Starting phenix.real_space_refine on Fri Jul 3 19:45:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzo_45072/07_2026/9bzo_45072_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzo_45072/07_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_45072/07_2026/9bzo_45072_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzo_45072/07_2026/9bzo_45072_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bzo_45072/07_2026/9bzo_45072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzo_45072/07_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-dev-6108/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, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.84, per 1000 atoms: 0.24 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: 1.26 Conformation dependent library (CDL) restraints added in 701.2 milliseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.104A 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: 2.88 Time building geometry restraints manager: 1.71 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 3.060 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 3.060 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 3.060 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.991 3.060 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: 1.770 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.870 Find NCS groups from input model: 0.370 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.740 ------------------------------------------------------------------------------- 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 : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.1479 time to fit residues: 203.4790 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 : 0.621 ------------------------------------------------------------------------------- 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 201 HIS ** 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 = 0.119828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.092232 restraints weight = 42113.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.094643 restraints weight = 28086.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.096833 restraints weight = 20912.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.098040 restraints weight = 17044.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.098917 restraints weight = 14220.174| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (14 function evaluations) r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16386 Z= 0.187 Angle : 0.642 9.393 22134 Z= 0.349 Chirality : 0.044 0.202 2360 Planarity : 0.004 0.053 2818 Dihedral : 9.532 128.635 2290 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.35 % Allowed : 2.86 % 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: 1.25 (0.19), residues: 1932 helix: 1.22 (0.15), residues: 1136 sheet: 0.02 (0.41), residues: 138 loop : 0.54 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 665 TYR 0.022 0.002 TYR B 36 PHE 0.041 0.003 PHE C 166 TRP 0.011 0.002 TRP B 558 HIS 0.009 0.002 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 (16386) covalent geometry : angle 0.64180 / 0.35 (22134) hydrogen bonds : bond 0.04737 / 2.96 ( 871) hydrogen bonds : angle 5.23323 / 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 771 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 765 time to evaluate : 0.529 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: A 89 PHE cc_start: 0.8743 (t80) cc_final: 0.8497 (t80) REVERT: A 101 TYR cc_start: 0.9409 (m-80) cc_final: 0.9119 (m-10) REVERT: A 109 ASN cc_start: 0.9541 (p0) cc_final: 0.9279 (m-40) REVERT: A 115 LEU cc_start: 0.9418 (mt) cc_final: 0.9108 (mt) REVERT: A 119 GLU cc_start: 0.9137 (mp0) cc_final: 0.7954 (tm-30) REVERT: A 120 ASP cc_start: 0.8983 (m-30) cc_final: 0.8515 (m-30) REVERT: A 122 ILE cc_start: 0.9451 (mt) cc_final: 0.9233 (mt) REVERT: A 144 MET cc_start: 0.8924 (mtm) cc_final: 0.8532 (mtm) REVERT: A 147 GLN cc_start: 0.8948 (mt0) cc_final: 0.8431 (mt0) REVERT: A 149 TYR cc_start: 0.9482 (t80) cc_final: 0.9045 (t80) REVERT: A 168 VAL cc_start: 0.8771 (t) cc_final: 0.8298 (t) REVERT: A 173 LEU cc_start: 0.9450 (mt) cc_final: 0.9213 (mt) REVERT: A 199 VAL cc_start: 0.9233 (t) cc_final: 0.8961 (t) REVERT: A 236 TYR cc_start: 0.8741 (t80) cc_final: 0.8218 (t80) REVERT: A 278 LEU cc_start: 0.9488 (tp) cc_final: 0.9087 (tp) REVERT: A 280 ILE cc_start: 0.8641 (pt) cc_final: 0.8381 (pt) REVERT: A 300 VAL cc_start: 0.9579 (m) cc_final: 0.9131 (m) REVERT: A 326 PHE cc_start: 0.9517 (m-80) cc_final: 0.9188 (m-80) REVERT: A 349 LEU cc_start: 0.9528 (mt) cc_final: 0.9289 (mt) REVERT: A 359 MET cc_start: 0.8560 (ttp) cc_final: 0.8244 (ttp) REVERT: A 370 ASN cc_start: 0.9445 (m-40) cc_final: 0.8988 (m-40) REVERT: A 375 LYS cc_start: 0.8656 (mmmt) cc_final: 0.8216 (mmtm) REVERT: A 377 LYS cc_start: 0.8703 (mttt) cc_final: 0.8185 (mtmm) REVERT: A 386 LEU cc_start: 0.9317 (mt) cc_final: 0.9114 (mt) REVERT: A 407 ILE cc_start: 0.8837 (mt) cc_final: 0.8522 (mt) REVERT: A 408 SER cc_start: 0.9184 (p) cc_final: 0.8983 (t) REVERT: A 459 LYS cc_start: 0.9019 (mttp) cc_final: 0.8315 (mtpt) REVERT: A 468 LEU cc_start: 0.9758 (tp) cc_final: 0.9551 (tp) REVERT: A 493 MET cc_start: 0.9288 (tmm) cc_final: 0.8891 (tmm) REVERT: A 501 GLN cc_start: 0.9494 (mm-40) cc_final: 0.8819 (tp-100) REVERT: A 515 ASP cc_start: 0.9213 (m-30) cc_final: 0.8625 (m-30) REVERT: A 516 GLN cc_start: 0.9096 (mp10) cc_final: 0.8706 (mp10) REVERT: A 561 LEU cc_start: 0.9649 (tp) cc_final: 0.9368 (tp) REVERT: A 598 MET cc_start: 0.8515 (ttt) cc_final: 0.8258 (ttt) REVERT: A 615 MET cc_start: 0.8651 (mmp) cc_final: 0.8266 (mmp) REVERT: A 650 GLN cc_start: 0.8299 (mt0) cc_final: 0.8032 (mt0) REVERT: A 677 ARG cc_start: 0.9299 (mmm-85) cc_final: 0.8690 (mmm-85) REVERT: B 8 LYS cc_start: 0.9317 (tptp) cc_final: 0.8979 (tptp) REVERT: B 16 ILE cc_start: 0.9726 (pt) cc_final: 0.9445 (pt) REVERT: B 30 LYS cc_start: 0.9745 (tmtt) cc_final: 0.9390 (tptt) REVERT: B 41 ILE cc_start: 0.9579 (mm) cc_final: 0.9295 (mt) REVERT: B 51 LEU cc_start: 0.9039 (tp) cc_final: 0.8710 (tp) REVERT: B 67 GLU cc_start: 0.9377 (mm-30) cc_final: 0.9160 (mm-30) REVERT: B 95 MET cc_start: 0.9539 (mmp) cc_final: 0.9071 (mmp) REVERT: B 144 MET cc_start: 0.9500 (mtm) cc_final: 0.9238 (mtm) REVERT: B 195 LEU cc_start: 0.9389 (mt) cc_final: 0.9179 (mt) REVERT: B 211 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8280 (mm-30) REVERT: B 227 MET cc_start: 0.9163 (mtp) cc_final: 0.8804 (mtp) REVERT: B 250 TYR cc_start: 0.8217 (m-80) cc_final: 0.7174 (m-80) REVERT: B 286 ASP cc_start: 0.8519 (m-30) cc_final: 0.8225 (m-30) REVERT: B 291 LEU cc_start: 0.9573 (mt) cc_final: 0.9361 (mt) REVERT: B 322 MET cc_start: 0.8647 (mmm) cc_final: 0.8124 (mmm) REVERT: B 326 PHE cc_start: 0.9042 (m-80) cc_final: 0.8652 (m-80) REVERT: B 375 LYS cc_start: 0.9244 (mmmm) cc_final: 0.9033 (mmmm) REVERT: B 379 SER cc_start: 0.8979 (t) cc_final: 0.8538 (t) REVERT: B 410 ASN cc_start: 0.8773 (m110) cc_final: 0.8407 (m110) REVERT: B 420 MET cc_start: 0.9096 (mmm) cc_final: 0.8884 (mmm) REVERT: B 458 MET cc_start: 0.9603 (mmm) cc_final: 0.9302 (mmm) REVERT: B 493 MET cc_start: 0.9242 (ppp) cc_final: 0.9037 (ppp) REVERT: B 500 ILE cc_start: 0.9658 (mt) cc_final: 0.9414 (mt) REVERT: B 558 TRP cc_start: 0.9086 (m100) cc_final: 0.8631 (m100) REVERT: B 570 MET cc_start: 0.8831 (mmm) cc_final: 0.8167 (mmm) REVERT: B 598 MET cc_start: 0.9222 (mtm) cc_final: 0.8927 (mtm) REVERT: B 612 TYR cc_start: 0.9178 (m-80) cc_final: 0.7893 (m-80) REVERT: B 613 TYR cc_start: 0.9136 (t80) cc_final: 0.8843 (t80) REVERT: B 648 ILE cc_start: 0.9364 (mm) cc_final: 0.9026 (mm) REVERT: B 656 LEU cc_start: 0.9591 (mt) cc_final: 0.9368 (mt) REVERT: B 673 TYR cc_start: 0.9095 (t80) cc_final: 0.8855 (t80) REVERT: C 17 PHE cc_start: 0.8654 (p90) cc_final: 0.7558 (p90) REVERT: C 21 PHE cc_start: 0.9215 (m-10) cc_final: 0.8577 (m-80) REVERT: C 92 PHE cc_start: 0.8102 (t80) cc_final: 0.7869 (t80) REVERT: C 96 MET cc_start: 0.8502 (tpt) cc_final: 0.8218 (tpt) REVERT: C 100 VAL cc_start: 0.6306 (t) cc_final: 0.6021 (t) REVERT: C 112 LEU cc_start: 0.7179 (mt) cc_final: 0.6951 (pp) REVERT: C 157 MET cc_start: 0.9570 (mtm) cc_final: 0.9222 (ptm) REVERT: C 163 LEU cc_start: 0.9609 (tt) cc_final: 0.9192 (tt) REVERT: C 178 PHE cc_start: 0.9211 (m-80) cc_final: 0.8998 (m-10) REVERT: C 214 ASN cc_start: 0.8502 (m-40) cc_final: 0.7948 (p0) REVERT: C 227 PHE cc_start: 0.7336 (m-80) cc_final: 0.7103 (m-80) REVERT: C 263 ASN cc_start: 0.6653 (m-40) cc_final: 0.6358 (m110) REVERT: C 285 ILE cc_start: 0.8971 (mm) cc_final: 0.8720 (mm) REVERT: D 17 PHE cc_start: 0.5317 (m-80) cc_final: 0.5063 (m-80) REVERT: D 21 PHE cc_start: 0.9147 (m-10) cc_final: 0.8883 (m-10) REVERT: D 74 MET cc_start: 0.8462 (mmp) cc_final: 0.7556 (mmt) REVERT: D 109 PHE cc_start: 0.8426 (m-80) cc_final: 0.7921 (m-10) REVERT: D 172 PHE cc_start: 0.9256 (m-80) cc_final: 0.8856 (m-80) REVERT: D 181 GLN cc_start: 0.7469 (pt0) cc_final: 0.6670 (pm20) REVERT: D 189 GLU cc_start: 0.9193 (pt0) cc_final: 0.8476 (pt0) REVERT: D 214 ASN cc_start: 0.9142 (m-40) cc_final: 0.8731 (p0) REVERT: D 239 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8392 (pp20) outliers start: 6 outliers final: 1 residues processed: 770 average time/residue: 0.1275 time to fit residues: 145.1463 Evaluate side-chains 620 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 618 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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: 10.0000 chunk 131 optimal weight: 0.7980 chunk 164 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 182 optimal weight: 4.9990 chunk 159 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 158 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** 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 ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN D 25 ASN D 71 ASN D 216 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.113404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.083720 restraints weight = 49264.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.087021 restraints weight = 30421.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.089513 restraints weight = 21209.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.091234 restraints weight = 15677.