Starting phenix.real_space_refine on Thu Aug 6 15:14:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzd_45064/08_2026/9bzd_45064_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzd_45064/08_2026/9bzd_45064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bzd_45064/08_2026/9bzd_45064_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzd_45064/08_2026/9bzd_45064_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bzd_45064/08_2026/9bzd_45064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzd_45064/08_2026/9bzd_45064.map" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.64, per 1000 atoms: 0.23 Number of scatterers: 16038 At special positions: 0 Unit cell: (93.288, 128.778, 129.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 760.7 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: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.515A 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: 4.128A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.694A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.627A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.074A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.677A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.878A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.645A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.729A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.027A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.068A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.544A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.934A 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: 7.902A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.478A pdb=" N LEU A 656 " --> pdb=" O ARG A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.185A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.049A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.309A 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: 2.89 Time building geometry restraints manager: 1.73 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: 4892 1.34 - 1.46: 3091 1.46 - 1.58: 8222 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" O3B TTP B 801 " pdb=" PG TTP B 801 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.83e+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 4.79e+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 1.18e+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 1.16e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 21530 2.10 - 4.19: 523 4.19 - 6.29: 64 6.29 - 8.38: 8 8.38 - 10.48: 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 110.54 116.60 -6.06 1.36e+00 5.41e-01 1.99e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.14 -4.43 1.15e+00 7.56e-01 1.48e+01 angle pdb=" N SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.22 -3.94 1.09e+00 8.42e-01 1.31e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.82 -4.32 1.23e+00 6.61e-01 1.23e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.73 -4.02 1.15e+00 7.56e-01 1.22e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.05: 9090 25.05 - 50.10: 654 50.10 - 75.15: 126 75.15 - 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 -95.65 122.67 1 2.00e+01 2.50e-03 3.70e+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 -134.38 12.38 0 2.50e+00 1.60e-01 2.45e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2142 0.093 - 0.187: 185 0.187 - 0.280: 28 0.280 - 0.373: 3 0.373 - 0.467: 2 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.44e+00 chirality pdb=" CA TYR C 169 " pdb=" N TYR C 169 " pdb=" C TYR C 169 " pdb=" CB TYR C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " -0.017 2.00e-02 2.50e+03 1.10e-02 2.13e+00 pdb=" CG PHE D 92 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 169 " 0.017 2.00e-02 2.50e+03 1.01e-02 2.04e+00 pdb=" CG TYR C 169 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR C 169 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR C 169 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 169 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 169 " 0.008 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 131 2.51 - 3.11: 11547 3.11 - 3.70: 27037 3.70 - 4.30: 41565 4.30 - 4.90: 65447 Nonbonded interactions: 145727 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.911 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.962 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.012 3.040 ... (remaining 145722 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.520 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.139 16386 Z= 0.334 Angle : 0.788 10.479 22134 Z= 0.472 Chirality : 0.058 0.467 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.675 125.244 6202 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.19 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: 0.57 (0.18), residues: 1932 helix: 0.59 (0.14), residues: 1149 sheet: 0.46 (0.42), residues: 124 loop : 0.24 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 196 TYR 0.021 0.002 TYR D 179 PHE 0.021 0.002 PHE C 168 TRP 0.009 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.33 (16386) covalent geometry : angle 0.78784 / 0.47 (22134) hydrogen bonds : bond 0.15424 / 9.51 ( 871) hydrogen bonds : angle 6.51733 / 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 1098 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 1075 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLN cc_start: 0.8048 (mt0) cc_final: 0.7539 (mt0) REVERT: A 12 LEU cc_start: 0.7978 (mt) cc_final: 0.7773 (mp) REVERT: A 28 LYS cc_start: 0.8502 (mmtm) cc_final: 0.8297 (tppp) REVERT: A 76 ASP cc_start: 0.7984 (m-30) cc_final: 0.7351 (m-30) REVERT: A 127 LEU cc_start: 0.8535 (mt) cc_final: 0.8222 (mt) REVERT: A 179 LEU cc_start: 0.8733 (tp) cc_final: 0.8515 (tp) REVERT: A 181 ASP cc_start: 0.7596 (m-30) cc_final: 0.7212 (m-30) REVERT: A 204 SER cc_start: 0.8470 (m) cc_final: 0.8039 (t) REVERT: A 265 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8590 (mmmt) REVERT: A 280 ILE cc_start: 0.8960 (pt) cc_final: 0.8670 (pt) REVERT: A 348 MET cc_start: 0.7366 (tmm) cc_final: 0.6798 (tmm) REVERT: A 352 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6376 (mt-10) REVERT: A 362 ASP cc_start: 0.5957 (m-30) cc_final: 0.5559 (m-30) REVERT: A 598 MET cc_start: 0.7520 (mtm) cc_final: 0.6916 (mtp) REVERT: A 604 ARG cc_start: 0.7657 (mmp80) cc_final: 0.6307 (mmt90) REVERT: A 606 TYR cc_start: 0.6419 (m-80) cc_final: 0.5936 (m-80) REVERT: A 645 GLN cc_start: 0.8195 (tp40) cc_final: 0.7666 (tp40) REVERT: B 11 GLN cc_start: 0.7881 (mt0) cc_final: 0.7483 (mt0) REVERT: B 12 LEU cc_start: 0.8243 (mt) cc_final: 0.7943 (mt) REVERT: B 33 VAL cc_start: 0.9342 (OUTLIER) cc_final: 0.9138 (t) REVERT: B 109 ASN cc_start: 0.8024 (m-40) cc_final: 0.7577 (p0) REVERT: B 121 ARG cc_start: 0.8401 (tpm170) cc_final: 0.7983 (tpp-160) REVERT: B 187 ASP cc_start: 0.6443 (t70) cc_final: 0.6238 (t0) REVERT: B 286 ASP cc_start: 0.6756 (OUTLIER) cc_final: 0.6117 (m-30) REVERT: B 295 ASP cc_start: 0.8037 (t0) cc_final: 0.7783 (t0) REVERT: B 348 MET cc_start: 0.6874 (tmm) cc_final: 0.6617 (ttp) REVERT: B 350 ARG cc_start: 0.7566 (mtp85) cc_final: 0.7299 (mtp85) REVERT: B 362 ASP cc_start: 0.6613 (m-30) cc_final: 0.6351 (m-30) REVERT: B 366 LYS cc_start: 0.8398 (ptpp) cc_final: 0.8183 (ttmt) REVERT: B 381 LEU cc_start: 0.8713 (tp) cc_final: 0.8398 (tp) REVERT: B 458 MET cc_start: 0.8485 (mmm) cc_final: 0.8224 (mmm) REVERT: B 460 SER cc_start: 0.8996 (t) cc_final: 0.8649 (p) REVERT: B 471 TYR cc_start: 0.8414 (t80) cc_final: 0.7955 (t80) REVERT: B 485 ARG cc_start: 0.7856 (mtm-85) cc_final: 0.7314 (mtm-85) REVERT: B 493 MET cc_start: 0.8356 (tmm) cc_final: 0.8147 (tmm) REVERT: B 496 ASN cc_start: 0.8372 (t0) cc_final: 0.8076 (t0) REVERT: B 500 ILE cc_start: 0.8730 (mt) cc_final: 0.8327 (mt) REVERT: B 546 LEU cc_start: 0.9032 (mt) cc_final: 0.8740 (mt) REVERT: B 550 MET cc_start: 0.7893 (mtm) cc_final: 0.7345 (mtm) REVERT: B 601 ILE cc_start: 0.8457 (mt) cc_final: 0.8138 (mt) REVERT: B 604 ARG cc_start: 0.7109 (mmp80) cc_final: 0.6767 (tpp80) REVERT: B 612 TYR cc_start: 0.7795 (m-80) cc_final: 0.7493 (m-80) REVERT: B 664 THR cc_start: 0.8952 (p) cc_final: 0.8745 (p) REVERT: C 106 SER cc_start: 0.7759 (m) cc_final: 0.6432 (m) REVERT: C 212 ILE cc_start: 0.6000 (mt) cc_final: 0.5753 (mt) REVERT: D 178 PHE cc_start: 0.5471 (m-80) cc_final: 0.5088 (m-80) REVERT: D 193 LEU cc_start: 0.7895 (mt) cc_final: 0.7625 (mt) REVERT: D 260 ILE cc_start: 0.7126 (mt) cc_final: 0.6763 (mt) REVERT: D 315 LEU cc_start: 0.7097 (mt) cc_final: 0.6817 (mt) outliers start: 23 outliers final: 7 residues processed: 1082 average time/residue: 0.1398 time to fit residues: 219.4297 Evaluate side-chains 725 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 716 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.0370 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 25 GLN B 320 ASN B 329 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 501 GLN B 676 HIS C 24 GLN C 28 GLN C 80 HIS C 85 GLN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN C 270 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN D 80 HIS D 91 ASN D 128 ASN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.134714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.097063 restraints weight = 35027.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.100811 restraints weight = 16322.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.103303 restraints weight = 9745.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.105001 restraints weight = 6604.