: 0.4062 (m-80) cc_final: 0.3634 (m-80) outliers start: 23 outliers final: 6 residues processed: 967 average time/residue: 0.1257 time to fit residues: 173.6067 Evaluate side-chains 662 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 653 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 GLN ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 HIS B 49 HIS ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN B 645 GLN B 676 HIS ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN C 233 ASN C 238 ASN ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.120396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.092452 restraints weight = 42020.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.094892 restraints weight = 27863.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.097203 restraints weight = 20853.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.098496 restraints weight = 16771.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.099386 restraints weight = 13986.106| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16386 Z= 0.189 Angle : 0.647 9.676 22134 Z= 0.352 Chirality : 0.044 0.210 2360 Planarity : 0.004 0.053 2818 Dihedral : 9.548 128.579 2290 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.29 % Allowed : 2.91 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.19), residues: 1932 helix: 1.22 (0.15), residues: 1134 sheet: 0.01 (0.41), residues: 138 loop : 0.50 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 256 TYR 0.021 0.002 TYR B 36 PHE 0.039 0.003 PHE C 166 TRP 0.011 0.002 TRP B 558 HIS 0.008 0.002 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.19 (16386) covalent geometry : angle 0.64690 / 0.35 (22134) hydrogen bonds : bond 0.04742 / 2.97 ( 871) hydrogen bonds : angle 5.23096 / 3.78 ( 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 770 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 765 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9192 (t0) cc_final: 0.8988 (t0) REVERT: A 41 ILE cc_start: 0.9534 (mm) cc_final: 0.9324 (mm) REVERT: A 89 PHE cc_start: 0.8760 (t80) cc_final: 0.8504 (t80) REVERT: A 101 TYR cc_start: 0.9411 (m-80) cc_final: 0.9122 (m-10) REVERT: A 109 ASN cc_start: 0.9537 (p0) cc_final: 0.9265 (m-40) REVERT: A 115 LEU cc_start: 0.9417 (mt) cc_final: 0.9132 (mt) REVERT: A 119 GLU cc_start: 0.9139 (mp0) cc_final: 0.7950 (tm-30) REVERT: A 120 ASP cc_start: 0.8989 (m-30) cc_final: 0.8523 (m-30) REVERT: A 122 ILE cc_start: 0.9453 (mt) cc_final: 0.9234 (mt) REVERT: A 144 MET cc_start: 0.8940 (mtm) cc_final: 0.8560 (mtm) REVERT: A 147 GLN cc_start: 0.8939 (mt0) cc_final: 0.8421 (mt0) REVERT: A 149 TYR cc_start: 0.9473 (t80) cc_final: 0.9040 (t80) REVERT: A 168 VAL cc_start: 0.8766 (t) cc_final: 0.8288 (t) REVERT: A 173 LEU cc_start: 0.9452 (mt) cc_final: 0.9212 (mt) REVERT: A 199 VAL cc_start: 0.9206 (t) cc_final: 0.8918 (t) REVERT: A 236 TYR cc_start: 0.8736 (t80) cc_final: 0.8208 (t80) REVERT: A 278 LEU cc_start: 0.9489 (tp) cc_final: 0.9094 (tp) REVERT: A 280 ILE cc_start: 0.8594 (pt) cc_final: 0.8340 (pt) REVERT: A 326 PHE cc_start: 0.9524 (m-80) cc_final: 0.9197 (m-80) REVERT: A 349 LEU cc_start: 0.9529 (mt) cc_final: 0.9289 (mt) REVERT: A 359 MET cc_start: 0.8563 (ttp) cc_final: 0.8328 (ttp) REVERT: A 370 ASN cc_start: 0.9448 (m-40) cc_final: 0.8993 (m-40) REVERT: A 375 LYS cc_start: 0.8648 (mmmt) cc_final: 0.8175 (mmtm) REVERT: A 377 LYS cc_start: 0.8698 (mttt) cc_final: 0.8187 (mtmm) REVERT: A 407 ILE cc_start: 0.8831 (mt) cc_final: 0.8517 (mt) REVERT: A 408 SER cc_start: 0.9182 (p) cc_final: 0.8981 (t) REVERT: A 459 LYS cc_start: 0.9019 (mttp) cc_final: 0.8313 (mtpt) REVERT: A 468 LEU cc_start: 0.9759 (tp) cc_final: 0.9555 (tp) REVERT: A 493 MET cc_start: 0.9309 (tmm) cc_final: 0.8910 (tmm) REVERT: A 501 GLN cc_start: 0.9495 (mm-40) cc_final: 0.8813 (tp-100) REVERT: A 515 ASP cc_start: 0.9215 (m-30) cc_final: 0.8623 (m-30) REVERT: A 516 GLN cc_start: 0.9092 (mp10) cc_final: 0.8702 (mp10) REVERT: A 561 LEU cc_start: 0.9644 (tp) cc_final: 0.9358 (tp) REVERT: A 598 MET cc_start: 0.8532 (ttt) cc_final: 0.8289 (ttt) REVERT: A 601 ILE cc_start: 0.9416 (mt) cc_final: 0.9118 (mt) REVERT: A 615 MET cc_start: 0.8652 (mmp) cc_final: 0.8324 (mmp) REVERT: A 650 GLN cc_start: 0.8293 (mt0) cc_final: 0.8037 (mt0) REVERT: A 677 ARG cc_start: 0.9299 (mmm-85) cc_final: 0.8573 (mmm-85) REVERT: B 8 LYS cc_start: 0.9327 (tptp) cc_final: 0.8987 (tptp) REVERT: B 16 ILE cc_start: 0.9726 (pt) cc_final: 0.9441 (pt) REVERT: B 30 LYS cc_start: 0.9743 (tmtt) cc_final: 0.9391 (tptt) REVERT: B 41 ILE cc_start: 0.9581 (mm) cc_final: 0.9296 (mt) REVERT: B 51 LEU cc_start: 0.9022 (tp) cc_final: 0.8696 (tp) REVERT: B 67 GLU cc_start: 0.9378 (mm-30) cc_final: 0.9160 (mm-30) REVERT: B 95 MET cc_start: 0.9545 (mmp) cc_final: 0.9074 (mmp) REVERT: B 100 PHE cc_start: 0.9554 (t80) cc_final: 0.9194 (t80) REVERT: B 144 MET cc_start: 0.9495 (mtm) cc_final: 0.9211 (mtm) REVERT: B 195 LEU cc_start: 0.9387 (mt) cc_final: 0.9175 (mt) REVERT: B 211 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8343 (mm-30) REVERT: B 227 MET cc_start: 0.9163 (mtp) cc_final: 0.8800 (mtp) REVERT: B 235 ARG cc_start: 0.8888 (ttm110) cc_final: 0.8532 (ttm110) REVERT: B 250 TYR cc_start: 0.8215 (m-80) cc_final: 0.7163 (m-80) REVERT: B 286 ASP cc_start: 0.8559 (m-30) cc_final: 0.8262 (m-30) REVERT: B 291 LEU cc_start: 0.9572 (mt) cc_final: 0.9361 (mt) REVERT: B 322 MET cc_start: 0.8656 (mmm) cc_final: 0.8183 (mmm) REVERT: B 375 LYS cc_start: 0.9252 (mmmm) cc_final: 0.9046 (mmmm) REVERT: B 379 SER cc_start: 0.8974 (t) cc_final: 0.8544 (t) REVERT: B 410 ASN cc_start: 0.8777 (m110) cc_final: 0.8442 (m110) REVERT: B 420 MET cc_start: 0.9094 (mmm) cc_final: 0.8875 (mmm) REVERT: B 458 MET cc_start: 0.9601 (mmm) cc_final: 0.9306 (mmm) REVERT: B 493 MET cc_start: 0.9244 (ppp) cc_final: 0.9040 (ppp) REVERT: B 500 ILE cc_start: 0.9664 (mt) cc_final: 0.9418 (mt) REVERT: B 558 TRP cc_start: 0.9078 (m100) cc_final: 0.8623 (m100) REVERT: B 570 MET cc_start: 0.8840 (mmm) cc_final: 0.8176 (mmm) REVERT: B 598 MET cc_start: 0.9213 (mtm) cc_final: 0.8914 (mtm) REVERT: B 612 TYR cc_start: 0.9177 (m-80) cc_final: 0.7893 (m-80) REVERT: B 613 TYR cc_start: 0.9104 (t80) cc_final: 0.8803 (t80) REVERT: B 648 ILE cc_start: 0.9360 (mm) cc_final: 0.9023 (mm) REVERT: B 656 LEU cc_start: 0.9590 (mt) cc_final: 0.9356 (mt) REVERT: B 673 TYR cc_start: 0.9099 (t80) cc_final: 0.8859 (t80) REVERT: C 17 PHE cc_start: 0.8695 (p90) cc_final: 0.7610 (p90) REVERT: C 21 PHE cc_start: 0.9220 (m-10) cc_final: 0.8578 (m-80) REVERT: C 92 PHE cc_start: 0.8079 (t80) cc_final: 0.7855 (t80) REVERT: C 96 MET cc_start: 0.8401 (tpt) cc_final: 0.8047 (tpt) REVERT: C 100 VAL cc_start: 0.6275 (t) cc_final: 0.5996 (t) REVERT: C 157 MET cc_start: 0.9575 (mtm) cc_final: 0.9212 (ptm) REVERT: C 163 LEU cc_start: 0.9611 (tt) cc_final: 0.9181 (tt) REVERT: C 178 PHE cc_start: 0.9214 (m-80) cc_final: 0.9003 (m-10) REVERT: C 214 ASN cc_start: 0.8507 (m-40) cc_final: 0.7959 (p0) REVERT: C 227 PHE cc_start: 0.7345 (m-80) cc_final: 0.7110 (m-80) REVERT: C 263 ASN cc_start: 0.6609 (m-40) cc_final: 0.6292 (m110) REVERT: C 285 ILE cc_start: 0.8978 (mm) cc_final: 0.8727 (mm) REVERT: D 17 PHE cc_start: 0.5331 (m-80) cc_final: 0.5090 (m-80) REVERT: D 21 PHE cc_start: 0.9150 (m-10) cc_final: 0.8895 (m-10) REVERT: D 74 MET cc_start: 0.8563 (mmp) cc_final: 0.8229 (mmt) REVERT: D 109 PHE cc_start: 0.8453 (m-80) cc_final: 0.7993 (m-80) REVERT: D 172 PHE cc_start: 0.9278 (m-80) cc_final: 0.9020 (m-80) REVERT: D 181 GLN cc_start: 0.7514 (pt0) cc_final: 0.7181 (pt0) REVERT: D 185 MET cc_start: 0.4148 (mmp) cc_final: 0.3348 (mmp) REVERT: D 189 GLU cc_start: 0.9203 (pt0) cc_final: 0.8531 (pt0) REVERT: D 214 ASN cc_start: 0.9145 (m-40) cc_final: 0.8734 (p0) outliers start: 5 outliers final: 1 residues processed: 769 average time/residue: 0.1072 time to fit residues: 122.0031 Evaluate side-chains 617 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 616 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 164 optimal weight: 9.9990 chunk 28 optimal weight: 0.6980 chunk 182 optimal weight: 6.9990 chunk 159 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN B 304 HIS B 320 ASN B 361 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN C 263 ASN D 25 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.108628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.079427 restraints weight = 50782.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.082370 restraints weight = 30546.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.084846 restraints weight = 20977.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.086263 restraints weight = 15495.