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.092436 restraints weight = 12358.180| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16386 Z= 0.152 Angle : 0.590 6.961 22134 Z= 0.317 Chirality : 0.042 0.173 2360 Planarity : 0.004 0.078 2818 Dihedral : 9.058 140.824 2290 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.06 % Allowed : 2.74 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.19), residues: 1932 helix: 1.13 (0.15), residues: 1134 sheet: -0.27 (0.39), residues: 144 loop : 0.37 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 164 TYR 0.019 0.001 TYR B 118 PHE 0.034 0.003 PHE C 109 TRP 0.007 0.001 TRP B 558 HIS 0.008 0.001 HIS A 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (16386) covalent geometry : angle 0.58960 / 0.32 (22134) hydrogen bonds : bond 0.04192 / 2.64 ( 871) hydrogen bonds : angle 5.00029 / 3.60 ( 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 721 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 720 time to evaluate : 0.640 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: A 29 ASP cc_start: 0.9323 (t0) cc_final: 0.9035 (t70) REVERT: A 67 GLU cc_start: 0.9591 (mp0) cc_final: 0.9322 (pm20) REVERT: A 101 TYR cc_start: 0.9427 (m-80) cc_final: 0.9016 (m-10) REVERT: A 115 LEU cc_start: 0.9562 (mt) cc_final: 0.9159 (mt) REVERT: A 122 ILE cc_start: 0.9461 (mt) cc_final: 0.9252 (mt) REVERT: A 144 MET cc_start: 0.8820 (mtm) cc_final: 0.8405 (mtm) REVERT: A 147 GLN cc_start: 0.8889 (mt0) cc_final: 0.8292 (mt0) REVERT: A 150 GLN cc_start: 0.9227 (tp40) cc_final: 0.9015 (tp40) REVERT: A 173 LEU cc_start: 0.9501 (mt) cc_final: 0.9284 (mt) REVERT: A 176 ASN cc_start: 0.8416 (t0) cc_final: 0.8076 (t0) REVERT: A 190 MET cc_start: 0.9180 (mtp) cc_final: 0.8930 (mtp) REVERT: A 199 VAL cc_start: 0.9496 (t) cc_final: 0.9231 (t) REVERT: A 205 LYS cc_start: 0.8206 (mttm) cc_final: 0.7964 (mttm) REVERT: A 224 VAL cc_start: 0.8846 (p) cc_final: 0.8409 (t) REVERT: A 235 ARG cc_start: 0.8448 (mtm110) cc_final: 0.8089 (mtm110) REVERT: A 236 TYR cc_start: 0.8853 (t80) cc_final: 0.8321 (t80) REVERT: A 279 SER cc_start: 0.8101 (m) cc_final: 0.7195 (p) REVERT: A 283 VAL cc_start: 0.9167 (t) cc_final: 0.8883 (t) REVERT: A 291 LEU cc_start: 0.9526 (mt) cc_final: 0.9110 (mp) REVERT: A 316 GLU cc_start: 0.9451 (tt0) cc_final: 0.9211 (tt0) REVERT: A 326 PHE cc_start: 0.9661 (m-10) cc_final: 0.9327 (m-80) REVERT: A 359 MET cc_start: 0.8663 (ttp) cc_final: 0.8386 (ttp) REVERT: A 362 ASP cc_start: 0.9023 (m-30) cc_final: 0.8633 (m-30) REVERT: A 370 ASN cc_start: 0.9450 (m-40) cc_final: 0.8945 (m-40) REVERT: A 375 LYS cc_start: 0.8847 (mmmt) cc_final: 0.8493 (mmtm) REVERT: A 377 LYS cc_start: 0.8824 (mttt) cc_final: 0.8237 (mtmm) REVERT: A 407 ILE cc_start: 0.9032 (mt) cc_final: 0.8696 (mt) REVERT: A 420 MET cc_start: 0.9319 (mmm) cc_final: 0.8952 (tpp) REVERT: A 459 LYS cc_start: 0.9037 (mttp) cc_final: 0.8334 (mtmm) REVERT: A 469 HIS cc_start: 0.8922 (t-170) cc_final: 0.8601 (t-170) REVERT: A 493 MET cc_start: 0.9333 (tmm) cc_final: 0.8927 (tmm) REVERT: A 501 GLN cc_start: 0.9398 (tp40) cc_final: 0.8720 (tp40) REVERT: A 515 ASP cc_start: 0.9239 (m-30) cc_final: 0.8634 (m-30) REVERT: A 516 GLN cc_start: 0.9196 (mp10) cc_final: 0.8874 (mp10) REVERT: A 561 LEU cc_start: 0.9619 (tp) cc_final: 0.9348 (tp) REVERT: A 562 LYS cc_start: 0.9618 (ttmt) cc_final: 0.9410 (ttmt) REVERT: A 598 MET cc_start: 0.8539 (ttt) cc_final: 0.8227 (ttt) REVERT: A 664 THR cc_start: 0.9515 (p) cc_final: 0.9184 (p) REVERT: A 677 ARG cc_start: 0.9389 (mmm-85) cc_final: 0.8887 (mmm-85) REVERT: B 8 LYS cc_start: 0.9349 (tptp) cc_final: 0.9034 (tptp) REVERT: B 16 ILE cc_start: 0.9768 (pt) cc_final: 0.9490 (pt) REVERT: B 30 LYS cc_start: 0.9774 (tmtt) cc_final: 0.9426 (tptt) REVERT: B 51 LEU cc_start: 0.9211 (tp) cc_final: 0.8830 (tp) REVERT: B 54 LYS cc_start: 0.9778 (ttmm) cc_final: 0.9376 (tttp) REVERT: B 95 MET cc_start: 0.9494 (mmp) cc_final: 0.9177 (ttp) REVERT: B 99 LYS cc_start: 0.9529 (mmmt) cc_final: 0.9176 (mmmt) REVERT: B 119 GLU cc_start: 0.9117 (mp0) cc_final: 0.8700 (mp0) REVERT: B 120 ASP cc_start: 0.9331 (m-30) cc_final: 0.9075 (m-30) REVERT: B 218 ASN cc_start: 0.9191 (m-40) cc_final: 0.8508 (m-40) REVERT: B 235 ARG cc_start: 0.8792 (ttm110) cc_final: 0.8296 (ttm110) REVERT: B 250 TYR cc_start: 0.8571 (m-80) cc_final: 0.7333 (m-80) REVERT: B 283 VAL cc_start: 0.9424 (t) cc_final: 0.9033 (t) REVERT: B 286 ASP cc_start: 0.8559 (m-30) cc_final: 0.7841 (m-30) REVERT: B 291 LEU cc_start: 0.9549 (mt) cc_final: 0.9298 (mt) REVERT: B 322 MET cc_start: 0.8832 (mmm) cc_final: 0.8191 (mmm) REVERT: B 326 PHE cc_start: 0.9427 (m-80) cc_final: 0.9014 (m-80) REVERT: B 359 MET cc_start: 0.8840 (ttt) cc_final: 0.8373 (tmm) REVERT: B 362 ASP cc_start: 0.8463 (m-30) cc_final: 0.7492 (m-30) REVERT: B 375 LYS cc_start: 0.9228 (mmmm) cc_final: 0.8968 (mmmm) REVERT: B 379 SER cc_start: 0.9191 (t) cc_final: 0.8437 (t) REVERT: B 402 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8284 (tm-30) REVERT: B 403 ILE cc_start: 0.9403 (mp) cc_final: 0.9003 (tp) REVERT: B 410 ASN cc_start: 0.8944 (m110) cc_final: 0.8554 (m110) REVERT: B 458 MET cc_start: 0.9563 (mmm) cc_final: 0.9248 (mmm) REVERT: B 570 MET cc_start: 0.8980 (mmm) cc_final: 0.8263 (mmm) REVERT: B 586 TYR cc_start: 0.8823 (m-10) cc_final: 0.8584 (m-80) REVERT: B 598 MET cc_start: 0.9288 (mtm) cc_final: 0.8936 (mtm) REVERT: B 612 TYR cc_start: 0.9016 (m-80) cc_final: 0.7864 (m-80) REVERT: B 613 TYR cc_start: 0.9060 (t80) cc_final: 0.7755 (t80) REVERT: B 631 ASP cc_start: 0.9372 (t70) cc_final: 0.9106 (t0) REVERT: B 639 ASP cc_start: 0.9298 (m-30) cc_final: 0.9039 (m-30) REVERT: B 640 MET cc_start: 0.9502 (tpp) cc_final: 0.9213 (tpp) REVERT: B 648 ILE cc_start: 0.9320 (mm) cc_final: 0.8983 (mm) REVERT: B 656 LEU cc_start: 0.9644 (mt) cc_final: 0.9401 (mt) REVERT: B 673 TYR cc_start: 0.9086 (t80) cc_final: 0.8860 (t80) REVERT: B 679 ILE cc_start: 0.9665 (mm) cc_final: 0.9446 (mm) REVERT: B 687 THR cc_start: 0.8848 (t) cc_final: 0.8014 (t) REVERT: C 17 PHE cc_start: 0.8503 (p90) cc_final: 0.7437 (p90) REVERT: C 20 MET cc_start: 0.8860 (ptp) cc_final: 0.8649 (pmm) REVERT: C 21 PHE cc_start: 0.9204 (m-10) cc_final: 0.8620 (m-80) REVERT: C 69 GLN cc_start: 0.9066 (tp-100) cc_final: 0.8660 (tp-100) REVERT: C 74 MET cc_start: 0.8331 (mmm) cc_final: 0.7976 (mmm) REVERT: C 90 LEU cc_start: 0.7603 (mt) cc_final: 0.7359 (mt) REVERT: C 112 LEU cc_start: 0.7446 (mt) cc_final: 0.7190 (pp) REVERT: C 157 MET cc_start: 0.9633 (mtm) cc_final: 0.9279 (ptm) REVERT: C 163 LEU cc_start: 0.9546 (tt) cc_final: 0.9140 (tt) REVERT: C 178 PHE cc_start: 0.9240 (m-80) cc_final: 0.8896 (m-10) REVERT: C 204 TYR cc_start: 0.8713 (t80) cc_final: 0.8397 (t80) REVERT: C 214 ASN cc_start: 0.8766 (m-40) cc_final: 0.8280 (p0) REVERT: C 239 GLU cc_start: 0.8673 (pt0) cc_final: 0.8465 (pt0) REVERT: C 263 ASN cc_start: 0.6697 (m110) cc_final: 0.6449 (p0) REVERT: C 283 ASN cc_start: 0.7603 (t0) cc_final: 0.7397 (t0) REVERT: D 109 PHE cc_start: 0.8901 (m-80) cc_final: 0.8127 (m-80) REVERT: D 172 PHE cc_start: 0.9394 (m-80) cc_final: 0.9145 (m-80) REVERT: D 189 GLU cc_start: 0.9234 (pt0) cc_final: 0.8950 (pt0) REVERT: D 315 LEU cc_start: 0.9117 (tt) cc_final: 0.8772 (pt) outliers start: 1 outliers final: 0 residues processed: 721 average time/residue: 0.1261 time to fit residues: 136.8803 Evaluate side-chains 596 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 596 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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: 0.9990 chunk 157 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 89 optimal weight: 0.0970 chunk 127 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 chunk 185 optimal weight: 9.9990 chunk 191 optimal weight: 20.0000 chunk 159 optimal weight: 8.9990 chunk 182 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 GLN 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** B 147 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN C 270 ASN D 23 ASN D 25 ASN D 210 GLN D 288 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.111875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.081394 restraints weight = 49084.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.084639 restraints weight = 29932.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.087104 restraints weight = 21028.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.088929 restraints weight = 15674.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.090215 restraints weight = 12335.223| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 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 = 0.3146 r_free = 0.3146 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: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.5947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16386 Z= 0.135 Angle : 0.577 7.419 22134 Z= 0.310 Chirality : 0.042 0.225 2360 Planarity : 0.004 0.041 2818 Dihedral : 8.827 152.450 2290 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.17 % Allowed : 2.21 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.18), residues: 1932 helix: 1.07 (0.15), residues: 1139 sheet: -0.39 (0.40), residues: 144 loop : 0.18 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 600 TYR 0.022 0.001 TYR D 174 PHE 0.049 0.002 PHE C 168 TRP 0.008 0.001 TRP A 558 HIS 0.009 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (16386) covalent geometry : angle 0.57655 / 0.31 (22134) hydrogen bonds : bond 0.03882 / 2.44 ( 871) hydrogen bonds : angle 4.95848 / 3.60 ( 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 701 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 698 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.9279 (t0) cc_final: 0.8922 (t0) REVERT: A 67 GLU cc_start: 0.9586 (mp0) cc_final: 0.9383 (pm20) REVERT: A 115 LEU cc_start: 0.9404 (mt) cc_final: 0.9201 (mt) REVERT: A 136 LYS cc_start: 0.9441 (tptp) cc_final: 0.9087 (tppt) REVERT: A 144 MET cc_start: 0.8767 (mtm) cc_final: 0.8368 (mtm) REVERT: A 147 GLN cc_start: 0.8834 (mt0) cc_final: 0.8318 (mt0) REVERT: A 150 GLN cc_start: 0.9302 (tp40) cc_final: 0.9075 (tp40) REVERT: A 172 LEU cc_start: 0.9450 (mp) cc_final: 0.9081 (mp) REVERT: A 173 LEU cc_start: 0.9454 (mt) cc_final: 0.9204 (mt) REVERT: A 184 ARG cc_start: 0.9281 (mmm-85) cc_final: 0.8846 (tpp80) REVERT: A 199 VAL cc_start: 0.9497 (t) cc_final: 0.9220 (t) REVERT: A 236 TYR cc_start: 0.8826 (t80) cc_final: 0.8407 (t80) REVERT: A 280 ILE cc_start: 0.8587 (pt) cc_final: 