Starting phenix.real_space_refine on Thu Aug 6 15:05:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzi_45068/08_2026/9bzi_45068_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzi_45068/08_2026/9bzi_45068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bzi_45068/08_2026/9bzi_45068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzi_45068/08_2026/9bzi_45068.map" model { file = "/net/cci-nas-00/data/ceres_data/9bzi_45068/08_2026/9bzi_45068_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzi_45068/08_2026/9bzi_45068_neut.cif" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 3.04, per 1000 atoms: 0.19 Number of scatterers: 16038 At special positions: 0 Unit cell: (96.33, 140.946, 130.806, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 621.8 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: 0.33 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: 3.986A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.953A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.664A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.575A 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: 3.693A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.628A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A 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: 4.073A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.579A 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: 3.676A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.878A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.645A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.729A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.027A 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: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.668A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.643A 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: 6.200A 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: 6.479A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.499A 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: 7.229A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.048A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A 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: 6.548A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A 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: 2.67 Time building geometry restraints manager: 1.29 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: 4853 1.34 - 1.46: 3064 1.46 - 1.58: 8288 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" O3B TTP A 803 " pdb=" PG TTP A 803 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.81e+01 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 4.80e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.061 1.25e-02 6.40e+03 2.37e+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 1.14e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 21529 2.10 - 4.19: 524 4.19 - 6.29: 64 6.29 - 8.39: 8 8.39 - 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 110.54 116.64 -6.10 1.36e+00 5.41e-01 2.01e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.15 -4.44 1.15e+00 7.56e-01 1.49e+01 angle pdb=" N SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.25 -3.97 1.09e+00 8.42e-01 1.33e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.84 -4.34 1.23e+00 6.61e-01 1.25e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.69 -3.98 1.15e+00 7.56e-01 1.20e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.05: 9093 25.05 - 50.09: 651 50.09 - 75.14: 126 75.14 - 100.19: 26 100.19 - 125.24: 2 Dihedral angle restraints: 9898 sinusoidal: 4140 harmonic: 5758 Sorted by residual: dihedral pdb=" O4' GDP A 802 " pdb=" C1' GDP A 802 " pdb=" N9 GDP A 802 " pdb=" C8 GDP A 802 " ideal model delta sinusoidal sigma weight residual 27.02 -98.21 125.24 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 -95.62 122.64 1 2.00e+01 2.50e-03 3.69e+01 dihedral pdb=" C VAL C 125 " pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual -122.00 -134.29 12.29 0 2.50e+00 1.60e-01 2.42e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2145 0.094 - 0.188: 182 0.188 - 0.282: 29 0.282 - 0.376: 2 0.376 - 0.470: 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 5.53e+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 4.66e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.70e+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 " 0.018 2.00e-02 2.50e+03 1.12e-02 2.20e+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 9.95e-03 1.98e+00 pdb=" CG TYR C 169 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 169 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 169 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 169 " 0.002 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: 129 2.51 - 3.11: 11556 3.11 - 3.70: 27051 3.70 - 4.30: 41551 4.30 - 4.90: 65481 Nonbonded interactions: 145768 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.012 3.040 ... (remaining 145763 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 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: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 12.860 Find NCS groups from input model: 0.230 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: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 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 10.483 22134 Z= 0.472 Chirality : 0.058 0.470 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.634 125.236 6202 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.34 % Allowed : 15.27 % Favored : 83.39 % 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 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.33 (16386) covalent geometry : angle 0.78758 / 0.47 (22134) hydrogen bonds : bond 0.15420 / 9.51 ( 871) hydrogen bonds : angle 6.51778 / 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 1108 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 1085 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8512 (mmtm) cc_final: 0.8195 (mtpp) REVERT: A 76 ASP cc_start: 0.8314 (m-30) cc_final: 0.7600 (m-30) REVERT: A 172 LEU cc_start: 0.8973 (mp) cc_final: 0.8508 (mp) REVERT: A 177 ASP cc_start: 0.8139 (t0) cc_final: 0.7845 (t0) REVERT: A 188 ILE cc_start: 0.8410 (mt) cc_final: 0.8066 (mt) REVERT: A 192 LEU cc_start: 0.9025 (mt) cc_final: 0.8774 (mt) REVERT: A 202 ASN cc_start: 0.9096 (t0) cc_final: 0.8841 (t0) REVERT: A 258 ILE cc_start: 0.8947 (tp) cc_final: 0.8697 (tp) REVERT: A 349 LEU cc_start: 0.8369 (mt) cc_final: 0.8146 (mt) REVERT: A 385 VAL cc_start: 0.8658 (t) cc_final: 0.8370 (t) REVERT: A 391 VAL cc_start: 0.9431 (p) cc_final: 0.9198 (p) REVERT: A 407 ILE cc_start: 0.8631 (mt) cc_final: 0.8200 (mt) REVERT: A 420 MET cc_start: 0.7021 (mmm) cc_final: 0.6674 (mmm) REVERT: A 485 ARG cc_start: 0.7711 (mtm-85) cc_final: 0.7485 (mtm-85) REVERT: A 501 GLN cc_start: 0.8151 (tt0) cc_final: 0.7764 (tt0) REVERT: A 546 LEU cc_start: 0.8784 (mt) cc_final: 0.8562 (mt) REVERT: A 550 MET cc_start: 0.6690 (mtm) cc_final: 0.6082 (mtm) REVERT: A 590 SER cc_start: 0.8929 (p) cc_final: 0.8282 (p) REVERT: A 631 ASP cc_start: 0.7860 (m-30) cc_final: 0.7412 (m-30) REVERT: B 118 TYR cc_start: 0.7321 (t80) cc_final: 0.7008 (t80) REVERT: B 122 ILE cc_start: 0.8631 (mt) cc_final: 0.8430 (mt) REVERT: B 191 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8224 (mm-40) REVERT: B 192 LEU cc_start: 0.9085 (mt) cc_final: 0.8857 (mt) REVERT: B 204 SER cc_start: 0.8867 (m) cc_final: 0.8149 (t) REVERT: B 226 VAL cc_start: 0.8791 (t) cc_final: 0.8582 (t) REVERT: B 265 LYS cc_start: 0.8645 (mmtt) cc_final: 0.8295 (mmmt) REVERT: B 286 ASP cc_start: 0.6672 (OUTLIER) cc_final: 0.6449 (m-30) REVERT: B 358 ILE cc_start: 0.8977 (mm) cc_final: 0.8719 (mm) REVERT: B 366 LYS cc_start: 0.8571 (ptpp) cc_final: 0.8221 (ttpp) REVERT: B 378 PHE cc_start: 0.8476 (p90) cc_final: 0.8115 (p90) REVERT: B 384 GLU cc_start: 0.8921 (pm20) cc_final: 0.8626 (pm20) REVERT: B 458 MET cc_start: 0.8141 (mmm) cc_final: 0.7834 (tpp) REVERT: B 468 LEU cc_start: 0.8484 (tp) cc_final: 0.8145 (tp) REVERT: B 471 TYR cc_start: 0.8185 (t80) cc_final: 0.7850 (t80) REVERT: B 546 LEU cc_start: 0.8826 (mt) cc_final: 0.8281 (mt) REVERT: B 583 SER cc_start: 0.6929 (m) cc_final: 0.6561 (t) REVERT: B 645 GLN cc_start: 0.8235 (tp-100) cc_final: 0.7984 (tp40) REVERT: B 650 GLN cc_start: 0.8332 (mt0) cc_final: 0.7615 (mt0) REVERT: B 670 ILE cc_start: 0.9064 (mt) cc_final: 0.8820 (mt) REVERT: B 687 THR cc_start: 0.7737 (m) cc_final: 0.7350 (p) REVERT: C 95 MET cc_start: 0.5372 (tmm) cc_final: 0.4514 (tmm) REVERT: C 131 LEU cc_start: 0.5653 (OUTLIER) cc_final: 0.5418 (tp) REVERT: C 153 LEU cc_start: 0.6621 (tp) cc_final: 0.6015 (tp) REVERT: C 155 LYS cc_start: 0.7675 (mttt) cc_final: 0.7442 (mmtt) REVERT: C 174 TYR cc_start: 0.4327 (OUTLIER) cc_final: 0.3652 (t80) REVERT: D 17 PHE cc_start: 0.6374 (p90) cc_final: 0.6076 (p90) REVERT: D 43 THR cc_start: 0.7141 (p) cc_final: 0.6894 (p) REVERT: D 89 VAL cc_start: 0.7381 (t) cc_final: 0.6656 (t) REVERT: D 178 PHE cc_start: 0.6753 (m-80) cc_final: 0.5555 (m-80) REVERT: D 265 ASN cc_start: 0.4532 (m-40) cc_final: 0.3794 (m110) outliers start: 23 outliers final: 7 residues processed: 1094 average time/residue: 0.1245 time to fit residues: 197.6790 Evaluate side-chains 716 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 706 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 216 VAL 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 131 LEU 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: 5.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 239 GLN A 304 HIS A 370 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN B 61 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 304 HIS B 329 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 127 GLN C 234 GLN C 263 ASN D 25 ASN D 71 ASN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.119921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.090423 restraints weight = 41093.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.093823 restraints weight = 21361.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.096158 restraints weight = 13379.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.097832 restraints weight = 9304.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.099022 restraints weight = 7037.333| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3216 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (16 function evaluations) r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4541 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= 0.179 Angle : 0.730 14.480 22134 Z= 0.385 Chirality : 0.047 0.190 2360 Planarity : 0.004 0.043 2818 Dihedral : 9.798 128.175 2306 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 4.25 % Allowed : 21.62 % Favored : 74.13 % 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: 1.23 (0.19), residues: 1932 helix: 1.23 (0.15), residues: 1130 sheet: 0.22 (0.42), residues: 126 loop : 0.42 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 243 TYR 0.021 0.002 TYR B 527 PHE 0.033 0.003 PHE D 172 TRP 0.022 0.003 TRP C 30 HIS 0.011 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (16386) covalent geometry : angle 0.73027 / 0.38 (22134) hydrogen bonds : bond 0.04911 / 3.12 ( 871) hydrogen bonds : angle 5.26276 / 3.77 ( 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 856 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 783 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8834 (tppt) cc_final: 0.8434 (tppt) REVERT: A 76 ASP cc_start: 0.9010 (m-30) cc_final: 0.8341 (m-30) REVERT: A 156 PHE cc_start: 0.9309 (t80) cc_final: 0.9055 (t80) REVERT: A 174 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7458 (mt-10) REVERT: A 191 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8275 (mm-40) REVERT: A 232 ASN cc_start: 0.9344 (OUTLIER) cc_final: 0.9040 (m-40) REVERT: A 250 TYR cc_start: 0.8773 (m-80) cc_final: 0.8471 (m-80) REVERT: A 255 HIS cc_start: 0.8861 (t-90) cc_final: 0.8072 (t-90) REVERT: A 257 ASP cc_start: 0.9203 (m-30) cc_final: 0.8934 (m-30) REVERT: A 291 LEU cc_start: 0.9557 (mt) cc_final: 0.9269 (mt) REVERT: A 335 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7927 (mt-10) REVERT: A 378 PHE cc_start: 0.8945 (p90) cc_final: 0.8598 (p90) REVERT: A 415 ASN cc_start: 0.9182 (t0) cc_final: 0.8768 (t0) REVERT: A 436 LEU cc_start: 0.9385 (mt) cc_final: 0.8973 (mt) REVERT: A 447 ASN cc_start: 0.8375 (m-40) cc_final: 0.7716 (t0) REVERT: A 471 TYR cc_start: 0.8910 (t80) cc_final: 0.8420 (t80) REVERT: A 505 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8583 (pt0) REVERT: A 515 ASP cc_start: 0.9035 (m-30) cc_final: 