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.087527 restraints weight = 12558.749| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.5677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16386 Z= 0.216 Angle : 0.641 7.856 22134 Z= 0.343 Chirality : 0.043 0.176 2360 Planarity : 0.004 0.065 2818 Dihedral : 9.268 143.453 2290 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.17 % Allowed : 2.86 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.19), residues: 1932 helix: 1.06 (0.15), residues: 1131 sheet: -0.35 (0.39), residues: 148 loop : 0.44 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 164 TYR 0.023 0.002 TYR B 118 PHE 0.034 0.003 PHE C 168 TRP 0.009 0.002 TRP A 623 HIS 0.009 0.002 HIS A 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.22 (16386) covalent geometry : angle 0.64121 / 0.34 (22134) hydrogen bonds : bond 0.04322 / 2.72 ( 871) hydrogen bonds : angle 5.11554 / 3.67 ( 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 706 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 703 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9298 (t0) cc_final: 0.9027 (t0) REVERT: A 67 GLU cc_start: 0.9579 (mp0) cc_final: 0.9366 (pm20) REVERT: A 89 PHE cc_start: 0.8865 (t80) cc_final: 0.8627 (t80) REVERT: A 95 MET cc_start: 0.9167 (mmm) cc_final: 0.8954 (tpt) REVERT: A 100 PHE cc_start: 0.9529 (t80) cc_final: 0.9201 (t80) REVERT: A 101 TYR cc_start: 0.9539 (m-80) cc_final: 0.9248 (m-10) REVERT: A 115 LEU cc_start: 0.9631 (mt) cc_final: 0.9315 (mt) REVERT: A 116 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7479 (tt0) REVERT: A 129 PHE cc_start: 0.9711 (m-10) cc_final: 0.9474 (m-10) REVERT: A 144 MET cc_start: 0.8892 (mtm) cc_final: 0.8504 (mtm) REVERT: A 147 GLN cc_start: 0.8842 (mt0) cc_final: 0.8367 (mt0) REVERT: A 172 LEU cc_start: 0.9383 (mp) cc_final: 0.8918 (mp) REVERT: A 173 LEU cc_start: 0.9551 (mt) cc_final: 0.9327 (mt) REVERT: A 191 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8646 (mm-40) REVERT: A 199 VAL cc_start: 0.9488 (t) cc_final: 0.9213 (t) REVERT: A 205 LYS cc_start: 0.8263 (mttm) cc_final: 0.8014 (mttm) REVERT: A 236 TYR cc_start: 0.8944 (t80) cc_final: 0.8589 (t80) REVERT: A 279 SER cc_start: 0.8159 (m) cc_final: 0.7368 (p) REVERT: A 291 LEU cc_start: 0.9561 (mt) cc_final: 0.9232 (mp) REVERT: A 300 VAL cc_start: 0.9630 (m) cc_final: 0.9393 (m) REVERT: A 313 HIS cc_start: 0.8851 (m-70) cc_final: 0.8650 (m-70) REVERT: A 316 GLU cc_start: 0.9440 (tt0) cc_final: 0.9205 (tt0) REVERT: A 326 PHE cc_start: 0.9685 (m-10) cc_final: 0.9415 (m-80) REVERT: A 335 GLU cc_start: 0.9230 (mm-30) cc_final: 0.8719 (mp0) REVERT: A 359 MET cc_start: 0.8720 (ttp) cc_final: 0.8396 (tmm) REVERT: A 360 PHE cc_start: 0.9358 (m-80) cc_final: 0.8753 (m-80) REVERT: A 362 ASP cc_start: 0.9099 (m-30) cc_final: 0.8749 (m-30) REVERT: A 370 ASN cc_start: 0.9555 (m-40) cc_final: 0.9152 (m-40) REVERT: A 375 LYS cc_start: 0.8888 (mmmt) cc_final: 0.8518 (mmtm) REVERT: A 406 ASP cc_start: 0.8409 (m-30) cc_final: 0.8125 (m-30) REVERT: A 407 ILE cc_start: 0.9107 (mt) cc_final: 0.8847 (mt) REVERT: A 459 LYS cc_start: 0.9073 (mttp) cc_final: 0.8824 (mppt) REVERT: A 466 MET cc_start: 0.9513 (ptt) cc_final: 0.9154 (ptt) REVERT: A 469 HIS cc_start: 0.9158 (t-170) cc_final: 0.8833 (t-170) REVERT: A 493 MET cc_start: 0.9288 (tmm) cc_final: 0.8935 (tmm) REVERT: A 501 GLN cc_start: 0.9438 (tp40) cc_final: 0.8717 (tp-100) REVERT: A 515 ASP cc_start: 0.9275 (m-30) cc_final: 0.8695 (m-30) REVERT: A 516 GLN cc_start: 0.9217 (mp10) cc_final: 0.8869 (mp10) REVERT: A 561 LEU cc_start: 0.9620 (tp) cc_final: 0.9372 (tp) REVERT: A 598 MET cc_start: 0.8607 (ttt) cc_final: 0.8402 (ttt) REVERT: A 599 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8197 (tm-30) REVERT: A 634 MET cc_start: 0.9263 (mmm) cc_final: 0.8751 (mmm) REVERT: A 657 PHE cc_start: 0.8775 (m-80) cc_final: 0.8357 (m-80) REVERT: B 8 LYS cc_start: 0.9361 (tptp) cc_final: 0.9048 (tptp) REVERT: B 30 LYS cc_start: 0.9780 (tmtt) cc_final: 0.9429 (tptt) REVERT: B 54 LYS cc_start: 0.9770 (ttmm) cc_final: 0.9368 (tttp) REVERT: B 95 MET cc_start: 0.9507 (mmp) cc_final: 0.9137 (mmm) REVERT: B 99 LYS cc_start: 0.9571 (mmmt) cc_final: 0.9219 (mttt) REVERT: B 118 TYR cc_start: 0.9324 (t80) cc_final: 0.9009 (t80) REVERT: B 218 ASN cc_start: 0.9259 (m-40) cc_final: 0.8714 (m-40) REVERT: B 250 TYR cc_start: 0.8688 (m-80) cc_final: 0.7379 (m-80) REVERT: B 251 LEU cc_start: 0.9606 (tp) cc_final: 0.9397 (tp) REVERT: B 283 VAL cc_start: 0.9526 (t) cc_final: 0.9179 (t) REVERT: B 291 LEU cc_start: 0.9535 (mt) cc_final: 0.9269 (mt) REVERT: B 322 MET cc_start: 0.8908 (mmm) cc_final: 0.8068 (mmm) REVERT: B 326 PHE cc_start: 0.9531 (m-10) cc_final: 0.9057 (m-80) REVERT: B 359 MET cc_start: 0.8923 (ttt) cc_final: 0.8448 (tmm) REVERT: B 362 ASP cc_start: 0.8560 (m-30) cc_final: 0.8350 (m-30) REVERT: B 370 ASN cc_start: 0.9482 (m-40) cc_final: 0.9257 (m110) REVERT: B 375 LYS cc_start: 0.9295 (mmmm) cc_final: 0.9026 (mmmm) REVERT: B 379 SER cc_start: 0.9246 (t) cc_final: 0.8493 (t) REVERT: B 403 ILE cc_start: 0.9394 (mp) cc_final: 0.9014 (tp) REVERT: B 410 ASN cc_start: 0.8955 (m110) cc_final: 0.8599 (m110) REVERT: B 416 ILE cc_start: 0.9647 (mt) cc_final: 0.9356 (mt) REVERT: B 419 VAL cc_start: 0.9679 (t) cc_final: 0.9475 (p) REVERT: B 420 MET cc_start: 0.9408 (mmm) cc_final: 0.8902 (mmm) REVERT: B 458 MET cc_start: 0.9593 (mmm) cc_final: 0.9284 (mmm) REVERT: B 468 LEU cc_start: 0.9683 (tp) cc_final: 0.9444 (tp) REVERT: B 500 ILE cc_start: 0.9691 (mt) cc_final: 0.9462 (mt) REVERT: B 570 MET cc_start: 0.8972 (mmm) cc_final: 0.8310 (mmm) REVERT: B 598 MET cc_start: 0.9337 (mtm) cc_final: 0.8993 (mtm) REVERT: B 612 TYR cc_start: 0.9052 (m-80) cc_final: 0.7926 (m-80) REVERT: B 613 TYR cc_start: 0.9118 (t80) cc_final: 0.8552 (t80) REVERT: B 615 MET cc_start: 0.8912 (mmp) cc_final: 0.8101 (mmt) REVERT: B 631 ASP cc_start: 0.9386 (t70) cc_final: 0.9104 (t0) REVERT: B 636 LYS cc_start: 0.9626 (mptt) cc_final: 0.9355 (mmtt) REVERT: B 639 ASP cc_start: 0.9323 (m-30) cc_final: 0.9023 (m-30) REVERT: B 640 MET cc_start: 0.9541 (tpp) cc_final: 0.9017 (tpp) REVERT: B 648 ILE cc_start: 0.9308 (mm) cc_final: 0.8969 (mm) REVERT: B 656 LEU cc_start: 0.9629 (mt) cc_final: 0.9379 (mt) REVERT: B 673 TYR cc_start: 0.9134 (t80) cc_final: 0.8864 (t80) REVERT: B 679 ILE cc_start: 0.9590 (mm) cc_final: 0.9367 (mm) REVERT: C 17 PHE cc_start: 0.8514 (p90) cc_final: 0.7542 (p90) REVERT: C 20 MET cc_start: 0.8861 (ptp) cc_final: 0.8522 (pmm) REVERT: C 21 PHE cc_start: 0.9216 (m-10) cc_final: 0.8423 (m-80) REVERT: C 90 LEU cc_start: 0.7517 (mt) cc_final: 0.7179 (mt) REVERT: C 93 MET cc_start: 0.8813 (mtt) cc_final: 0.8497 (mtt) REVERT: C 96 MET cc_start: 0.8434 (tpt) cc_final: 0.8007 (tpt) REVERT: C 105 TYR cc_start: 0.8751 (m-80) cc_final: 0.8388 (m-80) REVERT: C 122 PHE cc_start: 0.8729 (m-80) cc_final: 0.8388 (m-80) REVERT: C 157 MET cc_start: 0.9694 (mtm) cc_final: 0.9276 (ptm) REVERT: C 163 LEU cc_start: 0.9556 (tt) cc_final: 0.9139 (tt) REVERT: C 178 PHE cc_start: 0.9234 (m-80) cc_final: 0.8870 (m-10) REVERT: C 204 TYR cc_start: 0.8748 (t80) cc_final: 0.8251 (t80) REVERT: C 263 ASN cc_start: 0.6907 (m110) cc_final: 0.6560 (p0) REVERT: D 66 ASP cc_start: 0.6152 (OUTLIER) cc_final: 0.5770 (p0) REVERT: D 109 PHE cc_start: 0.8970 (m-80) cc_final: 0.8214 (m-80) REVERT: D 169 TYR cc_start: 0.8773 (m-10) cc_final: 0.8494 (m-80) REVERT: D 172 PHE cc_start: 0.9487 (m-80) cc_final: 0.9248 (m-80) outliers start: 3 outliers final: 0 residues processed: 705 average time/residue: 0.1225 time to fit residues: 130.0381 Evaluate side-chains 588 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 587 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 127 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 chunk 191 optimal weight: 0.7980 chunk 159 optimal weight: 7.9990 chunk 182 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN B 147 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN D 23 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.106317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.078341 restraints weight = 51417.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.081202 restraints weight = 31150.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.083425 restraints weight = 21615.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.085013 restraints weight = 16029.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.086177 restraints weight = 12531.699| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.6335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16386 Z= 0.207 Angle : 0.628 7.689 22134 Z= 0.337 Chirality : 0.043 0.177 2360 Planarity : 0.004 0.045 2818 Dihedral : 9.010 145.283 2290 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.06 % Allowed : 2.56 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.18), residues: 1932 helix: 0.92 (0.15), residues: 1150 sheet: -0.42 (0.40), residues: 144 loop : 0.04 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 604 TYR 0.026 0.002 TYR D 174 PHE 0.039 0.002 PHE C 168 TRP 0.048 0.002 TRP D 124 HIS 0.006 0.002 HIS B 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.21 (16386) covalent geometry : angle 0.62766 / 0.34 (22134) hydrogen bonds : bond 0.04146 / 2.60 ( 871) hydrogen bonds : angle 5.08428 / 3.68 ( 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 687 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 686 time to evaluate : 0.456 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 29 ASP cc_start: 0.9347 (t0) cc_final: 0.9092 (t0) REVERT: A 41 ILE cc_start: 0.9695 (mm) cc_final: 0.9418 (mt) REVERT: A 89 PHE cc_start: 0.8887 (t80) cc_final: 0.8569 (t80) REVERT: A 95 MET cc_start: 0.9226 (mmm) cc_final: 0.8923 (tpt) REVERT: A 119 GLU cc_start: 0.9178 (mp0) cc_final: 0.8829 (mp0) REVERT: A 120 ASP cc_start: 0.9329 (m-30) cc_final: 0.9014 (m-30) REVERT: A 136 LYS cc_start: 0.9467 (tptp) cc_final: 0.9122 (tppt) REVERT: A 144 MET cc_start: 0.8800 (mtm) cc_final: 0.8437 (mtm) REVERT: A 147 GLN cc_start: 0.8792 (mt0) cc_final: 0.8386 (mt0) REVERT: A 172 LEU cc_start: 0.9365 (mp) cc_final: 0.9032 (mp) REVERT: A 173 LEU cc_start: 0.9551 (mt) cc_final: 0.9348 (mt) REVERT: A 184 ARG cc_start: 0.9336 (mmm-85) cc_final: 0.8887 (tpp80) REVERT: A 190 MET cc_start: 0.9201 (mtp) cc_final: 0.8977 (mtp) REVERT: A 191 GLN cc_start: 0.8931 (mm-40) cc_final: 0.8640 (mm-40) REVERT: A 199 VAL cc_start: 0.9501 (t) cc_final: 0.9212 (t) REVERT: A 235 ARG cc_start: 0.8327 (mtm110) cc_final: 0.7983 (mtm110) REVERT: A 236 TYR cc_start: 0.9022 (t80) cc_final: 0.8713 (t80) REVERT: A 254 PHE cc_start: 0.8515 (m-80) cc_final: 0.8002 (m-10) REVERT: A 280 ILE cc_start: 0.8416 (pt) cc_final: 0.8037 (mp) REVERT: A 283 VAL cc_start: 0.9141 (t) cc_final: 0.8846 (t) REVERT: A 286 ASP cc_start: 0.9205 (m-30) cc_final: 0.8924 (m-30) REVERT: A 319 MET cc_start: 0.9171 (ttt) cc_final: 0.8869 (tpp) REVERT: A 326 PHE cc_start: 0.9700 (m-10) cc_final: 0.9479 (m-10) REVERT: A 335 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8824 (mp0) REVERT: A 359 MET cc_start: 0.8855 (ttp) cc_final: 0.8394 (ttp) REVERT: A 362 ASP cc_start: 0.9136 (m-30) cc_final: 0.8817 (m-30) REVERT: A 370 ASN cc_start: 0.9586 (m-40) cc_final: 0.9225 (m110) REVERT: A 375 LYS cc_start: 0.8844 (mmmt) cc_final: 0.8619 (mmtm) REVERT: A 406 ASP cc_start: 0.8587 (m-30) cc_final: 0.8270 (m-30) REVERT: A 407 ILE cc_start: 0.9213 (mt) cc_final: 0.8795 (mt) REVERT: A 468 LEU cc_start: 0.9747 (tp) cc_final: 0.9498 (tp) REVERT: A 469 HIS cc_start: 0.9086 (t-170) cc_final: 0.8850 (t-170) REVERT: A 474 GLN cc_start: 0.9320 (tm-30) cc_final: 0.9095 (tm-30) REVERT: A 479 TYR cc_start: 0.9296 (t80) cc_final: 0.8685 (t80) REVERT: A 493 MET cc_start: 0.9261 (tmm) cc_final: 0.8844 (tmm) REVERT: A 501 GLN cc_start: 0.9431 (tp40) cc_final: 0.8667 (tp-100) REVERT: A 515 ASP cc_start: 0.9337 (m-30) cc_final: 0.8776 (m-30) REVERT: A 516 GLN cc_start: 0.9241 (mp10) cc_final: 0.8975 (mp10) REVERT: A 561 LEU cc_start: 0.9640 (tp) cc_final: 0.9419 (tp) REVERT: A 598 MET cc_start: 0.8610 (ttt) cc_final: 0.8206 (ttt) REVERT: A 599 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8269 (tm-30) REVERT: A 602 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7418 (tm-30) REVERT: A 615 MET cc_start: 0.9069 (mmp) cc_final: 0.8845 (mmp) REVERT: A 628 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8873 (mt-10) REVERT: A 640 MET cc_start: 0.9410 (tpp) cc_final: 0.9127 (tpp) REVERT: A 653 SER cc_start: 0.8943 (p) cc_final: 0.8659 (p) REVERT: B 8 LYS cc_start: 0.9341 (tptp) cc_final: 0.9044 (tptp) REVERT: B 30 LYS cc_start: 0.9783 (tmtt) cc_final: 0.9412 (tptt) REVERT: B 95 MET cc_start: 0.9487 (mmp) cc_final: 0.9137 (mmm) REVERT: B 99 LYS cc_start: 0.9561 (mmmt) cc_final: 0.9189 (mttt) REVERT: B 117 ARG cc_start: 0.9053 (mtp180) cc_final: 0.8724 (mmm160) REVERT: B 119 GLU cc_start: 0.9304 (mp0) cc_final: 0.8930 (mp0) REVERT: B 120 ASP cc_start: 0.9385 (m-30) cc_final: 0.9175 (m-30) REVERT: B 144 MET cc_start: 0.9399 (mtm) cc_final: 0.9196 (mtm) REVERT: B 199 VAL cc_start: 0.8969 (t) cc_final: 0.8705 (p) REVERT: B 250 TYR cc_start: 0.8634 (m-80) cc_final: 0.7304 (m-80) REVERT: B 263 ASP cc_start: 0.9173 (m-30) cc_final: 0.8886 (m-30) REVERT: B 283 VAL cc_start: 0.9531 (t) cc_final: 0.9145 (t) REVERT: B 291 LEU cc_start: 0.9547 (mt) cc_final: 0.9308 (mt) REVERT: B 316 GLU cc_start: 0.9443 (tm-30) cc_final: 0.9209 (tm-30) REVERT: B 322 MET cc_start: 0.8847 (mmm) cc_final: 0.8563 (mmm) REVERT: B 359 MET cc_start: 0.8995 (ttt) cc_final: 0.8458 (tmm) REVERT: B 375 LYS cc_start: 0.9340 (mmmm) cc_final: 0.9102 (mmmm) REVERT: B 379 SER cc_start: 0.9153 (t) cc_final: 0.8570 (t) REVERT: B 403 ILE cc_start: 0.9322 (mp) cc_final: 0.8962 (tp) REVERT: B 410 ASN cc_start: 0.8911 (m110) cc_final: 0.8637 (m110) REVERT: B 415 ASN cc_start: 0.9387 (t0) cc_final: 0.8970 (t0) REVERT: B 420 MET cc_start: 0.9416 (mmm) cc_final: 0.9071 (mmm) REVERT: B 460 SER cc_start: 0.9300 (t) cc_final: 0.9032 (t) REVERT: B 468 LEU cc_start: 0.9623 (tp) cc_final: 0.9420 (tp) REVERT: B 494 MET cc_start: 0.9529 (ttm) cc_final: 0.9257 (ttm) REVERT: B 574 TYR cc_start: 0.9019 (m-10) cc_final: 0.8671 (m-80) REVERT: B 588 GLN cc_start: 0.9231 (mm110) cc_final: 0.8770 (mm110) REVERT: B 598 MET cc_start: 0.9411 (mtm) cc_final: 0.9090 (mtm) REVERT: B 601 ILE cc_start: 0.9175 (mm) cc_final: 0.8763 (tp) REVERT: B 612 TYR cc_start: 0.8903 (m-80) cc_final: 0.7850 (m-80) REVERT: B 613 TYR cc_start: 0.9068 (t80) cc_final: 0.8590 (t80) REVERT: B 615 MET cc_start: 0.8819 (mmp) cc_final: 0.8239 (mmp) REVERT: B 631 ASP cc_start: 0.9376 (t70) cc_final: 0.9096 (t0) REVERT: B 636 LYS cc_start: 0.9637 (mptt) cc_final: 0.9346 (mmtt) REVERT: B 639 ASP cc_start: 0.9352 (m-30) cc_final: 0.8917 (m-30) REVERT: B 640 MET cc_start: 0.9433 (tpp) cc_final: 0.8975 (tpp) REVERT: B 645 GLN cc_start: 0.9008 (tp-100) cc_final: 0.8793 (tp-100) REVERT: B 648 ILE cc_start: 0.9289 (mm) cc_final: 0.8970 (mm) REVERT: B 656 LEU cc_start: 0.9608 (mt) cc_final: 0.9345 (mt) REVERT: B 673 TYR cc_start: 0.9170 (t80) cc_final: 0.8744 (t80) REVERT: B 679 ILE cc_start: 0.9555 (mm) cc_final: 0.9311 (mm) REVERT: C 17 PHE cc_start: 0.8402 (p90) cc_final: 0.7504 (p90) REVERT: C 20 MET cc_start: 0.8885 (ptp) cc_final: 0.8624 (pmm) REVERT: C 21 PHE cc_start: 0.9144 (m-10) cc_final: 0.8553 (m-80) REVERT: C 90 LEU cc_start: 0.7678 (mt) cc_final: 0.7286 (mt) REVERT: C 93 MET cc_start: 0.8840 (mtt) cc_final: 0.8555 (mtt) REVERT: C 105 TYR cc_start: 0.8927 (m-80) cc_final: 0.8502 (m-80) REVERT: C 122 PHE cc_start: 0.8643 (m-80) cc_final: 0.8265 (m-80) REVERT: C 157 MET cc_start: 0.9688 (mtm) cc_final: 0.9437 (ttm) REVERT: C 178 PHE cc_start: 0.9230 (m-80) cc_final: 0.8856 (m-10) REVERT: C 204 TYR cc_start: 0.8839 (t80) cc_final: 0.8192 (t80) REVERT: D 109 PHE cc_start: 0.8941 (m-80) cc_final: 0.8267 (m-80) REVERT: D 112 LEU cc_start: 0.8625 (mm) cc_final: 0.7774 (pp) REVERT: D 169 TYR cc_start: 0.8760 (m-10) cc_final: 0.8396 (m-80) REVERT: D 172 PHE cc_start: 0.9492 (m-80) cc_final: 0.9067 (m-80) REVERT: D 224 LEU cc_start: 0.9448 (mt) cc_final: 0.9190 (mt) REVERT: D 252 LEU cc_start: 0.7555 (mp) cc_final: 0.7310 (mp) outliers start: 1 outliers final: 0 residues processed: 686 average time/residue: 0.1153 time to fit residues: 120.1481 Evaluate side-chains 577 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 577 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 ASN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN B 320 ASN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN D 25 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN D 288 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.102147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.074237 restraints weight = 53170.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.077003 restraints weight = 31855.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.079189 restraints weight = 21894.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.080737 restraints weight = 16322.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.081869 restraints weight = 12851.581| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.7085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16386 Z= 0.286 Angle : 0.712 8.524 22134 Z= 0.382 Chirality : 0.045 0.223 2360 Planarity : 0.005 0.054 2818 Dihedral : 9.209 147.160 2290 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 21.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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 are not related in a simple way. whole: 0.40 (0.18), residues: 1932 helix: 0.68 (0.15), residues: 1141 sheet: -0.47 (0.40), residues: 148 loop : -0.05 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 274 TYR 0.028 0.002 TYR D 130 PHE 0.036 0.003 PHE D 227 TRP 0.052 0.002 TRP D 124 HIS 0.013 0.002 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.29 (16386) covalent geometry : angle 0.71216 / 0.38 (22134) hydrogen bonds : bond 0.04352 / 2.74 ( 871) hydrogen bonds : angle 5.39800 / 3.91 ( 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 657 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 657 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9224 (tptp) cc_final: 0.8670 (tppt) REVERT: A 12 LEU cc_start: 0.9608 (mt) cc_final: 0.9303 (mt) REVERT: A 95 MET cc_start: 0.9362 (mmm) cc_final: 0.9065 (mmm) REVERT: A 115 LEU cc_start: 0.9671 (mt) cc_final: 0.9376 (mt) REVERT: A 116 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7715 (tt0) REVERT: A 120 ASP cc_start: 0.9394 (m-30) cc_final: 0.9153 (m-30) REVERT: A 136 LYS cc_start: 0.9529 (tptp) cc_final: 0.9228 (tppp) REVERT: A 144 MET cc_start: 0.8806 (mtm) cc_final: 0.8508 (mtm) REVERT: A 147 GLN cc_start: 0.8788 (mt0) cc_final: 0.8501 (mt0) REVERT: A 172 LEU cc_start: 0.9402 (mp) cc_final: 0.9061 (mp) REVERT: A 176 ASN cc_start: 0.8568 (t0) cc_final: 0.7876 (m-40) REVERT: A 184 ARG cc_start: 0.9298 (mmm-85) cc_final: 0.8879 (tpp80) REVERT: A 190 MET cc_start: 0.9208 (mtp) cc_final: 0.8857 (mtp) REVERT: A 191 GLN cc_start: 0.9040 (mm-40) cc_final: 0.8586 (mm-40) REVERT: A 199 VAL cc_start: 0.9474 (t) cc_final: 0.9237 (t) REVERT: A 235 ARG cc_start: 0.8301 (mtm110) cc_final: 0.7980 (mtm110) REVERT: A 236 TYR cc_start: 0.9038 (t80) cc_final: 0.8402 (t80) REVERT: A 252 ASN cc_start: 0.9306 (t0) cc_final: 0.9032 (t0) REVERT: A 280 ILE cc_start: 0.8525 (pt) cc_final: 0.8308 (mp) REVERT: A 286 ASP cc_start: 0.9198 (m-30) cc_final: 0.8898 (m-30) REVERT: A 313 HIS cc_start: 0.8988 (m-70) cc_final: 0.8568 (m-70) REVERT: A 322 MET cc_start: 0.9112 (mmp) cc_final: 0.8844 (mmm) REVERT: A 335 GLU cc_start: 0.9350 (mm-30) cc_final: 0.8983 (mp0) REVERT: A 352 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8623 (tm-30) REVERT: A 359 MET cc_start: 0.8952 (ttp) cc_final: 0.8503 (ttp) REVERT: A 362 ASP cc_start: 0.9132 (m-30) cc_final: 0.8838 (m-30) REVERT: A 370 ASN cc_start: 0.9611 (m-40) cc_final: 0.9314 (m110) REVERT: A 398 ASP cc_start: 0.8650 (p0) cc_final: 0.8376 (p0) REVERT: A 406 ASP cc_start: 0.8712 (m-30) cc_final: 0.8404 (m-30) REVERT: A 407 ILE cc_start: 0.9096 (mt) cc_final: 0.8638 (mt) REVERT: A 420 MET cc_start: 0.9395 (mmm) cc_final: 0.9028 (tpp) REVERT: A 441 GLU cc_start: 0.9225 (mm-30) cc_final: 0.9004 (mm-30) REVERT: A 469 HIS cc_start: 0.9245 (t-170) cc_final: 0.8879 (t-170) REVERT: A 490 THR cc_start: 0.9617 (m) cc_final: 0.8943 (m) REVERT: A 494 MET cc_start: 0.9492 (mpp) cc_final: 0.8997 (mmm) REVERT: A 501 GLN cc_start: 0.9437 (tp40) cc_final: 0.8545 (tp-100) REVERT: A 515 ASP cc_start: 0.9393 (m-30) cc_final: 0.8922 (m-30) REVERT: A 570 MET cc_start: 0.9205 (mtp) cc_final: 0.8856 (mtp) REVERT: A 583 SER cc_start: 0.9602 (m) cc_final: 0.9358 (p) REVERT: A 615 MET cc_start: 0.9016 (mmp) cc_final: 0.8788 (mmp) REVERT: A 628 GLU cc_start: 0.9285 (mt-10) cc_final: 0.8680 (mm-30) REVERT: A 632 MET cc_start: 0.8963 (mmm) cc_final: 0.8655 (mmm) REVERT: A 634 MET cc_start: 0.9341 (mmm) cc_final: 0.9081 (mmm) REVERT: A 636 LYS cc_start: 0.9818 (mmtp) cc_final: 0.9608 (mmmm) REVERT: A 647 