0.8049 (mp) REVERT: A 283 VAL cc_start: 0.9182 (t) cc_final: 0.8894 (t) REVERT: A 286 ASP cc_start: 0.9244 (m-30) cc_final: 0.8966 (m-30) REVERT: A 316 GLU cc_start: 0.9429 (tt0) cc_final: 0.9212 (tt0) REVERT: A 326 PHE cc_start: 0.9718 (m-10) cc_final: 0.9415 (m-80) REVERT: A 355 TYR cc_start: 0.8846 (m-10) cc_final: 0.8606 (m-10) REVERT: A 362 ASP cc_start: 0.9001 (m-30) cc_final: 0.8644 (m-30) REVERT: A 370 ASN cc_start: 0.9488 (m-40) cc_final: 0.8976 (m-40) REVERT: A 375 LYS cc_start: 0.8905 (mmmt) cc_final: 0.8476 (mmtm) REVERT: A 377 LYS cc_start: 0.8884 (mttt) cc_final: 0.8249 (mtmm) REVERT: A 406 ASP cc_start: 0.8542 (m-30) cc_final: 0.8282 (m-30) REVERT: A 407 ILE cc_start: 0.9039 (mt) cc_final: 0.8693 (mt) REVERT: A 426 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8314 (tm-30) REVERT: A 441 GLU cc_start: 0.9235 (mm-30) cc_final: 0.9031 (mm-30) REVERT: A 458 MET cc_start: 0.8893 (mmp) cc_final: 0.8571 (mmp) REVERT: A 459 LYS cc_start: 0.9109 (mttp) cc_final: 0.8447 (mtmm) REVERT: A 468 LEU cc_start: 0.9723 (tp) cc_final: 0.9460 (tp) REVERT: A 479 TYR cc_start: 0.9319 (t80) cc_final: 0.8780 (t80) REVERT: A 493 MET cc_start: 0.9340 (tmm) cc_final: 0.8893 (tmm) REVERT: A 501 GLN cc_start: 0.9358 (tp40) cc_final: 0.8691 (tp40) REVERT: A 515 ASP cc_start: 0.9274 (m-30) cc_final: 0.8405 (m-30) REVERT: A 516 GLN cc_start: 0.9216 (mp10) cc_final: 0.8658 (mp10) REVERT: A 558 TRP cc_start: 0.9432 (m100) cc_final: 0.9198 (m100) REVERT: A 561 LEU cc_start: 0.9610 (tp) cc_final: 0.9032 (tp) REVERT: A 598 MET cc_start: 0.8602 (ttt) cc_final: 0.8303 (ttt) REVERT: A 615 MET cc_start: 0.9080 (mmp) cc_final: 0.8733 (mmp) REVERT: B 8 LYS cc_start: 0.9344 (tptp) cc_final: 0.9037 (tptp) REVERT: B 16 ILE cc_start: 0.9760 (pt) cc_final: 0.9550 (pt) REVERT: B 30 LYS cc_start: 0.9769 (tmtt) cc_final: 0.9422 (tptt) REVERT: B 54 LYS cc_start: 0.9776 (ttmm) cc_final: 0.9414 (tttp) REVERT: B 65 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8226 (tm-30) REVERT: B 99 LYS cc_start: 0.9532 (mmmt) cc_final: 0.9189 (mttt) REVERT: B 119 GLU cc_start: 0.9102 (mp0) cc_final: 0.8665 (mp0) REVERT: B 120 ASP cc_start: 0.9346 (m-30) cc_final: 0.9145 (m-30) REVERT: B 149 TYR cc_start: 0.8937 (t80) cc_final: 0.8624 (t80) REVERT: B 187 ASP cc_start: 0.9457 (t70) cc_final: 0.9135 (t0) REVERT: B 211 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8369 (mm-30) REVERT: B 250 TYR cc_start: 0.8502 (m-80) cc_final: 0.7187 (m-80) REVERT: B 283 VAL cc_start: 0.9401 (t) cc_final: 0.8928 (t) REVERT: B 286 ASP cc_start: 0.8790 (m-30) cc_final: 0.8064 (m-30) REVERT: B 291 LEU cc_start: 0.9579 (mt) cc_final: 0.9329 (mt) REVERT: B 322 MET cc_start: 0.8820 (mmm) cc_final: 0.8249 (mmm) REVERT: B 326 PHE cc_start: 0.9461 (m-10) cc_final: 0.8944 (m-80) REVERT: B 359 MET cc_start: 0.8923 (ttt) cc_final: 0.8404 (tmm) REVERT: B 362 ASP cc_start: 0.8663 (m-30) cc_final: 0.7576 (m-30) REVERT: B 375 LYS cc_start: 0.9231 (mmmm) cc_final: 0.9011 (mmmm) REVERT: B 379 SER cc_start: 0.9152 (t) cc_final: 0.8397 (t) REVERT: B 390 GLN cc_start: 0.9155 (mm-40) cc_final: 0.8864 (mm-40) REVERT: B 402 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8240 (tm-30) REVERT: B 403 ILE cc_start: 0.9375 (mp) cc_final: 0.8964 (tp) REVERT: B 410 ASN cc_start: 0.8980 (m110) cc_final: 0.8535 (m110) REVERT: B 415 ASN cc_start: 0.9381 (t0) cc_final: 0.8649 (t0) REVERT: B 416 ILE cc_start: 0.9572 (mt) cc_final: 0.9347 (mt) REVERT: B 418 ASN cc_start: 0.9428 (m-40) cc_final: 0.9010 (m-40) REVERT: B 419 VAL cc_start: 0.9542 (p) cc_final: 0.9218 (p) REVERT: B 420 MET cc_start: 0.9337 (mmm) cc_final: 0.8835 (mmm) REVERT: B 458 MET cc_start: 0.9541 (mmm) cc_final: 0.9292 (mmm) REVERT: B 468 LEU cc_start: 0.9546 (tp) cc_final: 0.9295 (tp) REVERT: B 598 MET cc_start: 0.9372 (mtm) cc_final: 0.9000 (mtm) REVERT: B 601 ILE cc_start: 0.9119 (mm) cc_final: 0.8700 (tp) REVERT: B 612 TYR cc_start: 0.8906 (m-80) cc_final: 0.7973 (m-80) REVERT: B 613 TYR cc_start: 0.9019 (t80) cc_final: 0.8804 (t80) REVERT: B 615 MET cc_start: 0.8768 (mmp) cc_final: 0.8246 (mmp) REVERT: B 631 ASP cc_start: 0.9396 (t70) cc_final: 0.9114 (t0) REVERT: B 639 ASP cc_start: 0.9336 (m-30) cc_final: 0.8920 (m-30) REVERT: B 640 MET cc_start: 0.9522 (tpp) cc_final: 0.8883 (tpp) REVERT: B 641 ILE cc_start: 0.9729 (OUTLIER) cc_final: 0.9476 (mp) REVERT: B 645 GLN cc_start: 0.9001 (tp-100) cc_final: 0.8763 (tp-100) REVERT: B 648 ILE cc_start: 0.9246 (mm) cc_final: 0.9042 (mm) REVERT: B 656 LEU cc_start: 0.9578 (mt) cc_final: 0.9319 (mt) REVERT: B 673 TYR cc_start: 0.9164 (t80) cc_final: 0.8840 (t80) REVERT: B 679 ILE cc_start: 0.9623 (mm) cc_final: 0.9355 (mm) REVERT: C 17 PHE cc_start: 0.8362 (p90) cc_final: 0.7405 (p90) REVERT: C 20 MET cc_start: 0.8900 (ptp) cc_final: 0.8648 (pmm) REVERT: C 21 PHE cc_start: 0.9205 (m-10) cc_final: 0.8446 (m-80) REVERT: C 74 MET cc_start: 0.8467 (mmm) cc_final: 0.8115 (mmm) REVERT: C 112 LEU cc_start: 0.7544 (mt) cc_final: 0.7296 (pp) REVERT: C 122 PHE cc_start: 0.8733 (m-80) cc_final: 0.8453 (m-80) REVERT: C 157 MET cc_start: 0.9593 (mtm) cc_final: 0.9329 (ptm) REVERT: C 178 PHE cc_start: 0.9187 (m-80) cc_final: 0.8818 (m-10) REVERT: C 207 LEU cc_start: 0.8943 (tt) cc_final: 0.8709 (pp) REVERT: C 239 GLU cc_start: 0.8590 (pt0) cc_final: 0.7928 (pt0) REVERT: C 283 ASN cc_start: 0.7636 (t0) cc_final: 0.7337 (t0) REVERT: C 313 GLU cc_start: 0.9320 (mt-10) cc_final: 0.8879 (mp0) REVERT: D 109 PHE cc_start: 0.8773 (m-80) cc_final: 0.8090 (m-80) REVERT: D 112 LEU cc_start: 0.8527 (mm) cc_final: 0.7667 (pp) REVERT: D 164 GLU cc_start: 0.8586 (pt0) cc_final: 0.7935 (tt0) REVERT: D 169 TYR cc_start: 0.8698 (m-80) cc_final: 0.8456 (m-80) REVERT: D 172 PHE cc_start: 0.9459 (m-80) cc_final: 0.9087 (m-80) REVERT: D 189 GLU cc_start: 0.9221 (pt0) cc_final: 0.8946 (pp20) REVERT: D 201 HIS cc_start: 0.8272 (m170) cc_final: 0.7680 (m170) outliers start: 3 outliers final: 0 residues processed: 698 average time/residue: 0.1266 time to fit residues: 133.3606 Evaluate side-chains 595 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 594 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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: 9.9990 chunk 46 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 126 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 122 optimal weight: 0.0270 chunk 115 optimal weight: 10.0000 chunk 168 optimal weight: 8.9990 chunk 157 optimal weight: 9.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN 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 496 ASN ** 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 320 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.106972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.077667 restraints weight = 52029.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.080861 restraints weight = 31525.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.082996 restraints weight = 21558.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.084692 restraints weight = 16163.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.085940 restraints weight = 12669.630| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.6587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16386 Z= 0.205 Angle : 0.632 7.208 22134 Z= 0.341 Chirality : 0.043 0.211 2360 Planarity : 0.004 0.053 2818 Dihedral : 8.842 156.645 2290 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: 0.75 (0.18), residues: 1932 helix: 0.99 (0.15), residues: 1145 sheet: -0.45 (0.41), residues: 144 loop : 0.04 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 604 TYR 0.034 0.002 TYR C 276 PHE 0.042 0.003 PHE C 168 TRP 0.056 0.002 TRP D 124 HIS 0.013 0.002 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.20 (16386) covalent geometry : angle 0.63176 / 0.34 (22134) hydrogen bonds : bond 0.04059 / 2.56 ( 871) hydrogen bonds : angle 5.12261 / 3.71 ( 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 688 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 688 time to evaluate : 0.652 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 29 ASP cc_start: 0.9307 (t0) cc_final: 0.9050 (t0) REVERT: A 116 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7805 (tt0) REVERT: A 119 GLU cc_start: 0.9137 (mp0) cc_final: 0.8794 (mp0) REVERT: A 136 LYS cc_start: 0.9476 (tptp) cc_final: 0.9166 (tppp) REVERT: A 144 MET cc_start: 0.8740 (mtm) cc_final: 0.8413 (mtm) REVERT: A 147 GLN cc_start: 0.8818 (mt0) cc_final: 0.8381 (mt0) REVERT: A 164 ARG cc_start: 0.7892 (ptm-80) cc_final: 0.6697 (ptm-80) REVERT: A 168 VAL cc_start: 0.8590 (t) cc_final: 0.8389 (m) REVERT: A 172 LEU cc_start: 0.9435 (mp) cc_final: 0.9097 (mp) REVERT: A 173 LEU cc_start: 0.9527 (mt) cc_final: 0.9305 (mt) REVERT: A 184 ARG cc_start: 0.9349 (mmm-85) cc_final: 0.8972 (tpp80) REVERT: A 190 MET cc_start: 0.9196 (mtp) cc_final: 0.8918 (mtp) REVERT: A 199 VAL cc_start: 0.9582 (t) cc_final: 0.9299 (t) REVERT: A 235 ARG cc_start: 0.8400 (mtm110) cc_final: 0.8053 (mtm110) REVERT: A 236 TYR cc_start: 0.9044 (t80) cc_final: 0.8659 (t80) REVERT: A 286 ASP cc_start: 0.9216 (m-30) cc_final: 0.8944 (m-30) REVERT: A 316 GLU cc_start: 0.9395 (tt0) cc_final: 0.9191 (tt0) REVERT: A 352 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8664 (tm-30) REVERT: A 359 MET cc_start: 0.8662 (tmm) cc_final: 0.8093 (tmm) REVERT: A 362 ASP cc_start: 0.8981 (m-30) cc_final: 0.8642 (m-30) REVERT: A 370 ASN cc_start: 0.9578 (m-40) cc_final: 0.9125 (m110) REVERT: A 375 LYS cc_start: 0.8962 (mmmt) cc_final: 0.8444 (mmtm) REVERT: A 377 LYS cc_start: 0.8885 (mttt) cc_final: 0.8614 (mttp) REVERT: A 406 ASP cc_start: 0.8646 (m-30) cc_final: 0.8344 (m-30) REVERT: A 407 ILE cc_start: 0.9091 (mt) cc_final: 0.8749 (mt) REVERT: A 441 GLU cc_start: 0.9294 (mm-30) cc_final: 0.9006 (mm-30) REVERT: A 459 LYS cc_start: 0.9202 (mttp) cc_final: 0.8550 (mtmm) REVERT: A 468 LEU cc_start: 0.9711 (tp) cc_final: 0.9507 (tp) REVERT: A 469 HIS cc_start: 0.9069 (t-170) cc_final: 0.8827 (t-170) REVERT: A 487 PHE cc_start: 0.9778 (t80) cc_final: 0.9546 (t80) REVERT: A 490 THR cc_start: 0.9643 (m) cc_final: 0.9071 (m) REVERT: A 493 MET cc_start: 0.9089 (tmm) cc_final: 0.8711 (tmm) REVERT: A 515 ASP cc_start: 0.9330 (m-30) cc_final: 0.8749 (m-30) REVERT: A 516 GLN cc_start: 0.9214 (mp10) cc_final: 0.8888 (mp10) REVERT: A 598 MET cc_start: 0.8669 (ttt) cc_final: 0.8039 (ttt) REVERT: A 615 MET cc_start: 0.9214 (mmp) cc_final: 0.8910 (mmp) REVERT: A 628 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8689 (mt-10) REVERT: A 634 MET cc_start: 0.9313 (mmm) cc_final: 0.9092 (mmm) REVERT: A 645 GLN cc_start: 0.8781 (tp40) cc_final: 0.8555 (tp-100) REVERT: A 652 ILE cc_start: 0.9282 (mt) cc_final: 0.8806 (mt) REVERT: B 8 LYS cc_start: 0.9342 (tptp) cc_final: 0.9057 (tptp) REVERT: B 16 ILE cc_start: 0.9802 (pt) cc_final: 0.9599 (pt) REVERT: B 30 LYS cc_start: 0.9769 (tmtt) cc_final: 0.9373 (tptt) REVERT: B 95 MET cc_start: 0.9510 (mmp) cc_final: 0.9049 (mmt) REVERT: B 119 GLU cc_start: 0.9303 (mp0) cc_final: 0.8833 (mp0) REVERT: B 124 ILE cc_start: 0.9566 (mm) cc_final: 0.9292 (mm) REVERT: B 139 GLU cc_start: 0.9443 (mp0) cc_final: 0.9234 (mp0) REVERT: B 147 GLN cc_start: 0.9422 (mt0) cc_final: 0.8935 (mt0) REVERT: B 149 TYR cc_start: 0.8981 (t80) cc_final: 0.8750 (t80) REVERT: B 191 GLN cc_start: 0.9110 (mm-40) cc_final: 0.8740 (mm-40) REVERT: B 199 VAL cc_start: 0.8970 (t) cc_final: 0.8644 (p) REVERT: B 250 TYR cc_start: 0.8632 (m-80) cc_final: 0.7393 (m-80) REVERT: B 263 ASP cc_start: 0.9091 (m-30) cc_final: 0.8767 (m-30) REVERT: B 283 VAL cc_start: 0.9515 (t) cc_final: 0.9083 (t) REVERT: B 291 LEU cc_start: 0.9573 (mt) cc_final: 0.9317 (mt) REVERT: B 316 GLU cc_start: 0.9441 (tm-30) cc_final: 0.9188 (tm-30) REVERT: B 322 MET cc_start: 0.8770 (mmm) cc_final: 0.8414 (mmm) REVERT: B 359 MET cc_start: 0.8895 (ttt) cc_final: 0.8459 (tmm) REVERT: B 375 LYS cc_start: 0.9286 (mmmm) cc_final: 0.9034 (mmmm) REVERT: B 379 SER cc_start: 0.9155 (t) cc_final: 0.8558 (t) REVERT: B 403 ILE cc_start: 0.9350 (mp) cc_final: 0.8984 (tp) REVERT: B 410 ASN cc_start: 0.9032 (m110) cc_final: 0.8816 (m110) REVERT: B 416 ILE cc_start: 0.9645 (mt) cc_final: 0.9425 (mt) REVERT: B 418 ASN cc_start: 0.9422 (m-40) cc_final: 0.9009 (m-40) REVERT: B 420 MET cc_start: 0.9457 (mmm) cc_final: 0.9065 (mmm) REVERT: B 467 ASN cc_start: 0.8758 (m110) cc_final: 0.7996 (m110) REVERT: B 530 LYS cc_start: 0.9022 (ptmm) cc_final: 0.8611 (ptmm) REVERT: B 598 MET cc_start: 0.9408 (mtm) cc_final: 0.9091 (mtm) REVERT: B 601 ILE cc_start: 0.9281 (mm) cc_final: 0.8928 (tp) REVERT: B 612 TYR cc_start: 0.8735 (m-80) cc_final: 0.7950 (m-80) REVERT: B 613 TYR cc_start: 0.9167 (t80) cc_final: 0.8954 (t80) REVERT: B 615 MET cc_start: 0.8845 (mmp) cc_final: 0.8164 (mmp) REVERT: B 631 ASP cc_start: 0.9400 (t70) cc_final: 0.9139 (t0) REVERT: B 636 LYS cc_start: 0.9615 (mptt) cc_final: 0.9288 (mmtt) REVERT: B 639 ASP cc_start: 0.9314 (m-30) cc_final: 0.8838 (m-30) REVERT: B 640 MET cc_start: 0.9464 (tpp) cc_final: 0.8944 (tpp) REVERT: B 673 TYR cc_start: 0.9106 (t80) cc_final: 0.8704 (t80) REVERT: B 679 ILE cc_start: 0.9595 (mm) cc_final: 0.9341 (mm) REVERT: C 17 PHE cc_start: 0.8389 (p90) cc_final: 0.7148 (p90) REVERT: C 21 PHE cc_start: 0.9161 (m-10) cc_final: 0.8515 (m-80) REVERT: C 96 MET cc_start: 0.8385 (tpt) cc_final: 0.8145 (tpt) REVERT: C 105 TYR cc_start: 0.8882 (m-80) cc_final: 0.8433 (m-80) REVERT: C 122 PHE cc_start: 0.8652 (m-80) cc_final: 0.8286 (m-80) REVERT: C 178 PHE cc_start: 0.9174 (m-80) cc_final: 0.8876 (m-10) REVERT: C 233 ASN cc_start: 0.9485 (m110) cc_final: 0.9230 (p0) REVERT: C 239 GLU cc_start: 0.8625 (pt0) cc_final: 0.8072 (pt0) REVERT: C 283 ASN cc_start: 0.7748 (t0) cc_final: 0.7499 (t0) REVERT: C 285 ILE cc_start: 0.9125 (mm) cc_final: 0.8863 (mm) REVERT: D 21 PHE cc_start: 0.8805 (m-10) cc_final: 0.8582 (m-10) REVERT: D 109 PHE cc_start: 0.8626 (m-80) cc_final: 0.7870 (m-80) REVERT: D 112 LEU cc_start: 0.8581 (mm) cc_final: 0.8236 (mm) REVERT: D 157 MET cc_start: 0.9561 (ptp) cc_final: 0.9353 (ptt) REVERT: D 166 PHE cc_start: 0.7773 (t80) cc_final: 0.7538 (t80) REVERT: D 169 TYR cc_start: 0.9198 (m-80) cc_final: 0.8967 (m-80) REVERT: D 172 PHE cc_start: 0.9367 (m-80) cc_final: 0.9138 (m-80) REVERT: D 198 GLU cc_start: 0.9239 (mp0) cc_final: 0.8968 (mm-30) REVERT: D 244 GLU cc_start: 0.9234 (mp0) cc_final: 0.9014 (mm-30) outliers start: 0 outliers final: 0 residues processed: 688 average time/residue: 0.1275 time to fit residues: 132.2882 Evaluate side-chains 569 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 569 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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: 0.9980 chunk 183 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 496 ASN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 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 320 ASN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.107774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.079651 restraints weight = 50980.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.082740 restraints weight = 30619.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.084836 restraints weight = 20833.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.086471 restraints weight = 15580.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.087642 restraints weight = 12176.993| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 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 = 0.3091 r_free = 0.3091 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 (7 function evaluations) r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.6943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16386 Z= 0.165 Angle : 0.604 8.756 22134 Z= 0.326 Chirality : 0.043 0.256 2360 Planarity : 0.004 0.063 2818 Dihedral : 8.658 155.287 2290 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.17 % Allowed : 1.34 % 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: 0.67 (0.18), residues: 1932 helix: 0.97 (0.15), residues: 1142 sheet: -0.57 (0.40), residues: 144 loop : -0.05 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 225 TYR 0.026 0.002 TYR D 174 PHE 0.039 0.002 PHE C 168 TRP 0.052 0.002 TRP D 124 HIS 0.014 0.002 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (16386) covalent geometry : angle 0.60396 / 0.33 (22134) hydrogen bonds : bond 0.03937 / 2.49 ( 871) hydrogen bonds : angle 5.09657 / 3.71 ( 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 682 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 679 time to evaluate : 0.540 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: 0.9150 (tptp) cc_final: 0.8761 (tppt) REVERT: A 116 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7736 (tt0) REVERT: A 119 GLU cc_start: 0.9120 (mp0) cc_final: 0.8801 (mp0) REVERT: A 144 MET cc_start: 0.8698 (mtm) cc_final: 0.8367 (mtm) REVERT: A 147 GLN cc_start: 0.8697 (mt0) cc_final: 0.8470 (mt0) REVERT: A 172 LEU cc_start: 0.9383 (mp) cc_final: 0.9041 (mp) REVERT: A 173 LEU cc_start: 0.9492 (mt) cc_final: 0.9291 (mt) REVERT: A 184 ARG cc_start: 0.9345 (mmm-85) cc_final: 0.8999 (tpp80) REVERT: A 190 MET cc_start: 0.9158 (mtp) cc_final: 0.8921 (mtp) REVERT: A 199 VAL cc_start: 0.9546 (t) cc_final: 0.9096 (t) REVERT: A 228 LYS cc_start: 0.8919 (mmmt) cc_final: 0.8714 (mmtm) REVERT: A 235 ARG cc_start: 0.8330 (mtm110) cc_final: 0.7876 (mtm110) REVERT: A 236 TYR cc_start: 0.8937 (t80) cc_final: 0.8419 (t80) REVERT: A 261 PHE cc_start: 0.9052 (t80) cc_final: 0.8836 (t80) REVERT: A 280 ILE cc_start: 0.8560 (pt) cc_final: 0.8222 (mp) REVERT: A 316 GLU cc_start: 0.9386 (tt0) cc_final: 0.9180 (tt0) REVERT: A 322 MET cc_start: 0.9149 (mmp) cc_final: 0.8862 (tpp) REVERT: A 349 LEU cc_start: 0.9464 (mt) cc_final: 0.9213 (mt) REVERT: A 359 MET cc_start: 0.8577 (tmm) cc_final: 0.8121 (tmm) REVERT: A 362 ASP cc_start: 0.8836 (m-30) cc_final: 0.8463 (m-30) REVERT: A 370 ASN cc_start: 0.9569 (m-40) cc_final: 0.9115 (m110) REVERT: A 375 LYS cc_start: 0.8985 (mmmt) cc_final: 0.8501 (mmtm) REVERT: A 377 LYS cc_start: 0.8936 (mttt) cc_final: 0.8587 (mttp) REVERT: A 381 LEU cc_start: 0.8943 (tp) cc_final: 0.8549 (pt) REVERT: A 403 ILE cc_start: 0.8891 (tp) cc_final: 0.8592 (tp) REVERT: A 406 ASP cc_start: 0.8566 (m-30) cc_final: 0.8291 (m-30) REVERT: A 407 ILE cc_start: 0.9117 (mt) cc_final: 0.8782 (mt) REVERT: A 426 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8441 (tm-30) REVERT: A 441 GLU cc_start: 0.9283 (mm-30) cc_final: 0.8912 (mm-30) REVERT: A 459 LYS cc_start: 0.9248 (mttp) cc_final: 0.8604 (mtmm) REVERT: A 466 MET cc_start: 0.9232 (ptp) cc_final: 0.8392 (ptp) REVERT: A 468 LEU cc_start: 0.9676 (tp) cc_final: 0.9206 (tp) REVERT: A 479 TYR cc_start: 0.8925 (t80) cc_final: 0.7792 (t80) REVERT: A 490 THR cc_start: 0.9614 (m) cc_final: 0.9172 (p) REVERT: A 493 MET cc_start: 0.9090 (tmm) cc_final: 0.8568 (tmm) REVERT: A 494 MET cc_start: 0.9581 (mpp) cc_final: 0.9130 (mmm) REVERT: A 515 ASP cc_start: 0.9322 (m-30) cc_final: 0.8772 (m-30) REVERT: A 516 GLN cc_start: 0.9147 (mp10) cc_final: 0.8853 (mp10) REVERT: A 598 MET cc_start: 0.8685 (ttt) cc_final: 0.7936 (ttt) REVERT: A 615 MET cc_start: 0.9216 (mmp) cc_final: 0.8912 (mmp) REVERT: A 628 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8733 (mm-30) REVERT: A 632 MET cc_start: 0.8961 (mmm) cc_final: 0.8624 (mmm) REVERT: A 634 MET cc_start: 0.9357 (mmm) cc_final: 0.9143 (mmm) REVERT: A 636 LYS cc_start: 0.9813 (mmtp) cc_final: 0.9609 (mmmm) REVERT: A 640 MET cc_start: 0.9194 (tpp) cc_final: 0.8951 (tpp) REVERT: A 645 GLN cc_start: 0.8867 (tp40) cc_final: 0.8507 (tp-100) REVERT: A 652 ILE cc_start: 0.9207 (mt) cc_final: 0.8761 (mt) REVERT: B 8 LYS cc_start: 0.9386 (tptp) cc_final: 0.9084 (tptp) REVERT: B 30 LYS cc_start: 0.9778 (tmtt) cc_final: 0.9403 (tptt) REVERT: B 67 GLU cc_start: 0.8849 (mp0) cc_final: 0.8531 (mp0) REVERT: B 82 LYS cc_start: 0.9518 (ptpp) cc_final: 0.9232 (ptpt) REVERT: B 95 MET cc_start: 0.9447 (mmp) cc_final: 0.9026 (mmp) REVERT: B 116 GLU cc_start: 0.8218 (tt0) cc_final: 0.7906 (tt0) REVERT: B 119 GLU cc_start: 0.9182 (mp0) cc_final: 0.8708 (mp0) REVERT: B 120 ASP cc_start: 0.9423 (m-30) cc_final: 0.9194 (m-30) REVERT: B 144 MET cc_start: 0.9387 (mtm) cc_final: 0.9186 (mtm) REVERT: B 147 GLN cc_start: 0.9450 (mt0) cc_final: 0.9088 (mt0) REVERT: B 149 TYR cc_start: 0.9075 (t80) cc_final: 0.8722 (t80) REVERT: B 199 VAL cc_start: 0.9029 (t) cc_final: 0.8761 (p) REVERT: B 250 TYR cc_start: 0.8634 (m-80) cc_final: 0.7420 (m-80) REVERT: B 263 ASP cc_start: 0.9139 (m-30) cc_final: 0.8915 (m-30) REVERT: B 283 VAL cc_start: 0.9525 (t) cc_final: 0.9096 (t) REVERT: B 286 ASP cc_start: 0.8973 (m-30) cc_final: 0.8109 (m-30) REVERT: B 291 LEU cc_start: 0.9565 (mt) cc_final: 0.9311 (mt) REVERT: B 316 GLU cc_start: 0.9411 (tm-30) cc_final: 0.9191 (tm-30) REVERT: B 