0.8668 (m-30) REVERT: A 546 LEU cc_start: 0.9729 (mt) cc_final: 0.9403 (mt) REVERT: A 595 MET cc_start: 0.9252 (mmp) cc_final: 0.8945 (mmp) REVERT: A 615 MET cc_start: 0.9205 (mmt) cc_final: 0.8869 (mmm) REVERT: A 640 MET cc_start: 0.9101 (tpp) cc_final: 0.8847 (tpp) REVERT: A 645 GLN cc_start: 0.8608 (tp40) cc_final: 0.8246 (tp-100) REVERT: A 648 ILE cc_start: 0.9577 (mm) cc_final: 0.9182 (mm) REVERT: B 18 ILE cc_start: 0.9623 (mp) cc_final: 0.9336 (pt) REVERT: B 82 LYS cc_start: 0.9588 (mtpp) cc_final: 0.9289 (ptpp) REVERT: B 95 MET cc_start: 0.9030 (tpt) cc_final: 0.8718 (tpp) REVERT: B 99 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8571 (tptp) REVERT: B 102 ASN cc_start: 0.9415 (m110) cc_final: 0.9117 (m110) REVERT: B 107 LYS cc_start: 0.9329 (mttt) cc_final: 0.9127 (mmmm) REVERT: B 112 LYS cc_start: 0.9149 (pptt) cc_final: 0.8853 (pttm) REVERT: B 184 ARG cc_start: 0.9454 (tpp80) cc_final: 0.9075 (tpp80) REVERT: B 227 MET cc_start: 0.9236 (mtt) cc_final: 0.8981 (mtt) REVERT: B 322 MET cc_start: 0.9129 (mmm) cc_final: 0.8765 (mmt) REVERT: B 378 PHE cc_start: 0.9144 (p90) cc_final: 0.8874 (p90) REVERT: B 393 SER cc_start: 0.9349 (m) cc_final: 0.8800 (p) REVERT: B 399 GLU cc_start: 0.8932 (tp30) cc_final: 0.8596 (mm-30) REVERT: B 402 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7523 (tm-30) REVERT: B 471 TYR cc_start: 0.9272 (t80) cc_final: 0.8903 (t80) REVERT: B 475 ASN cc_start: 0.9096 (m-40) cc_final: 0.8666 (m110) REVERT: B 515 ASP cc_start: 0.9193 (m-30) cc_final: 0.8729 (m-30) REVERT: B 550 MET cc_start: 0.7778 (mtp) cc_final: 0.7530 (mtp) REVERT: B 558 TRP cc_start: 0.9262 (m100) cc_final: 0.8679 (m100) REVERT: B 570 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.7884 (mtm) REVERT: B 583 SER cc_start: 0.8828 (m) cc_final: 0.8287 (p) REVERT: B 620 SER cc_start: 0.9359 (OUTLIER) cc_final: 0.9113 (p) REVERT: B 632 MET cc_start: 0.8512 (mtm) cc_final: 0.8296 (mtm) REVERT: B 645 GLN cc_start: 0.9241 (tp-100) cc_final: 0.8832 (tp40) REVERT: C 21 PHE cc_start: 0.9313 (m-80) cc_final: 0.8891 (m-80) REVERT: C 30 TRP cc_start: 0.7523 (p-90) cc_final: 0.6919 (t60) REVERT: C 90 LEU cc_start: 0.8973 (mt) cc_final: 0.8648 (mt) REVERT: C 92 PHE cc_start: 0.9420 (t80) cc_final: 0.8454 (t80) REVERT: C 93 MET cc_start: 0.9390 (mtt) cc_final: 0.9008 (mtt) REVERT: C 95 MET cc_start: 0.9102 (tmm) cc_final: 0.8704 (tmm) REVERT: C 96 MET cc_start: 0.9119 (mmm) cc_final: 0.8122 (mmm) REVERT: C 101 HIS cc_start: 0.8953 (m170) cc_final: 0.8525 (m170) REVERT: C 109 PHE cc_start: 0.8392 (m-10) cc_final: 0.8144 (m-10) REVERT: C 130 TYR cc_start: 0.9614 (m-80) cc_final: 0.9342 (m-10) REVERT: C 145 ILE cc_start: 0.7481 (tp) cc_final: 0.7000 (tp) REVERT: C 155 LYS cc_start: 0.8723 (mttt) cc_final: 0.8285 (mmtt) REVERT: C 157 MET cc_start: 0.9250 (mtt) cc_final: 0.8991 (mtt) REVERT: C 173 TYR cc_start: 0.8448 (t80) cc_final: 0.7899 (t80) REVERT: C 174 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.7810 (t80) REVERT: C 197 ASP cc_start: 0.9471 (m-30) cc_final: 0.9115 (m-30) REVERT: C 198 GLU cc_start: 0.9609 (mm-30) cc_final: 0.9250 (mm-30) REVERT: C 201 HIS cc_start: 0.8962 (m-70) cc_final: 0.8709 (m90) REVERT: C 241 GLU cc_start: 0.9575 (mp0) cc_final: 0.9243 (mp0) REVERT: C 242 TYR cc_start: 0.9318 (t80) cc_final: 0.8760 (t80) REVERT: C 259 PHE cc_start: 0.8913 (t80) cc_final: 0.7894 (t80) REVERT: C 263 ASN cc_start: 0.9595 (OUTLIER) cc_final: 0.8549 (p0) REVERT: C 268 LEU cc_start: 0.9531 (mt) cc_final: 0.9218 (mt) REVERT: D 30 TRP cc_start: 0.8085 (p-90) cc_final: 0.7633 (p-90) REVERT: D 50 ASN cc_start: 0.8968 (m-40) cc_final: 0.8471 (p0) REVERT: D 63 THR cc_start: 0.9319 (m) cc_final: 0.9102 (p) REVERT: D 96 MET cc_start: 0.8408 (mmm) cc_final: 0.8127 (mmm) REVERT: D 131 LEU cc_start: 0.8534 (tt) cc_final: 0.8117 (tp) REVERT: D 167 LEU cc_start: 0.9715 (mt) cc_final: 0.9283 (mt) REVERT: D 168 PHE cc_start: 0.8481 (m-80) cc_final: 0.7824 (m-80) REVERT: D 174 TYR cc_start: 0.8760 (t80) cc_final: 0.8326 (t80) REVERT: D 198 GLU cc_start: 0.8590 (pp20) cc_final: 0.8309 (pp20) REVERT: D 254 HIS cc_start: 0.8933 (m90) cc_final: 0.8710 (m-70) outliers start: 73 outliers final: 32 residues processed: 811 average time/residue: 0.1154 time to fit residues: 140.6001 Evaluate side-chains 740 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 702 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain B residue 99 LYS 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 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 427 LYS Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 312 VAL 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: 1.9990 chunk 164 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 182 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 40 optimal weight: 0.0870 chunk 158 optimal weight: 0.7980 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 370 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 338 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 HIS ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN D 71 ASN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 181 GLN ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.118888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.088440 restraints weight = 41437.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.091896 restraints weight = 20791.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.094198 restraints weight = 12969.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.095863 restraints weight = 9064.