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.106058 restraints weight = 4999.471| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (15 function evaluations) r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16386 Z= 0.161 Angle : 0.713 15.134 22134 Z= 0.370 Chirality : 0.046 0.188 2360 Planarity : 0.004 0.044 2818 Dihedral : 9.810 129.954 2305 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.73 % Allowed : 21.79 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.18), residues: 1932 helix: 1.35 (0.15), residues: 1129 sheet: 1.02 (0.48), residues: 100 loop : 0.29 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 243 TYR 0.021 0.002 TYR B 72 PHE 0.030 0.002 PHE D 172 TRP 0.025 0.003 TRP D 30 HIS 0.009 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (16386) covalent geometry : angle 0.71330 / 0.37 (22134) hydrogen bonds : bond 0.04851 / 3.08 ( 871) hydrogen bonds : angle 5.13962 / 3.66 ( 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 854 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 790 time to evaluate : 0.633 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 65 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8213 (mm-30) REVERT: A 66 GLU cc_start: 0.8561 (tp30) cc_final: 0.8355 (tp30) REVERT: A 144 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8782 (mtm) REVERT: A 181 ASP cc_start: 0.8746 (m-30) cc_final: 0.8420 (m-30) REVERT: A 204 SER cc_start: 0.9231 (m) cc_final: 0.9027 (t) REVERT: A 218 ASN cc_start: 0.8913 (t0) cc_final: 0.8693 (t0) REVERT: A 221 LYS cc_start: 0.8873 (mmtp) cc_final: 0.8648 (mttp) REVERT: A 243 ARG cc_start: 0.7648 (ttp80) cc_final: 0.7402 (tmm-80) REVERT: A 274 ARG cc_start: 0.8154 (ttp80) cc_final: 0.7380 (mtm-85) REVERT: A 322 MET cc_start: 0.8762 (mmm) cc_final: 0.8302 (mmm) REVERT: A 335 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8578 (mm-30) REVERT: A 348 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7245 (tmm) REVERT: A 352 GLU cc_start: 0.7829 (mt-10) cc_final: 0.6898 (mt-10) REVERT: A 384 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.7915 (pm20) REVERT: A 415 ASN cc_start: 0.9354 (t0) cc_final: 0.9097 (t0) REVERT: A 420 MET cc_start: 0.9285 (mmm) cc_final: 0.8954 (mmm) REVERT: A 444 ASP cc_start: 0.8575 (t70) cc_final: 0.8345 (t70) REVERT: A 492 PHE cc_start: 0.9161 (m-80) cc_final: 0.8927 (m-10) REVERT: A 493 MET cc_start: 0.8985 (tmm) cc_final: 0.8542 (tmm) REVERT: A 494 MET cc_start: 0.9351 (mtm) cc_final: 0.8948 (mtt) REVERT: A 505 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8610 (mt-10) REVERT: A 528 PHE cc_start: 0.8974 (m-80) cc_final: 0.8619 (m-80) REVERT: A 586 TYR cc_start: 0.8619 (m-80) cc_final: 0.8307 (m-10) REVERT: A 598 MET cc_start: 0.8663 (mtm) cc_final: 0.8400 (mtp) REVERT: A 602 GLU cc_start: 0.7755 (pt0) cc_final: 0.6831 (pt0) REVERT: A 604 ARG cc_start: 0.8791 (mmp80) cc_final: 0.8202 (mmt90) REVERT: A 615 MET cc_start: 0.9327 (mmm) cc_final: 0.9116 (mmm) REVERT: A 630 TYR cc_start: 0.8381 (m-80) cc_final: 0.7682 (m-80) REVERT: A 686 ARG cc_start: 0.8374 (mmm-85) cc_final: 0.7747 (ttm-80) REVERT: B 18 ILE cc_start: 0.9506 (mm) cc_final: 0.9294 (pt) REVERT: B 20 LYS cc_start: 0.9478 (OUTLIER) cc_final: 0.9122 (mmmm) REVERT: B 41 ILE cc_start: 0.9552 (mm) cc_final: 0.9302 (mm) REVERT: B 65 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8009 (mp0) REVERT: B 99 LYS cc_start: 0.9540 (mmmm) cc_final: 0.9273 (mmmm) REVERT: B 106 LEU cc_start: 0.9129 (tp) cc_final: 0.8744 (tt) REVERT: B 109 ASN cc_start: 0.9106 (m-40) cc_final: 0.8465 (p0) REVERT: B 147 GLN cc_start: 0.8723 (mt0) cc_final: 0.8022 (mm110) REVERT: B 184 ARG cc_start: 0.9222 (mmm-85) cc_final: 0.8946 (tpp80) REVERT: B 243 ARG cc_start: 0.6836 (ttp80) cc_final: 0.6632 (tmm-80) REVERT: B 257 ASP cc_start: 0.8774 (m-30) cc_final: 0.8371 (m-30) REVERT: B 286 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7339 (m-30) REVERT: B 288 PHE cc_start: 0.9383 (t80) cc_final: 0.9133 (t80) REVERT: B 290 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8531 (tm-30) REVERT: B 312 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8598 (pm20) REVERT: B 317 MET cc_start: 0.8481 (ptp) cc_final: 0.8027 (pmm) REVERT: B 321 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8332 (tm-30) REVERT: B 322 MET cc_start: 0.9287 (mmm) cc_final: 0.8928 (mmm) REVERT: B 362 ASP cc_start: 0.8557 (m-30) cc_final: 0.7385 (m-30) REVERT: B 374 SER cc_start: 0.8911 (t) cc_final: 0.8523 (t) REVERT: B 447 ASN cc_start: 0.8492 (m-40) cc_final: 0.7893 (t0) REVERT: B 471 TYR cc_start: 0.9426 (t80) cc_final: 0.9167 (t80) REVERT: B 477 ILE cc_start: 0.9281 (mp) cc_final: 0.9056 (pt) REVERT: B 492 PHE cc_start: 0.9494 (m-80) cc_final: 0.9042 (m-10) REVERT: B 493 MET cc_start: 0.9698 (tmm) cc_final: 0.8953 (tmm) REVERT: B 496 ASN cc_start: 0.9807 (t0) cc_final: 0.9558 (t0) REVERT: B 515 ASP cc_start: 0.9125 (m-30) cc_final: 0.8684 (m-30) REVERT: B 558 TRP cc_start: 0.9210 (m100) cc_final: 0.8516 (m100) REVERT: B 610 LYS cc_start: 0.8795 (mmmt) cc_final: 0.8530 (mmmt) REVERT: B 612 TYR cc_start: 0.8761 (m-80) cc_final: 0.8283 (m-80) REVERT: B 640 MET cc_start: 0.9343 (tpp) cc_final: 0.9092 (tpp) REVERT: C 41 LEU cc_start: 0.8452 (mm) cc_final: 0.8217 (mm) REVERT: C 47 LEU cc_start: 0.8051 (mt) cc_final: 0.7788 (tp) REVERT: C 55 TYR cc_start: 0.8142 (t80) cc_final: 0.7353 (t80) REVERT: C 56 MET cc_start: 0.5642 (ttt) cc_final: 0.5256 (ttt) REVERT: C 69 GLN cc_start: 0.8954 (tp40) cc_final: 0.8719 (tp40) REVERT: C 91 ASN cc_start: 0.9301 (m-40) cc_final: 0.8941 (m-40) REVERT: C 93 MET cc_start: 0.9299 (mtt) cc_final: 0.8997 (mtt) REVERT: C 95 MET cc_start: 0.9037 (tmm) cc_final: 0.8576 (tmm) REVERT: C 96 MET cc_start: 0.8879 (mmt) cc_final: 0.8441 (mmm) REVERT: C 97 GLU cc_start: 0.6857 (mm-30) cc_final: 0.6078 (mm-30) REVERT: C 111 THR cc_start: 0.8092 (m) cc_final: 0.7891 (p) REVERT: C 130 TYR cc_start: 0.9448 (m-10) cc_final: 0.9238 (m-10) REVERT: C 164 GLU cc_start: 0.9356 (mm-30) cc_final: 0.8766 (mm-30) REVERT: C 172 PHE cc_start: 0.8507 (m-10) cc_final: 0.8289 (m-80) REVERT: C 178 PHE cc_start: 0.9019 (m-80) cc_final: 0.7842 (m-80) REVERT: C 185 MET cc_start: 0.8384 (pmm) cc_final: 0.7086 (pmm) REVERT: C 186 GLN cc_start: 0.9444 (mm110) cc_final: 0.8973 (mp10) REVERT: C 198 GLU cc_start: 0.9399 (mm-30) cc_final: 0.9044 (mm-30) REVERT: C 259 PHE cc_start: 0.8982 (t80) cc_final: 0.8716 (t80) REVERT: C 270 ASN cc_start: 0.7822 (m110) cc_final: 0.7473 (m110) REVERT: D 30 TRP cc_start: 0.8633 (p-90) cc_final: 0.7520 (p-90) REVERT: D 46 TYR cc_start: 0.9211 (m-80) cc_final: 0.8860 (m-80) REVERT: D 96 MET cc_start: 0.8458 (mmt) cc_final: 0.8185 (mmt) REVERT: D 178 PHE cc_start: 0.9023 (m-80) cc_final: 0.8141 (m-80) REVERT: D 186 GLN cc_start: 0.9077 (mm-40) cc_final: 0.8687 (mp10) REVERT: D 200 ILE cc_start: 0.7950 (tt) cc_final: 0.7514 (tt) REVERT: D 212 ILE cc_start: 0.9084 (mt) cc_final: 0.8579 (tp) REVERT: D 227 PHE cc_start: 0.8341 (t80) cc_final: 0.8072 (m-80) REVERT: D 247 TYR cc_start: 0.8675 (m-10) cc_final: 0.8455 (m-10) outliers start: 64 outliers final: 31 residues processed: 817 average time/residue: 0.1189 time to fit residues: 147.3740 Evaluate side-chains 743 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 706 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 164 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 232 ASN B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN B 668 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN D 23 ASN D 28 GLN D 91 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.125678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.089270 restraints weight = 36013.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.092870 restraints weight = 16652.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.094965 restraints weight = 9878.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.096678 restraints weight = 7017.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.097711 restraints weight = 5232.640| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (13 function evaluations) r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16386 Z= 0.159 Angle : 0.677 14.493 22134 Z= 0.351 Chirality : 0.045 0.232 2360 Planarity : 0.004 0.043 2818 Dihedral : 9.293 129.824 2297 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.73 % Allowed : 25.06 % Favored : 71.21 % 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: 1.20 (0.19), residues: 1932 helix: 1.27 (0.15), residues: 1133 sheet: 0.78 (0.48), residues: 104 loop : 0.18 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 164 TYR 0.017 0.001 TYR A 612 PHE 0.040 0.002 PHE C 168 TRP 0.014 0.002 TRP D 44 HIS 0.006 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (16386) covalent geometry : angle 0.67731 / 0.35 (22134) hydrogen bonds : bond 0.04345 / 2.75 ( 871) hydrogen bonds : angle 5.07453 / 3.61 ( 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 808 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 744 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.9015 (m-10) cc_final: 0.8271 (m-10) REVERT: A 65 GLU cc_start: 0.8533 (mm-30) cc_final: 0.7808 (mp0) REVERT: A 66 GLU cc_start: 0.8544 (tp30) cc_final: 0.8275 (tp30) REVERT: A 82 LYS cc_start: 0.9650 (mmmm) cc_final: 0.9328 (mmmm) REVERT: A 95 MET cc_start: 0.9356 (mmm) cc_final: 0.9135 (tpp) REVERT: A 99 LYS cc_start: 0.9398 (mmtm) cc_final: 0.9194 (mmtm) REVERT: A 127 LEU cc_start: 0.9382 (mt) cc_final: 0.9112 (mm) REVERT: A 144 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8696 (mtm) REVERT: A 163 ARG cc_start: 0.8365 (mmp80) cc_final: 0.8125 (mmm-85) REVERT: A 181 ASP cc_start: 0.8799 (m-30) cc_final: 0.8464 (m-30) REVERT: A 187 ASP cc_start: 0.9059 (t70) cc_final: 0.8750 (t70) REVERT: A 218 ASN cc_start: 0.9100 (t0) cc_final: 0.8655 (t0) REVERT: A 243 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7656 (tmm-80) REVERT: A 257 ASP cc_start: 0.9361 (m-30) cc_final: 0.8866 (m-30) REVERT: A 274 ARG cc_start: 0.8236 (ttp80) cc_final: 0.7959 (ptp90) REVERT: A 286 ASP cc_start: 0.8439 (m-30) cc_final: 0.8150 (m-30) REVERT: A 321 GLU cc_start: 0.8685 (tp30) cc_final: 0.8256 (tp30) REVERT: A 322 MET cc_start: 0.9059 (mmm) cc_final: 0.8185 (mmm) REVERT: A 326 PHE cc_start: 0.9618 (m-10) cc_final: 0.9389 (m-80) REVERT: A 335 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8575 (mm-30) REVERT: A 348 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7494 (tmm) REVERT: A 352 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7398 (mt-10) REVERT: A 359 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8000 (ttp) REVERT: A 362 ASP cc_start: 0.8647 (m-30) cc_final: 0.8122 (m-30) REVERT: A 384 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8004 (pm20) REVERT: A 415 ASN cc_start: 0.9272 (t0) cc_final: 0.9015 (t0) REVERT: A 447 ASN cc_start: 0.8487 (m-40) cc_final: 0.7984 (t0) REVERT: A 466 MET cc_start: 0.9115 (ptt) cc_final: 0.8802 (ptt) REVERT: A 479 TYR cc_start: 0.9345 (t80) cc_final: 0.8680 (t80) REVERT: A 493 MET cc_start: 0.9012 (tmm) cc_final: 0.8565 (tmm) REVERT: A 505 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8583 (mt-10) REVERT: A 510 LYS cc_start: 0.9060 (mtpt) cc_final: 0.8610 (mtpt) REVERT: A 586 TYR cc_start: 0.8632 (m-80) cc_final: 0.8384 (m-10) REVERT: A 602 GLU cc_start: 0.7542 (pt0) cc_final: 0.6571 (pt0) REVERT: A 604 ARG cc_start: 0.8831 (mmp80) cc_final: 0.8150 (mmt90) REVERT: A 610 LYS cc_start: 0.8041 (tptp) cc_final: 0.7735 (tptt) REVERT: A 632 MET cc_start: 0.8646 (mtm) cc_final: 0.7880 (mtp) REVERT: A 640 MET cc_start: 0.9507 (tpp) cc_final: 0.9090 (tpp) REVERT: A 647 