322 MET cc_start: 0.8737 (mmm) cc_final: 0.8348 (mmm) REVERT: B 359 MET cc_start: 0.9049 (ttt) cc_final: 0.8523 (tmm) REVERT: B 362 ASP cc_start: 0.8472 (m-30) cc_final: 0.7526 (m-30) REVERT: B 375 LYS cc_start: 0.9271 (mmmm) cc_final: 0.8982 (mmmm) REVERT: B 379 SER cc_start: 0.9121 (t) cc_final: 0.8529 (t) REVERT: B 402 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8320 (tm-30) REVERT: B 403 ILE cc_start: 0.9313 (mp) cc_final: 0.8968 (tp) REVERT: B 410 ASN cc_start: 0.8938 (m110) cc_final: 0.8673 (m110) REVERT: B 416 ILE cc_start: 0.9638 (mt) cc_final: 0.9431 (mt) REVERT: B 418 ASN cc_start: 0.9397 (m-40) cc_final: 0.9069 (m-40) REVERT: B 420 MET cc_start: 0.9460 (mmm) cc_final: 0.9092 (mmm) REVERT: B 467 ASN cc_start: 0.8665 (m110) cc_final: 0.7895 (m110) REVERT: B 494 MET cc_start: 0.9562 (ttm) cc_final: 0.9256 (ttm) REVERT: B 530 LYS cc_start: 0.9019 (ptmm) cc_final: 0.8617 (ptmm) REVERT: B 570 MET cc_start: 0.8971 (mmm) cc_final: 0.8308 (mmm) REVERT: B 598 MET cc_start: 0.9402 (mtm) cc_final: 0.9067 (mtm) REVERT: B 601 ILE cc_start: 0.9239 (mm) cc_final: 0.8846 (tp) REVERT: B 612 TYR cc_start: 0.8658 (m-80) cc_final: 0.7681 (m-80) REVERT: B 613 TYR cc_start: 0.9156 (t80) cc_final: 0.8863 (t80) REVERT: B 615 MET cc_start: 0.8862 (mmp) cc_final: 0.8165 (mmp) REVERT: B 631 ASP cc_start: 0.9397 (t70) cc_final: 0.9139 (t0) REVERT: B 636 LYS cc_start: 0.9599 (mptt) cc_final: 0.9253 (mmtt) REVERT: B 640 MET cc_start: 0.9443 (tpp) cc_final: 0.9033 (tpp) REVERT: B 679 ILE cc_start: 0.9594 (mm) cc_final: 0.9357 (mm) REVERT: C 17 PHE cc_start: 0.8418 (p90) cc_final: 0.7409 (p90) REVERT: C 21 PHE cc_start: 0.9044 (m-10) cc_final: 0.8414 (m-80) REVERT: C 96 MET cc_start: 0.8403 (tpt) cc_final: 0.8054 (tpt) REVERT: C 105 TYR cc_start: 0.8975 (m-80) cc_final: 0.8537 (m-80) REVERT: C 120 GLU cc_start: 0.9387 (OUTLIER) cc_final: 0.8990 (pm20) REVERT: C 178 PHE cc_start: 0.9176 (m-80) cc_final: 0.8885 (m-10) REVERT: C 233 ASN cc_start: 0.9459 (m110) cc_final: 0.9207 (p0) REVERT: C 239 GLU cc_start: 0.8557 (pt0) cc_final: 0.8030 (pt0) REVERT: C 283 ASN cc_start: 0.7691 (t0) cc_final: 0.7447 (t0) REVERT: C 285 ILE cc_start: 0.9131 (mm) cc_final: 0.8853 (mm) REVERT: D 21 PHE cc_start: 0.8797 (m-10) cc_final: 0.8520 (m-10) REVERT: D 96 MET cc_start: 0.8498 (mmp) cc_final: 0.8051 (mmp) REVERT: D 109 PHE cc_start: 0.8737 (m-80) cc_final: 0.7979 (m-80) REVERT: D 112 LEU cc_start: 0.8583 (mm) cc_final: 0.8177 (mm) REVERT: D 169 TYR cc_start: 0.9157 (m-80) cc_final: 0.8875 (m-80) REVERT: D 172 PHE cc_start: 0.9474 (m-80) cc_final: 0.9070 (m-80) REVERT: D 179 TYR cc_start: 0.8077 (t80) cc_final: 0.7645 (t80) REVERT: D 185 MET cc_start: 0.5820 (mmp) cc_final: 0.5468 (mmm) REVERT: D 239 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8651 (pm20) outliers start: 3 outliers final: 0 residues processed: 682 average time/residue: 0.1235 time to fit residues: 127.6214 Evaluate side-chains 575 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 573 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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: 5.9990 chunk 51 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 186 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 115 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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 668 ASN ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** B 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 HIS ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.110765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.082248 restraints weight = 49903.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.085342 restraints weight = 29677.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.087541 restraints weight = 20262.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.089212 restraints weight = 15073.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.090450 restraints weight = 11814.602| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 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 = 0.3143 r_free = 0.3143 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: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.7229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16386 Z= 0.138 Angle : 0.616 8.185 22134 Z= 0.331 Chirality : 0.043 0.288 2360 Planarity : 0.003 0.044 2818 Dihedral : 8.459 155.283 2290 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.06 % Allowed : 1.34 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.18), residues: 1932 helix: 0.97 (0.15), residues: 1146 sheet: -0.56 (0.41), residues: 144 loop : -0.11 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 164 TYR 0.026 0.001 TYR D 174 PHE 0.035 0.002 PHE C 168 TRP 0.055 0.002 TRP D 124 HIS 0.010 0.001 HIS A 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (16386) covalent geometry : angle 0.61571 / 0.33 (22134) hydrogen bonds : bond 0.03951 / 2.49 ( 871) hydrogen bonds : angle 5.15008 / 3.73 ( 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 684 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 683 time to evaluate : 0.624 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: 0.9153 (tptp) cc_final: 0.8707 (tppt) REVERT: A 116 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7707 (tt0) REVERT: A 119 GLU cc_start: 0.9064 (mp0) cc_final: 0.8773 (mp0) REVERT: A 120 ASP cc_start: 0.9170 (m-30) cc_final: 0.8936 (m-30) REVERT: A 129 PHE cc_start: 0.9711 (m-10) cc_final: 0.9505 (m-80) REVERT: A 144 MET cc_start: 0.8625 (mtm) cc_final: 0.8272 (mtm) REVERT: A 147 GLN cc_start: 0.8717 (mt0) cc_final: 0.8429 (mt0) REVERT: A 172 LEU cc_start: 0.9333 (mp) cc_final: 0.9118 (mp) REVERT: A 184 ARG cc_start: 0.9288 (mmm-85) cc_final: 0.8922 (tpp80) REVERT: A 235 ARG cc_start: 0.8408 (mtm110) cc_final: 0.8066 (mtm110) REVERT: A 236 TYR cc_start: 0.8886 (t80) cc_final: 0.8439 (t80) REVERT: A 280 ILE cc_start: 0.8539 (pt) cc_final: 0.8031 (mp) REVERT: A 290 GLU cc_start: 0.9449 (mm-30) cc_final: 0.9248 (mm-30) REVERT: A 316 GLU cc_start: 0.9376 (tt0) cc_final: 0.9009 (tt0) REVERT: A 322 MET cc_start: 0.9176 (mmp) cc_final: 0.8917 (tpp) REVERT: A 345 LYS cc_start: 0.8947 (tttt) cc_final: 0.8740 (tttt) REVERT: A 349 LEU cc_start: 0.9473 (mt) cc_final: 0.9217 (mt) REVERT: A 352 GLU cc_start: 0.9052 (tm-30) cc_final: 0.8633 (tm-30) REVERT: A 359 MET cc_start: 0.8538 (tmm) cc_final: 0.8106 (tmm) REVERT: A 362 ASP cc_start: 0.8761 (m-30) cc_final: 0.8353 (m-30) REVERT: A 370 ASN cc_start: 0.9552 (m-40) cc_final: 0.9159 (m110) REVERT: A 375 LYS cc_start: 0.8962 (mmmt) cc_final: 0.8502 (mmtm) REVERT: A 377 LYS cc_start: 0.8944 (mttt) cc_final: 0.8567 (mttp) REVERT: A 381 LEU cc_start: 0.8936 (tp) cc_final: 0.8544 (pt) REVERT: A 406 ASP cc_start: 0.8596 (m-30) cc_final: 0.8321 (m-30) REVERT: A 407 ILE cc_start: 0.9116 (mt) cc_final: 0.8779 (mt) REVERT: A 420 MET cc_start: 0.9379 (mmm) cc_final: 0.8929 (tpp) REVERT: A 426 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8425 (tm-30) REVERT: A 468 LEU cc_start: 0.9659 (tp) cc_final: 0.9318 (tp) REVERT: A 469 HIS cc_start: 0.8811 (t-170) cc_final: 0.8601 (t-170) REVERT: A 479 TYR cc_start: 0.8838 (t80) cc_final: 0.7823 (t80) REVERT: A 490 THR cc_start: 0.9548 (m) cc_final: 0.9287 (p) REVERT: A 493 MET cc_start: 0.9065 (tmm) cc_final: 0.8513 (tmm) REVERT: A 494 MET cc_start: 0.9512 (mpp) cc_final: 0.9046 (mmm) REVERT: A 515 ASP cc_start: 0.9373 (m-30) cc_final: 0.8824 (m-30) REVERT: A 516 GLN cc_start: 0.9144 (mp10) cc_final: 0.8860 (mp10) REVERT: A 570 MET cc_start: 0.9346 (mtp) cc_final: 0.9043 (mtp) REVERT: A 598 MET cc_start: 0.8760 (ttt) cc_final: 0.7988 (ttt) REVERT: A 602 GLU cc_start: 0.8513 (pp20) cc_final: 0.7257 (pp20) REVERT: A 628 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8694 (mm-30) REVERT: A 632 MET cc_start: 0.8984 (mmm) cc_final: 0.8764 (mmm) REVERT: A 636 LYS cc_start: 0.9790 (mmtp) cc_final: 0.9587 (mmmm) REVERT: A 640 MET cc_start: 0.9202 (tpp) cc_final: 0.8960 (tpp) REVERT: A 650 GLN cc_start: 0.8822 (mt0) cc_final: 0.8430 (mm-40) REVERT: A 653 SER cc_start: 0.9203 (p) cc_final: 0.8943 (p) REVERT: A 677 ARG cc_start: 0.9383 (mmm-85) cc_final: 0.8904 (mmm-85) REVERT: A 686 ARG cc_start: 0.7178 (mmm160) cc_final: 0.6632 (tpt90) REVERT: B 8 LYS cc_start: 0.9437 (tptp) cc_final: 0.9140 (tptp) REVERT: B 16 ILE cc_start: 0.9750 (tt) cc_final: 0.9345 (pt) REVERT: B 30 LYS cc_start: 0.9825 (tmtt) cc_final: 0.9527 (tptt) REVERT: B 67 GLU cc_start: 0.8923 (mp0) cc_final: 0.8509 (mp0) REVERT: B 82 LYS cc_start: 0.9502 (ptpp) cc_final: 0.9177 (ptpt) REVERT: B 99 LYS cc_start: 0.9507 (mmmt) cc_final: 0.9231 (mttt) REVERT: B 116 GLU cc_start: 0.8172 (tt0) cc_final: 0.7720 (tp30) REVERT: B 119 GLU cc_start: 0.9170 (mp0) cc_final: 0.8678 (mp0) REVERT: B 120 ASP cc_start: 0.9432 (m-30) cc_final: 0.9016 (m-30) REVERT: B 144 MET cc_start: 0.9360 (mtm) cc_final: 0.9120 (mtm) REVERT: B 147 GLN cc_start: 0.9422 (mt0) cc_final: 0.8948 (mt0) REVERT: B 149 TYR cc_start: 0.9112 (t80) cc_final: 0.8681 (t80) REVERT: B 227 MET cc_start: 0.9194 (ttp) cc_final: 0.8931 (ttp) REVERT: B 250 TYR cc_start: 0.8606 (m-80) cc_final: 0.7399 (m-80) REVERT: B 260 ASP cc_start: 0.9437 (p0) cc_final: 0.9204 (p0) REVERT: B 263 ASP cc_start: 0.8997 (m-30) cc_final: 0.8768 (m-30) REVERT: B 283 VAL cc_start: 0.9518 (t) cc_final: 0.9188 (t) REVERT: B 286 ASP cc_start: 0.8836 (m-30) cc_final: 0.8276 (m-30) REVERT: B 291 LEU cc_start: 0.9555 (mt) cc_final: 0.9322 (mt) REVERT: B 316 GLU cc_start: 0.9378 (tm-30) cc_final: 0.9172 (tm-30) REVERT: B 322 MET cc_start: 0.8682 (mmm) cc_final: 0.8313 (mmm) REVERT: B 350 ARG cc_start: 0.8491 (mtp85) cc_final: 0.7751 (mtp85) REVERT: B 359 MET cc_start: 0.9081 (ttt) cc_final: 0.8500 (tmm) REVERT: B 375 LYS cc_start: 0.9253 (mmmm) cc_final: 0.8975 (mmmm) REVERT: B 379 SER cc_start: 0.9060 (t) cc_final: 0.8455 (t) REVERT: B 402 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8300 (tm-30) REVERT: B 403 ILE cc_start: 0.9318 (mp) cc_final: 0.8958 (tp) REVERT: B 410 ASN cc_start: 0.8924 (m110) cc_final: 0.8575 (m110) REVERT: B 415 ASN cc_start: 0.9229 (t0) cc_final: 0.8389 (t0) REVERT: B 418 ASN cc_start: 0.9397 (m-40) cc_final: 0.9035 (m-40) REVERT: B 467 ASN cc_start: 0.8612 (m110) cc_final: 0.8280 (m-40) REVERT: B 469 HIS cc_start: 0.8757 (t-170) cc_final: 0.8408 (t70) REVERT: B 494 MET cc_start: 0.9546 (ttm) cc_final: 0.9239 (ttm) REVERT: B 530 LYS