HIS cc_start: 0.9348 (m-70) cc_final: 0.7825 (m170) REVERT: A 653 SER cc_start: 0.8882 (p) cc_final: 0.8678 (p) REVERT: A 658 LEU cc_start: 0.9530 (mt) cc_final: 0.9219 (mt) REVERT: A 662 MET cc_start: 0.8496 (pmm) cc_final: 0.8274 (pmm) REVERT: A 672 LEU cc_start: 0.9343 (mt) cc_final: 0.9143 (mt) REVERT: A 675 HIS cc_start: 0.9328 (t-90) cc_final: 0.8771 (t70) REVERT: B 8 LYS cc_start: 0.9372 (tptp) cc_final: 0.9163 (tptp) REVERT: B 28 LYS cc_start: 0.9493 (mtpt) cc_final: 0.9285 (ttpp) REVERT: B 30 LYS cc_start: 0.9791 (tmtt) cc_final: 0.9401 (tptt) REVERT: B 95 MET cc_start: 0.9379 (mmp) cc_final: 0.8985 (tpp) REVERT: B 104 TYR cc_start: 0.8783 (m-80) cc_final: 0.8321 (m-80) REVERT: B 116 GLU cc_start: 0.8529 (mt-10) cc_final: 0.7728 (mt-10) REVERT: B 119 GLU cc_start: 0.9381 (mp0) cc_final: 0.8937 (mp0) REVERT: B 120 ASP cc_start: 0.9484 (m-30) cc_final: 0.9200 (m-30) REVERT: B 124 ILE cc_start: 0.9577 (mm) cc_final: 0.9310 (mm) REVERT: B 139 GLU cc_start: 0.9456 (mp0) cc_final: 0.9130 (mp0) REVERT: B 179 LEU cc_start: 0.9784 (tp) cc_final: 0.9554 (tp) REVERT: B 187 ASP cc_start: 0.9466 (t70) cc_final: 0.9248 (t70) REVERT: B 199 VAL cc_start: 0.8983 (t) cc_final: 0.8679 (p) REVERT: B 211 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8879 (mm-30) REVERT: B 218 ASN cc_start: 0.9144 (m-40) cc_final: 0.8811 (m-40) REVERT: B 235 ARG cc_start: 0.8712 (ttm110) cc_final: 0.8137 (ttm110) REVERT: B 250 TYR cc_start: 0.8834 (m-80) cc_final: 0.7599 (m-80) REVERT: B 251 LEU cc_start: 0.9691 (tp) cc_final: 0.9433 (tp) REVERT: B 260 ASP cc_start: 0.9563 (p0) cc_final: 0.9344 (p0) REVERT: B 263 ASP cc_start: 0.9265 (m-30) cc_final: 0.9039 (m-30) REVERT: B 291 LEU cc_start: 0.9544 (mt) cc_final: 0.9292 (mt) REVERT: B 316 GLU cc_start: 0.9425 (tm-30) cc_final: 0.9219 (tm-30) REVERT: B 322 MET cc_start: 0.8748 (mmm) cc_final: 0.8484 (mmm) REVERT: B 359 MET cc_start: 0.9211 (ttt) cc_final: 0.8617 (tmm) REVERT: B 375 LYS cc_start: 0.9361 (mmmm) cc_final: 0.9080 (mmmm) REVERT: B 379 SER cc_start: 0.9279 (t) cc_final: 0.8661 (t) REVERT: B 402 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8344 (tm-30) REVERT: B 403 ILE cc_start: 0.9299 (mp) cc_final: 0.8938 (tp) REVERT: B 407 ILE cc_start: 0.8816 (mt) cc_final: 0.8547 (mt) REVERT: B 415 ASN cc_start: 0.9145 (t0) cc_final: 0.8800 (t0) REVERT: B 420 MET cc_start: 0.9428 (mmm) cc_final: 0.9086 (mmm) REVERT: B 446 ARG cc_start: 0.9126 (mmm-85) cc_final: 0.8579 (mmm-85) REVERT: B 458 MET cc_start: 0.9524 (mmm) cc_final: 0.8831 (mmm) REVERT: B 494 MET cc_start: 0.9561 (ttm) cc_final: 0.9201 (ttm) REVERT: B 598 MET cc_start: 0.9356 (mtm) cc_final: 0.9110 (mtm) REVERT: B 601 ILE cc_start: 0.9191 (mm) cc_final: 0.8752 (tp) REVERT: B 612 TYR cc_start: 0.8751 (m-80) cc_final: 0.7879 (m-80) REVERT: B 613 TYR cc_start: 0.9145 (t80) cc_final: 0.8467 (t80) REVERT: B 615 MET cc_start: 0.8851 (mmp) cc_final: 0.8209 (mmt) REVERT: B 631 ASP cc_start: 0.9320 (t70) cc_final: 0.8956 (t0) REVERT: B 640 MET cc_start: 0.9385 (tpp) cc_final: 0.8867 (tpp) REVERT: B 679 ILE cc_start: 0.9562 (mm) cc_final: 0.9348 (mm) REVERT: C 17 PHE cc_start: 0.8553 (p90) cc_final: 0.7760 (p90) REVERT: C 21 PHE cc_start: 0.8975 (m-10) cc_final: 0.8529 (m-80) REVERT: C 105 TYR cc_start: 0.8895 (m-80) cc_final: 0.8520 (m-80) REVERT: C 122 PHE cc_start: 0.8621 (m-80) cc_final: 0.8247 (m-80) REVERT: C 178 PHE cc_start: 0.9244 (m-80) cc_final: 0.8993 (m-10) REVERT: C 204 TYR cc_start: 0.8936 (t80) cc_final: 0.8568 (t80) REVERT: D 21 PHE cc_start: 0.8823 (m-10) cc_final: 0.8594 (m-10) REVERT: D 109 PHE cc_start: 0.8912 (m-80) cc_final: 0.8283 (m-80) REVERT: D 112 LEU cc_start: 0.8625 (mm) cc_final: 0.7773 (pp) REVERT: D 166 PHE cc_start: 0.8234 (t80) cc_final: 0.7748 (t80) REVERT: D 169 TYR cc_start: 0.9106 (m-10) cc_final: 0.8871 (m-80) REVERT: D 172 PHE cc_start: 0.9513 (m-80) cc_final: 0.9260 (m-80) REVERT: D 179 TYR cc_start: 0.8266 (t80) cc_final: 0.7887 (t80) REVERT: D 185 MET cc_start: 0.5779 (mmp) cc_final: 0.5523 (mmm) REVERT: D 244 GLU cc_start: 0.9081 (mp0) cc_final: 0.8847 (mm-30) REVERT: D 260 ILE cc_start: 0.8499 (mt) cc_final: 0.7816 (mt) REVERT: D 263 ASN cc_start: 0.8903 (m-40) cc_final: 0.8639 (p0) outliers start: 0 outliers final: 0 residues processed: 657 average time/residue: 0.1086 time to fit residues: 107.8258 Evaluate side-chains 571 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 571 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 28 optimal weight: 0.0670 chunk 75 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 136 optimal weight: 0.0030 overall best weight: 2.2134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN B 410 ASN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.106197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.077653 restraints weight = 50806.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.080471 restraints weight = 30358.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.082855 restraints weight = 20812.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.084299 restraints weight = 15453.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.085556 restraints weight = 12349.263| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.7366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16386 Z= 0.174 Angle : 0.632 7.784 22134 Z= 0.339 Chirality : 0.044 0.265 2360 Planarity : 0.003 0.044 2818 Dihedral : 8.950 145.901 2290 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.12 % Allowed : 1.75 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.18), residues: 1932 helix: 0.95 (0.15), residues: 1126 sheet: -0.55 (0.40), residues: 148 loop : 0.01 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 86 TYR 0.025 0.002 TYR B 574 PHE 0.030 0.002 PHE C 168 TRP 0.056 0.002 TRP D 124 HIS 0.016 0.002 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (16386) covalent geometry : angle 0.63190 / 0.34 (22134) hydrogen bonds : bond 0.04108 / 2.59 ( 871) hydrogen bonds : angle 5.16652 / 3.75 ( 2571) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 674 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9264 (tptp) cc_final: 0.8828 (tppt) REVERT: A 58 LEU cc_start: 0.9816 (mm) cc_final: 0.9433 (pp) REVERT: A 95 MET cc_start: 0.9325 (mmm) cc_final: 0.8885 (mmm) REVERT: A 116 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7578 (tt0) REVERT: A 120 ASP cc_start: 0.9316 (m-30) cc_final: 0.9064 (m-30) REVERT: A 128 PHE cc_start: 0.9581 (t80) cc_final: 0.9372 (t80) REVERT: A 136 LYS cc_start: 0.9468 (tptp) cc_final: 0.9252 (tppp) REVERT: A 144 MET cc_start: 0.8623 (mtm) cc_final: 0.8375 (mtm) REVERT: A 173 LEU cc_start: 0.9465 (mt) cc_final: 0.9207 (mt) REVERT: A 176 ASN cc_start: 0.8439 (t0) cc_final: 0.7832 (m110) REVERT: A 184 ARG cc_start: 0.9302 (mmm-85) cc_final: 0.9036 (tpp80) REVERT: A 190 MET cc_start: 0.9150 (mtp) cc_final: 0.8886 (mtp) REVERT: A 191 GLN cc_start: 0.9012 (mm-40) cc_final: 0.8714 (mm-40) REVERT: A 214 LYS cc_start: 0.9468 (mmmt) cc_final: 0.9235 (mmtt) REVERT: A 235 ARG cc_start: 0.8329 (mtm110) cc_final: 0.8008 (mtm110) REVERT: A 236 TYR cc_start: 0.8966 (t80) cc_final: 0.8289 (t80) REVERT: A 280 ILE cc_start: 0.8528 (pt) cc_final: 0.8101 (mp) REVERT: A 335 GLU cc_start: 0.9307 (mm-30) cc_final: 0.9007 (mp0) REVERT: A 359 MET cc_start: 0.8893 (ttp) cc_final: 0.8550 (ttp) REVERT: A 362 ASP cc_start: 0.9054 (m-30) cc_final: 0.8787 (m-30) REVERT: A 370 ASN cc_start: 0.9571 (m-40) cc_final: 0.9107 (m110) REVERT: A 381 LEU cc_start: 0.8953 (tp) cc_final: 0.8596 (pt) REVERT: A 398 ASP cc_start: 0.8585 (p0) cc_final: 0.8309 (p0) REVERT: A 403 ILE cc_start: 0.8917 (tp) cc_final: 0.8554 (tp) REVERT: A 407 ILE cc_start: 0.9150 (mt) cc_final: 0.8762 (mt) REVERT: A 426 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8430 (tm-30) REVERT: A 468 LEU cc_start: 0.9741 (tp) cc_final: 0.9327 (tp) REVERT: A 469 HIS cc_start: 0.9026 (t-170) cc_final: 0.8745 (t-170) REVERT: A 472 LEU cc_start: 0.9630 (mt) cc_final: 0.9378 (mt) REVERT: A 479 TYR cc_start: 0.9030 (t80) cc_final: 0.7824 (t80) REVERT: A 494 MET cc_start: 0.9400 (mpp) cc_final: 0.9089 (mmm) REVERT: A 501 GLN cc_start: 0.9430 (tp40) cc_final: 0.9166 (mm-40) REVERT: A 515 ASP cc_start: 0.9350 (m-30) cc_final: 0.8796 (m-30) REVERT: A 516 GLN cc_start: 0.9077 (mp10) cc_final: 0.8517 (mp10) REVERT: A 570 MET cc_start: 0.9340 (mtp) cc_final: 0.8884 (mtp) REVERT: A 598 MET cc_start: 0.8877 (ttt) cc_final: 0.8562 (ttt) REVERT: A 599 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8126 (tm-30) REVERT: A 615 MET cc_start: 0.9097 (mmp) cc_final: 0.8401 (mmp) REVERT: A 628 GLU cc_start: 0.9280 (mt-10) cc_final: 0.8846 (mt-10) REVERT: A 632 MET cc_start: 0.8927 (mmm) cc_final: 0.8627 (mmm) REVERT: A 634 MET cc_start: 0.9375 (mmm) cc_final: 0.9109 (mmm) REVERT: A 636 LYS cc_start: 0.9799 (mmtp) cc_final: 0.9577 (mmmm) REVERT: A 640 MET cc_start: 0.9333 (tpp) cc_final: 0.8952 (tpp) REVERT: A 653 SER cc_start: 0.8883 (p) cc_final: 0.8677 (p) REVERT: B 8 LYS cc_start: 0.9384 (tptp) cc_final: 0.9123 (tptp) REVERT: B 30 LYS cc_start: 0.9801 (tmtt) cc_final: 0.9413 (tptt) REVERT: B 82 LYS cc_start: 0.9478 (ptpp) cc_final: 0.9155 (ptpt) REVERT: B 95 MET cc_start: 0.9366 (mmp) cc_final: 0.9032 (mmt) REVERT: B 99 LYS cc_start: 0.9570 (mmmt) cc_final: 0.9286 (mttt) REVERT: B 106 LEU cc_start: 0.9439 (tt) cc_final: 0.9173 (tt) REVERT: B 116 GLU cc_start: 0.8640 (mt-10) cc_final: 0.7784 (tt0) REVERT: B 119 GLU cc_start: 0.9339 (mp0) cc_final: 0.8898 (mp0) REVERT: B 144 MET cc_start: 0.9376 (mtm) cc_final: 0.9155 (mtm) REVERT: B 149 TYR cc_start: 0.9156 (t80) cc_final: 0.8893 (t80) REVERT: B 168 VAL cc_start: 0.9357 (t) cc_final: 0.9138 (m) REVERT: B 199 VAL cc_start: 0.9007 (t) cc_final: 0.8731 (p) REVERT: B 211 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8950 (mm-30) REVERT: B 235 ARG cc_start: 0.8724 (ttm110) cc_final: 0.8150 (ttm110) REVERT: B 250 TYR cc_start: 0.8742 (m-80) cc_final: 