HIS cc_start: 0.8820 (m-70) cc_final: 0.8416 (m-70) REVERT: B 15 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8572 (tm-30) REVERT: B 17 MET cc_start: 0.8568 (mmm) cc_final: 0.8153 (mmm) REVERT: B 65 GLU cc_start: 0.8656 (mm-30) cc_final: 0.7911 (mp0) REVERT: B 99 LYS cc_start: 0.9561 (mmmm) cc_final: 0.9310 (mmmm) REVERT: B 106 LEU cc_start: 0.9294 (tp) cc_final: 0.9003 (tt) REVERT: B 109 ASN cc_start: 0.9092 (m-40) cc_final: 0.8559 (p0) REVERT: B 184 ARG cc_start: 0.9261 (mmm-85) cc_final: 0.8982 (tpp80) REVERT: B 202 ASN cc_start: 0.9204 (t0) cc_final: 0.8088 (t0) REVERT: B 257 ASP cc_start: 0.9010 (m-30) cc_final: 0.8507 (m-30) REVERT: B 271 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8561 (mm-30) REVERT: B 286 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.7437 (m-30) REVERT: B 290 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8481 (tm-30) REVERT: B 312 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8691 (pm20) REVERT: B 317 MET cc_start: 0.8543 (ptp) cc_final: 0.8147 (pmm) REVERT: B 348 MET cc_start: 0.9059 (ttp) cc_final: 0.8614 (ttp) REVERT: B 362 ASP cc_start: 0.8587 (m-30) cc_final: 0.7480 (m-30) REVERT: B 370 ASN cc_start: 0.9302 (m-40) cc_final: 0.9052 (m110) REVERT: B 374 SER cc_start: 0.9006 (t) cc_final: 0.8619 (t) REVERT: B 399 GLU cc_start: 0.8183 (mp0) cc_final: 0.7905 (mp0) REVERT: B 467 ASN cc_start: 0.9381 (t0) cc_final: 0.9133 (m-40) REVERT: B 471 TYR cc_start: 0.9398 (t80) cc_final: 0.9098 (t80) REVERT: B 477 ILE cc_start: 0.9313 (mp) cc_final: 0.9086 (pt) REVERT: B 493 MET cc_start: 0.9667 (tmm) cc_final: 0.8966 (tmm) REVERT: B 515 ASP cc_start: 0.9114 (m-30) cc_final: 0.8696 (m-30) REVERT: B 558 TRP cc_start: 0.9454 (m100) cc_final: 0.8695 (m100) REVERT: B 610 LYS cc_start: 0.8727 (mmmt) cc_final: 0.8433 (mmmt) REVERT: B 612 TYR cc_start: 0.8759 (m-80) cc_final: 0.8307 (m-80) REVERT: B 668 ASN cc_start: 0.9292 (m-40) cc_final: 0.9083 (m110) REVERT: C 19 GLN cc_start: 0.7830 (mp10) cc_final: 0.7446 (pm20) REVERT: C 20 MET cc_start: 0.9083 (tpp) cc_final: 0.8875 (tpp) REVERT: C 55 TYR cc_start: 0.8304 (t80) cc_final: 0.7888 (t80) REVERT: C 56 MET cc_start: 0.5783 (ttt) cc_final: 0.5279 (ttt) REVERT: C 66 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.7097 (t0) REVERT: C 91 ASN cc_start: 0.9325 (m-40) cc_final: 0.9062 (m-40) REVERT: C 93 MET cc_start: 0.9395 (mtt) cc_final: 0.9040 (mtt) REVERT: C 130 TYR cc_start: 0.9460 (m-10) cc_final: 0.9258 (m-10) REVERT: C 164 GLU cc_start: 0.9356 (mm-30) cc_final: 0.9057 (mm-30) REVERT: C 178 PHE cc_start: 0.9141 (m-80) cc_final: 0.8161 (m-80) REVERT: C 185 MET cc_start: 0.8468 (pmm) cc_final: 0.7442 (pmm) REVERT: C 186 GLN cc_start: 0.9353 (mm110) cc_final: 0.8886 (mp10) REVERT: C 198 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8630 (mm-30) REVERT: C 223 GLU cc_start: 0.8876 (tm-30) cc_final: 0.7876 (pt0) REVERT: C 259 PHE cc_start: 0.8907 (t80) cc_final: 0.8516 (t80) REVERT: C 268 LEU cc_start: 0.9026 (tp) cc_final: 0.8508 (pp) REVERT: C 270 ASN cc_start: 0.7834 (m110) cc_final: 0.7570 (m110) REVERT: C 274 ASP cc_start: 0.7515 (p0) cc_final: 0.7288 (p0) REVERT: D 28 GLN cc_start: 0.8969 (tt0) cc_final: 0.8725 (tt0) REVERT: D 30 TRP cc_start: 0.8736 (p-90) cc_final: 0.8345 (p-90) REVERT: D 46 TYR cc_start: 0.9291 (m-80) cc_final: 0.8878 (m-80) REVERT: D 178 PHE cc_start: 0.9008 (m-10) cc_final: 0.8142 (m-80) REVERT: D 186 GLN cc_start: 0.9086 (mm-40) cc_final: 0.8695 (mp10) REVERT: D 212 ILE cc_start: 0.9332 (mt) cc_final: 0.9064 (mm) REVERT: D 287 LEU cc_start: 0.6903 (mt) cc_final: 0.6627 (mt) outliers start: 64 outliers final: 41 residues processed: 766 average time/residue: 0.1131 time to fit residues: 132.9514 Evaluate side-chains 743 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 695 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 281 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 168 optimal weight: 7.9990 chunk 89 optimal weight: 0.0970 chunk 127 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 185 optimal weight: 5.9990 chunk 191 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 GLN B 410 ASN B 418 ASN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.124813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.088645 restraints weight = 36264.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.092172 restraints weight = 17140.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.094576 restraints weight = 10092.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.095943 restraints weight = 6863.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.096916 restraints weight = 5239.143| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.5775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16386 Z= 0.174 Angle : 0.688 15.092 22134 Z= 0.350 Chirality : 0.045 0.240 2360 Planarity : 0.004 0.045 2818 Dihedral : 9.068 130.916 2295 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.31 % Allowed : 26.52 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.19), residues: 1932 helix: 1.18 (0.15), residues: 1126 sheet: -0.08 (0.43), residues: 136 loop : 0.16 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 235 TYR 0.017 0.001 TYR A 236 PHE 0.035 0.002 PHE D 172 TRP 0.022 0.002 TRP C 44 HIS 0.006 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (16386) covalent geometry : angle 0.68799 / 0.35 (22134) hydrogen bonds : bond 0.04098 / 2.61 ( 871) hydrogen bonds : angle 5.07245 / 3.63 ( 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 812 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 738 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.9073 (m-10) cc_final: 0.8407 (m-10) REVERT: A 65 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8061 (mp0) REVERT: A 66 GLU cc_start: 0.8529 (tp30) cc_final: 0.8312 (tp30) REVERT: A 82 LYS cc_start: 0.9647 (mmmm) cc_final: 0.9341 (mmmm) REVERT: A 127 LEU cc_start: 0.9402 (mt) cc_final: 0.9187 (mm) REVERT: A 134 THR cc_start: 0.9486 (OUTLIER) cc_final: 0.9128 (t) REVERT: A 144 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8702 (mtm) REVERT: A 147 GLN cc_start: 0.9117 (mt0) cc_final: 0.8868 (mt0) REVERT: A 181 ASP cc_start: 0.8818 (m-30) cc_final: 0.8543 (m-30) REVERT: A 187 ASP cc_start: 0.9042 (t70) cc_final: 0.8712 (t70) REVERT: A 202 ASN cc_start: 0.9543 (t0) cc_final: 0.9250 (t0) REVERT: A 218 ASN cc_start: 0.9137 (t0) cc_final: 0.8750 (t0) REVERT: A 243 ARG cc_start: 0.7730 (ttp80) cc_final: 0.7277 (ttp80) REVERT: A 257 ASP cc_start: 0.9426 (m-30) cc_final: 0.9014 (m-30) REVERT: A 321 GLU cc_start: 0.8726 (tp30) cc_final: 0.8275 (tp30) REVERT: A 359 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8214 (ttp) REVERT: A 370 ASN cc_start: 0.9188 (m-40) cc_final: 0.8893 (m-40) REVERT: A 384 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.7435 (pm20) REVERT: A 415 ASN cc_start: 0.9279 (t0) cc_final: 0.9066 (t0) REVERT: A 447 ASN cc_start: 0.8529 (m-40) cc_final: 0.8012 (t0) REVERT: A 466 MET cc_start: 0.9194 (ptt) cc_final: 0.8924 (ptt) REVERT: A 479 TYR cc_start: 0.9480 (t80) cc_final: 0.9105 (t80) REVERT: A 493 MET cc_start: 0.9046 (tmm) cc_final: 0.8479 (tmm) REVERT: A 505 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8772 (mt-10) REVERT: A 512 GLU cc_start: 0.8486 (pt0) cc_final: 0.8065 (pt0) REVERT: A 602 GLU cc_start: 0.7634 (pt0) cc_final: 0.7012 (pt0) REVERT: A 604 ARG cc_start: 0.8775 (mmp80) cc_final: 0.8243 (mmt-90) REVERT: A 610 LYS cc_start: 0.7925 (tptp) cc_final: 0.7648 (tptt) REVERT: A 632 MET cc_start: 0.8743 (mtm) cc_final: 0.8051 (mtp) REVERT: A 634 MET cc_start: 0.8980 (mmm) cc_final: 0.8698 (mmt) REVERT: A 640 MET cc_start: 0.9598 (tpp) cc_final: 0.8855 (tpp) REVERT: A 643 THR cc_start: 0.9605 (m) cc_final: 0.9391 (t) REVERT: A 686 ARG cc_start: 0.8613 (mmm-85) cc_final: 0.8306 (mmm-85) REVERT: B 8 LYS cc_start: 0.9040 (tppt) cc_final: 0.8759 (tppt) REVERT: B 15 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8635 (tm-30) REVERT: B 17 MET cc_start: 0.8614 (mmm) cc_final: 0.8227 (mmm) REVERT: B 21 ASP cc_start: 0.8760 (m-30) cc_final: 0.8333 (t0) REVERT: B 99 LYS cc_start: 0.9561 (mmmm) cc_final: 0.9298 (mmmm) REVERT: B 109 ASN cc_start: 0.9220 (m-40) cc_final: 0.8533 (p0) REVERT: B 174 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8244 (mm-30) REVERT: B 202 ASN cc_start: 0.9407 (t0) cc_final: 0.8749 (t0) REVERT: B 257 ASP cc_start: 0.9032 (m-30) cc_final: 0.8513 (m-30) REVERT: B 276 LYS cc_start: 0.9083 (mmtt) cc_final: 0.8677 (mmtt) REVERT: B 286 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.7548 (m-30) REVERT: B 290 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8447 (tm-30) REVERT: B 312 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8738 (pm20) REVERT: B 317 MET cc_start: 0.8568 (ptp) cc_final: 0.8063 (pmm) REVERT: B 362 ASP cc_start: 0.8630 (m-30) cc_final: 0.7430 (m-30) REVERT: B 374 SER cc_start: 0.9135 (t) cc_final: 0.8746 (t) REVERT: B 378 PHE cc_start: 0.9277 (p90) cc_final: 0.9001 (p90) REVERT: B 393 SER cc_start: 0.9445 (m) cc_final: 0.9087 (p) REVERT: B 415 ASN cc_start: 0.9145 (t0) cc_final: 0.8921 (t0) REVERT: B 434 ASP cc_start: 0.8978 (m-30) cc_final: 0.8728 (m-30) REVERT: B 467 ASN cc_start: 0.9405 (t0) cc_final: 0.9170 (m-40) REVERT: B 471 TYR cc_start: 0.9284 (t80) cc_final: 0.9064 (t80) REVERT: B 483 GLU cc_start: 0.9470 (mp0) cc_final: 0.9260 (mp0) REVERT: B 493 MET cc_start: 0.9679 (tmm) cc_final: 0.8857 (tmm) REVERT: B 515 ASP cc_start: 0.9040 (m-30) cc_final: 0.8730 (m-30) REVERT: B 602 GLU cc_start: 0.8682 (tt0) cc_final: 0.7952 (tt0) REVERT: B 610 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8521 (mmmt) REVERT: B 612 TYR cc_start: 0.8653 (m-80) cc_final: 0.8212 (m-80) REVERT: B 628 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7995 (mm-30) REVERT: B 640 MET cc_start: 0.9229 (tpp) cc_final: 0.8991 (tpp) REVERT: C 19 GLN cc_start: 0.7706 (mp10) cc_final: 0.7386 (pm20) REVERT: C 55 TYR cc_start: 0.8361 (t80) cc_final: 0.7741 (t80) REVERT: C 56 MET cc_start: 0.5870 (ttt) cc_final: 0.5345 (ttt) REVERT: C 80 HIS cc_start: 0.8576 (m90) cc_final: 0.7889 (m90) REVERT: C 92 PHE cc_start: 0.7855 (t80) cc_final: 0.7641 (t80) REVERT: C 130 TYR cc_start: 0.9315 (m-10) cc_final: 0.9036 (m-10) REVERT: C 164 GLU cc_start: 0.9372 (mm-30) cc_final: 0.9155 (mm-30) REVERT: C 178 PHE cc_start: 0.9296 (m-80) cc_final: 0.8406 (m-10) REVERT: C 185 MET cc_start: 0.8474 (pmm) cc_final: 0.7335 (pmm) REVERT: C 186 GLN cc_start: 0.9358 (mm110) cc_final: 0.8860 (mp10) REVERT: C 223 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8111 (pt0) REVERT: C 242 TYR cc_start: 0.9383 (t80) cc_final: 0.9062 (t80) REVERT: C 259 PHE cc_start: 0.8883 (t80) cc_final: 0.8440 (t80) REVERT: C 268 LEU cc_start: 0.9034 (tp) cc_final: 0.8778 (tp) REVERT: C 270 ASN cc_start: 0.7983 (m110) cc_final: 0.7687 (m110) REVERT: D 28 GLN cc_start: 0.8888 (tt0) cc_final: 0.8366 (tt0) REVERT: D 30 TRP cc_start: 0.8680 (p-90) cc_final: 0.8371 (p-90) REVERT: D 34 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8330 (mm-30) REVERT: D 46 TYR cc_start: 0.9245 (m-80) cc_final: 0.8843 (m-80) REVERT: D 56 MET cc_start: 0.7244 (mmp) cc_final: 0.6625 (mtt) REVERT: D 178 PHE cc_start: 0.9098 (m-10) cc_final: 0.8283 (m-80) REVERT: D 186 GLN cc_start: 0.9085 (mm-40) cc_final: 0.8670 (mp10) REVERT: D 207 LEU cc_start: 0.9200 (mm) cc_final: 0.8868 (mm) REVERT: D 247 TYR cc_start: 0.8824 (m-10) cc_final: 0.8462 (m-10) outliers start: 74 outliers final: 47 residues processed: 763 average time/residue: 0.1143 time to fit residues: 132.0913 Evaluate side-chains 748 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 695 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 122 optimal weight: 0.0980 chunk 115 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 GLN A 668 ASN B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN C 84 HIS ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN D 25 ASN ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 127 GLN D 128 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.126062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.090332 restraints weight = 36124.