cc_start: 0.9030 (ptmm) cc_final: 0.8751 (ptmm) REVERT: B 598 MET cc_start: 0.9384 (mtm) cc_final: 0.9013 (mtm) REVERT: B 612 TYR cc_start: 0.8601 (m-80) cc_final: 0.7903 (m-80) REVERT: B 613 TYR cc_start: 0.9112 (t80) cc_final: 0.8650 (t80) REVERT: B 615 MET cc_start: 0.8736 (mmp) cc_final: 0.8040 (mmp) REVERT: B 631 ASP cc_start: 0.9412 (t70) cc_final: 0.9166 (t0) REVERT: B 636 LYS cc_start: 0.9572 (mptt) cc_final: 0.9309 (mmtt) REVERT: B 640 MET cc_start: 0.9399 (tpp) cc_final: 0.8877 (tpp) REVERT: B 648 ILE cc_start: 0.9250 (mm) cc_final: 0.8882 (mm) REVERT: B 667 LEU cc_start: 0.9646 (tp) cc_final: 0.9439 (tp) REVERT: B 679 ILE cc_start: 0.9585 (mm) cc_final: 0.9362 (mm) REVERT: C 17 PHE cc_start: 0.8414 (p90) cc_final: 0.7536 (p90) REVERT: C 21 PHE cc_start: 0.9063 (m-10) cc_final: 0.8383 (m-80) REVERT: C 96 MET cc_start: 0.8385 (tpt) cc_final: 0.7920 (tpt) REVERT: C 105 TYR cc_start: 0.8980 (m-80) cc_final: 0.8538 (m-80) REVERT: C 157 MET cc_start: 0.9522 (ptm) cc_final: 0.9025 (ppp) REVERT: C 178 PHE cc_start: 0.9180 (m-80) cc_final: 0.8913 (m-10) REVERT: C 230 ASP cc_start: 0.8939 (t0) cc_final: 0.8451 (m-30) REVERT: C 239 GLU cc_start: 0.8480 (pt0) cc_final: 0.7974 (pt0) REVERT: D 21 PHE cc_start: 0.8733 (m-10) cc_final: 0.8511 (m-10) REVERT: D 109 PHE cc_start: 0.8513 (m-80) cc_final: 0.7647 (m-80) REVERT: D 112 LEU cc_start: 0.8576 (mm) cc_final: 0.8216 (mm) REVERT: D 119 ASN cc_start: 0.8786 (m-40) cc_final: 0.8582 (m110) REVERT: D 157 MET cc_start: 0.9344 (ptp) cc_final: 0.8853 (ptt) REVERT: D 166 PHE cc_start: 0.7621 (t80) cc_final: 0.7388 (t80) REVERT: D 172 PHE cc_start: 0.9422 (m-80) cc_final: 0.9024 (m-80) REVERT: D 179 TYR cc_start: 0.8088 (t80) cc_final: 0.7652 (t80) REVERT: D 185 MET cc_start: 0.6040 (mmp) cc_final: 0.5681 (mmm) REVERT: D 211 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8975 (mt-10) REVERT: D 244 GLU cc_start: 0.9138 (mp0) cc_final: 0.8935 (mm-30) REVERT: D 271 LEU cc_start: 0.8591 (mt) cc_final: 0.8349 (mt) outliers start: 1 outliers final: 0 residues processed: 684 average time/residue: 0.1246 time to fit residues: 129.1019 Evaluate side-chains 581 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 581 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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: 7.9990 chunk 99 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 153 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 151 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 ASN A 645 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 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 320 ASN B 410 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.108101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.079127 restraints weight = 51472.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.082254 restraints weight = 31207.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.084431 restraints weight = 21540.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.086020 restraints weight = 16101.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.087254 restraints weight = 12776.689| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.7559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16386 Z= 0.190 Angle : 0.659 16.344 22134 Z= 0.353 Chirality : 0.044 0.301 2360 Planarity : 0.004 0.041 2818 Dihedral : 8.545 156.630 2290 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: 0.48 (0.18), residues: 1932 helix: 0.81 (0.15), residues: 1138 sheet: -0.64 (0.41), residues: 144 loop : -0.12 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 164 TYR 0.043 0.002 TYR C 142 PHE 0.036 0.002 PHE C 168 TRP 0.061 0.002 TRP D 124 HIS 0.010 0.002 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 (16386) covalent geometry : angle 0.65897 / 0.35 (22134) hydrogen bonds : bond 0.04125 / 2.58 ( 871) hydrogen bonds : angle 5.24357 / 3.82 ( 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 662 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 662 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.9205 (tptp) cc_final: 0.8758 (tppt) REVERT: A 15 GLU cc_start: 0.9144 (tp30) cc_final: 0.8844 (tp30) REVERT: A 95 MET cc_start: 0.9363 (mmm) cc_final: 0.9000 (tpt) REVERT: A 116 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7713 (tt0) REVERT: A 119 GLU cc_start: 0.9143 (mp0) cc_final: 0.8812 (mp0) REVERT: A 120 ASP cc_start: 0.9266 (m-30) cc_final: 0.9048 (m-30) REVERT: A 147 GLN cc_start: 0.8740 (mt0) cc_final: 0.8389 (mt0) REVERT: A 173 LEU cc_start: 0.9505 (mt) cc_final: 0.9242 (mt) REVERT: A 176 ASN cc_start: 0.8518 (t0) cc_final: 0.7910 (m-40) REVERT: A 184 ARG cc_start: 0.9317 (mmm-85) cc_final: 0.8883 (tpp80) REVERT: A 190 MET cc_start: 0.9164 (mtp) cc_final: 0.8859 (mtp) REVERT: A 235 ARG cc_start: 0.8307 (mtm110) cc_final: 0.8014 (mtm110) REVERT: A 236 TYR cc_start: 0.8989 (t80) cc_final: 0.8359 (t80) REVERT: A 261 PHE cc_start: 0.9033 (t80) cc_final: 0.8759 (t80) REVERT: A 280 ILE cc_start: 0.8591 (pt) cc_final: 0.7999 (mp) REVERT: A 290 GLU cc_start: 0.9449 (mm-30) cc_final: 0.9242 (mm-30) REVERT: A 316 GLU cc_start: 0.9365 (tt0) cc_final: 0.9124 (tt0) REVERT: A 352 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8648 (tm-30) REVERT: A 355 TYR cc_start: 0.8714 (m-10) cc_final: 0.8487 (m-10) REVERT: A 359 MET cc_start: 0.8547 (tmm) cc_final: 0.8224 (tmm) REVERT: A 362 ASP cc_start: 0.8755 (m-30) cc_final: 0.8370 (m-30) REVERT: A 370 ASN cc_start: 0.9500 (m-40) cc_final: 0.9175 (m110) REVERT: A 375 LYS cc_start: 0.8959 (mmmt) cc_final: 0.8236 (mmtp) REVERT: A 377 LYS cc_start: 0.8922 (mttt) cc_final: 0.8481 (mttp) REVERT: A 381 LEU cc_start: 0.9027 (tp) cc_final: 0.8557 (pt) REVERT: A 407 ILE cc_start: 0.9245 (mt) cc_final: 0.8940 (mt) REVERT: A 426 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8485 (tm-30) REVERT: A 469 HIS cc_start: 0.8922 (t-170) cc_final: 0.8617 (t-170) REVERT: A 479 TYR cc_start: 0.8932 (t80) cc_final: 0.8609 (t80) REVERT: A 490 THR cc_start: 0.9512 (m) cc_final: 0.9186 (p) REVERT: A 494 MET cc_start: 0.9463 (mpp) cc_final: 0.8999 (mmm) REVERT: A 496 ASN cc_start: 0.9338 (m-40) cc_final: 0.9120 (m110) REVERT: A 515 ASP cc_start: 0.9430 (m-30) cc_final: 0.8921 (m-30) REVERT: A 516 GLN cc_start: 0.9172 (mp10) cc_final: 0.8877 (mp10) REVERT: A 570 MET cc_start: 0.9337 (mtp) cc_final: 0.8933 (mtp) REVERT: A 598 MET cc_start: 0.8726 (ttt) cc_final: 0.7876 (ttt) REVERT: A 628 GLU cc_start: 0.9250 (mt-10) cc_final: 0.8728 (mm-30) REVERT: A 632 MET cc_start: 0.9031 (mmm) cc_final: 0.8769 (mmm) REVERT: A 636 LYS cc_start: 0.9800 (mmtp) cc_final: 0.9597 (mmmm) REVERT: A 640 MET cc_start: 0.9242 (tpp) cc_final: 0.8826 (tpp) REVERT: A 646 GLN cc_start: 0.9137 (pm20) cc_final: 0.8861 (pm20) REVERT: A 647 HIS cc_start: 0.9277 (m-70) cc_final: 0.7749 (m170) REVERT: A 653 SER cc_start: 0.9250 (p) cc_final: 0.9040 (p) REVERT: A 672 LEU cc_start: 0.9343 (mt) cc_final: 0.9123 (mt) REVERT: B 8 LYS cc_start: 0.9462 (tptp) cc_final: 0.9165 (tptp) REVERT: B 30 LYS cc_start: 0.9826 (tmtt) cc_final: 0.9522 (tptt) REVERT: B 67 GLU cc_start: 0.9205 (mp0) cc_final: 0.8930 (mp0) REVERT: B 82 LYS cc_start: 0.9502 (ptpp) cc_final: 0.9197 (ptpt) REVERT: B 99 LYS cc_start: 0.9504 (mmmt) cc_final: 0.9201 (mttp) REVERT: B 119 GLU cc_start: 0.9201 (mp0) cc_final: 0.8750 (mp0) REVERT: B 120 ASP cc_start: 0.9422 (m-30) cc_final: 0.9205 (m-30) REVERT: B 147 GLN cc_start: 0.9451 (mt0) cc_final: 0.8866 (mt0) REVERT: B 149 TYR cc_start: 0.9145 (t80) cc_final: 0.8791 (t80) REVERT: B 227 MET cc_start: 0.9174 (ttp) cc_final: 0.8915 (ttp) REVERT: B 235 ARG cc_start: 0.8707 (ttm110) cc_final: 0.8091 (ttm110) REVERT: B 250 TYR cc_start: 0.8743 (m-80) cc_final: 0.7593 (m-80) REVERT: B 263 ASP cc_start: 0.9170 (m-30) cc_final: 0.8813 (m-30) REVERT: B 283 VAL cc_start: 0.9545 (t) cc_final: 0.9217 (t) REVERT: B 286 ASP cc_start: 0.8864 (m-30) cc_final: 0.8035 (m-30) REVERT: B 291 LEU cc_start: 0.9549 (mt) cc_final: 0.9314 (mt) REVERT: B 316 GLU cc_start: 0.9434 (tm-30) cc_final: 0.9196 (tm-30) REVERT: B 325 LYS cc_start: 0.8864 (mptt) cc_final: 0.8636 (tptt) REVERT: B 359 MET cc_start: 0.9059 (ttt) cc_final: 0.8477 (tmm) REVERT: B 362 ASP cc_start: 0.8430 (m-30) cc_final: 0.7631 (m-30) REVERT: B 375 LYS cc_start: 0.9284 (mmmm) cc_final: 0.8987 (mmmm) REVERT: B 379 SER cc_start: 0.9128 (t) cc_final: 0.8571 (t) REVERT: B 403 ILE cc_start: 0.9320 (mp) cc_final: 0.8958 (tp) REVERT: B 410 ASN cc_start: 0.9024 (m-40) cc_final: 0.8792 (m-40) REVERT: B 415 ASN cc_start: 0.9198 (t0) cc_final: 0.8324 (t0) REVERT: B 420 MET cc_start: 0.9481 (mmm) cc_final: 0.9073 (mmm) REVERT: B 467 ASN cc_start: 0.8523 (m110) cc_final: 0.8239 (m-40) REVERT: B 494 MET cc_start: 0.9552 (ttm) cc_final: 0.9246 (ttm) REVERT: B 598 MET cc_start: 0.9364 (mtm) cc_final: 0.9033 (mtm) REVERT: B 612 TYR cc_start: 0.8582 (m-80) cc_final: 0.7781 (m-80) REVERT: B 613 TYR cc_start: 0.9185 (t80) cc_final: 0.8911 (t80) REVERT: B 615 MET cc_start: 0.8732 (mmp) cc_final: 0.8071 (mmp) REVERT: B 631 ASP cc_start: 0.9407 (t70) cc_final: 0.9188 (t0) REVERT: B 639 ASP cc_start: 0.9414 (m-30) cc_final: 0.8910 (m-30) REVERT: B 640 MET cc_start: 0.9439 (tpp) cc_final: 0.8896 (tpp) REVERT: B 641 ILE cc_start: 0.9649 (mp) cc_final: 0.9435 (mp) REVERT: B 656 LEU cc_start: 0.9537 (mt) cc_final: 0.9290 (mt) REVERT: B 673 TYR cc_start: 0.9061 (t80) cc_final: 0.8629 (t80) REVERT: B 679 ILE cc_start: 0.9612 (mm) cc_final: 0.9347 (mm) REVERT: C 17 PHE cc_start: 0.8603 (p90) cc_final: 0.7623 (p90) REVERT: C 20 MET cc_start: 0.8958 (pmm) cc_final: 0.8613 (pmm) REVERT: C 21 PHE cc_start: 0.9023 (m-10) cc_final: 0.8246 (m-80) REVERT: C 72 THR cc_start: 0.8199 (m) cc_final: 0.7918 (p) REVERT: C 96 MET cc_start: 0.8572 (tpt) cc_final: 0.8299 (tpt) REVERT: C 100 VAL cc_start: 0.6286 (t) cc_final: 0.5941 (t) REVERT: C 105 TYR cc_start: 0.9081 (m-80) cc_final: 0.8717 (m-80) REVERT: C 204 TYR cc_start: 0.8941 (t80) cc_final: 0.8723 (t80) REVERT: C 230 ASP cc_start: 0.8905 (t0) cc_final: 0.8425 (m-30) REVERT: C 239 GLU cc_start: 0.8486 (pt0) cc_final: 0.7963 (pt0) REVERT: C 320 PHE cc_start: 0.7862 (m-10) cc_final: 0.7456 (m-10) REVERT: D 21 PHE cc_start: 0.8639 (m-10) cc_final: 0.8404 (m-10) REVERT: D 109 PHE cc_start: 0.8539 (m-80) cc_final: 0.7698 (m-80) REVERT: D 112 LEU cc_start: 0.8625 (mm) cc_final: 0.8171 (mm) REVERT: D 166 PHE cc_start: 0.7694 (t80) cc_final: 0.7355 (t80) REVERT: D 172 PHE cc_start: 0.9508 (m-80) cc_final: 0.9163 (m-80) REVERT: D 179 TYR cc_start: 0.8116 (t80) cc_final: 0.7660 (t80) REVERT: D 185 MET cc_start: 0.6257 (mmp) cc_final: 0.5972 (mmm) REVERT: D 214 ASN cc_start: 0.9622 (t0) cc_final: 0.9356 (p0) REVERT: D 224 LEU cc_start: 0.9352 (mt) cc_final: 0.9129 (mt) REVERT: D 244 GLU cc_start: 0.9082 (mp0) cc_final: 0.8810 (mm-30) outliers start: 0 outliers final: 0 residues processed: 662 average time/residue: 0.1241 time to fit residues: 124.7688 Evaluate side-chains 573 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 573 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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: 0.4980 chunk 133 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 71 optimal weight: 0.1980 chunk 100 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 501 GLN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** 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** B 668 ASN D 146 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.114638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.085626 restraints weight = 49623.