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.097152 restraints weight = 6914.760| |-----------------------------------------------------------------------------| 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) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.5526 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= 0.166 Angle : 0.710 14.615 22134 Z= 0.367 Chirality : 0.047 0.271 2360 Planarity : 0.004 0.037 2818 Dihedral : 9.298 130.148 2298 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.96 % Allowed : 24.83 % 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: 1.17 (0.18), residues: 1932 helix: 1.28 (0.15), residues: 1106 sheet: 0.72 (0.45), residues: 110 loop : 0.13 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 243 TYR 0.036 0.002 TYR D 142 PHE 0.038 0.002 PHE C 172 TRP 0.011 0.002 TRP C 44 HIS 0.011 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (16386) covalent geometry : angle 0.70958 / 0.37 (22134) hydrogen bonds : bond 0.04511 / 2.88 ( 871) hydrogen bonds : angle 5.23745 / 3.73 ( 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 839 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 771 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ILE cc_start: 0.9097 (mm) cc_final: 0.8883 (mm) REVERT: A 76 ASP cc_start: 0.8926 (m-30) cc_final: 0.8615 (m-30) REVERT: A 138 LYS cc_start: 0.9200 (mmtt) cc_final: 0.8949 (mmtp) REVERT: A 146 ASN cc_start: 0.8788 (m-40) cc_final: 0.8387 (m110) REVERT: A 174 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7541 (mt-10) REVERT: A 211 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7877 (mm-30) REVERT: A 221 LYS cc_start: 0.8924 (mttp) cc_final: 0.8581 (mttm) REVERT: A 232 ASN cc_start: 0.9214 (OUTLIER) cc_final: 0.9004 (m110) REVERT: A 250 TYR cc_start: 0.8841 (m-80) cc_final: 0.8582 (m-80) REVERT: A 294 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8744 (tm-30) REVERT: A 325 LYS cc_start: 0.9563 (mmmt) cc_final: 0.9121 (mmtp) REVERT: A 335 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8054 (mt-10) REVERT: A 360 PHE cc_start: 0.9071 (m-80) cc_final: 0.8786 (m-80) REVERT: A 383 SER cc_start: 0.8916 (p) cc_final: 0.8705 (p) REVERT: A 420 MET cc_start: 0.8854 (mmm) cc_final: 0.8631 (mmm) REVERT: A 447 ASN cc_start: 0.8317 (m-40) cc_final: 0.7684 (t0) REVERT: A 471 TYR cc_start: 0.8916 (t80) cc_final: 0.8441 (t80) REVERT: A 505 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8667 (mt-10) REVERT: A 515 ASP cc_start: 0.9129 (m-30) cc_final: 0.8792 (m-30) REVERT: A 526 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8722 (mp0) REVERT: A 528 PHE cc_start: 0.8943 (m-80) cc_final: 0.8716 (m-80) REVERT: A 546 LEU cc_start: 0.9748 (mt) cc_final: 0.9410 (mt) REVERT: A 550 MET cc_start: 0.6884 (mtm) cc_final: 0.6299 (mtm) REVERT: A 590 SER cc_start: 0.9630 (t) cc_final: 0.8884 (p) REVERT: A 595 MET cc_start: 0.9252 (mmp) cc_final: 0.8851 (mmp) REVERT: A 615 MET cc_start: 0.9293 (mmt) cc_final: 0.8953 (mmm) REVERT: A 645 GLN cc_start: 0.8981 (tp40) cc_final: 0.8340 (tp-100) REVERT: A 648 ILE cc_start: 0.9541 (mm) cc_final: 0.9121 (mm) REVERT: A 650 GLN cc_start: 0.8843 (mt0) cc_final: 0.8355 (mm-40) REVERT: B 8 LYS cc_start: 0.9226 (tptm) cc_final: 0.9009 (tptm) REVERT: B 18 ILE cc_start: 0.9576 (mp) cc_final: 0.9297 (pt) REVERT: B 54 LYS cc_start: 0.9644 (tttt) cc_final: 0.9333 (tttt) REVERT: B 82 LYS cc_start: 0.9602 (mtpp) cc_final: 0.9182 (ptpp) REVERT: B 95 MET cc_start: 0.9116 (tpt) cc_final: 0.8576 (tpp) REVERT: B 99 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.8568 (tptp) REVERT: B 102 ASN cc_start: 0.9497 (m110) cc_final: 0.9204 (m110) REVERT: B 112 LYS cc_start: 0.9233 (pptt) cc_final: 0.8986 (pttm) REVERT: B 181 ASP cc_start: 0.8823 (m-30) cc_final: 0.8561 (m-30) REVERT: B 184 ARG cc_start: 0.9496 (tpp80) cc_final: 0.9262 (tpp80) REVERT: B 232 ASN cc_start: 0.9500 (OUTLIER) cc_final: 0.9137 (m110) REVERT: B 235 ARG cc_start: 0.9125 (mtm110) cc_final: 0.8765 (ptp-110) REVERT: B 236 TYR cc_start: 0.9314 (t80) cc_final: 0.8490 (t80) REVERT: B 263 ASP cc_start: 0.9269 (m-30) cc_final: 0.8898 (m-30) REVERT: B 266 LYS cc_start: 0.9086 (mtpp) cc_final: 0.8793 (mttp) REVERT: B 322 MET cc_start: 0.9259 (mmm) cc_final: 0.8926 (mmt) REVERT: B 335 GLU cc_start: 0.8267 (mt-10) cc_final: 0.8029 (mm-30) REVERT: B 341 LYS cc_start: 0.9619 (mmtm) cc_final: 0.9262 (mmmt) REVERT: B 344 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8887 (pt0) REVERT: B 348 MET cc_start: 0.8720 (tmm) cc_final: 0.8343 (tpt) REVERT: B 362 ASP cc_start: 0.8535 (m-30) cc_final: 0.8148 (m-30) REVERT: B 393 SER cc_start: 0.9311 (m) cc_final: 0.8990 (p) REVERT: B 396 ASP cc_start: 0.8827 (p0) cc_final: 0.8467 (p0) REVERT: B 399 GLU cc_start: 0.9001 (tp30) cc_final: 0.8605 (mm-30) REVERT: B 402 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7531 (tm-30) REVERT: B 471 TYR cc_start: 0.9142 (t80) cc_final: 0.8918 (t80) REVERT: B 475 ASN cc_start: 0.9077 (m-40) cc_final: 0.8695 (m110) REVERT: B 515 ASP cc_start: 0.9215 (m-30) cc_final: 0.8694 (m-30) REVERT: B 548 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7529 (mm-30) REVERT: B 550 MET cc_start: 0.8037 (mtp) cc_final: 0.7834 (mtp) REVERT: B 570 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7503 (ttm) REVERT: B 583 SER cc_start: 0.8947 (m) cc_final: 0.8398 (p) REVERT: B 584 ILE cc_start: 0.9453 (tp) cc_final: 0.9200 (tp) REVERT: B 599 GLU cc_start: 0.9001 (pm20) cc_final: 0.8717 (pm20) REVERT: B 602 GLU cc_start: 0.8396 (pt0) cc_final: 0.8089 (pt0) REVERT: B 604 ARG cc_start: 0.8830 (mmp80) cc_final: 0.8401 (mmt-90) REVERT: B 632 MET cc_start: 0.8461 (mtm) cc_final: 0.8160 (mtm) REVERT: B 645 GLN cc_start: 0.9302 (tp-100) cc_final: 0.8887 (tp40) REVERT: B 668 ASN cc_start: 0.9017 (m110) cc_final: 0.8512 (m-40) REVERT: C 20 MET cc_start: 0.9526 (tmm) cc_final: 0.9183 (tmm) REVERT: C 21 PHE cc_start: 0.9482 (m-80) cc_final: 0.8732 (m-80) REVERT: C 86 ARG cc_start: 0.4588 (mpt180) cc_final: 0.4354 (mpt180) REVERT: C 90 LEU cc_start: 0.9091 (mt) cc_final: 0.8828 (mt) REVERT: C 92 PHE cc_start: 0.9495 (t80) cc_final: 0.9107 (t80) REVERT: C 101 HIS cc_start: 0.8362 (m170) cc_final: 0.7872 (m90) REVERT: C 134 LYS cc_start: 0.9437 (pttm) cc_final: 0.9179 (pttm) REVERT: C 155 LYS cc_start: 0.8820 (mttt) cc_final: 0.8522 (mmtt) REVERT: C 174 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.7907 (t80) REVERT: C 198 GLU cc_start: 0.9297 (mm-30) cc_final: 0.8854 (mm-30) REVERT: C 201 HIS cc_start: 0.9166 (m-70) cc_final: 0.8805 (m-70) REVERT: C 242 TYR cc_start: 0.9485 (t80) cc_final: 0.8836 (t80) REVERT: C 259 PHE cc_start: 0.9056 (t80) cc_final: 0.8535 (t80) REVERT: C 266 LYS cc_start: 0.9424 (mttt) cc_final: 0.8975 (mmmm) REVERT: D 20 MET cc_start: 0.9282 (ppp) cc_final: 0.9050 (ppp) REVERT: D 30 TRP cc_start: 0.8306 (p-90) cc_final: 0.8106 (p-90) REVERT: D 96 MET cc_start: 0.8160 (mmm) cc_final: 0.7871 (mmm) REVERT: D 131 LEU cc_start: 0.8742 (tt) cc_final: 0.8416 (tp) REVERT: D 168 PHE cc_start: 0.8585 (m-80) cc_final: 0.8100 (m-80) REVERT: D 172 PHE cc_start: 0.8789 (m-80) cc_final: 0.8273 (m-80) REVERT: D 174 TYR cc_start: 