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.093770 restraints weight = 16827.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.096177 restraints weight = 10265.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.097686 restraints weight = 6963.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.098663 restraints weight = 5285.009| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.6136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16386 Z= 0.145 Angle : 0.727 15.452 22134 Z= 0.359 Chirality : 0.046 0.372 2360 Planarity : 0.004 0.050 2818 Dihedral : 8.894 130.659 2295 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.67 % Allowed : 29.02 % Favored : 67.31 % 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: 0.83 (0.19), residues: 1932 helix: 1.02 (0.15), residues: 1138 sheet: -0.25 (0.42), residues: 138 loop : 0.10 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 243 TYR 0.024 0.001 TYR B 574 PHE 0.032 0.002 PHE C 172 TRP 0.013 0.001 TRP D 44 HIS 0.006 0.001 HIS A 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (16386) covalent geometry : angle 0.72719 / 0.36 (22134) hydrogen bonds : bond 0.04077 / 2.61 ( 871) hydrogen bonds : angle 5.07092 / 3.62 ( 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 774 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 711 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.9007 (m-10) cc_final: 0.8406 (m-10) REVERT: A 65 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8155 (mp0) REVERT: A 66 GLU cc_start: 0.8496 (tp30) cc_final: 0.8260 (tp30) REVERT: A 82 LYS cc_start: 0.9645 (mmmm) cc_final: 0.9342 (mmmm) REVERT: A 181 ASP cc_start: 0.8802 (m-30) cc_final: 0.8546 (m-30) REVERT: A 187 ASP cc_start: 0.9056 (t70) cc_final: 0.8697 (t70) REVERT: A 218 ASN cc_start: 0.9196 (t0) cc_final: 0.8799 (t0) REVERT: A 257 ASP cc_start: 0.9419 (m-30) cc_final: 0.9032 (m-30) REVERT: A 286 ASP cc_start: 0.8520 (m-30) cc_final: 0.8252 (m-30) REVERT: A 321 GLU cc_start: 0.8743 (tp30) cc_final: 0.8284 (tp30) REVERT: A 341 LYS cc_start: 0.9233 (mmmm) cc_final: 0.8769 (ptpp) REVERT: A 348 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7991 (tmm) REVERT: A 362 ASP cc_start: 0.8531 (m-30) cc_final: 0.8110 (m-30) REVERT: A 370 ASN cc_start: 0.9208 (m-40) cc_final: 0.8884 (m-40) REVERT: A 384 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.7307 (pm20) REVERT: A 389 SER cc_start: 0.9323 (OUTLIER) cc_final: 0.9000 (p) REVERT: A 415 ASN cc_start: 0.9278 (t0) cc_final: 0.9061 (t0) REVERT: A 420 MET cc_start: 0.9396 (mmm) cc_final: 0.9194 (mmm) REVERT: A 441 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8595 (mm-30) REVERT: A 447 ASN cc_start: 0.8489 (m-40) cc_final: 0.7994 (t0) REVERT: A 466 MET cc_start: 0.9157 (ptt) cc_final: 0.8884 (ptt) REVERT: A 493 MET cc_start: 0.8953 (tmm) cc_final: 0.8526 (tmm) REVERT: A 505 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8783 (mt-10) REVERT: A 509 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8476 (tm-30) REVERT: A 510 LYS cc_start: 0.9344 (mtpt) cc_final: 0.8897 (mtpt) REVERT: A 512 GLU cc_start: 0.8367 (pt0) cc_final: 0.7955 (pt0) REVERT: A 526 GLU cc_start: 0.8270 (mm-30) cc_final: 0.8069 (mm-30) REVERT: A 588 GLN cc_start: 0.9036 (mm-40) cc_final: 0.8696 (tp40) REVERT: A 602 GLU cc_start: 0.7664 (pt0) cc_final: 0.6335 (pt0) REVERT: A 604 ARG cc_start: 0.8788 (mmp80) cc_final: 0.8088 (mmt90) REVERT: A 632 MET cc_start: 0.8616 (mtm) cc_final: 0.7965 (mtp) REVERT: A 640 MET cc_start: 0.9638 (tpp) cc_final: 0.8737 (tpp) REVERT: A 643 THR cc_start: 0.9653 (m) cc_final: 0.9399 (t) REVERT: A 686 ARG cc_start: 0.8619 (mmm-85) cc_final: 0.8163 (ttm-80) REVERT: B 8 LYS cc_start: 0.9036 (tppt) cc_final: 0.8801 (tppt) REVERT: B 17 MET cc_start: 0.8666 (mmm) cc_final: 0.8280 (mmm) REVERT: B 21 ASP cc_start: 0.8794 (m-30) cc_final: 0.8389 (t0) REVERT: B 31 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8130 (mt-10) REVERT: B 99 LYS cc_start: 0.9539 (mmmm) cc_final: 0.9230 (mmmm) REVERT: B 108 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.8147 (p) REVERT: B 109 ASN cc_start: 0.9239 (m-40) cc_final: 0.8801 (p0) REVERT: B 112 LYS cc_start: 0.9139 (pttm) cc_final: 0.8929 (pttm) REVERT: B 181 ASP cc_start: 0.9093 (OUTLIER) cc_final: 0.8566 (t0) REVERT: B 202 ASN cc_start: 0.9403 (t0) cc_final: 0.9039 (t0) REVERT: B 257 ASP cc_start: 0.8974 (m-30) cc_final: 0.8478 (m-30) REVERT: B 286 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.7644 (m-30) REVERT: B 290 GLU cc_start: 0.8769 (tm-30) cc_final: 0.7986 (tm-30) REVERT: B 317 MET cc_start: 0.8411 (ptp) cc_final: 0.8071 (pmm) REVERT: B 333 LYS cc_start: 0.8850 (tttt) cc_final: 0.8463 (tttm) REVERT: B 348 MET cc_start: 0.9112 (ttp) cc_final: 0.8677 (ttp) REVERT: B 362 ASP cc_start: 0.8618 (m-30) cc_final: 0.7474 (m-30) REVERT: B 374 SER cc_start: 0.9120 (t) cc_final: 0.8850 (t) REVERT: B 393 SER cc_start: 0.9397 (m) cc_final: 0.9022 (p) REVERT: B 394 TYR cc_start: 0.9132 (m-80) cc_final: 0.8692 (m-80) REVERT: B 415 ASN cc_start: 0.9142 (t0) cc_final: 0.8798 (t0) REVERT: B 434 ASP cc_start: 0.9018 (m-30) cc_final: 0.8775 (m-30) REVERT: B 467 ASN cc_start: 0.9398 (t0) cc_final: 0.9067 (m-40) REVERT: B 471 TYR cc_start: 0.9411 (t80) cc_final: 0.9015 (t80) REVERT: B 483 GLU cc_start: 0.9431 (mp0) cc_final: 0.9211 (mp0) REVERT: B 493 MET cc_start: 0.9673 (tmm) cc_final: 0.8850 (tmm) REVERT: B 515 ASP cc_start: 0.9027 (m-30) cc_final: 0.8754 (m-30) REVERT: B 602 GLU cc_start: 0.8445 (tt0) cc_final: 0.8166 (tt0) REVERT: B 610 LYS cc_start: 0.8867 (mmmt) cc_final: 0.8613 (mmmt) REVERT: B 612 TYR cc_start: 0.8615 (m-80) cc_final: 0.8206 (m-80) REVERT: B 627 LYS cc_start: 0.8879 (ttpp) cc_final: 0.8485 (tttp) REVERT: B 628 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8056 (mm-30) REVERT: C 19 GLN cc_start: 0.7691 (mp10) cc_final: 0.7390 (pm20) REVERT: C 20 MET cc_start: 0.9060 (tpp) cc_final: 0.8743 (tmm) REVERT: C 55 TYR cc_start: 0.8349 (t80) cc_final: 0.7719 (t80) REVERT: C 56 MET cc_start: 0.5809 (ttt) cc_final: 0.5378 (ttt) REVERT: C 80 HIS cc_start: 0.8616 (m90) cc_final: 0.8122 (m90) REVERT: C 134 LYS cc_start: 0.9682 (pttm) cc_final: 0.9382 (pttm) REVERT: C 153 LEU cc_start: 0.9271 (pp) cc_final: 0.9064 (pp) REVERT: C 178 PHE cc_start: 0.9277 (m-80) cc_final: 0.8301 (m-10) REVERT: C 185 MET cc_start: 0.8553 (pmm) cc_final: 0.7415 (pmm) REVERT: C 186 GLN cc_start: 0.9346 (mm110) cc_final: 0.8837 (mp10) REVERT: C 198 GLU cc_start: 0.9451 (mm-30) cc_final: 0.9172 (mm-30) REVERT: C 223 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8034 (pt0) REVERT: C 259 PHE cc_start: 0.8899 (t80) cc_final: 0.8348 (t80) REVERT: C 268 LEU cc_start: 0.8992 (tp) cc_final: 0.8764 (tp) REVERT: C 270 ASN cc_start: 0.8092 (m110) cc_final: 0.7841 (m110) REVERT: C 313 GLU cc_start: 0.8966 (tt0) cc_final: 0.8691 (tt0) REVERT: C 316 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8747 (mmtt) REVERT: D 30 TRP cc_start: 0.8629 (p-90) cc_final: 0.7993 (p-90) REVERT: D 46 TYR cc_start: 0.9183 (m-80) cc_final: 0.8833 (m-10) REVERT: D 130 TYR cc_start: 0.6012 (m-10) cc_final: 0.5652 (m-10) REVERT: D 178 PHE cc_start: 0.9139 (m-10) cc_final: 0.8442 (m-80) REVERT: D 186 GLN cc_start: 0.9113 (mm-40) cc_final: 0.8674 (mp10) REVERT: D 244 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: D 252 LEU cc_start: 0.6393 (mt) cc_final: 0.6079 (mm) REVERT: D 268 LEU cc_start: 0.6017 (mt) cc_final: 0.5757 (tp) outliers start: 63 outliers final: 42 residues processed: 735 average time/residue: 0.1220 time to fit residues: 136.2604 Evaluate side-chains 724 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 675 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 4.9990 chunk 183 optimal weight: 0.5980 chunk 72 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN A 668 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 98 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN D 28 GLN D 50 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.125861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.090110 restraints weight = 35697.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.093622 restraints weight = 17017.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.095976 restraints weight = 10228.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.097520 restraints weight = 7067.