0.7549 (m-80) REVERT: B 263 ASP cc_start: 0.9163 (m-30) cc_final: 0.8807 (m-30) REVERT: B 283 VAL cc_start: 0.9588 (t) cc_final: 0.9333 (t) REVERT: B 291 LEU cc_start: 0.9569 (mt) cc_final: 0.9325 (mt) REVERT: B 316 GLU cc_start: 0.9412 (tm-30) cc_final: 0.9209 (tm-30) REVERT: B 359 MET cc_start: 0.9183 (ttt) cc_final: 0.8467 (tmm) REVERT: B 375 LYS cc_start: 0.9332 (mmmm) cc_final: 0.9034 (mmmm) REVERT: B 379 SER cc_start: 0.9228 (t) cc_final: 0.8645 (t) REVERT: B 403 ILE cc_start: 0.9265 (mp) cc_final: 0.8883 (tp) REVERT: B 407 ILE cc_start: 0.8660 (mt) cc_final: 0.8428 (mt) REVERT: B 408 SER cc_start: 0.9443 (p) cc_final: 0.9233 (p) REVERT: B 410 ASN cc_start: 0.9107 (m-40) cc_final: 0.8830 (m-40) REVERT: B 415 ASN cc_start: 0.9308 (t0) cc_final: 0.8856 (t0) REVERT: B 416 ILE cc_start: 0.9717 (mt) cc_final: 0.9514 (mt) REVERT: B 420 MET cc_start: 0.9413 (mmm) cc_final: 0.9043 (mmm) REVERT: B 446 ARG cc_start: 0.9084 (mmm-85) cc_final: 0.8463 (mmm-85) REVERT: B 458 MET cc_start: 0.9412 (mmm) cc_final: 0.8857 (mmm) REVERT: B 468 LEU cc_start: 0.9604 (tp) cc_final: 0.9403 (tp) REVERT: B 494 MET cc_start: 0.9566 (ttm) cc_final: 0.9221 (ttm) REVERT: B 530 LYS cc_start: 0.9007 (ptmm) cc_final: 0.8580 (ptmm) REVERT: B 574 TYR cc_start: 0.8954 (m-10) cc_final: 0.8683 (m-80) REVERT: B 588 GLN cc_start: 0.9542 (mm-40) cc_final: 0.9227 (mm-40) REVERT: B 598 MET cc_start: 0.9359 (mtm) cc_final: 0.9094 (mtm) REVERT: B 601 ILE cc_start: 0.9193 (mm) cc_final: 0.8879 (tp) REVERT: B 612 TYR cc_start: 0.8855 (m-80) cc_final: 0.7870 (m-80) REVERT: B 613 TYR cc_start: 0.9215 (t80) cc_final: 0.8812 (t80) REVERT: B 615 MET cc_start: 0.8862 (mmp) cc_final: 0.8389 (mmp) REVERT: B 631 ASP cc_start: 0.9344 (t70) cc_final: 0.8972 (t0) REVERT: B 636 LYS cc_start: 0.9604 (mptt) cc_final: 0.9303 (mmtt) REVERT: B 639 ASP cc_start: 0.9454 (m-30) cc_final: 0.8925 (m-30) REVERT: B 640 MET cc_start: 0.9336 (tpp) cc_final: 0.8854 (tpp) REVERT: B 673 TYR cc_start: 0.9144 (t80) cc_final: 0.8700 (t80) REVERT: C 17 PHE cc_start: 0.8435 (p90) cc_final: 0.7649 (p90) REVERT: C 21 PHE cc_start: 0.8991 (m-10) cc_final: 0.8460 (m-80) REVERT: C 96 MET cc_start: 0.8221 (tpt) cc_final: 0.7908 (tpt) REVERT: C 105 TYR cc_start: 0.8958 (m-80) cc_final: 0.8564 (m-80) REVERT: C 122 PHE cc_start: 0.8623 (m-80) cc_final: 0.8261 (m-80) REVERT: C 178 PHE cc_start: 0.9243 (m-80) cc_final: 0.9018 (m-10) REVERT: C 204 TYR cc_start: 0.8986 (t80) cc_final: 0.8530 (t80) REVERT: C 207 LEU cc_start: 0.9054 (tt) cc_final: 0.8830 (pp) REVERT: D 21 PHE cc_start: 0.8714 (m-10) cc_final: 0.8469 (m-10) REVERT: D 109 PHE cc_start: 0.8850 (m-80) cc_final: 0.8221 (m-80) REVERT: D 112 LEU cc_start: 0.8661 (mm) cc_final: 0.7809 (pp) REVERT: D 169 TYR cc_start: 0.9031 (m-10) cc_final: 0.8675 (m-10) REVERT: D 172 PHE cc_start: 0.9508 (m-80) cc_final: 0.9201 (m-80) REVERT: D 179 TYR cc_start: 0.8314 (t80) cc_final: 0.7835 (t80) REVERT: D 185 MET cc_start: 0.5585 (mmp) cc_final: 0.5214 (mmm) REVERT: D 239 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8599 (pm20) REVERT: D 260 ILE cc_start: 0.8476 (mt) cc_final: 0.7817 (mt) REVERT: D 281 ASP cc_start: 0.8234 (p0) cc_final: 0.8020 (p0) outliers start: 2 outliers final: 0 residues processed: 676 average time/residue: 0.1144 time to fit residues: 117.0407 Evaluate side-chains 567 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 566 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 3.9990 chunk 51 optimal weight: 0.0970 chunk 74 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 HIS ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.105969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.078066 restraints weight = 50697.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.081042 restraints weight = 30628.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.083197 restraints weight = 20892.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.084644 restraints weight = 15478.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.085842 restraints weight = 12353.619| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.7682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16386 Z= 0.178 Angle : 0.638 8.161 22134 Z= 0.346 Chirality : 0.044 0.251 2360 Planarity : 0.004 0.044 2818 Dihedral : 8.799 147.404 2290 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.06 % Allowed : 1.46 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.18), residues: 1932 helix: 0.87 (0.15), residues: 1129 sheet: -0.34 (0.41), residues: 132 loop : -0.15 (0.22), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 164 TYR 0.033 0.002 TYR C 276 PHE 0.046 0.002 PHE D 227 TRP 0.057 0.002 TRP D 124 HIS 0.014 0.002 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 (16386) covalent geometry : angle 0.63758 / 0.35 (22134) hydrogen bonds : bond 0.04006 / 2.52 ( 871) hydrogen bonds : angle 5.19245 / 3.75 ( 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 665 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 664 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9281 (tptp) cc_final: 0.8845 (tppt) REVERT: A 15 GLU cc_start: 0.9166 (tp30) cc_final: 0.8860 (tp30) REVERT: A 58 LEU cc_start: 0.9799 (mm) cc_final: 0.9442 (pp) REVERT: A 87 LYS cc_start: 0.9492 (tppt) cc_final: 0.9130 (tppp) REVERT: A 116 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7595 (tt0) REVERT: A 119 GLU cc_start: 0.9104 (mp0) cc_final: 0.8845 (mp0) REVERT: A 120 ASP cc_start: 0.9298 (m-30) cc_final: 0.9026 (m-30) REVERT: A 128 PHE cc_start: 0.9586 (t80) cc_final: 0.9313 (t80) REVERT: A 136 LYS cc_start: 0.9523 (tptp) cc_final: 0.9204 (tppp) REVERT: A 164 ARG cc_start: 0.8022 (ptm-80) cc_final: 0.6555 (ptm-80) REVERT: A 173 LEU cc_start: 0.9494 (mt) cc_final: 0.9201 (mt) REVERT: A 176 ASN cc_start: 0.8528 (t0) cc_final: 0.7883 (m110) REVERT: A 184 ARG cc_start: 0.9324 (mmm-85) cc_final: 0.9118 (tpp80) REVERT: A 190 MET cc_start: 0.9151 (mtp) cc_final: 0.8809 (mtp) REVERT: A 214 LYS cc_start: 0.9470 (mmmt) cc_final: 0.9244 (mmtt) REVERT: A 221 LYS cc_start: 0.9109 (tppt) cc_final: 0.8674 (tppt) REVERT: A 236 TYR cc_start: 0.8962 (t80) cc_final: 0.8109 (t80) REVERT: A 263 ASP cc_start: 0.9054 (m-30) cc_final: 0.8813 (m-30) REVERT: A 280 ILE cc_start: 0.8471 (pt) cc_final: 0.8247 (mp) REVERT: A 286 ASP cc_start: 0.9215 (m-30) cc_final: 0.8825 (m-30) REVERT: A 307 TYR cc_start: 0.9452 (t80) cc_final: 0.9128 (t80) REVERT: A 335 GLU cc_start: 0.9299 (mm-30) cc_final: 0.8987 (mp0) REVERT: A 349 LEU cc_start: 0.9457 (mt) cc_final: 0.9117 (mt) REVERT: A 362 ASP cc_start: 0.9066 (m-30) cc_final: 0.8590 (m-30) REVERT: A 370 ASN cc_start: 0.9603 (m-40) cc_final: 0.9221 (m110) REVERT: A 381 LEU cc_start: 0.8968 (tp) cc_final: 0.8601 (pt) REVERT: A 398 ASP cc_start: 0.8543 (p0) cc_final: 0.8274 (p0) REVERT: A 407 ILE cc_start: 0.9187 (mt) cc_final: 0.8933 (mt) REVERT: A 426 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8432 (tm-30) REVERT: A 469 HIS cc_start: 0.8977 (t-170) cc_final: 0.8704 (t-170) REVERT: A 479 TYR cc_start: 0.9035 (t80) cc_final: 0.8600 (t80) REVERT: A 494 MET cc_start: 0.9340 (mpp) cc_final: 0.8993 (mmm) REVERT: A 501 GLN cc_start: 0.9428 (tp40) cc_final: 0.9162 (mm-40) REVERT: A 515 ASP cc_start: 0.9372 (m-30) cc_final: 0.8819 (m-30) REVERT: A 516 GLN cc_start: 0.9071 (mp10) cc_final: 0.8499 (mp10) REVERT: A 562 LYS cc_start: 0.9721 (ttmm) cc_final: 0.9389 (tttt) REVERT: A 570 MET cc_start: 0.9288 (mtp) cc_final: 0.9015 (mtp) REVERT: A 615 MET cc_start: 0.9071 (mmp) cc_final: 0.8772 (mmp) REVERT: A 628 GLU cc_start: 0.9229 (mt-10) cc_final: 0.8781 (mt-10) REVERT: A 632 MET cc_start: 0.8952 (mmm) cc_final: 0.8572 (mmm) REVERT: A 634 MET cc_start: 0.9374 (mmm) cc_final: 0.9138 (mmm) REVERT: A 636 LYS cc_start: 0.9799 (mmtp) cc_final: 0.9572 (mmmm) REVERT: A 640 MET cc_start: 0.9327 (tpp) cc_final: 0.8933 (tpp) REVERT: A 653 SER cc_start: 0.9007 (p) cc_final: 0.8782 (p) REVERT: A 675 HIS cc_start: 0.9394 (t-90) cc_final: 0.8666 (t70) REVERT: A 686 ARG cc_start: 0.7348 (tpt170) cc_final: 0.7073 (tpt170) REVERT: B 8 LYS cc_start: 0.9397 (tptp) cc_final: 0.9180 (tptp) REVERT: B 30 LYS cc_start: 0.9767 (tmtt) cc_final: 0.9418 (tptt) REVERT: B 82 LYS cc_start: 0.9472 (ptpp) cc_final: 0.9182 (ptpt) REVERT: B 87 LYS cc_start: 0.9603 (tptp) cc_final: 0.9356 (tptp) REVERT: B 89 PHE cc_start: 0.8756 (t80) cc_final: 0.8513 (t80) REVERT: B 99 LYS cc_start: 0.9599 (mmmt) cc_final: 0.9306 (mttt) REVERT: B 106 LEU cc_start: 0.9430 (tt) cc_final: 0.8780 (tt) REVERT: B 116 GLU cc_start: 0.8560 (mt-10) cc_final: 0.7882 (tt0) REVERT: B 119 GLU cc_start: 0.9268 (mp0) cc_final: 0.8843 (mp0) REVERT: B 149 TYR cc_start: 0.9210 (t80) cc_final: 0.8826 (t80) REVERT: B 235 ARG cc_start: 0.8679 (ttm110) cc_final: 0.8081 (ttm110) REVERT: B 250 TYR cc_start: 0.8713 (m-80) cc_final: 0.7521 (m-80) REVERT: B 263 ASP cc_start: 0.9159 (m-30) cc_final: 0.8912 (m-30) REVERT: B 283 VAL cc_start: 0.9553 (t) cc_final: 0.9247 (t) REVERT: B 291 LEU cc_start: 0.9559 (mt) cc_final: 0.9304 (mt) REVERT: B 322 MET cc_start: 0.8805 (mmm) cc_final: 0.8395 (mmm) REVERT: B 348 MET cc_start: 0.8929 (tpt) cc_final: 0.8454 (tpp) REVERT: B 359 MET cc_start: 0.9114 (ttt) cc_final: 0.8465 (tmm) REVERT: B 375 LYS cc_start: 0.9173 (mmmm) cc_final: 0.8817 (mmmm) REVERT: B 379 SER cc_start: 0.9260 (t) cc_final: 0.8664 (t) REVERT: B 403 ILE cc_start: 0.9336 (mp) cc_final: 0.9007 (tp) REVERT: B 410 ASN cc_start: 0.9176 (m-40) cc_final: 0.8939 (m-40) REVERT: B 415 ASN cc_start: 0.9351 (t0) cc_final: 0.8850 (t0) REVERT: B 420 MET cc_start: 0.9431 (mmm) cc_final: 0.9115 (mmm) REVERT: B 446 ARG cc_start: 0.9100 (mmm-85) cc_final: 0.8520 (mmm-85) REVERT: B 458 MET cc_start: 0.9409 (mmm) cc_final: 0.8843 (mmm) REVERT: B 468 LEU cc_start: 0.9577 (tp) cc_final: 0.9366 (tp) REVERT: B 494 MET cc_start: 0.9545 (ttm) cc_final: 0.9226 (ttm) REVERT: B 530 LYS cc_start: 0.8975 (ptmm) cc_final: 0.8518 (ptmm) REVERT: B 598 MET