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.088786 restraints weight = 29733.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.091079 restraints weight = 20469.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.092802 restraints weight = 15237.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.094095 restraints weight = 11920.971| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.7797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16386 Z= 0.134 Angle : 0.655 11.210 22134 Z= 0.348 Chirality : 0.045 0.351 2360 Planarity : 0.004 0.038 2818 Dihedral : 8.374 155.761 2290 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 0.48 (0.18), residues: 1932 helix: 0.84 (0.15), residues: 1138 sheet: -0.77 (0.42), residues: 144 loop : -0.15 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 164 TYR 0.030 0.001 TYR C 142 PHE 0.041 0.002 PHE C 109 TRP 0.056 0.002 TRP D 124 HIS 0.010 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (16386) covalent geometry : angle 0.65468 / 0.35 (22134) hydrogen bonds : bond 0.04061 / 2.55 ( 871) hydrogen bonds : angle 5.22940 / 3.82 ( 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 670 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 670 time to evaluate : 0.620 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: 0.9190 (tptp) cc_final: 0.8718 (tppt) REVERT: A 15 GLU cc_start: 0.9177 (tp30) cc_final: 0.8800 (tp30) REVERT: A 81 PHE cc_start: 0.9574 (m-80) cc_final: 0.9365 (m-80) REVERT: A 95 MET cc_start: 0.9269 (mmm) cc_final: 0.8964 (tpt) REVERT: A 116 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7584 (tt0) REVERT: A 119 GLU cc_start: 0.9023 (mp0) cc_final: 0.8776 (mp0) REVERT: A 120 ASP cc_start: 0.9133 (m-30) cc_final: 0.8870 (m-30) REVERT: A 129 PHE cc_start: 0.9637 (m-10) cc_final: 0.9385 (m-10) REVERT: A 136 LYS cc_start: 0.9563 (ttpp) cc_final: 0.9346 (ttpt) REVERT: A 147 GLN cc_start: 0.8792 (mt0) cc_final: 0.8441 (mt0) REVERT: A 164 ARG cc_start: 0.8076 (ptm-80) cc_final: 0.6671 (ptm-80) REVERT: A 173 LEU cc_start: 0.9501 (mt) cc_final: 0.9194 (mt) REVERT: A 184 ARG cc_start: 0.9275 (mmm-85) cc_final: 0.8857 (tpp80) REVERT: A 190 MET cc_start: 0.9138 (mtp) cc_final: 0.8936 (mtp) REVERT: A 236 TYR cc_start: 0.8929 (t80) cc_final: 0.8411 (t80) REVERT: A 261 PHE cc_start: 0.9072 (t80) cc_final: 0.8822 (t80) REVERT: A 280 ILE cc_start: 0.8528 (pt) cc_final: 0.7913 (mp) REVERT: A 290 GLU cc_start: 0.9459 (mm-30) cc_final: 0.9215 (mm-30) REVERT: A 307 TYR cc_start: 0.9514 (t80) cc_final: 0.9078 (t80) REVERT: A 316 GLU cc_start: 0.9348 (tt0) cc_final: 0.9061 (tt0) REVERT: A 349 LEU cc_start: 0.9438 (mt) cc_final: 0.9200 (mt) REVERT: A 352 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8623 (tm-30) REVERT: A 359 MET cc_start: 0.8417 (tmm) cc_final: 0.8181 (tmm) REVERT: A 362 ASP cc_start: 0.8737 (m-30) cc_final: 0.8448 (m-30) REVERT: A 370 ASN cc_start: 0.9397 (m-40) cc_final: 0.9070 (m110) REVERT: A 375 LYS cc_start: 0.8938 (mmmt) cc_final: 0.8205 (mmtm) REVERT: A 377 LYS cc_start: 0.8943 (mttt) cc_final: 0.8591 (mttp) REVERT: A 381 LEU cc_start: 0.9025 (tp) cc_final: 0.8613 (pt) REVERT: A 426 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8429 (tm-30) REVERT: A 441 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8994 (mm-30) REVERT: A 496 ASN cc_start: 0.9415 (m-40) cc_final: 0.9198 (m110) REVERT: A 501 GLN cc_start: 0.9467 (mm110) cc_final: 0.9079 (mt0) REVERT: A 515 ASP cc_start: 0.9400 (m-30) cc_final: 0.8806 (m-30) REVERT: A 516 GLN cc_start: 0.9154 (mp10) cc_final: 0.8893 (mp10) REVERT: A 561 LEU cc_start: 0.9665 (tp) cc_final: 0.9461 (tp) REVERT: A 562 LYS cc_start: 0.9735 (ttmt) cc_final: 0.9213 (tttt) REVERT: A 570 MET cc_start: 0.9376 (mtp) cc_final: 0.9061 (mtp) REVERT: A 595 MET cc_start: 0.9007 (mmm) cc_final: 0.8720 (mtt) REVERT: A 598 MET cc_start: 0.8804 (ttt) cc_final: 0.7927 (ttt) REVERT: A 628 GLU cc_start: 0.9309 (mt-10) cc_final: 0.8836 (mm-30) REVERT: A 632 MET cc_start: 0.9002 (mmm) cc_final: 0.8756 (mmm) REVERT: A 636 LYS cc_start: 0.9785 (mmtp) cc_final: 0.9575 (mmmm) REVERT: A 640 MET cc_start: 0.9234 (tpp) cc_final: 0.8733 (tpp) REVERT: A 646 GLN cc_start: 0.9124 (pm20) cc_final: 0.8867 (pm20) REVERT: A 647 HIS cc_start: 0.9232 (m-70) cc_final: 0.7732 (m170) REVERT: A 677 ARG cc_start: 0.9376 (mmm-85) cc_final: 0.8958 (mmm-85) REVERT: B 8 LYS cc_start: 0.9452 (tptp) cc_final: 0.9169 (tptp) REVERT: B 30 LYS cc_start: 0.9819 (tmtt) cc_final: 0.9490 (tptt) REVERT: B 67 GLU cc_start: 0.9214 (mp0) cc_final: 0.8889 (mp0) REVERT: B 82 LYS cc_start: 0.9491 (ptpp) cc_final: 0.9133 (ptpt) REVERT: B 99 LYS cc_start: 0.9519 (mmmt) cc_final: 0.9221 (mttp) REVERT: B 117 ARG cc_start: 0.8898 (mtp180) cc_final: 0.8525 (mmm160) REVERT: B 119 GLU cc_start: 0.9121 (mp0) cc_final: 0.8702 (mp0) REVERT: B 147 GLN cc_start: 0.9424 (mt0) cc_final: 0.9067 (mt0) REVERT: B 149 TYR cc_start: 0.9161 (t80) cc_final: 0.8701 (t80) REVERT: B 227 MET cc_start: 0.9165 (ttp) cc_final: 0.8951 (ttp) REVERT: B 235 ARG cc_start: 0.8729 (ttm110) cc_final: 0.8216 (ttm110) REVERT: B 250 TYR cc_start: 0.8485 (m-80) cc_final: 0.7335 (m-80) REVERT: B 260 ASP cc_start: 0.9420 (p0) cc_final: 0.9217 (p0) REVERT: B 263 ASP cc_start: 0.9130 (m-30) cc_final: 0.8764 (m-30) REVERT: B 283 VAL cc_start: 0.9520 (t) cc_final: 0.9194 (t) REVERT: B 286 ASP cc_start: 0.8847 (m-30) cc_final: 0.7990 (m-30) REVERT: B 291 LEU cc_start: 0.9566 (mt) cc_final: 0.9358 (mt) REVERT: B 322 MET cc_start: 0.9010 (mmp) cc_final: 0.8372 (mmm) REVERT: B 359 MET cc_start: 0.9040 (ttt) cc_final: 0.8492 (tmm) REVERT: B 362 ASP cc_start: 0.8707 (m-30) cc_final: 0.7605 (m-30) REVERT: B 375 LYS cc_start: 0.9249 (mmmm) cc_final: 0.8964 (mmmm) REVERT: B 379 SER cc_start: 0.9010 (t) cc_final: 0.8435 (t) REVERT: B 402 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8289 (tm-30) REVERT: B 403 ILE cc_start: 0.9267 (mp) cc_final: 0.8860 (tp) REVERT: B 410 ASN cc_start: 0.9028 (m-40) cc_final: 0.8701 (m-40) REVERT: B 415 ASN cc_start: 0.9316 (t0) cc_final: 0.8951 (t0) REVERT: B 467 ASN cc_start: 0.8563 (m110) cc_final: 0.8285 (m-40) REVERT: B 469 HIS cc_start: 0.8629 (t-170) cc_final: 0.8245 (t70) REVERT: B 494 MET cc_start: 0.9558 (ttm) cc_final: 0.9279 (ttm) REVERT: B 500 ILE cc_start: 0.9635 (mt) cc_final: 0.8981 (mt) REVERT: B 530 LYS cc_start: 0.9121 (ptmm) cc_final: 0.8759 (ptmm) REVERT: B 531 TYR cc_start: 0.7937 (m-80) cc_final: 0.7731 (m-10) REVERT: B 575 ARG cc_start: 0.8625 (mtm-85) cc_final: 0.7722 (mpp80) REVERT: B 598 MET cc_start: 0.9314 (mtm) cc_final: 0.9015 (mtm) REVERT: B 602 GLU cc_start: 0.8762 (pp20) cc_final: 0.7746 (pp20) REVERT: B 612 TYR cc_start: 0.8604 (m-80) cc_final: 0.7881 (m-80) REVERT: B 631 ASP cc_start: 0.9415 (t70) cc_final: 0.9188 (t0) REVERT: B 640 MET cc_start: 0.9404 (tpp) cc_final: 0.8795 (tpp) REVERT: B 648 ILE cc_start: 0.9208 (mm) cc_final: 0.8829 (mm) REVERT: B 679 ILE cc_start: 0.9552 (mm) cc_final: 0.9323 (mm) REVERT: C 17 PHE cc_start: 0.8569 (p90) cc_final: 0.7545 (p90) REVERT: C 20 MET cc_start: 0.9005 (pmm) cc_final: 0.8592 (pmm) REVERT: C 21 PHE cc_start: 0.9045 (m-10) cc_final: 0.8105 (m-80) REVERT: C 96 MET cc_start: 0.8593 (tpt) cc_final: 0.8153 (tpt) REVERT: C 100 VAL cc_start: 0.6657 (t) cc_final: 0.6338 (t) REVERT: C 105 TYR cc_start: 0.8946 (m-80) cc_final: 0.8572 (m-80) REVERT: C 154 PHE cc_start: 0.9561 (t80) cc_final: 0.9243 (t80) REVERT: C 157 MET cc_start: 0.9649 (ptm) cc_final: 0.9068 (ppp) REVERT: C 178 PHE cc_start: 0.9168 (m-80) cc_final: 0.8936 (m-10) REVERT: C 230 ASP cc_start: 0.8862 (t0) cc_final: 0.8368 (m-30) REVERT: C 239 GLU cc_start: 0.8408 (pt0) cc_final: 0.7681 (pt0) REVERT: D 21 PHE cc_start: 0.8679 (m-10) cc_final: 0.8447 (m-10) REVERT: D 108 ILE cc_start: 0.9438 (pt) cc_final: 0.9204 (pt) REVERT: D 109 PHE cc_start: 0.8532 (m-80) cc_final: 0.7665 (m-80) REVERT: D 112 LEU cc_start: 0.8646 (mm) cc_final: 0.8217 (mm) REVERT: D 166 PHE cc_start: 0.7419 (t80) cc_final: 0.7036 (t80) REVERT: D 169 TYR cc_start: 0.8891 (m-80) cc_final: 0.8365 (m-80) REVERT: D 172 PHE cc_start: 0.9359 (m-80) cc_final: 0.9010 (m-80) REVERT: D 179 TYR cc_start: 0.8011 (t80) cc_final: 0.7583 (t80) REVERT: D 185 MET cc_start: 0.6107 (mmp) cc_final: 0.5840 (mmm) REVERT: D 214 ASN cc_start: 0.9635 (t0) cc_final: 0.9323 (p0) REVERT: D 224 LEU cc_start: 0.9426 (mt) cc_final: 0.9118 (mt) REVERT: D 244 GLU cc_start: 0.9076 (mp0) cc_final: 0.8763 (mm-30) REVERT: D 285 ILE cc_start: 0.9273 (tp) cc_final: 0.9071 (tp) outliers start: 0 outliers final: 0 residues processed: 670 average time/residue: 0.1245 time to fit residues: 126.2062 Evaluate side-chains 569 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 569 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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: 8.9990 chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 189 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 165 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** 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 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.112860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.083774 restraints weight = 50894.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.086894 restraints weight = 30545.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.089058 restraints weight = 21004.