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.098510 restraints weight = 5393.850| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.6506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16386 Z= 0.145 Angle : 0.734 15.785 22134 Z= 0.362 Chirality : 0.045 0.203 2360 Planarity : 0.004 0.045 2818 Dihedral : 8.701 131.211 2294 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.08 % Allowed : 29.84 % Favored : 66.08 % 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: 0.67 (0.19), residues: 1932 helix: 0.95 (0.15), residues: 1146 sheet: -0.39 (0.42), residues: 138 loop : -0.08 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 261 TYR 0.022 0.001 TYR D 242 PHE 0.031 0.002 PHE C 172 TRP 0.015 0.001 TRP D 44 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (16386) covalent geometry : angle 0.73429 / 0.36 (22134) hydrogen bonds : bond 0.04018 / 2.59 ( 871) hydrogen bonds : angle 5.08424 / 3.64 ( 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 765 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 695 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.9504 (mmtm) cc_final: 0.9282 (tppp) REVERT: A 54 LYS cc_start: 0.9639 (tttt) cc_final: 0.9415 (ttmt) REVERT: A 64 TYR cc_start: 0.9063 (m-10) cc_final: 0.8625 (m-10) REVERT: A 65 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8367 (mp0) REVERT: A 66 GLU cc_start: 0.8528 (tp30) cc_final: 0.8255 (tp30) REVERT: A 82 LYS cc_start: 0.9658 (mmmm) cc_final: 0.9346 (mmmm) REVERT: A 144 MET cc_start: 0.9115 (mtm) cc_final: 0.8744 (mtm) REVERT: A 147 GLN cc_start: 0.9073 (mt0) cc_final: 0.8786 (mt0) REVERT: A 163 ARG cc_start: 0.8347 (mmp80) cc_final: 0.8139 (mmm-85) REVERT: A 181 ASP cc_start: 0.8819 (m-30) cc_final: 0.8541 (m-30) REVERT: A 187 ASP cc_start: 0.9027 (t70) cc_final: 0.8722 (t70) REVERT: A 202 ASN cc_start: 0.9508 (t0) cc_final: 0.9247 (t0) REVERT: A 218 ASN cc_start: 0.9237 (t0) cc_final: 0.8833 (t0) REVERT: A 257 ASP cc_start: 0.9379 (m-30) cc_final: 0.9045 (m-30) REVERT: A 286 ASP cc_start: 0.8430 (m-30) cc_final: 0.8156 (m-30) REVERT: A 321 GLU cc_start: 0.8847 (tp30) cc_final: 0.8414 (tp30) REVERT: A 348 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7968 (tmm) REVERT: A 357 TYR cc_start: 0.8949 (m-10) cc_final: 0.8584 (m-80) REVERT: A 359 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8170 (ttp) REVERT: A 362 ASP cc_start: 0.8571 (m-30) cc_final: 0.7894 (m-30) REVERT: A 370 ASN cc_start: 0.9200 (m-40) cc_final: 0.8875 (m-40) REVERT: A 384 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.7437 (pm20) REVERT: A 389 SER cc_start: 0.9410 (OUTLIER) cc_final: 0.9063 (p) REVERT: A 405 LEU cc_start: 0.8981 (mt) cc_final: 0.8675 (mt) REVERT: A 415 ASN cc_start: 0.9288 (t0) cc_final: 0.9041 (t0) REVERT: A 447 ASN cc_start: 0.8442 (m-40) cc_final: 0.7986 (t0) REVERT: A 453 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.8173 (ttt180) REVERT: A 466 MET cc_start: 0.9211 (ptt) cc_final: 0.8869 (ptt) REVERT: A 493 MET cc_start: 0.9030 (tmm) cc_final: 0.8431 (tmm) REVERT: A 494 MET cc_start: 0.9206 (mtm) cc_final: 0.8852 (mtt) REVERT: A 496 ASN cc_start: 0.9542 (t0) cc_final: 0.9085 (t0) REVERT: A 505 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8753 (mt-10) REVERT: A 509 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8547 (tm-30) REVERT: A 510 LYS cc_start: 0.9366 (mtpt) cc_final: 0.8851 (mtpt) REVERT: A 512 GLU cc_start: 0.8354 (pt0) cc_final: 0.8130 (pt0) REVERT: A 602 GLU cc_start: 0.7827 (pt0) cc_final: 0.7441 (pt0) REVERT: A 610 LYS cc_start: 0.7960 (tptt) cc_final: 0.7705 (tptt) REVERT: A 632 MET cc_start: 0.8666 (mtm) cc_final: 0.7938 (mtp) REVERT: A 640 MET cc_start: 0.9653 (tpp) cc_final: 0.8664 (tpp) REVERT: A 645 GLN cc_start: 0.9003 (tp40) cc_final: 0.8759 (tp-100) REVERT: A 686 ARG cc_start: 0.8766 (mmm-85) cc_final: 0.8498 (mtp85) REVERT: B 8 LYS cc_start: 0.9001 (tppt) cc_final: 0.8772 (tppt) REVERT: B 17 MET cc_start: 0.8832 (mmm) cc_final: 0.8615 (mmm) REVERT: B 21 ASP cc_start: 0.8805 (m-30) cc_final: 0.8391 (t0) REVERT: B 31 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7883 (mt-10) REVERT: B 65 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8070 (mp0) REVERT: B 99 LYS cc_start: 0.9494 (mmmm) cc_final: 0.9190 (mmmm) REVERT: B 109 ASN cc_start: 0.9241 (m-40) cc_final: 0.8603 (p0) REVERT: B 128 PHE cc_start: 0.9579 (t80) cc_final: 0.9349 (t80) REVERT: B 181 ASP cc_start: 0.9132 (OUTLIER) cc_final: 0.8662 (t0) REVERT: B 257 ASP cc_start: 0.8933 (m-30) cc_final: 0.8473 (m-30) REVERT: B 263 ASP cc_start: 0.9194 (m-30) cc_final: 0.8780 (p0) REVERT: B 286 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.7679 (m-30) REVERT: B 290 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8262 (tm-30) REVERT: B 312 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8647 (pm20) REVERT: B 333 LYS cc_start: 0.8877 (tttt) cc_final: 0.8579 (tttp) REVERT: B 362 ASP cc_start: 0.8625 (m-30) cc_final: 0.7452 (m-30) REVERT: B 374 SER cc_start: 0.9216 (t) cc_final: 0.8961 (t) REVERT: B 378 PHE cc_start: 0.9320 (p90) cc_final: 0.9010 (p90) REVERT: B 393 SER cc_start: 0.9375 (m) cc_final: 0.9030 (p) REVERT: B 394 TYR cc_start: 0.9049 (m-80) cc_final: 0.8737 (m-80) REVERT: B 415 ASN cc_start: 0.9139 (t0) cc_final: 0.8736 (t0) REVERT: B 467 ASN cc_start: 0.9378 (t0) cc_final: 0.9074 (m-40) REVERT: B 471 TYR cc_start: 0.9217 (t80) cc_final: 0.8983 (t80) REVERT: B 483 GLU cc_start: 0.9443 (mp0) cc_final: 0.9208 (mp0) REVERT: B 493 MET cc_start: 0.9662 (tmm) cc_final: 0.8865 (tmm) REVERT: B 515 ASP cc_start: 0.8994 (m-30) cc_final: 0.8746 (m-30) REVERT: B 602 GLU cc_start: 0.8498 (tt0) cc_final: 0.8112 (tt0) REVERT: B 610 LYS cc_start: 0.8957 (mmmt) cc_final: 0.8728 (mmmt) REVERT: B 612 TYR cc_start: 0.8592 (m-80) cc_final: 0.8183 (m-80) REVERT: B 628 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8307 (mm-30) REVERT: B 632 MET cc_start: 0.8872 (mtp) cc_final: 0.8596 (mtm) REVERT: C 19 GLN cc_start: 0.7716 (mp10) cc_final: 0.7349 (pm20) REVERT: C 20 MET cc_start: 0.9053 (tpp) cc_final: 0.8761 (tmm) REVERT: C 42 LEU cc_start: 0.8149 (pt) cc_final: 0.7937 (pp) REVERT: C 55 TYR cc_start: 0.8312 (t80) cc_final: 0.7684 (t80) REVERT: C 56 MET cc_start: 0.5716 (ttt) cc_final: 0.5286 (ttt) REVERT: C 68 GLU cc_start: 0.9264 (tm-30) cc_final: 0.8956 (tm-30) REVERT: C 80 HIS cc_start: 0.8665 (m90) cc_final: 0.8278 (m90) REVERT: C 98 ASN cc_start: 0.7356 (m-40) cc_final: 0.7082 (m-40) REVERT: C 112 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7323 (tp) REVERT: C 145 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7804 (tp) REVERT: C 154 PHE cc_start: 0.8332 (m-80) cc_final: 0.8023 (m-80) REVERT: C 164 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8816 (tp30) REVERT: C 169 TYR cc_start: 0.8469 (m-80) cc_final: 0.8118 (m-80) REVERT: C 178 PHE cc_start: 0.9298 (m-80) cc_final: 0.8318 (m-10) REVERT: C 185 MET cc_start: 0.8609 (pmm) cc_final: 0.7523 (pmm) REVERT: C 186 GLN cc_start: 0.9363 (mm110) cc_final: 0.8854 (mp10) REVERT: C 216 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.6925 (mp10) REVERT: C 242 TYR cc_start: 0.9305 (t80) cc_final: 0.9079 (t80) REVERT: C 259 PHE cc_start: 0.8915 (t80) cc_final: 0.8418 (t80) REVERT: C 261 ARG cc_start: 0.9153 (mtm-85) cc_final: 0.8717 (ptt-90) REVERT: C 268 LEU cc_start: 0.8942 (tp) cc_final: 0.8693 (tp) REVERT: C 269 MET cc_start: 0.9173 (ppp) cc_final: 0.8931 (ppp) REVERT: C 270 ASN cc_start: 0.8183 (m110) cc_final: 0.7814 (m110) REVERT: C 313 GLU cc_start: 0.8986 (tt0) cc_final: 0.8663 (tt0) REVERT: C 316 LYS cc_start: 0.9105 (mmtt) cc_final: 0.8828 (mmtt) REVERT: D 17 PHE cc_start: 0.7376 (m-80) cc_final: 0.6764 (m-80) REVERT: D 28 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.8797 (tp40) REVERT: D 30 TRP cc_start: 0.8451 (p-90) cc_final: 0.8012 (p-90) REVERT: D 46 TYR cc_start: 0.9107 (m-80) cc_final: 0.8829 (m-10) REVERT: D 56 MET cc_start: 0.7627 (mmm) cc_final: 0.6637 (ptp) REVERT: D 96 MET cc_start: 0.8334 (mmt) cc_final: 0.7885 (mmm) REVERT: D 136 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8300 (mt0) REVERT: D 178 PHE cc_start: 0.9174 (m-10) cc_final: 0.8573 (m-80) REVERT: D 186 GLN cc_start: 0.9147 (mm-40) cc_final: 0.8697 (mp10) REVERT: D 207 LEU cc_start: 0.9148 (mm) cc_final: 0.8945 (mm) REVERT: D 210 GLN cc_start: 0.9412 (tm-30) cc_final: 0.9141 (pt0) REVERT: D 246 LEU cc_start: 0.7926 (tp) cc_final: 0.7569 (mt) REVERT: D 247 TYR cc_start: 0.8755 (m-10) cc_final: 0.8448 (m-10) REVERT: D 252 LEU cc_start: 0.6362 (mt) cc_final: 0.5997 (mm) REVERT: D 269 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8158 (ppp) outliers start: 70 outliers final: 50 residues processed: 724 average time/residue: 0.1122 time to fit residues: 123.9956 Evaluate side-chains 723 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 659 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain D residue 28 GLN Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 186 optimal weight: 20.0000 chunk 140 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 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 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.119270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.084250 restraints weight = 35933.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.087458 restraints weight = 17273.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.089623 restraints weight = 10659.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.091073 restraints weight = 7352.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.092049 restraints weight = 5647.571| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.6865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 16386 Z= 0.272 Angle : 0.796 15.580 22134 Z= 0.403 Chirality : 0.047 0.194 2360 Planarity : 0.004 0.045 2818 Dihedral : 8.971 136.293 2294 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 5.13 % Allowed : 29.90 % Favored : 64.98 % 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: 0.51 (0.19), residues: 1932 helix: 0.79 (0.15), residues: 1168 sheet: -0.62 (0.41), residues: 148 loop : -0.06 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 235 TYR 0.027 0.002 TYR B 527 PHE 0.031 0.002 PHE A 261 TRP 0.016 0.002 TRP D 44 HIS 0.006 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.27 (16386) covalent geometry : angle 0.79581 / 0.40 (22134) hydrogen bonds : bond 0.04228 / 2.68 ( 871) hydrogen bonds : angle 5.22244 / 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 755 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 667 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9235 (mmmm) cc_final: 0.9008 (ttmm) REVERT: A 17 MET cc_start: 0.8350 (mpp) cc_final: 0.8041 (mpp) REVERT: A 55 LEU cc_start: 0.9813 (mt) cc_final: 0.9548 (pp) REVERT: A 65 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8409 (mp0) REVERT: A 66 GLU cc_start: 0.8458 (tp30) cc_final: 0.8217 (tp30) REVERT: A 82 LYS cc_start: 0.9653 (mmmm) cc_final: 0.9340 (mmmm) REVERT: A 144 MET cc_start: 0.9149 (mtm) cc_final: 0.8732 (mtm) REVERT: A 149 TYR cc_start: 0.9358 (t80) cc_final: 0.8615 (t80) REVERT: A 181 ASP cc_start: 0.8811 (m-30) cc_final: 0.8564 (m-30) REVERT: A 187 ASP cc_start: 0.9067 (t70) cc_final: 0.8668 (t70) REVERT: A 218 ASN cc_start: 0.9362 (t0) cc_final: 0.9078 (t0) REVERT: A 257 ASP cc_start: 0.9410 (m-30) cc_final: 0.9011 (m-30) REVERT: A 286 ASP cc_start: 0.8582 (m-30) cc_final: 0.8300 (m-30) REVERT: A 321 GLU cc_start: 0.8916 (tp30) cc_final: 0.8501 (tp30) REVERT: A 348 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.7673 (tmm) REVERT: A 352 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7644 (mt-10) REVERT: A 359 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8323 (ttp) REVERT: A 362 ASP cc_start: 0.8704 (m-30) cc_final: 0.7906 (m-30) REVERT: A 384 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.7779 (pm20) REVERT: A 389 SER cc_start: 0.9546 (OUTLIER) cc_final: 0.9172 (p) REVERT: A 447 ASN cc_start: 0.8555 (m-40) cc_final: 0.8243 (m-40) REVERT: A 466 MET cc_start: 0.9317 (ptt) cc_final: 0.8938 (ptt) REVERT: A 493 MET cc_start: 0.9053 (tmm) cc_final: 0.8412 (tmm) REVERT: A 496 ASN cc_start: 0.9520 (t0) cc_final: 0.9122 (t0) REVERT: A 505 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8454 (mt-10) REVERT: A 510 LYS cc_start: 0.9317 (mtpt) cc_final: 0.8976 (mtpt) REVERT: A 512 GLU cc_start: 0.8448 (pt0) cc_final: 0.8237 (pt0) REVERT: A 602 GLU cc_start: 0.7847 (pt0) cc_final: 0.6151 (pt0) REVERT: A 604 ARG cc_start: 0.8806 (mmp80) cc_final: 0.7948 (mmt90) REVERT: A 632 MET cc_start: 0.8922 (mtm) cc_final: 0.8144 (mtp) REVERT: A 640 MET cc_start: 0.9558 (tpp) cc_final: 0.8759 (tpp) REVERT: A 659 LYS cc_start: 0.9076 (mmmt) cc_final: 0.8818 (mmtt) REVERT: B 8 LYS cc_start: 0.9066 (tppt) cc_final: 0.8848 (tppt) REVERT: B 17 MET cc_start: 0.8987 (mmm) cc_final: 0.8781 (mmm) REVERT: B 21 ASP cc_start: 0.8838 (m-30) cc_final: 0.8447 (t0) REVERT: B 31 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8007 (mt-10) REVERT: B 65 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8406 (mm-30) REVERT: B 71 LEU cc_start: 0.9717 (mm) cc_final: 0.9431 (mp) REVERT: B 99 LYS cc_start: 0.9573 (mmmm) cc_final: 0.9333 (mmmm) REVERT: B 109 ASN cc_start: 0.9237 (m-40) cc_final: 0.8735 (p0) REVERT: B 116 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8367 (mt-10) REVERT: B 174 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8397 (mm-30) REVERT: B 181 ASP cc_start: 0.9173 (OUTLIER) cc_final: 0.8721 (t0) REVERT: B 257 ASP cc_start: 0.8863 (m-30) cc_final: 0.8414 (m-30) REVERT: B 263 ASP cc_start: 0.9151 (m-30) cc_final: 0.8806 (p0) REVERT: B 286 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.7652 (m-30) REVERT: B 290 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8260 (tm-30) REVERT: B 322 MET cc_start: 0.9019 (mmt) cc_final: 0.8713 (mmt) REVERT: B 362 ASP cc_start: 0.8698 (m-30) cc_final: 0.7400 (m-30) REVERT: B 434 ASP cc_start: 0.9319 (m-30) cc_final: 0.9085 (m-30) REVERT: B 471 TYR cc_start: 0.9475 (t80) cc_final: 0.8760 (t80) REVERT: B 483 GLU cc_start: 0.9491 (mp0) cc_final: 0.9248 (mp0) REVERT: B 493 MET cc_start: 0.9697 (tmm) cc_final: 0.8884 (tmm) REVERT: B 494 MET cc_start: 0.9428 (mtp) cc_final: 0.9128 (mtp) REVERT: B 515 ASP cc_start: 0.9090 (m-30) cc_final: 0.8872 (m-30) REVERT: B 546 LEU cc_start: 0.9667 (mt) cc_final: 0.9372 (mt) REVERT: B 595 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8891 (mmm) REVERT: B 602 GLU cc_start: 0.8427 (tt0) cc_final: 0.8149 (tt0) REVERT: B 606 TYR cc_start: 0.8556 (m-80) cc_final: 0.8162 (m-80) REVERT: B 610 LYS cc_start: 0.9003 (mmmt) cc_final: 0.8714 (mmmt) REVERT: B 612 TYR cc_start: 0.8598 (m-80) cc_final: 0.8274 (m-80) REVERT: B 627 LYS cc_start: 0.8923 (ttpp) cc_final: 0.8635 (ttpp) REVERT: B 628 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8202 (mm-30) REVERT: B 668 ASN cc_start: 0.9326 (m110) cc_final: 0.9032 (m110) REVERT: C 19 GLN cc_start: 0.7701 (mp10) cc_final: 0.7361 (pm20) REVERT: C 20 MET cc_start: 0.9058 (tpp) cc_final: 0.8785 (tmm) REVERT: C 29 PHE cc_start: 0.8350 (t80) cc_final: 0.7835 (t80) REVERT: C 55 TYR cc_start: 0.8401 (t80) cc_final: 0.7825 (t80) REVERT: C 56 MET cc_start: 0.5919 (ttt) cc_final: 0.5554 (ttt) REVERT: C 80 HIS cc_start: 0.8789 (m90) cc_final: 0.8360 (m90) REVERT: C 96 MET cc_start: 0.8839 (mmt) cc_final: 0.8066 (mmm) REVERT: C 105 TYR cc_start: 0.9088 (m-10) cc_final: 0.8882 (m-10) REVERT: C 121 VAL cc_start: 0.9153 (OUTLIER) cc_final: 0.8899 (p) REVERT: C 134 LYS cc_start: 0.9585 (pttm) cc_final: 0.9235 (pttm) REVERT: C 164 GLU cc_start: 0.9295 (mm-30) cc_final: 0.9020 (tp30) REVERT: C 169 TYR cc_start: 0.8701 (m-80) cc_final: 0.8390 (m-80) REVERT: C 174 TYR cc_start: 0.9319 (OUTLIER) cc_final: 0.8592 (t80) REVERT: C 216 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.6916 (mp10) REVERT: C 242 TYR cc_start: 0.9328 (t80) cc_final: 0.9084 (t80) REVERT: C 259 PHE cc_start: 0.8998 (t80) cc_final: 0.8464 (t80) REVERT: C 268 LEU cc_start: 0.8907 (tp) cc_final: 0.8625 (tp) REVERT: C 269 MET cc_start: 0.9116 (ppp) cc_final: 0.8880 (ppp) REVERT: C 270 ASN cc_start: 0.8350 (m110) cc_final: 0.8010 (m110) REVERT: C 313 GLU cc_start: 0.9036 (tt0) cc_final: 0.8784 (tt0) REVERT: D 21 PHE cc_start: 0.9316 (m-80) cc_final: 0.9052 (m-80) REVERT: D 30 TRP cc_start: 0.8679 (p-90) cc_final: 0.7821 (p-90) REVERT: D 34 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8531 (mm-30) REVERT: D 46 TYR cc_start: 0.9113 (m-80) cc_final: 0.8797 (m-10) REVERT: D 153 LEU cc_start: 0.9168 (tp) cc_final: 0.8784 (mt) REVERT: D 178 PHE cc_start: 0.9346 (m-10) cc_final: 0.8636 (m-80) REVERT: D 186 GLN cc_start: 0.9161 (mm-40) cc_final: 0.8700 (mp10) REVERT: D 207 LEU cc_start: 0.9101 (mm) cc_final: 0.8821 (mm) REVERT: D 210 GLN cc_start: 0.9400 (tm-30) cc_final: 0.9138 (pt0) REVERT: D 244 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7616 (mp0) REVERT: D 246 LEU cc_start: 0.8114 (tp) cc_final: 0.7615 (mt) REVERT: D 247 TYR cc_start: 0.8869 (m-10) cc_final: 0.8540 (m-10) REVERT: D 252 LEU cc_start: 0.6328 (mt) cc_final: 0.5964 (mm) REVERT: D 269 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8164 (ppp) outliers start: 88 outliers final: 65 residues processed: 695 average time/residue: 0.1167 time to fit residues: 124.5802 Evaluate side-chains 706 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 629 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 134 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 151 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.122113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.087483 restraints weight = 36188.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.090934 restraints weight = 17338.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.093177 restraints weight = 10438.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.094686 restraints weight = 7240.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.095686 restraints weight = 5529.267| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.7144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16386 Z= 0.159 Angle : 0.780 16.183 22134 Z= 0.382 Chirality : 0.046 0.223 2360 Planarity : 0.004 0.046 2818 Dihedral : 8.776 135.946 2294 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.55 % Allowed : 33.39 % Favored : 63.05 % 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: 0.51 (0.19), residues: 1932 helix: 0.87 (0.15), residues: 1152 sheet: -0.67 (0.42), residues: 148 loop : -0.20 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 196 TYR 0.023 0.001 TYR B 394 PHE 0.034 0.002 PHE C 154 TRP 0.015 0.002 TRP C 44 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (16386) covalent geometry : angle 0.77956 / 0.38 (22134) hydrogen bonds : bond 0.04094 / 2.62 ( 871) hydrogen bonds : angle 5.12866 / 3.68 ( 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 730 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 669 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9178 (mmmm) cc_final: 0.8932 (ttmm) REVERT: A 64 TYR cc_start: 0.9157 (m-10) cc_final: 0.8536 (m-10) REVERT: A 65 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8381 (mp0) REVERT: A 82 LYS cc_start: 0.9653 (mmmm) cc_final: 0.9351 (mmmm) REVERT: A 144 MET cc_start: 0.9158 (mtm) cc_final: 0.8647 (mtm) REVERT: A 149 TYR cc_start: 0.9326 (t80) cc_final: 0.8757 (t80) REVERT: A 181 ASP cc_start: 0.8810 (m-30) cc_final: 0.8557 (m-30) REVERT: A 187 ASP cc_start: 0.9017 (t70) cc_final: 0.8650 (t70) REVERT: A 218 ASN cc_start: 0.9331 (t0) cc_final: 0.9125 (t0) REVERT: A 228 LYS cc_start: 0.9317 (mmmm) cc_final: 0.8710 (mmtt) REVERT: A 257 ASP cc_start: 0.9428 (m-30) cc_final: 0.9051 (m-30) REVERT: A 270 ASP cc_start: 0.9282 (p0) cc_final: 0.8964 (p0) REVERT: A 321 GLU cc_start: 0.8849 (tp30) cc_final: 0.8420 (tp30) REVERT: A 348 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7597 (tmm) REVERT: A 350 ARG cc_start: 0.9321 (mtp85) cc_final: 0.9011 (mtp180) REVERT: A 352 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7682 (mt-10) REVERT: A 359 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8236 (ttp) REVERT: A 362 ASP cc_start: 0.8693 (m-30) cc_final: 0.8035 (m-30) REVERT: A 384 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.7644 (pm20) REVERT: A 447 ASN cc_start: 0.8511 (m-40) cc_final: 0.7906 (t0) REVERT: A 466 MET cc_start: 0.9208 (ptt) cc_final: 0.8985 (ptt) REVERT: A 493 MET cc_start: 0.9013 (tmm) cc_final: 0.8244 (tmm) REVERT: A 494 MET cc_start: 0.9142 (mtm) cc_final: 0.8731 (mtt) REVERT: A 496 ASN cc_start: 0.9509 (t0) cc_final: 0.9118 (t0) REVERT: A 505 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8733 (mt-10) REVERT: A 516 GLN cc_start: 0.9045 (mt0) cc_final: 0.8602 (mt0) REVERT: A 550 MET cc_start: 0.7915 (mtm) cc_final: 0.7692 (mtm) REVERT: A 583 SER cc_start: 0.9374 (m) cc_final: 0.8806 (t) REVERT: A 598 MET cc_start: 0.8643 (mtp) cc_final: 0.7774 (mmm) REVERT: A 602 GLU cc_start: 0.7743 (pt0) cc_final: 0.6233 (pt0) REVERT: A 604 ARG cc_start: 0.8861 (mmp80) cc_final: 0.7952 (mmt-90) REVERT: A 632 MET cc_start: 0.8661 (mtm) cc_final: 0.7884 (mtp) REVERT: A 640 MET cc_start: 0.9610 (tpp) cc_final: 0.8680 (tpp) REVERT: A 659 LYS cc_start: 0.8980 (mmmt) cc_final: 0.8710 (mmtt) REVERT: A 686 ARG cc_start: 0.8850 (mmm-85) cc_final: 0.8494 (mmm-85) REVERT: B 8 LYS cc_start: 0.9070 (tppt) cc_final: 0.8845 (tppt) REVERT: B 17 MET cc_start: 0.8932 (mmm) cc_final: 0.8632 (mmm) REVERT: B 21 ASP cc_start: 0.8856 (m-30) cc_final: 0.8442 (t0) REVERT: B 28 LYS cc_start: 0.9323 (mmtt) cc_final: 0.8696 (mmmm) REVERT: B 31 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8031 (mt-10) REVERT: B 65 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8022 (mp0) REVERT: B 99 LYS cc_start: 0.9509 (mmmm) cc_final: 0.9280 (mmmm) REVERT: B 109 ASN cc_start: 0.9242 (m-40) cc_final: 0.8700 (p0) REVERT: B 181 ASP cc_start: 0.9087 (OUTLIER) cc_final: 0.8469 (t0) REVERT: B 