cc_start: 0.9335 (mtm) cc_final: 0.9072 (mtm) REVERT: B 601 ILE cc_start: 0.9140 (mm) cc_final: 0.8642 (tp) REVERT: B 612 TYR cc_start: 0.8802 (m-80) cc_final: 0.8087 (m-10) REVERT: B 613 TYR cc_start: 0.9275 (t80) cc_final: 0.8932 (t80) REVERT: B 615 MET cc_start: 0.8753 (mmp) cc_final: 0.8240 (mmp) REVERT: B 631 ASP cc_start: 0.9314 (t70) cc_final: 0.8978 (t0) REVERT: B 639 ASP cc_start: 0.9411 (m-30) cc_final: 0.8855 (m-30) REVERT: B 640 MET cc_start: 0.9330 (tpp) cc_final: 0.8805 (tpp) REVERT: B 644 ILE cc_start: 0.9705 (mt) cc_final: 0.9471 (mt) REVERT: B 673 TYR cc_start: 0.9051 (t80) cc_final: 0.8675 (t80) REVERT: B 679 ILE cc_start: 0.9577 (mm) cc_final: 0.9348 (mm) REVERT: C 17 PHE cc_start: 0.8543 (p90) cc_final: 0.7766 (p90) REVERT: C 21 PHE cc_start: 0.8991 (m-10) cc_final: 0.8490 (m-80) REVERT: C 55 TYR cc_start: 0.7298 (t80) cc_final: 0.6947 (t80) REVERT: C 96 MET cc_start: 0.8290 (tpt) cc_final: 0.7951 (tpt) REVERT: C 105 TYR cc_start: 0.8948 (m-80) cc_final: 0.8578 (m-80) REVERT: C 122 PHE cc_start: 0.8712 (m-80) cc_final: 0.8338 (m-80) REVERT: C 204 TYR cc_start: 0.8971 (t80) cc_final: 0.8507 (t80) REVERT: C 207 LEU cc_start: 0.9023 (tt) cc_final: 0.8781 (pp) REVERT: D 109 PHE cc_start: 0.8802 (m-80) cc_final: 0.8204 (m-80) REVERT: D 112 LEU cc_start: 0.8729 (mm) cc_final: 0.7901 (pp) REVERT: D 166 PHE cc_start: 0.7907 (t80) cc_final: 0.7413 (t80) REVERT: D 172 PHE cc_start: 0.9597 (m-80) cc_final: 0.9218 (m-80) REVERT: D 179 TYR cc_start: 0.8364 (t80) cc_final: 0.7940 (t80) REVERT: D 185 MET cc_start: 0.5691 (mmp) cc_final: 0.5470 (mmm) REVERT: D 211 GLU cc_start: 0.9136 (mt-10) cc_final: 0.8881 (mt-10) REVERT: D 244 GLU cc_start: 0.9081 (mp0) cc_final: 0.8788 (mm-30) REVERT: D 318 ASP cc_start: 0.9116 (t0) cc_final: 0.8777 (t70) outliers start: 1 outliers final: 0 residues processed: 665 average time/residue: 0.1134 time to fit residues: 114.0638 Evaluate side-chains 571 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 571 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 151 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 HIS ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.105831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.078054 restraints weight = 52811.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.080848 restraints weight = 31552.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.082966 restraints weight = 21863.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.084487 restraints weight = 16304.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.085632 restraints weight = 12881.287| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.7990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16386 Z= 0.224 Angle : 0.689 8.945 22134 Z= 0.371 Chirality : 0.046 0.270 2360 Planarity : 0.004 0.045 2818 Dihedral : 8.906 148.993 2290 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.18), residues: 1932 helix: 0.83 (0.15), residues: 1125 sheet: -0.21 (0.43), residues: 128 loop : -0.23 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 261 TYR 0.049 0.002 TYR C 142 PHE 0.038 0.002 PHE C 320 TRP 0.060 0.002 TRP D 124 HIS 0.010 0.002 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.22 (16386) covalent geometry : angle 0.68934 / 0.37 (22134) hydrogen bonds : bond 0.04266 / 2.66 ( 871) hydrogen bonds : angle 5.36146 / 3.89 ( 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 653 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 653 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9270 (tptp) cc_final: 0.8806 (tppt) REVERT: A 15 GLU cc_start: 0.9182 (tp30) cc_final: 0.8740 (tp30) REVERT: A 58 LEU cc_start: 0.9798 (mm) cc_final: 0.9503 (pp) REVERT: A 116 GLU cc_start: 0.8421 (mt-10) cc_final: 0.7547 (tt0) REVERT: A 128 PHE cc_start: 0.9617 (t80) cc_final: 0.9404 (t80) REVERT: A 173 LEU cc_start: 0.9547 (mt) cc_final: 0.9295 (mt) REVERT: A 176 ASN cc_start: 0.8598 (t0) cc_final: 0.8026 (m-40) REVERT: A 190 MET cc_start: 0.9190 (mtp) cc_final: 0.8782 (mtp) REVERT: A 191 GLN cc_start: 0.8885 (mm-40) cc_final: 0.8610 (mm-40) REVERT: A 195 LEU cc_start: 0.9623 (mm) cc_final: 0.9023 (tp) REVERT: A 221 LYS cc_start: 0.9135 (tppt) cc_final: 0.8711 (tppt) REVERT: A 235 ARG cc_start: 0.8264 (mtm110) cc_final: 0.8031 (mtm110) REVERT: A 236 TYR cc_start: 0.9022 (t80) cc_final: 0.8177 (t80) REVERT: A 280 ILE cc_start: 0.8501 (pt) cc_final: 0.8190 (mp) REVERT: A 307 TYR cc_start: 0.9421 (t80) cc_final: 0.9119 (t80) REVERT: A 313 HIS cc_start: 0.8849 (m-70) cc_final: 0.8587 (m170) REVERT: A 335 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8999 (mp0) REVERT: A 349 LEU cc_start: 0.9492 (mt) cc_final: 0.9210 (mt) REVERT: A 362 ASP cc_start: 0.8969 (m-30) cc_final: 0.8681 (m-30) REVERT: A 370 ASN cc_start: 0.9580 (m-40) cc_final: 0.9238 (m110) REVERT: A 381 LEU cc_start: 0.9023 (tp) cc_final: 0.8608 (pt) REVERT: A 426 GLU cc_start: 0.9108 (tm-30) cc_final: 0.8417 (tm-30) REVERT: A 466 MET cc_start: 0.9330 (ptp) cc_final: 0.9125 (ptp) REVERT: A 469 HIS cc_start: 0.9050 (t-170) cc_final: 0.8695 (t-170) REVERT: A 479 TYR cc_start: 0.9090 (t80) cc_final: 0.8672 (t80) REVERT: A 501 GLN cc_start: 0.9431 (tp40) cc_final: 0.8583 (tp-100) REVERT: A 515 ASP cc_start: 0.9371 (m-30) cc_final: 0.8746 (m-30) REVERT: A 516 GLN cc_start: 0.9032 (mp10) cc_final: 0.8501 (mp10) REVERT: A 562 LYS cc_start: 0.9715 (ttmm) cc_final: 0.9400 (tttt) REVERT: A 570 MET cc_start: 0.9258 (mtp) cc_final: 0.8962 (mtp) REVERT: A 588 GLN cc_start: 0.9215 (mm-40) cc_final: 0.8562 (tm-30) REVERT: A 628 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8709 (mt-10) REVERT: A 632 MET cc_start: 0.8960 (mmm) cc_final: 0.8621 (mmm) REVERT: A 636 LYS cc_start: 0.9794 (mmtp) cc_final: 0.9577 (mmmm) REVERT: A 640 MET cc_start: 0.9284 (tpp) cc_final: 0.8966 (tpp) REVERT: A 646 GLN cc_start: 0.9129 (pm20) cc_final: 0.8907 (pm20) REVERT: A 647 HIS cc_start: 0.9266 (m-70) cc_final: 0.7640 (m170) REVERT: A 653 SER cc_start: 0.9104 (p) cc_final: 0.8850 (p) REVERT: B 8 LYS cc_start: 0.9403 (tptp) cc_final: 0.9188 (tptp) REVERT: B 30 LYS cc_start: 0.9824 (tmtt) cc_final: 0.9433 (tptt) REVERT: B 87 LYS cc_start: 0.9622 (tptp) cc_final: 0.9362 (tptp) REVERT: B 95 MET cc_start: 0.9272 (mmt) cc_final: 0.8875 (mmt) REVERT: B 106 LEU cc_start: 0.9385 (tt) cc_final: 0.9059 (tt) REVERT: B 116 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8018 (tt0) REVERT: B 149 TYR cc_start: 0.9252 (t80) cc_final: 0.8836 (t80) REVERT: B 181 ASP cc_start: 0.9042 (m-30) cc_final: 0.8839 (m-30) REVERT: B 187 ASP cc_start: 0.9465 (t70) cc_final: 0.9261 (t0) REVERT: B 199 VAL cc_start: 0.8981 (t) cc_final: 0.8736 (p) REVERT: B 235 ARG cc_start: 0.8689 (ttm110) cc_final: 0.8102 (ttm110) REVERT: B 250 TYR cc_start: 0.8747 (m-80) cc_final: 0.7635 (m-80) REVERT: B 260 ASP cc_start: 0.9480 (p0) cc_final: 0.9274 (p0) REVERT: B 263 ASP cc_start: 0.9067 (m-30) cc_final: 0.8818 (m-30) REVERT: B 291 LEU cc_start: 0.9576 (mt) cc_final: 0.9328 (mt) REVERT: B 322 MET cc_start: 0.8877 (mmm) cc_final: 0.8513 (mmm) REVERT: B 348 MET cc_start: 0.8943 (tpt) cc_final: 0.8460 (tpp) REVERT: B 359 MET cc_start: 0.9181 (ttt) cc_final: 0.8578 (tmm) REVERT: B 362 ASP cc_start: 0.8709 (m-30) cc_final: 0.8220 (m-30) REVERT: B 375 LYS cc_start: 0.9245 (mmmm) cc_final: 0.8877 (mmmm) REVERT: B 379 SER cc_start: 0.9274 (t) cc_final: 0.8778 (t) REVERT: B 392 SER cc_start: 0.9267 (m) cc_final: 0.7926 (t) REVERT: B 394 TYR cc_start: 0.9224 (m-80) cc_final: 0.8010 (m-80) REVERT: B 403 ILE cc_start: 0.9213 (mp) cc_final: 0.8960 (tp) REVERT: B 415 ASN cc_start: 0.9348 (t0) cc_final: 0.8897 (t0) REVERT: B 420 MET cc_start: 0.9446 (mmm) cc_final: 0.9109 (mmm) REVERT: B 446 ARG cc_start: 0.9061 (mmm-85) cc_final: 0.8512 (mmm-85) REVERT: B 459 LYS cc_start: 0.9185 (mttp) cc_final: 0.8491 (mtmt) REVERT: B 494 MET cc_start: 0.9495 (ttm) cc_final: 0.9183 (ttm) REVERT: B 574 TYR cc_start: 0.8757 (m-80) cc_final: 0.8470 (m-80) REVERT: B 598 MET cc_start: 0.9283 (mtm) cc_final: 0.9048 (mtm) REVERT: B 601 ILE cc_start: 0.9189 (mm) cc_final: 0.8751 (tp) REVERT: B 612 TYR cc_start: 0.8703 (m-80) cc_final: 0.8008 (m-10) REVERT: B 613 TYR cc_start: 0.9349 (t80) cc_final: 0.8924 (t80) REVERT: B 615 MET cc_start: 0.8787 (mmp) cc_final: 0.8042 (mmt) REVERT: B 631 ASP cc_start: 0.9306 (t70) cc_final: 0.8960 (t0) REVERT: B 639 ASP cc_start: 0.9394 (m-30) cc_final: 0.8826 (m-30) REVERT: B 640 MET cc_start: 0.9309 (tpp) cc_final: 0.8806 (tpp) REVERT: B 667 LEU cc_start: 0.9674 (tp) cc_final: 0.9467 (tp) REVERT: B 673 TYR cc_start: 0.9043 (t80) cc_final: 0.8636 (t80) REVERT: B 679 ILE cc_start: 0.9597 (mm) cc_final: 0.9363 (mm) REVERT: C 17 PHE cc_start: 0.8564 (p90) cc_final: 0.7765 (p90) REVERT: C 20 MET cc_start: 0.8892 (pmm) cc_final: 0.8576 (pmm) REVERT: C 21 PHE cc_start: 0.8971 (m-10) cc_final: 0.8456 (m-80) REVERT: C 24 GLN cc_start: 0.8789 (mp10) cc_final: 0.8573 (mp10) REVERT: C 44 TRP cc_start: 0.7198 (t-100) cc_final: 0.6772 (t-100) REVERT: C 55 TYR cc_start: 0.7658 (t80) cc_final: 0.7188 (t80) REVERT: C 96 MET cc_start: 0.8456 (tpt) cc_final: 0.8036 (tpt) REVERT: C 105 TYR cc_start: 0.9000 (m-80) cc_final: 0.8643 (m-80) REVERT: C 122 PHE cc_start: 0.8554 (m-80) cc_final: 0.8182 (m-10) REVERT: C 157 MET cc_start: 0.9660 (ptm) cc_final: 0.9150 (ppp) REVERT: C 172 PHE cc_start: 0.8689 (m-80) cc_final: 0.8458 (m-80) REVERT: C 204 TYR cc_start: 0.9017 (t80) cc_final: 0.8483 (t80) REVERT: C 315 LEU cc_start: 0.8993 (tt) cc_final: 0.8765 (tt) REVERT: D 96 MET cc_start: 0.8666 (mmp) cc_final: 0.8440 (mmm) REVERT: D 109 PHE cc_start: 0.8773 (m-80) cc_final: 0.8166 (m-80) REVERT: D 112 LEU cc_start: 0.8801 (mm) cc_final: 0.8011 (pp) REVERT: D 166 PHE cc_start: 0.7711 (t80) cc_final: 0.7290 (t80) REVERT: D 169 TYR cc_start: 0.9367 (m-80) cc_final: 0.9045 (m-80) REVERT: D 172 PHE cc_start: 0.9505 (m-80) cc_final: 0.9182 (m-80) REVERT: D 179 TYR cc_start: 0.8384 (t80) cc_final: 0.7895 (t80) REVERT: D 185 MET cc_start: 0.5883 (mmp) cc_final: 0.5677 (mmm) REVERT: D 211 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8875 (mt-10) REVERT: D 244 GLU cc_start: 0.9060 (mp0) cc_final: 0.8750 (mm-30) REVERT: D 318 ASP cc_start: 0.9117 (t0) cc_final: 0.8742 (t70) outliers start: 0 outliers final: 0 residues processed: 653 average time/residue: 0.1120 time to fit residues: 110.8227 Evaluate side-chains 570 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 570 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 114 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.110106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.081778 restraints weight = 50946.