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.090772 restraints weight = 15803.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.092031 restraints weight = 12396.583| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 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 = 0.3145 r_free = 0.3145 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: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.7999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16386 Z= 0.159 Angle : 0.686 11.082 22134 Z= 0.368 Chirality : 0.045 0.362 2360 Planarity : 0.004 0.060 2818 Dihedral : 8.415 157.048 2290 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.18), residues: 1932 helix: 0.75 (0.15), residues: 1138 sheet: -0.71 (0.42), residues: 144 loop : -0.21 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 235 TYR 0.039 0.002 TYR C 142 PHE 0.029 0.002 PHE C 168 TRP 0.060 0.002 TRP D 124 HIS 0.010 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (16386) covalent geometry : angle 0.68599 / 0.37 (22134) hydrogen bonds : bond 0.04199 / 2.61 ( 871) hydrogen bonds : angle 5.30197 / 3.88 ( 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 654 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 654 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9243 (tptp) cc_final: 0.8832 (tppt) REVERT: A 15 GLU cc_start: 0.9124 (tp30) cc_final: 0.8820 (tp30) REVERT: A 81 PHE cc_start: 0.9572 (m-80) cc_final: 0.9355 (m-80) REVERT: A 116 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7545 (tt0) REVERT: A 119 GLU cc_start: 0.9038 (mp0) cc_final: 0.8802 (mp0) REVERT: A 136 LYS cc_start: 0.9559 (ttpp) cc_final: 0.9256 (ttpt) REVERT: A 147 GLN cc_start: 0.8790 (mt0) cc_final: 0.8467 (mt0) REVERT: A 164 ARG cc_start: 0.8061 (ptm-80) cc_final: 0.6663 (ptm-80) REVERT: A 184 ARG cc_start: 0.9301 (mmm-85) cc_final: 0.8917 (tpp80) REVERT: A 190 MET cc_start: 0.9179 (mtp) cc_final: 0.8931 (mtp) REVERT: A 206 LEU cc_start: 0.8833 (mt) cc_final: 0.8522 (mt) REVERT: A 235 ARG cc_start: 0.8352 (mtm110) cc_final: 0.7986 (mtm110) REVERT: A 236 TYR cc_start: 0.8980 (t80) cc_final: 0.8341 (t80) REVERT: A 261 PHE cc_start: 0.9067 (t80) cc_final: 0.8764 (t80) REVERT: A 280 ILE cc_start: 0.8534 (pt) cc_final: 0.8116 (mp) REVERT: A 289 VAL cc_start: 0.9757 (p) cc_final: 0.9525 (m) REVERT: A 290 GLU cc_start: 0.9497 (mm-30) cc_final: 0.9253 (mm-30) REVERT: A 307 TYR cc_start: 0.9531 (t80) cc_final: 0.9272 (t80) REVERT: A 345 LYS cc_start: 0.9079 (tttt) cc_final: 0.8821 (tttt) REVERT: A 349 LEU cc_start: 0.9458 (mt) cc_final: 0.9229 (mt) REVERT: A 352 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8630 (tm-30) REVERT: A 362 ASP cc_start: 0.8717 (m-30) cc_final: 0.8378 (m-30) REVERT: A 370 ASN cc_start: 0.9430 (m-40) cc_final: 0.9088 (m110) REVERT: A 375 LYS cc_start: 0.8947 (mmmt) cc_final: 0.8628 (mmtp) REVERT: A 377 LYS cc_start: 0.8824 (mttt) cc_final: 0.8276 (mtmm) REVERT: A 381 LEU cc_start: 0.9082 (tp) cc_final: 0.8736 (pt) REVERT: A 426 GLU cc_start: 0.9099 (tm-30) cc_final: 0.8431 (tm-30) REVERT: A 441 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8985 (mm-30) REVERT: A 468 LEU cc_start: 0.9662 (tp) cc_final: 0.9462 (tp) REVERT: A 479 TYR cc_start: 0.8830 (t80) cc_final: 0.8420 (t80) REVERT: A 496 ASN cc_start: 0.9403 (m-40) cc_final: 0.9183 (m110) REVERT: A 515 ASP cc_start: 0.9405 (m-30) cc_final: 0.8832 (m-30) REVERT: A 516 GLN cc_start: 0.9163 (mp10) cc_final: 0.8917 (mp10) REVERT: A 570 MET cc_start: 0.9335 (mtp) cc_final: 0.8933 (mtp) REVERT: A 583 SER cc_start: 0.9588 (m) cc_final: 0.9259 (t) REVERT: A 595 MET cc_start: 0.8987 (mmm) cc_final: 0.8761 (mtt) REVERT: A 598 MET cc_start: 0.8733 (ttt) cc_final: 0.8272 (ttt) REVERT: A 628 GLU cc_start: 0.9318 (mt-10) cc_final: 0.8796 (mm-30) REVERT: A 632 MET cc_start: 0.8986 (mmm) cc_final: 0.8749 (mmm) REVERT: A 636 LYS cc_start: 0.9802 (mmtp) cc_final: 0.9595 (mmmm) REVERT: A 640 MET cc_start: 0.9286 (tpp) cc_final: 0.8790 (tpp) REVERT: A 646 GLN cc_start: 0.9130 (pm20) cc_final: 0.8896 (pm20) REVERT: A 647 HIS cc_start: 0.9268 (m-70) cc_final: 0.7758 (m170) REVERT: A 650 GLN cc_start: 0.8938 (mt0) cc_final: 0.8522 (mt0) REVERT: A 677 ARG cc_start: 0.9347 (mmm-85) cc_final: 0.8907 (mmm-85) REVERT: A 679 ILE cc_start: 0.9560 (mm) cc_final: 0.9316 (mm) REVERT: B 8 LYS cc_start: 0.9445 (tptp) cc_final: 0.9173 (tptp) REVERT: B 30 LYS cc_start: 0.9743 (tmtt) cc_final: 0.9494 (tptt) REVERT: B 82 LYS cc_start: 0.9503 (ptpp) cc_final: 0.9185 (ptpt) REVERT: B 99 LYS cc_start: 0.9491 (mmmt) cc_final: 0.9248 (mttp) REVERT: B 119 GLU cc_start: 0.9142 (mp0) cc_final: 0.8730 (mp0) REVERT: B 120 ASP cc_start: 0.9437 (m-30) cc_final: 0.9186 (m-30) REVERT: B 144 MET cc_start: 0.9423 (mtm) cc_final: 0.9156 (mtm) REVERT: B 147 GLN cc_start: 0.9435 (mt0) cc_final: 0.9133 (mt0) REVERT: B 149 TYR cc_start: 0.9184 (t80) cc_final: 0.8724 (t80) REVERT: B 180 ASN cc_start: 0.9116 (m-40) cc_final: 0.8374 (t0) REVERT: B 235 ARG cc_start: 0.8703 (ttm110) cc_final: 0.8276 (ttm110) REVERT: B 250 TYR cc_start: 0.8654 (m-80) cc_final: 0.7451 (m-80) REVERT: B 260 ASP cc_start: 0.9409 (p0) cc_final: 0.9186 (p0) REVERT: B 263 ASP cc_start: 0.9133 (m-30) cc_final: 0.8731 (m-30) REVERT: B 283 VAL cc_start: 0.9495 (t) cc_final: 0.9158 (t) REVERT: B 286 ASP cc_start: 0.8797 (m-30) cc_final: 0.7906 (m-30) REVERT: B 291 LEU cc_start: 0.9584 (mt) cc_final: 0.9373 (mt) REVERT: B 322 MET cc_start: 0.8899 (mmp) cc_final: 0.8249 (mmm) REVERT: B 359 MET cc_start: 0.9009 (ttt) cc_final: 0.8486 (tmm) REVERT: B 362 ASP cc_start: 0.8646 (m-30) cc_final: 0.7522 (m-30) REVERT: B 375 LYS cc_start: 0.9250 (mmmm) cc_final: 0.8933 (mmmm) REVERT: B 379 SER cc_start: 0.9067 (t) cc_final: 0.8474 (t) REVERT: B 402 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8321 (tm-30) REVERT: B 403 ILE cc_start: 0.9276 (mp) cc_final: 0.8899 (tp) REVERT: B 410 ASN cc_start: 0.9084 (m-40) cc_final: 0.8865 (m-40) REVERT: B 415 ASN cc_start: 0.9307 (t0) cc_final: 0.8956 (t0) REVERT: B 420 MET cc_start: 0.9525 (mmm) cc_final: 0.9119 (mmm) REVERT: B 467 ASN cc_start: 0.8385 (m110) cc_final: 0.8125 (m-40) REVERT: B 469 HIS cc_start: 0.8925 (t-170) cc_final: 0.8346 (t70) REVERT: B 494 MET cc_start: 0.9537 (ttm) cc_final: 0.9215 (ttm) REVERT: B 530 LYS cc_start: 0.9081 (ptmm) cc_final: 0.8424 (ptmm) REVERT: B 598 MET cc_start: 0.9343 (mtm) cc_final: 0.9076 (mtm) REVERT: B 601 ILE cc_start: 0.9029 (tp) cc_final: 0.8571 (tp) REVERT: B 612 TYR cc_start: 0.8587 (m-80) cc_final: 0.7933 (m-80) REVERT: B 631 ASP cc_start: 0.9426 (t70) cc_final: 0.9069 (t0) REVERT: B 636 LYS cc_start: 0.9672 (mptt) cc_final: 0.9372 (mmtt) REVERT: B 640 MET cc_start: 0.9411 (tpp) cc_final: 0.8795 (tpp) REVERT: B 641 ILE cc_start: 0.9589 (mp) cc_final: 0.9334 (mp) REVERT: B 679 ILE cc_start: 0.9587 (mm) cc_final: 0.9312 (mm) REVERT: C 17 PHE cc_start: 0.8569 (p90) cc_final: 0.7564 (p90) REVERT: C 20 MET cc_start: 0.9021 (pmm) cc_final: 0.8696 (pmm) REVERT: C 21 PHE cc_start: 0.9005 (m-10) cc_final: 0.8136 (m-80) REVERT: C 96 MET cc_start: 0.8537 (tpt) cc_final: 0.8107 (tpt) REVERT: C 100 VAL cc_start: 0.6639 (t) cc_final: 0.6358 (p) REVERT: C 105 TYR cc_start: 0.9029 (m-80) cc_final: 0.8627 (m-80) REVERT: C 154 PHE cc_start: 0.9585 (t80) cc_final: 0.9226 (t80) REVERT: C 157 MET cc_start: 0.9651 (ptm) cc_final: 0.9060 (ppp) REVERT: C 178 PHE cc_start: 0.9191 (m-80) cc_final: 0.8973 (m-10) REVERT: C 230 ASP cc_start: 0.8859 (t0) cc_final: 0.8343 (m-30) REVERT: C 239 GLU cc_start: 0.8395 (pt0) cc_final: 0.7877 (pt0) REVERT: D 21 PHE cc_start: 0.8702 (m-10) cc_final: 0.8470 (m-10) REVERT: D 108 ILE cc_start: 0.9453 (pt) cc_final: 0.9144 (pt) REVERT: D 109 PHE cc_start: 0.8505 (m-80) cc_final: 0.7709 (m-80) REVERT: D 112 LEU cc_start: 0.8709 (mm) cc_final: 0.7860 (pp) REVERT: D 166 PHE cc_start: 0.7436 (t80) cc_final: 0.7232 (t80) REVERT: D 169 TYR cc_start: 0.9063 (m-80) cc_final: 0.8407 (m-80) REVERT: D 172 PHE cc_start: 0.9336 (m-80) cc_final: 0.8960 (m-80) REVERT: D 179 TYR cc_start: 0.8047 (t80) cc_final: 0.7587 (t80) REVERT: D 185 MET cc_start: 0.6162 (mmp) cc_final: 0.5901 (mmm) REVERT: D 224 LEU cc_start: 0.9364 (mt) cc_final: 0.9152 (mt) REVERT: D 244 GLU cc_start: 0.9096 (mp0) cc_final: 0.8838 (mm-30) REVERT: D 318 ASP cc_start: 0.9261 (t0) cc_final: 0.8971 (t70) outliers start: 0 outliers final: 0 residues processed: 654 average time/residue: 0.1219 time to fit residues: 121.3413 Evaluate side-chains 568 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 568 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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: 1.9990 chunk 39 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 148 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN A 645 GLN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.111658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.083046 restraints weight = 49861.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.086011 restraints weight = 30420.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.088417 restraints weight = 20870.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.090009 restraints weight = 15517.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.091293 restraints weight = 12288.448| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.090 | | 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) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (24 function evaluations) r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.8182 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= 0.143 Angle : 0.685 10.372 22134 Z= 0.367 Chirality : 0.045 0.364 2360 Planarity : 0.004 0.040 2818 Dihedral : 8.342 157.603 2290 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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: 0.36 (0.18), residues: 1932 helix: 0.75 (0.15), residues: 1137 sheet: -0.79 (0.41), residues: 144 loop : -0.20 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 161 TYR 0.037 0.002 TYR C 142 PHE 0.026 0.002 PHE C 168 TRP 0.060 0.002 TRP D 124 HIS 0.008 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (16386) covalent geometry : angle 0.68541 / 0.37 (22134) hydrogen bonds : bond 0.04133 / 2.57 ( 871) hydrogen bonds : angle 5.31177 / 3.88 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3475.25 seconds wall clock time: 61 minutes 9.94 seconds (3669.94 seconds total)