202 ASN cc_start: 0.9423 (t0) cc_final: 0.9146 (t0) REVERT: B 257 ASP cc_start: 0.8907 (m-30) cc_final: 0.8350 (m-30) REVERT: B 286 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.7720 (m-30) REVERT: B 290 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8140 (tm-30) REVERT: B 314 MET cc_start: 0.9259 (tmm) cc_final: 0.8992 (ttt) REVERT: B 362 ASP cc_start: 0.8720 (m-30) cc_final: 0.7521 (m-30) REVERT: B 394 TYR cc_start: 0.8884 (m-80) cc_final: 0.8383 (m-80) REVERT: B 471 TYR cc_start: 0.9281 (t80) cc_final: 0.8471 (t80) REVERT: B 492 PHE cc_start: 0.9733 (m-80) cc_final: 0.9486 (m-80) REVERT: B 493 MET cc_start: 0.9680 (tmm) cc_final: 0.8890 (tmm) REVERT: B 515 ASP cc_start: 0.9046 (m-30) cc_final: 0.8803 (m-30) REVERT: B 546 LEU cc_start: 0.9620 (mt) cc_final: 0.9310 (mt) REVERT: B 610 LYS cc_start: 0.9041 (mmmt) cc_final: 0.8778 (mmmt) REVERT: B 612 TYR cc_start: 0.8565 (m-80) cc_final: 0.8171 (m-80) REVERT: B 627 LYS cc_start: 0.8842 (ttpp) cc_final: 0.8529 (ttpp) REVERT: B 628 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8281 (mm-30) REVERT: B 668 ASN cc_start: 0.9295 (m110) cc_final: 0.9070 (m-40) REVERT: C 19 GLN cc_start: 0.7654 (mp10) cc_final: 0.7249 (pm20) REVERT: C 20 MET cc_start: 0.9025 (tpp) cc_final: 0.8697 (tmm) REVERT: C 29 PHE cc_start: 0.8243 (t80) cc_final: 0.7792 (t80) REVERT: C 55 TYR cc_start: 0.8202 (t80) cc_final: 0.7233 (t80) REVERT: C 56 MET cc_start: 0.5875 (ttt) cc_final: 0.5498 (ttt) REVERT: C 80 HIS cc_start: 0.8685 (m90) cc_final: 0.8272 (m90) REVERT: C 96 MET cc_start: 0.8749 (mmt) cc_final: 0.8149 (mmm) REVERT: C 105 TYR cc_start: 0.9084 (m-10) cc_final: 0.8858 (m-10) REVERT: C 121 VAL cc_start: 0.9105 (OUTLIER) cc_final: 0.8826 (p) REVERT: C 131 LEU cc_start: 0.9454 (mt) cc_final: 0.9240 (mt) REVERT: C 145 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7816 (tp) REVERT: C 154 PHE cc_start: 0.8127 (m-80) cc_final: 0.7478 (m-80) REVERT: C 164 GLU cc_start: 0.9236 (mm-30) cc_final: 0.8874 (tp30) REVERT: C 169 TYR cc_start: 0.8727 (m-80) cc_final: 0.8335 (m-80) REVERT: C 178 PHE cc_start: 0.9376 (m-80) cc_final: 0.8388 (m-10) REVERT: C 186 GLN cc_start: 0.9211 (mm110) cc_final: 0.8666 (mp10) REVERT: C 189 GLU cc_start: 0.8616 (tp30) cc_final: 0.8337 (mm-30) REVERT: C 229 ILE cc_start: 0.8531 (mm) cc_final: 0.8187 (mm) REVERT: C 259 PHE cc_start: 0.9013 (t80) cc_final: 0.8527 (t80) REVERT: C 268 LEU cc_start: 0.8856 (tp) cc_final: 0.8594 (tp) REVERT: C 269 MET cc_start: 0.9048 (ppp) cc_final: 0.8800 (ppp) REVERT: C 270 ASN cc_start: 0.8413 (m110) cc_final: 0.8071 (m110) REVERT: C 313 GLU cc_start: 0.8967 (tt0) cc_final: 0.8619 (tt0) REVERT: C 316 LYS cc_start: 0.9202 (mmtt) cc_final: 0.8893 (mmtt) REVERT: D 30 TRP cc_start: 0.8436 (p-90) cc_final: 0.8024 (p-90) REVERT: D 46 TYR cc_start: 0.9078 (m-80) cc_final: 0.8770 (m-10) REVERT: D 186 GLN cc_start: 0.9099 (mm-40) cc_final: 0.8613 (mp10) REVERT: D 207 LEU cc_start: 0.9060 (mm) cc_final: 0.8718 (mm) REVERT: D 210 GLN cc_start: 0.9378 (tm-30) cc_final: 0.9099 (pt0) REVERT: D 244 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: D 246 LEU cc_start: 0.8048 (tp) cc_final: 0.7525 (mt) REVERT: D 247 TYR cc_start: 0.8797 (m-10) cc_final: 0.8452 (m-10) REVERT: D 252 LEU cc_start: 0.6241 (mt) cc_final: 0.5998 (mm) REVERT: D 269 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7982 (ppp) outliers start: 61 outliers final: 46 residues processed: 693 average time/residue: 0.1176 time to fit residues: 125.0469 Evaluate side-chains 699 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 644 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 149 optimal weight: 20.0000 chunk 16 optimal weight: 0.0970 chunk 114 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 100 optimal weight: 0.0870 chunk 88 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN A 418 ASN A 588 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.125794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.090003 restraints weight = 35498.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.093432 restraints weight = 17287.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.095734 restraints weight = 10590.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.097281 restraints weight = 7381.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.098331 restraints weight = 5656.433| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.7417 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= 0.146 Angle : 0.795 15.863 22134 Z= 0.387 Chirality : 0.047 0.264 2360 Planarity : 0.004 0.046 2818 Dihedral : 8.618 137.944 2294 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.26 % Allowed : 33.92 % Favored : 62.82 % 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: 0.42 (0.18), residues: 1932 helix: 0.78 (0.15), residues: 1148 sheet: -0.75 (0.43), residues: 142 loop : -0.19 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 235 TYR 0.027 0.001 TYR B 527 PHE 0.033 0.002 PHE C 172 TRP 0.019 0.001 TRP D 44 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (16386) covalent geometry : angle 0.79473 / 0.39 (22134) hydrogen bonds : bond 0.04137 / 2.64 ( 871) hydrogen bonds : angle 5.15082 / 3.69 ( 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 743 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 687 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9236 (mmmm) cc_final: 0.8950 (ttmm) REVERT: A 64 TYR cc_start: 0.9134 (m-10) cc_final: 0.8544 (m-10) REVERT: A 82 LYS cc_start: 0.9632 (mmmm) cc_final: 0.9318 (mmmm) REVERT: A 102 ASN cc_start: 0.9223 (m110) cc_final: 0.8794 (m110) REVERT: A 149 TYR cc_start: 0.9343 (t80) cc_final: 0.8739 (t80) REVERT: A 163 ARG cc_start: 0.8320 (mmm-85) cc_final: 0.7641 (mmm160) REVERT: A 181 ASP cc_start: 0.8877 (m-30) cc_final: 0.8672 (m-30) REVERT: A 187 ASP cc_start: 0.8943 (t70) cc_final: 0.8606 (t70) REVERT: A 218 ASN cc_start: 0.9302 (t0) cc_final: 0.9051 (t0) REVERT: A 228 LYS cc_start: 0.9334 (mmmm) cc_final: 0.8725 (mmtt) REVERT: A 257 ASP cc_start: 0.9371 (m-30) cc_final: 0.9063 (m-30) REVERT: A 270 ASP cc_start: 0.9223 (p0) cc_final: 0.8852 (p0) REVERT: A 290 GLU cc_start: 0.8769 (tp30) cc_final: 0.8440 (tm-30) REVERT: A 321 GLU cc_start: 0.8860 (tp30) cc_final: 0.8443 (tp30) REVERT: A 348 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7429 (tmm) REVERT: A 350 ARG cc_start: 0.9298 (mtp85) cc_final: 0.9036 (mtp180) REVERT: A 352 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7630 (mt-10) REVERT: A 357 TYR cc_start: 0.9020 (m-10) cc_final: 0.8312 (m-10) REVERT: A 359 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8103 (ttp) REVERT: A 384 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8005 (pm20) REVERT: A 389 SER cc_start: 0.9442 (OUTLIER) cc_final: 0.9119 (p) REVERT: A 435 SER cc_start: 0.9469 (OUTLIER) cc_final: 0.9205 (t) REVERT: A 441 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8157 (mm-30) REVERT: A 447 ASN cc_start: 0.8401 (m110) cc_final: 0.7927 (t0) REVERT: A 493 MET cc_start: 0.8994 (tmm) cc_final: 0.8231 (tmm) REVERT: A 496 ASN cc_start: 0.9509 (t0) cc_final: 0.9122 (t0) REVERT: A 505 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8733 (mt-10) REVERT: A 571 TYR cc_start: 0.8204 (t80) cc_final: 0.7875 (t80) REVERT: A 583 SER cc_start: 0.9351 (m) cc_final: 0.8787 (t) REVERT: A 598 MET cc_start: 0.8554 (mtp) cc_final: 0.8350 (mmm) REVERT: A 602 GLU cc_start: 0.7784 (pt0) cc_final: 0.5963 (pt0) REVERT: A 604 ARG cc_start: 0.8827 (mmp80) cc_final: 0.7921 (mmt-90) REVERT: A 632 MET cc_start: 0.8578 (mtm) cc_final: 0.7882 (mtp) REVERT: A 640 MET cc_start: 0.9599 (tpp) cc_final: 0.8682 (tpp) REVERT: A 659 LYS cc_start: 0.9116 (mmmt) cc_final: 0.8852 (mmtt) REVERT: B 8 LYS cc_start: 0.9041 (tppt) cc_final: 0.8825 (tppt) REVERT: B 21 ASP cc_start: 0.8845 (m-30) cc_final: 0.8488 (t0) REVERT: B 28 LYS cc_start: 0.9271 (mmtt) cc_final: 0.8584 (mmmm) REVERT: B 31 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7995 (mt-10) REVERT: B 65 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8496 (mm-30) REVERT: B 99 LYS cc_start: 0.9501 (mmmm) cc_final: 0.9274 (mmmm) REVERT: B 109 ASN cc_start: 0.9203 (m-40) cc_final: 0.8619 (p0) REVERT: B 119 GLU cc_start: 0.8605 (mp0) cc_final: 0.8297 (mp0) REVERT: B 161 ARG cc_start: 0.9040 (mmm-85) cc_final: 0.8636 (mmm-85) REVERT: B 181 ASP cc_start: 0.9024 (OUTLIER) cc_final: 0.8390 (t0) REVERT: B 257 ASP cc_start: 0.8804 (m-30) cc_final: 0.8303 (m-30) REVERT: B 286 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.7810 (m-30) REVERT: B 290 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7943 (tm-30) REVERT: B 314 MET cc_start: 0.9193 (tmm) cc_final: 0.8990 (ttt) REVERT: B 335 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7957 (mt-10) REVERT: B 362 ASP cc_start: 0.8710 (m-30) cc_final: 0.7542 (m-30) REVERT: B 374 SER cc_start: 0.9329 (t) cc_final: 0.9035 (t) REVERT: B 394 TYR cc_start: 0.8755 (m-80) cc_final: 0.8548 (m-80) REVERT: B 447 ASN cc_start: 0.8527 (t0) cc_final: 0.7374 (m-40) REVERT: B 467 ASN cc_start: 0.9215 (m-40) cc_final: 0.8956 (m-40) REVERT: B 471 TYR cc_start: 0.9243 (t80) cc_final: 0.8771 (t80) REVERT: B 492 PHE cc_start: 0.9718 (m-80) cc_final: 0.9483 (m-80) REVERT: B 493 MET cc_start: 0.9657 (tmm) cc_final: 0.8893 (tmm) REVERT: B 515 ASP cc_start: 0.8979 (m-30) cc_final: 0.8735 (m-30) REVERT: B 548 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8119 (mm-30) REVERT: B 610 LYS cc_start: 0.9041 (mmmt) cc_final: 0.8788 (mmmt) REVERT: B 627 LYS cc_start: 0.8809 (ttpp) cc_final: 0.8537 (ttpp) REVERT: B 628 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8343 (mm-30) REVERT: C 19 GLN cc_start: 0.7590 (mp10) cc_final: 0.7164 (pm20) REVERT: C 20 MET cc_start: 0.8958 (tpp) cc_final: 0.8631 (tmm) REVERT: C 80 HIS cc_start: 0.8801 (m90) cc_final: 0.8443 (m90) REVERT: C 96 MET cc_start: 0.8643 (mmt) cc_final: 0.7999 (mmm) REVERT: C 105 TYR cc_start: 0.9050 (m-10) cc_final: 0.8838 (m-10) REVERT: C 112 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7186 (tp) REVERT: C 121 VAL cc_start: 0.9088 (OUTLIER) cc_final: 0.8867 (p) REVERT: C 145 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7848 (tp) REVERT: C 164 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8720 (tp30) REVERT: C 169 TYR cc_start: 0.8812 (m-80) cc_final: 0.8527 (m-80) REVERT: C 178 PHE cc_start: 0.9378 (m-80) cc_final: 0.8758 (m-10) REVERT: C 229 ILE cc_start: 0.8443 (mm) cc_final: 0.8112 (mm) REVERT: C 259 PHE cc_start: 0.9011 (t80) cc_final: 0.8569 (t80) REVERT: C 268 LEU cc_start: 0.8809 (tp) cc_final: 0.8547 (tp) REVERT: C 269 MET cc_start: 0.9024 (ppp) cc_final: 0.8795 (ppp) REVERT: C 270 ASN cc_start: 0.8504 (m110) cc_final: 0.8118 (m110) REVERT: D 28 GLN cc_start: 0.9239 (tt0) cc_final: 0.8678 (tt0) REVERT: D 30 TRP cc_start: 0.8645 (p-90) cc_final: 0.7907 (p-90) REVERT: D 46 TYR cc_start: 0.9054 (m-80) cc_final: 0.8817 (m-10) REVERT: D 96 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8115 (mmm) REVERT: D 109 PHE cc_start: 0.7279 (m-80) cc_final: 0.6560 (m-80) REVERT: D 186 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8609 (mp10) REVERT: D 207 LEU cc_start: 0.9050 (mm) cc_final: 0.8705 (mm) REVERT: D 210 GLN cc_start: 0.9370 (tm-30) cc_final: 0.9074 (pt0) REVERT: D 246 LEU cc_start: 0.7828 (tp) cc_final: 0.7388 (mt) REVERT: D 247 TYR cc_start: 0.8823 (m-10) cc_final: 0.8456 (m-10) REVERT: D 252 LEU cc_start: 0.6142 (mt) cc_final: 0.5939 (mm) REVERT: D 269 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7944 (ppp) outliers start: 56 outliers final: 39 residues processed: 709 average time/residue: 0.1048 time to fit residues: 114.1660 Evaluate side-chains 697 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 646 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 189 optimal weight: 9.9990 chunk 181 optimal weight: 0.8980 chunk 165 optimal weight: 0.5980 chunk 16 optimal weight: 0.0770 chunk 54 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN B 218 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN C 98 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.125510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.090623 restraints weight = 35806.