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.084839 restraints weight = 30247.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.087013 restraints weight = 20645.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.088633 restraints weight = 15233.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.089842 restraints weight = 11855.115| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.8164 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= 0.141 Angle : 0.652 7.863 22134 Z= 0.350 Chirality : 0.045 0.307 2360 Planarity : 0.004 0.043 2818 Dihedral : 8.543 148.184 2290 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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 are not related in a simple way. whole: 0.49 (0.18), residues: 1932 helix: 0.83 (0.15), residues: 1131 sheet: -0.02 (0.44), residues: 124 loop : -0.29 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 164 TYR 0.041 0.002 TYR C 142 PHE 0.031 0.002 PHE C 168 TRP 0.059 0.002 TRP D 124 HIS 0.014 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (16386) covalent geometry : angle 0.65244 / 0.35 (22134) hydrogen bonds : bond 0.04056 / 2.54 ( 871) hydrogen bonds : angle 5.24665 / 3.83 ( 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 663 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 663 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9295 (tptp) cc_final: 0.8810 (tppt) REVERT: A 15 GLU cc_start: 0.9234 (tp30) cc_final: 0.8751 (tp30) REVERT: A 58 LEU cc_start: 0.9818 (mm) cc_final: 0.9469 (pp) REVERT: A 81 PHE cc_start: 0.9555 (m-80) cc_final: 0.9324 (m-80) REVERT: A 116 GLU cc_start: 0.8403 (mt-10) cc_final: 0.7543 (tt0) REVERT: A 120 ASP cc_start: 0.9325 (m-30) cc_final: 0.9076 (m-30) REVERT: A 129 PHE cc_start: 0.9616 (m-10) cc_final: 0.9383 (m-80) REVERT: A 136 LYS cc_start: 0.9523 (tptp) cc_final: 0.9252 (ttpt) REVERT: A 173 LEU cc_start: 0.9480 (mt) cc_final: 0.9276 (mt) REVERT: A 176 ASN cc_start: 0.8416 (t0) cc_final: 0.7855 (m-40) REVERT: A 190 MET cc_start: 0.9106 (mtp) cc_final: 0.8865 (mtp) REVERT: A 214 LYS cc_start: 0.9471 (mmmt) cc_final: 0.9240 (mmtt) REVERT: A 221 LYS cc_start: 0.9046 (tppt) cc_final: 0.8608 (tppt) REVERT: A 235 ARG cc_start: 0.8324 (mtm110) cc_final: 0.8121 (mtm110) REVERT: A 236 TYR cc_start: 0.8919 (t80) cc_final: 0.8205 (t80) REVERT: A 307 TYR cc_start: 0.9440 (t80) cc_final: 0.9106 (t80) REVERT: A 335 GLU cc_start: 0.9261 (mm-30) cc_final: 0.8868 (mp0) REVERT: A 349 LEU cc_start: 0.9440 (mt) cc_final: 0.9116 (mt) REVERT: A 362 ASP cc_start: 0.8983 (m-30) cc_final: 0.8525 (m-30) REVERT: A 370 ASN cc_start: 0.9530 (m-40) cc_final: 0.9188 (m110) REVERT: A 381 LEU cc_start: 0.9046 (tp) cc_final: 0.8682 (pt) REVERT: A 385 VAL cc_start: 0.9550 (t) cc_final: 0.9296 (t) REVERT: A 426 GLU cc_start: 0.9087 (tm-30) cc_final: 0.8432 (tm-30) REVERT: A 469 HIS cc_start: 0.8884 (t-170) cc_final: 0.8593 (t-170) REVERT: A 479 TYR cc_start: 0.8950 (t80) cc_final: 0.8519 (t80) REVERT: A 515 ASP cc_start: 0.9388 (m-30) cc_final: 0.8746 (m-30) REVERT: A 516 GLN cc_start: 0.9006 (mp10) cc_final: 0.8463 (mp10) REVERT: A 562 LYS cc_start: 0.9795 (ttmm) cc_final: 0.9329 (tttt) REVERT: A 583 SER cc_start: 0.9534 (m) cc_final: 0.9294 (t) REVERT: A 588 GLN cc_start: 0.9234 (mm-40) cc_final: 0.8397 (tp-100) REVERT: A 598 MET cc_start: 0.9180 (ttt) cc_final: 0.8462 (ttt) REVERT: A 599 GLU cc_start: 0.8334 (tm-30) cc_final: 0.7906 (tm-30) REVERT: A 628 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8735 (mt-10) REVERT: A 632 MET cc_start: 0.8982 (mmm) cc_final: 0.8604 (mmm) REVERT: A 636 LYS cc_start: 0.9779 (mmtp) cc_final: 0.9549 (mmmm) REVERT: A 640 MET cc_start: 0.9305 (tpp) cc_final: 0.8976 (tpp) REVERT: A 647 HIS cc_start: 0.9185 (m-70) cc_final: 0.7656 (m170) REVERT: A 650 GLN cc_start: 0.9010 (mt0) cc_final: 0.8133 (mt0) REVERT: A 686 ARG cc_start: 0.7200 (tpt170) cc_final: 0.6937 (tpt170) REVERT: B 8 LYS cc_start: 0.9408 (tptp) cc_final: 0.9185 (tptp) REVERT: B 30 LYS cc_start: 0.9808 (tmtt) cc_final: 0.9390 (tptt) REVERT: B 82 LYS cc_start: 0.9453 (ptpp) cc_final: 0.9155 (ptpt) REVERT: B 95 MET cc_start: 0.9339 (mmt) cc_final: 0.9034 (mmt) REVERT: B 99 LYS cc_start: 0.9576 (mmmt) cc_final: 0.9247 (mttt) REVERT: B 106 LEU cc_start: 0.9398 (tt) cc_final: 0.8899 (tt) REVERT: B 107 LYS cc_start: 0.9506 (mppt) cc_final: 0.9084 (mptt) REVERT: B 116 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8058 (tt0) REVERT: B 149 TYR cc_start: 0.9268 (t80) cc_final: 0.8679 (t80) REVERT: B 202 ASN cc_start: 0.6908 (p0) cc_final: 0.6592 (p0) REVERT: B 211 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8770 (mm-30) REVERT: B 235 ARG cc_start: 0.8762 (ttm110) cc_final: 0.8220 (ttm110) REVERT: B 250 TYR cc_start: 0.8667 (m-80) cc_final: 0.7481 (m-80) REVERT: B 263 ASP cc_start: 0.9124 (m-30) cc_final: 0.8681 (m-30) REVERT: B 283 VAL cc_start: 0.9537 (t) cc_final: 0.9224 (t) REVERT: B 286 ASP cc_start: 0.8735 (m-30) cc_final: 0.7911 (m-30) REVERT: B 291 LEU cc_start: 0.9563 (mt) cc_final: 0.9324 (mt) REVERT: B 322 MET cc_start: 0.8895 (mmm) cc_final: 0.8475 (mmm) REVERT: B 348 MET cc_start: 0.9003 (tpt) cc_final: 0.8541 (tpp) REVERT: B 359 MET cc_start: 0.9151 (ttt) cc_final: 0.8456 (tmm) REVERT: B 362 ASP cc_start: 0.8701 (m-30) cc_final: 0.7496 (m-30) REVERT: B 375 LYS cc_start: 0.9251 (mmmm) cc_final: 0.8875 (mmmm) REVERT: B 379 SER cc_start: 0.9153 (t) cc_final: 0.8635 (t) REVERT: B 392 SER cc_start: 0.9236 (m) cc_final: 0.8134 (t) REVERT: B 394 TYR cc_start: 0.9198 (m-80) cc_final: 0.8884 (m-80) REVERT: B 403 ILE cc_start: 0.9327 (mp) cc_final: 0.9040 (tp) REVERT: B 415 ASN cc_start: 0.9361 (t0) cc_final: 0.8898 (t0) REVERT: B 416 ILE cc_start: 0.9715 (mt) cc_final: 0.9490 (mt) REVERT: B 420 MET cc_start: 0.9461 (mmm) cc_final: 0.9087 (mmm) REVERT: B 446 ARG cc_start: 0.9016 (mmm-85) cc_final: 0.8090 (mmm-85) REVERT: B 468 LEU cc_start: 0.9501 (tp) cc_final: 0.9228 (tp) REVERT: B 469 HIS cc_start: 0.8747 (t-170) cc_final: 0.8532 (t70) REVERT: B 494 MET cc_start: 0.9531 (ttm) cc_final: 0.9229 (ttm) REVERT: B 530 LYS cc_start: 0.9022 (ptmm) cc_final: 0.8397 (ptmm) REVERT: B 598 MET cc_start: 0.9349 (mtm) cc_final: 0.9093 (mtm) REVERT: B 601 ILE cc_start: 0.9187 (mm) cc_final: 0.8667 (tp) REVERT: B 613 TYR cc_start: 0.9356 (t80) cc_final: 0.8938 (t80) REVERT: B 615 MET cc_start: 0.8779 (mmp) cc_final: 0.8230 (mmp) REVERT: B 631 ASP cc_start: 0.9335 (t70) cc_final: 0.9038 (t0) REVERT: B 636 LYS cc_start: 0.9615 (mptt) cc_final: 0.9342 (mmtt) REVERT: B 640 MET cc_start: 0.9305 (tpp) cc_final: 0.8790 (tpp) REVERT: B 641 ILE cc_start: 0.9721 (mm) cc_final: 0.9494 (mm) REVERT: B 667 LEU cc_start: 0.9692 (tp) cc_final: 0.9490 (tp) REVERT: B 679 ILE cc_start: 0.9585 (mm) cc_final: 0.9384 (mm) REVERT: C 17 PHE cc_start: 0.8558 (p90) cc_final: 0.7827 (p90) REVERT: C 21 PHE cc_start: 0.8934 (m-10) cc_final: 0.8467 (m-80) REVERT: C 55 TYR cc_start: 0.7564 (t80) cc_final: 0.7323 (t80) REVERT: C 96 MET cc_start: 0.8508 (tpt) cc_final: 0.7983 (tpt) REVERT: C 105 TYR cc_start: 0.8942 (m-80) cc_final: 0.8611 (m-80) REVERT: C 122 PHE cc_start: 0.8594 (m-80) cc_final: 0.8234 (m-10) REVERT: C 172 PHE cc_start: 0.8618 (m-80) cc_final: 0.8415 (m-80) REVERT: C 204 TYR cc_start: 0.9013 (t80) cc_final: 0.8704 (t80) REVERT: C 207 LEU cc_start: 0.8970 (tt) cc_final: 0.8704 (pp) REVERT: D 109 PHE cc_start: 0.8701 (m-80) cc_final: 0.8469 (m-80) REVERT: D 112 LEU cc_start: 0.8842 (mm) cc_final: 0.8008 (pp) REVERT: D 157 MET cc_start: 0.9488 (ppp) cc_final: 0.8756 (ppp) REVERT: D 166 PHE cc_start: 0.7590 (t80) cc_final: 0.7274 (t80) REVERT: D 169 TYR cc_start: 0.9344 (m-80) cc_final: 0.8876 (m-80) REVERT: D 172 PHE cc_start: 0.9481 (m-80) cc_final: 0.9151 (m-80) REVERT: D 179 TYR cc_start: 0.8347 (t80) cc_final: 0.7860 (t80) REVERT: D 198 GLU cc_start: 0.9471 (pm20) cc_final: 0.9054 (mp0) REVERT: D 244 GLU cc_start: 0.9083 (mp0) cc_final: 0.8844 (mm-30) REVERT: D 318 ASP cc_start: 0.9087 (t0) cc_final: 0.8677 (t70) outliers start: 0 outliers final: 0 residues processed: 663 average time/residue: 0.1239 time to fit residues: 124.0651 Evaluate side-chains 577 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 577 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 165 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN A 365 ASN A 387 GLN A 390 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.110647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.082905 restraints weight = 51278.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.085851 restraints weight = 30397.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.087967 restraints weight = 20851.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.089542 restraints weight = 15356.