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.094006 restraints weight = 17588.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.096241 restraints weight = 10639.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.097843 restraints weight = 7433.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.098711 restraints weight = 5664.022| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.7650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16386 Z= 0.156 Angle : 0.844 16.670 22134 Z= 0.409 Chirality : 0.048 0.231 2360 Planarity : 0.004 0.046 2818 Dihedral : 8.578 139.028 2294 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.38 % Allowed : 35.26 % Favored : 61.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.19), residues: 1932 helix: 0.68 (0.15), residues: 1146 sheet: -0.56 (0.45), residues: 142 loop : -0.22 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 243 TYR 0.030 0.002 TYR A 471 PHE 0.033 0.002 PHE C 172 TRP 0.013 0.001 TRP C 44 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (16386) covalent geometry : angle 0.84369 / 0.41 (22134) hydrogen bonds : bond 0.04146 / 2.63 ( 871) hydrogen bonds : angle 5.23952 / 3.77 ( 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 717 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 659 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.9113 (m-10) cc_final: 0.8501 (m-10) REVERT: A 82 LYS cc_start: 0.9640 (mmmm) cc_final: 0.9341 (mmmm) REVERT: A 102 ASN cc_start: 0.9259 (m110) cc_final: 0.8885 (m110) REVERT: A 149 TYR cc_start: 0.9377 (t80) cc_final: 0.8694 (t80) REVERT: A 163 ARG cc_start: 0.8396 (mmm-85) cc_final: 0.7735 (mmm160) REVERT: A 181 ASP cc_start: 0.8844 (m-30) cc_final: 0.8565 (m-30) REVERT: A 187 ASP cc_start: 0.8950 (t70) cc_final: 0.8563 (t70) REVERT: A 218 ASN cc_start: 0.9330 (t0) cc_final: 0.9071 (t0) REVERT: A 257 ASP cc_start: 0.9339 (m-30) cc_final: 0.9074 (m-30) REVERT: A 270 ASP cc_start: 0.9188 (p0) cc_final: 0.8782 (p0) REVERT: A 290 GLU cc_start: 0.8756 (tp30) cc_final: 0.8408 (tm-30) REVERT: A 321 GLU cc_start: 0.8838 (tp30) cc_final: 0.8162 (tp30) REVERT: A 348 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.7575 (tmm) REVERT: A 350 ARG cc_start: 0.9271 (mtp85) cc_final: 0.9036 (mtp180) REVERT: A 352 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7731 (mt-10) REVERT: A 357 TYR cc_start: 0.8995 (m-10) cc_final: 0.8225 (m-10) REVERT: A 384 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.7583 (pm20) REVERT: A 389 SER cc_start: 0.9448 (OUTLIER) cc_final: 0.9100 (p) REVERT: A 435 SER cc_start: 0.9475 (OUTLIER) cc_final: 0.9221 (t) REVERT: A 447 ASN cc_start: 0.8375 (m110) cc_final: 0.7894 (t0) REVERT: A 458 MET cc_start: 0.9151 (mmm) cc_final: 0.8661 (tpp) REVERT: A 493 MET cc_start: 0.8948 (tmm) cc_final: 0.8165 (tmm) REVERT: A 496 ASN cc_start: 0.9491 (t0) cc_final: 0.9157 (t0) REVERT: A 505 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8748 (mt-10) REVERT: A 583 SER cc_start: 0.9348 (m) cc_final: 0.8776 (t) REVERT: A 598 MET cc_start: 0.8713 (mtp) cc_final: 0.8358 (mmt) REVERT: A 599 GLU cc_start: 0.8514 (mp0) cc_final: 0.8264 (mp0) REVERT: A 602 GLU cc_start: 0.7803 (pt0) cc_final: 0.6856 (pt0) REVERT: A 604 ARG cc_start: 0.8807 (mmp80) cc_final: 0.8090 (mmt-90) REVERT: A 632 MET cc_start: 0.8537 (mtm) cc_final: 0.7907 (mtp) REVERT: A 640 MET cc_start: 0.9582 (tpp) cc_final: 0.8661 (tpp) REVERT: A 659 LYS cc_start: 0.9040 (mmmt) cc_final: 0.8586 (mmtt) REVERT: B 21 ASP cc_start: 0.8829 (m-30) cc_final: 0.8482 (t0) REVERT: B 27 ASP cc_start: 0.8830 (p0) cc_final: 0.8447 (p0) REVERT: B 28 LYS cc_start: 0.9278 (mmtt) cc_final: 0.8933 (mmmm) REVERT: B 65 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8493 (mm-30) REVERT: B 99 LYS cc_start: 0.9482 (mmmm) cc_final: 0.9264 (mmmm) REVERT: B 119 GLU cc_start: 0.8713 (mp0) cc_final: 0.8384 (mp0) REVERT: B 161 ARG cc_start: 0.9024 (mmm-85) cc_final: 0.8659 (mmm-85) REVERT: B 181 ASP cc_start: 0.9023 (OUTLIER) cc_final: 0.8390 (t0) REVERT: B 257 ASP cc_start: 0.8805 (m-30) cc_final: 0.8328 (m-30) REVERT: B 286 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.7881 (m-30) REVERT: B 314 MET cc_start: 0.9181 (tmm) cc_final: 0.8971 (ttt) REVERT: B 319 MET cc_start: 0.8949 (ttm) cc_final: 0.8678 (tmm) REVERT: B 335 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7946 (mt-10) REVERT: B 362 ASP cc_start: 0.8677 (m-30) cc_final: 0.7646 (m-30) REVERT: B 374 SER cc_start: 0.9308 (t) cc_final: 0.9001 (t) REVERT: B 440 SER cc_start: 0.9573 (OUTLIER) cc_final: 0.9210 (p) REVERT: B 471 TYR cc_start: 0.9201 (t80) cc_final: 0.8726 (t80) REVERT: B 493 MET cc_start: 0.9654 (tmm) cc_final: 0.8891 (tmm) REVERT: B 515 ASP cc_start: 0.8926 (m-30) cc_final: 0.8692 (m-30) REVERT: B 548 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8058 (mm-30) REVERT: B 610 LYS cc_start: 0.9004 (mmmt) cc_final: 0.8791 (mmmt) REVERT: B 628 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8495 (mm-30) REVERT: C 20 MET cc_start: 0.8932 (tpp) cc_final: 0.8508 (tmm) REVERT: C 29 PHE cc_start: 0.8140 (t80) cc_final: 0.7784 (t80) REVERT: C 69 GLN cc_start: 0.8999 (tp40) cc_final: 0.8342 (tm-30) REVERT: C 80 HIS cc_start: 0.8840 (m90) cc_final: 0.8485 (m90) REVERT: C 96 MET cc_start: 0.8558 (mmt) cc_final: 0.8105 (mmm) REVERT: C 105 TYR cc_start: 0.9045 (m-10) cc_final: 0.8811 (m-10) REVERT: C 145 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7785 (tp) REVERT: C 164 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8797 (tp30) REVERT: C 169 TYR cc_start: 0.8779 (m-80) cc_final: 0.8552 (m-80) REVERT: C 178 PHE cc_start: 0.9465 (m-80) cc_final: 0.8754 (m-10) REVERT: C 186 GLN cc_start: 0.9272 (mm110) cc_final: 0.8824 (mp10) REVERT: C 229 ILE cc_start: 0.8392 (mm) cc_final: 0.8032 (mm) REVERT: C 259 PHE cc_start: 0.8975 (t80) cc_final: 0.8539 (t80) REVERT: C 268 LEU cc_start: 0.8782 (tp) cc_final: 0.8524 (tp) REVERT: C 269 MET cc_start: 0.9021 (ppp) cc_final: 0.8805 (ppp) REVERT: C 270 ASN cc_start: 0.8585 (m110) cc_final: 0.8239 (m110) REVERT: C 316 LYS cc_start: 0.9284 (mmtt) cc_final: 0.9002 (mmtt) REVERT: D 17 PHE cc_start: 0.7999 (m-80) cc_final: 0.7430 (m-10) REVERT: D 21 PHE cc_start: 0.9253 (m-80) cc_final: 0.8903 (m-10) REVERT: D 30 TRP cc_start: 0.8696 (p-90) cc_final: 0.8052 (p-90) REVERT: D 96 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8140 (mmm) REVERT: D 109 PHE cc_start: 0.7275 (m-80) cc_final: 0.6494 (m-80) REVERT: D 153 LEU cc_start: 0.9117 (tp) cc_final: 0.8914 (mt) REVERT: D 186 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8455 (mp10) REVERT: D 207 LEU cc_start: 0.9096 (mm) cc_final: 0.8766 (mm) REVERT: D 210 GLN cc_start: 0.9347 (tm-30) cc_final: 0.9034 (pt0) REVERT: D 240 LEU cc_start: 0.8676 (mt) cc_final: 0.8091 (pp) REVERT: D 246 LEU cc_start: 0.7679 (tp) cc_final: 0.7290 (mt) REVERT: D 247 TYR cc_start: 0.8847 (m-10) cc_final: 0.8463 (m-10) REVERT: D 252 LEU cc_start: 0.6281 (mt) cc_final: 0.6072 (mm) REVERT: D 269 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7819 (ppp) outliers start: 58 outliers final: 40 residues processed: 685 average time/residue: 0.1142 time to fit residues: 120.6810 Evaluate side-chains 690 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 640 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 0.4980 chunk 148 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 34 optimal weight: 0.0870 chunk 13 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 ASN B 19 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 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 = 0.3657 r_free = 0.3657 target = 0.126430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.091490 restraints weight = 35715.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.095036 restraints weight = 17347.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.097315 restraints weight = 10460.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.098889 restraints weight = 7261.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.099932 restraints weight = 5545.573| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.7879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16386 Z= 0.155 Angle : 0.860 16.506 22134 Z= 0.420 Chirality : 0.048 0.263 2360 Planarity : 0.004 0.040 2818 Dihedral : 8.548 140.365 2294 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.86 % Allowed : 36.01 % Favored : 61.13 % 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: 0.26 (0.19), residues: 1932 helix: 0.61 (0.15), residues: 1149 sheet: -0.48 (0.44), residues: 152 loop : -0.24 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 502 TYR 0.023 0.001 TYR D 46 PHE 0.035 0.002 PHE B 74 TRP 0.023 0.001 TRP D 44 HIS 0.005 0.001 HIS D 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (16386) covalent geometry : angle 0.86026 / 0.42 (22134) hydrogen bonds : bond 0.04221 / 2.69 ( 871) hydrogen bonds : angle 5.23390 / 3.77 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3357.57 seconds wall clock time: 58 minutes 50.83 seconds (3530.83 seconds total)