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.090714 restraints weight = 11936.225| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.8350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16386 Z= 0.145 Angle : 0.668 8.452 22134 Z= 0.359 Chirality : 0.045 0.328 2360 Planarity : 0.004 0.049 2818 Dihedral : 8.521 149.290 2290 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.06 % Allowed : 0.23 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.18), residues: 1932 helix: 0.79 (0.15), residues: 1142 sheet: 0.02 (0.44), residues: 124 loop : -0.32 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 604 TYR 0.041 0.002 TYR C 142 PHE 0.030 0.002 PHE C 168 TRP 0.060 0.002 TRP D 124 HIS 0.012 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (16386) covalent geometry : angle 0.66765 / 0.36 (22134) hydrogen bonds : bond 0.04092 / 2.55 ( 871) hydrogen bonds : angle 5.29077 / 3.86 ( 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 661 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 660 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9266 (tptp) cc_final: 0.8767 (tppt) REVERT: A 15 GLU cc_start: 0.9195 (tp30) cc_final: 0.8695 (tp30) REVERT: A 81 PHE cc_start: 0.9511 (m-80) cc_final: 0.9249 (m-80) REVERT: A 87 LYS cc_start: 0.9441 (tppt) cc_final: 0.9153 (tptp) REVERT: A 95 MET cc_start: 0.9096 (mmm) cc_final: 0.8689 (tpt) REVERT: A 116 GLU cc_start: 0.8615 (mt-10) cc_final: 0.7572 (tt0) REVERT: A 120 ASP cc_start: 0.9256 (m-30) cc_final: 0.9047 (m-30) REVERT: A 129 PHE cc_start: 0.9596 (m-10) cc_final: 0.9334 (m-80) REVERT: A 136 LYS cc_start: 0.9531 (tptp) cc_final: 0.9288 (ttpt) REVERT: A 173 LEU cc_start: 0.9493 (mt) cc_final: 0.9174 (mt) REVERT: A 176 ASN cc_start: 0.8483 (t0) cc_final: 0.7876 (m-40) REVERT: A 190 MET cc_start: 0.9100 (mtp) cc_final: 0.8850 (mtp) REVERT: A 191 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8126 (mm-40) REVERT: A 214 LYS cc_start: 0.9474 (mmmt) cc_final: 0.9254 (mmtt) REVERT: A 236 TYR cc_start: 0.8915 (t80) cc_final: 0.8192 (t80) REVERT: A 286 ASP cc_start: 0.9268 (m-30) cc_final: 0.8816 (m-30) REVERT: A 307 TYR cc_start: 0.9423 (t80) cc_final: 0.9130 (t80) REVERT: A 349 LEU cc_start: 0.9435 (mt) cc_final: 0.9153 (mt) REVERT: A 362 ASP cc_start: 0.8880 (m-30) cc_final: 0.8494 (m-30) REVERT: A 370 ASN cc_start: 0.9491 (m-40) cc_final: 0.9214 (m110) REVERT: A 375 LYS cc_start: 0.8967 (mmpt) cc_final: 0.8667 (mmmt) REVERT: A 381 LEU cc_start: 0.9064 (tp) cc_final: 0.8616 (pt) REVERT: A 385 VAL cc_start: 0.9507 (t) cc_final: 0.9173 (t) REVERT: A 386 LEU cc_start: 0.9514 (mt) cc_final: 0.9258 (mt) REVERT: A 469 HIS cc_start: 0.8811 (t-170) cc_final: 0.8525 (t-170) REVERT: A 479 TYR cc_start: 0.8943 (t80) cc_final: 0.8446 (t80) REVERT: A 515 ASP cc_start: 0.9382 (m-30) cc_final: 0.8741 (m-30) REVERT: A 516 GLN cc_start: 0.8996 (mp10) cc_final: 0.8502 (mp10) REVERT: A 562 LYS cc_start: 0.9791 (ttmm) cc_final: 0.9505 (tttp) REVERT: A 588 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8397 (tp-100) REVERT: A 598 MET cc_start: 0.9117 (ttt) cc_final: 0.8451 (ttt) REVERT: A 599 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7796 (tm-30) REVERT: A 604 ARG cc_start: 0.8929 (mmm-85) cc_final: 0.8726 (mmm160) REVERT: A 628 GLU cc_start: 0.9255 (mt-10) cc_final: 0.8814 (mt-10) REVERT: A 632 MET cc_start: 0.9002 (mmm) cc_final: 0.8677 (mmm) REVERT: A 634 MET cc_start: 0.9345 (mmt) cc_final: 0.9127 (mmt) REVERT: A 636 LYS cc_start: 0.9790 (mmtp) cc_final: 0.9556 (mmmm) REVERT: A 640 MET cc_start: 0.9294 (tpp) cc_final: 0.8817 (tpp) REVERT: A 641 ILE cc_start: 0.9841 (mm) cc_final: 0.9632 (mm) REVERT: A 646 GLN cc_start: 0.9122 (pm20) cc_final: 0.8916 (pm20) REVERT: A 647 HIS cc_start: 0.9190 (m-70) cc_final: 0.7705 (m170) REVERT: A 650 GLN cc_start: 0.8983 (mt0) cc_final: 0.8083 (mt0) REVERT: A 653 SER cc_start: 0.9147 (p) cc_final: 0.8901 (p) REVERT: A 675 HIS cc_start: 0.9364 (t-90) cc_final: 0.8694 (t70) REVERT: A 677 ARG cc_start: 0.9369 (mmm-85) cc_final: 0.8788 (mmm-85) REVERT: A 679 ILE cc_start: 0.9581 (mm) cc_final: 0.9371 (mm) REVERT: B 8 LYS cc_start: 0.9380 (tptp) cc_final: 0.9166 (tptp) REVERT: B 30 LYS cc_start: 0.9810 (tmtt) cc_final: 0.9378 (tptt) REVERT: B 82 LYS cc_start: 0.9436 (ptpp) cc_final: 0.9158 (ptpt) REVERT: B 87 LYS cc_start: 0.9580 (tptp) cc_final: 0.9350 (tptp) REVERT: B 95 MET cc_start: 0.9350 (mmt) cc_final: 0.8941 (mmt) REVERT: B 99 LYS cc_start: 0.9589 (mmmt) cc_final: 0.9262 (mttt) REVERT: B 106 LEU cc_start: 0.9416 (tt) cc_final: 0.8893 (tt) REVERT: B 107 LYS cc_start: 0.9488 (mppt) cc_final: 0.9054 (mptt) REVERT: B 116 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8041 (tt0) REVERT: B 143 LEU cc_start: 0.9536 (tp) cc_final: 0.9212 (tp) REVERT: B 147 GLN cc_start: 0.9495 (mt0) cc_final: 0.9098 (mt0) REVERT: B 149 TYR cc_start: 0.9405 (t80) cc_final: 0.8395 (t80) REVERT: B 191 GLN cc_start: 0.9189 (mm-40) cc_final: 0.8937 (mm-40) REVERT: B 211 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8676 (mm-30) REVERT: B 235 ARG cc_start: 0.8684 (ttm110) cc_final: 0.8258 (ttm110) REVERT: B 250 TYR cc_start: 0.8544 (m-80) cc_final: 0.7317 (m-80) REVERT: B 263 ASP cc_start: 0.9133 (m-30) cc_final: 0.8753 (m-30) REVERT: B 283 VAL cc_start: 0.9509 (t) cc_final: 0.9171 (t) REVERT: B 286 ASP cc_start: 0.8633 (m-30) cc_final: 0.7782 (m-30) REVERT: B 291 LEU cc_start: 0.9564 (mt) cc_final: 0.9329 (mt) REVERT: B 322 MET cc_start: 0.8835 (mmm) cc_final: 0.8441 (mmm) REVERT: B 348 MET cc_start: 0.8923 (tpt) cc_final: 0.8405 (tpp) REVERT: B 359 MET cc_start: 0.9108 (ttt) cc_final: 0.8479 (tmm) REVERT: B 362 ASP cc_start: 0.8651 (m-30) cc_final: 0.7408 (m-30) REVERT: B 375 LYS cc_start: 0.9218 (mmmm) cc_final: 0.8843 (mmmm) REVERT: B 379 SER cc_start: 0.9241 (t) cc_final: 0.8623 (t) REVERT: B 392 SER cc_start: 0.9199 (m) cc_final: 0.8474 (m) REVERT: B 403 ILE cc_start: 0.9279 (mp) cc_final: 0.9023 (tp) REVERT: B 410 ASN cc_start: 0.8868 (m-40) cc_final: 0.8621 (m-40) REVERT: B 411 LEU cc_start: 0.9315 (mp) cc_final: 0.9109 (mp) REVERT: B 415 ASN cc_start: 0.9374 (t0) cc_final: 0.8909 (t0) REVERT: B 420 MET cc_start: 0.9465 (mmm) cc_final: 0.9110 (mmm) REVERT: B 446 ARG cc_start: 0.8910 (mmm-85) cc_final: 0.8189 (mmm-85) REVERT: B 458 MET cc_start: 0.9358 (mmm) cc_final: 0.8763 (mmm) REVERT: B 459 LYS cc_start: 0.9176 (mttp) cc_final: 0.8505 (mtmt) REVERT: B 494 MET cc_start: 0.9456 (ttm) cc_final: 0.9193 (ttm) REVERT: B 500 ILE cc_start: 0.9638 (mt) cc_final: 0.8977 (mt) REVERT: B 530 LYS cc_start: 0.9105 (ptmm) cc_final: 0.8594 (ptmm) REVERT: B 575 ARG cc_start: 0.8771 (mtm-85) cc_final: 0.7983 (mpp80) REVERT: B 586 TYR cc_start: 0.9297 (m-80) cc_final: 0.8661 (m-10) REVERT: B 588 GLN cc_start: 0.9451 (mm-40) cc_final: 0.9140 (mm-40) REVERT: B 598 MET cc_start: 0.9348 (mtm) cc_final: 0.9075 (mtm) REVERT: B 601 ILE cc_start: 0.9027 (mm) cc_final: 0.8632 (tp) REVERT: B 613 TYR cc_start: 0.9276 (t80) cc_final: 0.8712 (t80) REVERT: B 615 MET cc_start: 0.8821 (mmp) cc_final: 0.8367 (mmm) REVERT: B 631 ASP cc_start: 0.9253 (t70) cc_final: 0.8929 (t0) REVERT: B 636 LYS cc_start: 0.9646 (mptt) cc_final: 0.9303 (mmtt) REVERT: B 639 ASP cc_start: 0.9443 (m-30) cc_final: 0.8854 (m-30) REVERT: B 640 MET cc_start: 0.9259 (tpp) cc_final: 0.8706 (tpp) REVERT: B 641 ILE cc_start: 0.9713 (mm) cc_final: 0.9470 (mm) REVERT: B 648 ILE cc_start: 0.9261 (mm) cc_final: 0.9056 (mm) REVERT: B 673 TYR cc_start: 0.8950 (t80) cc_final: 0.8682 (t80) REVERT: B 679 ILE cc_start: 0.9593 (mm) cc_final: 0.9372 (mm) REVERT: B 684 TYR cc_start: 0.7460 (t80) cc_final: 0.7260 (t80) REVERT: C 17 PHE cc_start: 0.8552 (p90) cc_final: 0.7804 (p90) REVERT: C 21 PHE cc_start: 0.8916 (m-10) cc_final: 0.8477 (m-80) REVERT: C 69 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8646 (pp30) REVERT: C 96 MET cc_start: 0.8508 (tpt) cc_final: 0.7920 (tpt) REVERT: C 105 TYR cc_start: 0.8987 (m-80) cc_final: 0.8659 (m-80) REVERT: C 122 PHE cc_start: 0.8602 (m-80) cc_final: 0.8228 (m-10) REVERT: C 157 MET cc_start: 0.9745 (ptm) cc_final: 0.9181 (ppp) REVERT: C 204 TYR cc_start: 0.9019 (t80) cc_final: 0.8667 (t80) REVERT: D 109 PHE cc_start: 0.8661 (m-80) cc_final: 0.8429 (m-80) REVERT: D 112 LEU cc_start: 0.8838 (mm) cc_final: 0.8051 (pp) REVERT: D 157 MET cc_start: 0.9485 (ppp) cc_final: 0.8733 (ppp) REVERT: D 166 PHE cc_start: 0.7643 (t80) cc_final: 0.7308 (t80) REVERT: D 169 TYR cc_start: 0.9349 (m-80) cc_final: 0.8905 (m-80) REVERT: D 172 PHE cc_start: 0.9384 (m-80) cc_final: 0.9080 (m-80) REVERT: D 179 TYR cc_start: 0.8336 (t80) cc_final: 0.7807 (t80) REVERT: D 198 GLU cc_start: 0.9417 (pm20) cc_final: 0.9192 (mp0) REVERT: D 244 GLU cc_start: 0.9069 (mp0) cc_final: 0.8832 (mm-30) REVERT: D 318 ASP cc_start: 0.8940 (t0) cc_final: 0.8524 (t70) outliers start: 1 outliers final: 0 residues processed: 660 average time/residue: 0.1272 time to fit residues: 126.0014 Evaluate side-chains 580 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 579 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 chunk 125 optimal weight: 0.0570 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.115637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.087925 restraints weight = 51181.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.090937 restraints weight = 30730.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.092975 restraints weight = 20865.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.094515 restraints weight = 15489.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.095725 restraints weight = 12038.412| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.8522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16386 Z= 0.136 Angle : 0.660 9.051 22134 Z= 0.353 Chirality : 0.045 0.329 2360 Planarity : 0.004 0.041 2818 Dihedral : 8.469 149.622 2290 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.19), residues: 1932 helix: 0.84 (0.15), residues: 1138 sheet: -0.47 (0.41), residues: 144 loop : -0.27 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 235 TYR 0.044 0.002 TYR C 142 PHE 0.045 0.002 PHE C 109 TRP 0.058 0.002 TRP D 124 HIS 0.009 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (16386) covalent geometry : angle 0.65958 / 0.35 (22134) hydrogen bonds : bond 0.04012 / 2.48 ( 871) hydrogen bonds : angle 5.23852 / 3.82 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3128.52 seconds wall clock time: 55 minutes 7.05 seconds (3307.05 seconds total)