0.8595 (t80) cc_final: 0.8238 (t80) REVERT: D 242 TYR cc_start: 0.8848 (t80) cc_final: 0.8571 (t80) REVERT: D 254 HIS cc_start: 0.8950 (m90) cc_final: 0.8729 (m-70) REVERT: D 268 LEU cc_start: 0.8889 (mm) cc_final: 0.8673 (mt) REVERT: D 282 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7184 (pt) outliers start: 68 outliers final: 41 residues processed: 796 average time/residue: 0.1276 time to fit residues: 152.7208 Evaluate side-chains 763 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 716 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN 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 267 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 6.9990 chunk 157 optimal weight: 0.7980 chunk 168 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 185 optimal weight: 9.9990 chunk 191 optimal weight: 0.9980 chunk 159 optimal weight: 20.0000 chunk 182 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 127 GLN C 238 ASN C 270 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 210 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.118483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.088206 restraints weight = 41447.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.091585 restraints weight = 21013.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.093881 restraints weight = 13127.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.095536 restraints weight = 9170.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.096746 restraints weight = 6955.728| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16386 Z= 0.173 Angle : 0.718 12.594 22134 Z= 0.368 Chirality : 0.047 0.245 2360 Planarity : 0.004 0.066 2818 Dihedral : 9.084 133.568 2297 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.60 % Allowed : 26.11 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.18), residues: 1932 helix: 1.17 (0.15), residues: 1109 sheet: 0.37 (0.43), residues: 118 loop : 0.15 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 261 TYR 0.028 0.002 TYR D 142 PHE 0.040 0.002 PHE C 168 TRP 0.009 0.002 TRP C 44 HIS 0.010 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (16386) covalent geometry : angle 0.71834 / 0.37 (22134) hydrogen bonds : bond 0.04360 / 2.79 ( 871) hydrogen bonds : angle 5.18799 / 3.67 ( 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 806 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 727 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASP cc_start: 0.9008 (m-30) cc_final: 0.8653 (m-30) REVERT: A 95 MET cc_start: 0.8982 (mmm) cc_final: 0.8657 (tpp) REVERT: A 138 LYS cc_start: 0.9229 (mmtt) cc_final: 0.9021 (mmtp) REVERT: A 144 MET cc_start: 0.8444 (mmp) cc_final: 0.8200 (mmp) REVERT: A 146 ASN cc_start: 0.8770 (m-40) cc_final: 0.8273 (m110) REVERT: A 161 ARG cc_start: 0.8525 (ttm110) cc_final: 0.7702 (ptp-170) REVERT: A 174 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7341 (mt-10) REVERT: A 221 LYS cc_start: 0.8923 (mttp) cc_final: 0.8698 (mttm) REVERT: A 243 ARG cc_start: 0.8397 (ttp80) cc_final: 0.8137 (ppt170) REVERT: A 250 TYR cc_start: 0.8944 (m-80) cc_final: 0.8706 (m-80) REVERT: A 255 HIS cc_start: 0.8759 (t-90) cc_final: 0.8541 (t-90) REVERT: A 335 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8074 (mt-10) REVERT: A 383 SER cc_start: 0.8856 (p) cc_final: 0.8651 (p) REVERT: A 403 ILE cc_start: 0.9158 (mm) cc_final: 0.8904 (mm) REVERT: A 420 MET cc_start: 0.8934 (mmm) cc_final: 0.8638 (mmm) REVERT: A 447 ASN cc_start: 0.8266 (m-40) cc_final: 0.7689 (t0) REVERT: A 471 TYR cc_start: 0.8972 (t80) cc_final: 0.8556 (t80) REVERT: A 493 MET cc_start: 0.8951 (tmm) cc_final: 0.8475 (tmm) REVERT: A 505 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8509 (mt-10) REVERT: A 515 ASP cc_start: 0.9173 (m-30) cc_final: 0.8835 (m-30) REVERT: A 516 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8427 (tp40) REVERT: A 546 LEU cc_start: 0.9719 (mt) cc_final: 0.9413 (mt) REVERT: A 550 MET cc_start: 0.6950 (mtm) cc_final: 0.6542 (mtm) REVERT: A 590 SER cc_start: 0.9532 (t) cc_final: 0.9073 (p) REVERT: A 595 MET cc_start: 0.9253 (mmp) cc_final: 0.8796 (mmp) REVERT: A 600 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7891 (mtt-85) REVERT: A 615 MET cc_start: 0.9313 (mmt) cc_final: 0.8997 (mmm) REVERT: A 639 ASP cc_start: 0.8882 (m-30) cc_final: 0.8174 (m-30) REVERT: A 640 MET cc_start: 0.9334 (tpp) cc_final: 0.8985 (tpp) REVERT: A 645 GLN cc_start: 0.8938 (tp40) cc_final: 0.8489 (tp-100) REVERT: A 650 GLN cc_start: 0.8903 (mt0) cc_final: 0.8386 (mt0) REVERT: A 657 PHE cc_start: 0.9127 (m-80) cc_final: 0.8843 (m-80) REVERT: A 677 ARG cc_start: 0.8863 (mmm160) cc_final: 0.8552 (tpp80) REVERT: B 8 LYS cc_start: 0.9284 (tptm) cc_final: 0.8854 (tppt) REVERT: B 18 ILE cc_start: 0.9616 (mp) cc_final: 0.9368 (pt) REVERT: B 82 LYS cc_start: 0.9606 (mtpp) cc_final: 0.9128 (ptpp) REVERT: B 95 MET cc_start: 0.9130 (tpt) cc_final: 0.8572 (tpp) REVERT: B 99 LYS cc_start: 0.9371 (tptp) cc_final: 0.8691 (tptp) REVERT: B 102 ASN cc_start: 0.9467 (m110) cc_final: 0.9217 (m110) REVERT: B 107 LYS cc_start: 0.9367 (mmmm) cc_final: 0.9060 (mmmm) REVERT: B 232 ASN cc_start: 0.9463 (OUTLIER) cc_final: 0.9262 (m110) REVERT: B 235 ARG cc_start: 0.9178 (mtm110) cc_final: 0.8809 (ptp-110) REVERT: B 236 TYR cc_start: 0.9317 (t80) cc_final: 0.8397 (t80) REVERT: B 257 ASP cc_start: 0.8829 (m-30) cc_final: 0.8491 (m-30) REVERT: B 263 ASP cc_start: 0.9245 (m-30) cc_final: 0.8765 (m-30) REVERT: B 266 LYS cc_start: 0.9105 (mtpp) cc_final: 0.8449 (mttm) REVERT: B 274 ARG cc_start: 0.8642 (ttm110) cc_final: 0.8277 (ttm170) REVERT: B 322 MET cc_start: 0.9299 (mmm) cc_final: 0.8959 (mmt) REVERT: B 333 LYS cc_start: 0.9137 (tttm) cc_final: 0.8611 (tttm) REVERT: B 335 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8174 (mm-30) REVERT: B 341 LYS cc_start: 0.9644 (mmtm) cc_final: 0.9330 (mmmt) REVERT: B 344 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8757 (pt0) REVERT: B 348 MET cc_start: 0.8794 (tmm) cc_final: 0.8398 (tpt) REVERT: B 362 ASP cc_start: 0.8571 (m-30) cc_final: 0.8321 (m-30) REVERT: B 393 SER cc_start: 0.9302 (m) cc_final: 0.9059 (p) REVERT: B 396 ASP cc_start: 0.8906 (p0) cc_final: 0.8538 (p0) REVERT: B 399 GLU cc_start: 0.8997 (tp30) cc_final: 0.8616 (mm-30) REVERT: B 402 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7716 (tm-30) REVERT: B 475 ASN cc_start: 0.9170 (m-40) cc_final: 0.8836 (m110) REVERT: B 483 GLU cc_start: 0.9464 (mp0) cc_final: 0.9138 (mp0) REVERT: B 515 ASP cc_start: 0.9203 (m-30) cc_final: 0.8664 (m-30) REVERT: B 522 TYR cc_start: 0.8844 (m-10) cc_final: 0.8625 (m-10) REVERT: B 548 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7713 (mm-30) REVERT: B 558 TRP cc_start: 0.9566 (m100) cc_final: 0.8800 (m100) REVERT: B 570 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.7060 (mtm) REVERT: B 573 SER cc_start: 0.9625 (OUTLIER) cc_final: 0.9346 (p) REVERT: B 583 SER cc_start: 0.9024 (m) cc_final: 0.8532 (p) REVERT: B 645 GLN cc_start: 0.9413 (tp40) cc_final: 0.8921 (tp40) REVERT: B 668 ASN cc_start: 0.9128 (m110) cc_final: 0.8718 (m-40) REVERT: B 686 ARG cc_start: 0.8370 (ttm170) cc_final: 0.7998 (mpt-90) REVERT: C 20 MET cc_start: 0.9532 (tmm) cc_final: 0.9167 (tmm) REVERT: C 21 PHE cc_start: 0.9520 (m-80) cc_final: 0.8799 (m-80) REVERT: C 55 TYR cc_start: 0.8843 (t80) cc_final: 0.8121 (m-10) REVERT: C 74 MET cc_start: 0.8927 (mtt) cc_final: 0.8639 (mtt) REVERT: C 90 LEU cc_start: 0.9184 (mt) cc_final: 0.8606 (mt) REVERT: C 92 PHE cc_start: 0.9513 (t80) cc_final: 0.8843 (t80) REVERT: C 96 MET cc_start: 0.9392 (mmm) cc_final: 0.8659 (mmm) REVERT: C 134 LYS cc_start: 0.9464 (pttm) cc_final: 0.9176 (pttm) REVERT: C 155 LYS cc_start: 0.9025 (mttt) cc_final: 0.8671 (mmtt) REVERT: C 174 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.7286 (t80) REVERT: C 204 TYR cc_start: 0.8987 (t80) cc_final: 0.8766 (t80) REVERT: C 242 TYR cc_start: 0.9549 (t80) cc_final: 0.8722 (t80) REVERT: C 259 PHE cc_start: 0.9059 (t80) cc_final: 0.8782 (t80) REVERT: C 269 MET cc_start: 0.9620 (ptt) cc_final: 0.9197 (mmt) REVERT: C 274 ASP cc_start: 0.8338 (p0) cc_final: 0.7754 (p0) REVERT: C 309 LYS cc_start: 0.6642 (pptt) cc_final: 0.6119 (ttpp) REVERT: D 30 TRP cc_start: 0.8274 (p-90) cc_final: 0.7959 (p-90) REVERT: D 51 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7450 (mm-30) REVERT: D 96 MET cc_start: 0.8210 (mmm) cc_final: 0.7840 (mmm) REVERT: D 131 LEU cc_start: 0.8896 (tt) cc_final: 0.8584 (tp) REVERT: D 155 LYS cc_start: 0.8038 (mttt) cc_final: 0.7639 (mtmm) REVERT: D 168 PHE cc_start: 0.8668 (m-80) cc_final: 0.7665 (m-80) REVERT: D 169 TYR cc_start: 0.8197 (m-80) cc_final: 0.7413 (m-80) REVERT: D 174 TYR cc_start: 0.8658 (t80) cc_final: 0.8246 (t80) REVERT: D 242 TYR cc_start: 0.8833 (t80) cc_final: 0.8517 (t80) REVERT: D 268 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8492 (mp) REVERT: D 282 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7467 (mm) outliers start: 79 outliers final: 45 residues processed: 760 average time/residue: 0.1270 time to fit residues: 145.3250 Evaluate side-chains 718 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 666 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 37 optimal weight: 0.3980 chunk 126 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 157 optimal weight: 0.7980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN B 158 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 210 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.116300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.087447 restraints weight = 41522.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.090523 restraints weight = 21267.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.092736 restraints weight = 13499.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.094318 restraints weight = 9457.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.095477 restraints weight = 7163.517| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.6534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16386 Z= 0.160 Angle : 0.716 13.483 22134 Z= 0.367 Chirality : 0.047 0.261 2360 Planarity : 0.004 0.037 2818 Dihedral : 8.915 135.225 2297 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.31 % Allowed : 27.86 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.18), residues: 1932 helix: 1.13 (0.15), residues: 1112 sheet: 0.15 (0.44), residues: 114 loop : 0.16 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 604 TYR 0.046 0.002 TYR D 142 PHE 0.040 0.002 PHE C 168 TRP 0.009 0.001 TRP D 44 HIS 0.010 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (16386) covalent geometry : angle 0.71562 / 0.37 (22134) hydrogen bonds : bond 0.04286 / 2.70 ( 871) hydrogen bonds : angle 5.18085 / 3.66 ( 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 782 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 708 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASP cc_start: 0.9030 (m-30) cc_final: 0.8637 (m-30) REVERT: A 82 LYS cc_start: 0.9503 (mttm) cc_final: 0.9224 (mmtt) REVERT: A 95 MET cc_start: 0.8901 (mmm) cc_final: 0.8503 (tpp) REVERT: A 138 LYS cc_start: 0.9262 (mmtt) cc_final: 0.8960 (mmtp) REVERT: A 150 GLN cc_start: 0.9506 (tp40) cc_final: 0.8730 (tm-30) REVERT: A 161 ARG cc_start: 0.8423 (ttm110) cc_final: 0.7760 (ptp-170) REVERT: A 174 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7450 (mt-10) REVERT: A 221 LYS cc_start: 0.8902 (mttp) cc_final: 0.8643 (mttm) REVERT: A 375 LYS cc_start: 0.8688 (mmtp) cc_final: 0.8476 (mmtm) REVERT: A 383 SER cc_start: 0.8914 (p) cc_final: 0.8702 (p) REVERT: A 403 ILE cc_start: 0.9204 (mm) cc_final: 0.8988 (mm) REVERT: A 420 MET cc_start: 0.8879 (mmm) cc_final: 0.8538 (mmm) REVERT: A 447 ASN cc_start: 0.7759 (m-40) cc_final: 0.7472 (t0) REVERT: A 471 TYR cc_start: 0.9028 (t80) cc_final: 0.8618 (t80) REVERT: A 493 MET cc_start: 0.8964 (tmm) cc_final: 0.8528 (tmm) REVERT: A 505 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8292 (mt-10) REVERT: A 515 ASP cc_start: 0.9061 (m-30) cc_final: 0.8747 (m-30) REVERT: A 516 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8365 (tp40) REVERT: A 546 LEU cc_start: 0.9682 (mt) cc_final: 0.9345 (mt) REVERT: A 550 MET cc_start: 0.6959 (mtm) cc_final: 0.6729 (mtm) REVERT: A 590 SER cc_start: 0.9520 (t) cc_final: 0.8943 (p) REVERT: A 595 MET cc_start: 0.9149 (mmp) cc_final: 0.8748 (mmp) REVERT: A 600 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8035 (mtt-85) REVERT: A 639 ASP cc_start: 0.8737 (m-30) cc_final: 0.8038 (m-30) REVERT: A 640 MET cc_start: 0.9435 (tpp) cc_final: 0.8899 (tpp) REVERT: A 645 GLN cc_start: 0.8991 (tp40) cc_final: 0.8501 (tp-100) REVERT: A 657 PHE cc_start: 0.9008 (m-80) cc_final: 0.8806 (m-80) REVERT: A 677 ARG cc_start: 0.8894 (mmm160) cc_final: 0.8537 (tpp80) REVERT: B 8 LYS cc_start: 0.9229 (tptm) cc_final: 0.9009 (tptm) REVERT: B 82 LYS cc_start: 0.9552 (mtpp) cc_final: 0.9057 (ptpp) REVERT: B 95 MET cc_start: 0.9020 (tpt) cc_final: 0.8478 (tpp) REVERT: B 99 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.8782 (tptp) REVERT: B 102 ASN cc_start: 0.9478 (m110) cc_final: 0.9246 (m110) REVERT: B 168 VAL cc_start: 0.9332 (t) cc_final: 0.9056 (m) REVERT: B 181 ASP cc_start: 0.8835 (m-30) cc_final: 0.8510 (m-30) REVERT: B 236 TYR cc_start: 0.9234 (t80) cc_final: 0.8266 (t80) REVERT: B 263 ASP cc_start: 0.9111 (m-30) cc_final: 0.8638 (m-30) REVERT: B 266 LYS cc_start: 0.9053 (mtpp) cc_final: 0.8448 (mttm) REVERT: B 274 ARG cc_start: 0.8607 (ttm110) cc_final: 0.8297 (ttm170) REVERT: B 322 MET cc_start: 0.9209 (mmm) cc_final: 0.8845 (mmt) REVERT: B 341 LYS cc_start: 0.9578 (mmtm) cc_final: 0.9257 (mmmt) REVERT: B 344 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8483 (pt0) REVERT: B 348 MET cc_start: 0.8661 (tmm) cc_final: 0.8290 (tpt) REVERT: B 362 ASP cc_start: 0.8493 (m-30) cc_final: 0.8260 (m-30) REVERT: B 387 GLN cc_start: 0.8190 (mp10) cc_final: 0.7970 (mm-40) REVERT: B 393 SER cc_start: 0.9315 (m) cc_final: 0.9071 (p) REVERT: B 396 ASP cc_start: 0.8852 (p0) cc_final: 0.8486 (p0) REVERT: B 399 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8510 (mm-30) REVERT: B 402 GLU cc_start: 0.8404 (tm-30) cc_final: 0.7828 (tm-30) REVERT: B 471 TYR cc_start: 0.9158 (t80) cc_final: 0.8813 (t80) REVERT: B 475 ASN cc_start: 0.9297 (m-40) cc_final: 0.8866 (m-40) REVERT: B 500 ILE cc_start: 0.9696 (OUTLIER) cc_final: 0.9373 (tp) REVERT: B 515 ASP cc_start: 0.9102 (m-30) cc_final: 0.8656 (m-30) REVERT: B 548 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7598 (mm-30) REVERT: B 558 TRP cc_start: 0.9465 (m100) cc_final: 0.8662 (m100) REVERT: B 561 LEU cc_start: 0.9688 (tp) cc_final: 0.9480 (tt) REVERT: B 583 SER cc_start: 0.9010 (m) cc_final: 0.8374 (p) REVERT: B 610 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8514 (ptmm) REVERT: B 632 MET cc_start: 0.8109 (mtm) cc_final: 0.7827 (mtt) REVERT: B 645 GLN cc_start: 0.9385 (tp40) cc_final: 0.9000 (tp40) REVERT: B 668 ASN cc_start: 0.9048 (m110) cc_final: 0.8531 (m110) REVERT: B 683 TYR cc_start: 0.8905 (t80) cc_final: 0.8440 (t80) REVERT: B 684 TYR cc_start: 0.7696 (OUTLIER) cc_final: 0.7442 (m-80) REVERT: C 20 MET cc_start: 0.9459 (tmm) cc_final: 0.9106 (tmm) REVERT: C 21 PHE cc_start: 0.9496 (m-80) cc_final: 0.8738 (m-80) REVERT: C 55 TYR cc_start: 0.8825 (t80) cc_final: 0.7914 (m-80) REVERT: C 74 MET cc_start: 0.8851 (mtt) cc_final: 0.8502 (mtt) REVERT: C 86 ARG cc_start: 0.5116 (mpt180) cc_final: 0.4412 (mpt180) REVERT: C 90 LEU cc_start: 0.9208 (mt) cc_final: 0.8678 (mt) REVERT: C 92 PHE cc_start: 0.9533 (t80) cc_final: 0.8956 (t80) REVERT: C 96 MET cc_start: 0.9300 (mmm) cc_final: 0.8489 (mmm) REVERT: C 109 PHE cc_start: 0.8324 (m-10) cc_final: 0.7812 (m-10) REVERT: C 134 LYS cc_start: 0.9456 (pttm) cc_final: 0.9150 (pttt) REVERT: C 143 LYS cc_start: 0.9127 (tptp) cc_final: 0.8902 (tppt) REVERT: C 155 LYS cc_start: 0.9202 (mttt) cc_final: 0.8836 (mmtt) REVERT: C 174 TYR cc_start: 0.7903 (OUTLIER) cc_final: 0.7217 (t80) REVERT: C 194 ILE cc_start: 0.9612 (mt) cc_final: 0.8997 (tp) REVERT: C 198 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8691 (mm-30) REVERT: C 252 LEU cc_start: 0.8459 (pp) cc_final: 0.7852 (tt) REVERT: C 259 PHE cc_start: 0.9088 (t80) cc_final: 0.8361 (t80) REVERT: C 260 ILE cc_start: 0.9026 (pt) cc_final: 0.8661 (pp) REVERT: C 263 ASN cc_start: 0.9681 (m110) cc_final: 0.9426 (p0) REVERT: C 269 MET cc_start: 0.9540 (ptt) cc_final: 0.9207 (mmt) REVERT: C 274 ASP cc_start: 0.8205 (p0) cc_final: 0.7673 (p0) REVERT: D 30 TRP cc_start: 0.8201 (p-90) cc_final: 0.7789 (p-90) REVERT: D 46 TYR cc_start: 0.8954 (m-10) cc_final: 0.8522 (m-10) REVERT: D 96 MET cc_start: 0.8246 (mmm) cc_final: 0.7859 (mmt) REVERT: D 131 LEU cc_start: 0.8959 (tt) cc_final: 0.8638 (tp) REVERT: D 137 MET cc_start: 0.8259 (mmt) cc_final: 0.7627 (mpp) REVERT: D 168 PHE cc_start: 0.8586 (m-80) cc_final: 0.7639 (m-80) REVERT: D 169 TYR cc_start: 0.8205 (m-80) cc_final: 0.7527 (m-80) REVERT: D 174 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.8320 (t80) REVERT: D 242 TYR cc_start: 0.8717 (t80) cc_final: 0.8419 (t80) REVERT: D 268 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8538 (mt) outliers start: 74 outliers final: 50 residues processed: 743 average time/residue: 0.1224 time to fit residues: 136.8413 Evaluate side-chains 719 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 660 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 136 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.120059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.090942 restraints weight = 40708.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.094235 restraints weight = 21296.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.096414 restraints weight = 13431.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.097999 restraints weight = 9499.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.099184 restraints weight = 7272.129| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 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 = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.6919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16386 Z= 0.145 Angle : 0.738 14.185 22134 Z= 0.372 Chirality : 0.047 0.254 2360 Planarity : 0.004 0.037 2818 Dihedral : 8.755 133.669 2297 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.08 % Allowed : 29.31 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.19), residues: 1932 helix: 1.08 (0.15), residues: 1124 sheet: -0.78 (0.39), residues: 162 loop : 0.25 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 350 TYR 0.030 0.001 TYR D 142 PHE 0.039 0.002 PHE C 178 TRP 0.007 0.001 TRP B 9 HIS 0.009 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (16386) covalent geometry : angle 0.73802 / 0.37 (22134) hydrogen bonds : bond 0.04191 / 2.63 ( 871) hydrogen bonds : angle 5.19438 / 3.66 ( 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 789 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 719 time to evaluate : 0.634 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: A 76 ASP cc_start: 0.9026 (m-30) cc_final: 0.8755 (m-30) REVERT: A 87 LYS cc_start: 0.9088 (tptm) cc_final: 0.8804 (ttmt) REVERT: A 95 MET cc_start: 0.8867 (mmm) cc_final: 0.8586 (tpp) REVERT: A 138 LYS cc_start: 0.9241 (mmtt) cc_final: 0.9007 (mmtt) REVERT: A 144 MET cc_start: 0.8301 (mmp) cc_final: 0.8078 (mmp) REVERT: A 150 GLN cc_start: 0.9412 (tp-100) cc_final: 0.9165 (tp-100) REVERT: A 161 ARG cc_start: 0.8490 (ttm110) cc_final: 0.7936 (ptp-170) REVERT: A 174 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7474 (mt-10) REVERT: A 214 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8462 (mmtt) REVERT: A 221 LYS cc_start: 0.8888 (mttp) cc_final: 0.8635 (mttm) REVERT: A 250 TYR cc_start: 0.8765 (m-80) cc_final: 0.8561 (m-10) REVERT: A 255 HIS cc_start: 0.8955 (t-90) cc_final: 0.8637 (t-90) REVERT: A 266 LYS cc_start: 0.8745 (ptmm) cc_final: 0.8186 (ptmm) REVERT: A 290 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8620 (tm-30) REVERT: A 390 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8606 (mm-40) REVERT: A 403 ILE cc_start: 0.9162 (mm) cc_final: 0.8933 (mm) REVERT: A 413 SER cc_start: 0.9462 (m) cc_final: 0.8998 (t) REVERT: A 420 MET cc_start: 0.8972 (mmm) cc_final: 0.8534 (mmm) REVERT: A 443 THR cc_start: 0.8498 (t) cc_final: 0.8294 (t) REVERT: A 447 ASN cc_start: 0.7803 (m-40) cc_final: 0.7577 (t0) REVERT: A 471 TYR cc_start: 0.9067 (t80) cc_final: 0.8730 (t80) REVERT: A 493 MET cc_start: 0.8871 (tmm) cc_final: 0.8415 (tmm) REVERT: A 494 MET cc_start: 0.9090 (mtp) cc_final: 0.8712 (mtp) REVERT: A 505 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8314 (mt-10) REVERT: A 515 ASP cc_start: 0.9075 (m-30) cc_final: 0.8744 (m-30) REVERT: A 516 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8358 (tp40) REVERT: A 546 LEU cc_start: 0.9680 (mt) cc_final: 0.9344 (mt) REVERT: A 590 SER cc_start: 0.9540 (t) cc_final: 0.8971 (p) REVERT: A 600 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8273 (mtt180) REVERT: A 639 ASP cc_start: 0.8750 (m-30) cc_final: 0.7963 (m-30) REVERT: A 640 MET cc_start: 0.9496 (tpp) cc_final: 0.9287 (tpp) REVERT: A 645 GLN cc_start: 0.9015 (tp40) cc_final: 0.8551 (tp-100) REVERT: A 677 ARG cc_start: 0.8922 (mmm160) cc_final: 0.8633 (tpp80) REVERT: B 8 LYS cc_start: 0.9248 (tptm) cc_final: 0.9033 (tptm) REVERT: B 82 LYS cc_start: 0.9546 (mtpp) cc_final: 0.9208 (ptpp) REVERT: B 95 MET cc_start: 0.9017 (tpt) cc_final: 0.8262 (tpp) REVERT: B 99 LYS cc_start: 0.9322 (tptp) cc_final: 0.8793 (tptp) REVERT: B 102 ASN cc_start: 0.9494 (m110) cc_final: 0.9279 (m110) REVERT: B 110 ASP cc_start: 0.9138 (p0) cc_final: 0.8921 (p0) REVERT: B 112 LYS cc_start: 0.9146 (pptt) cc_final: 0.8901 (pttm) REVERT: B 119 GLU cc_start: 0.9026 (mp0) cc_final: 0.8449 (mp0) REVERT: B 181 ASP cc_start: 0.8819 (m-30) cc_final: 0.8414 (m-30) REVERT: B 191 GLN cc_start: 0.9076 (mm-40) cc_final: 0.8723 (mm-40) REVERT: B 235 ARG cc_start: 0.9083 (mtm110) cc_final: 0.8784 (mtm-85) REVERT: B 236 TYR cc_start: 0.9333 (t80) cc_final: 0.8279 (t80) REVERT: B 263 ASP cc_start: 0.9109 (m-30) cc_final: 0.8724 (m-30) REVERT: B 266 LYS cc_start: 0.9104 (mtpp) cc_final: 0.8495 (mttm) REVERT: B 274 ARG cc_start: 0.8638 (ttm110) cc_final: 0.8345 (ttm170) REVERT: B 322 MET cc_start: 0.9306 (mmm) cc_final: 0.8929 (mmt) REVERT: B 333 LYS cc_start: 0.9082 (tttm) cc_final: 0.8737 (tttm) REVERT: B 341 LYS cc_start: 0.9612 (mmtm) cc_final: 0.9259 (mmmt) REVERT: B 344 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8574 (pt0) REVERT: B 348 MET cc_start: 0.8738 (tmm) cc_final: 0.8302 (tpt) REVERT: B 358 ILE cc_start: 0.9650 (mm) cc_final: 0.9199 (tp) REVERT: B 362 ASP cc_start: 0.8579 (m-30) cc_final: 0.8328 (m-30) REVERT: B 387 GLN cc_start: 0.8423 (mp10) cc_final: 0.7667 (mp10) REVERT: B 393 SER cc_start: 0.9251 (m) cc_final: 0.9032 (p) REVERT: B 396 ASP cc_start: 0.8845 (p0) cc_final: 0.8496 (p0) REVERT: B 399 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8578 (mm-30) REVERT: B 402 GLU cc_start: 0.8456 (tm-30) cc_final: 0.7810 (tm-30) REVERT: B 475 ASN cc_start: 0.9260 (m-40) cc_final: 0.8930 (m110) REVERT: B 483 GLU cc_start: 0.9478 (mp0) cc_final: 0.9225 (mp0) REVERT: B 500 ILE cc_start: 0.9705 (OUTLIER) cc_final: 0.9423 (tp) REVERT: B 515 ASP cc_start: 0.9094 (m-30) cc_final: 0.8644 (m-30) REVERT: B 548 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7653 (mm-30) REVERT: B 558 TRP cc_start: 0.9445 (m100) cc_final: 0.8744 (m100) REVERT: B 583 SER cc_start: 0.8999 (m) cc_final: 0.8513 (p) REVERT: B 586 TYR cc_start: 0.9235 (m-80) cc_final: 0.9000 (m-80) REVERT: B 588 GLN cc_start: 0.9319 (mm110) cc_final: 0.9047 (mm-40) REVERT: B 602 GLU cc_start: 0.8554 (pt0) cc_final: 0.5377 (pt0) REVERT: B 610 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8516 (ptmm) REVERT: B 632 MET cc_start: 0.7992 (mtm) cc_final: 0.7716 (mtt) REVERT: B 645 GLN cc_start: 0.9325 (tp40) cc_final: 0.8992 (tp40) REVERT: B 650 GLN cc_start: 0.7994 (mt0) cc_final: 0.7720 (mt0) REVERT: B 668 ASN cc_start: 0.9055 (m110) cc_final: 0.8522 (m110) REVERT: B 683 TYR cc_start: 0.8894 (t80) cc_final: 0.8462 (t80) REVERT: C 20 MET cc_start: 0.9470 (tmm) cc_final: 0.9126 (tmm) REVERT: C 21 PHE cc_start: 0.9548 (m-80) cc_final: 0.8771 (m-80) REVERT: C 74 MET cc_start: 0.8912 (mtt) cc_final: 0.8545 (mtt) REVERT: C 90 LEU cc_start: 0.8982 (mt) cc_final: 0.8779 (mt) REVERT: C 92 PHE cc_start: 0.9619 (t80) cc_final: 0.9108 (t80) REVERT: C 96 MET cc_start: 0.8978 (mmm) cc_final: 0.8464 (mmm) REVERT: C 109 PHE cc_start: 0.8146 (m-10) cc_final: 0.7734 (m-10) REVERT: C 130 TYR cc_start: 0.9571 (m-80) cc_final: 0.9210 (m-10) REVERT: C 134 LYS cc_start: 0.9568 (pttm) cc_final: 0.9365 (pttm) REVERT: C 155 LYS cc_start: 0.9266 (mttt) cc_final: 0.8928 (mmtt) REVERT: C 174 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.7587 (t80) REVERT: C 198 GLU cc_start: 0.9225 (mm-30) cc_final: 0.8660 (mm-30) REVERT: C 242 TYR cc_start: 0.9478 (t80) cc_final: 0.9168 (t80) REVERT: C 259 PHE cc_start: 0.9221 (t80) cc_final: 0.8687 (t80) REVERT: C 260 ILE cc_start: 0.9001 (pt) cc_final: 0.8671 (pp) REVERT: C 269 MET cc_start: 0.9549 (OUTLIER) cc_final: 0.9238 (mmt) REVERT: D 30 TRP cc_start: 0.8104 (p-90) cc_final: 0.7625 (p-90) REVERT: D 71 ASN cc_start: 0.9429 (m110) cc_final: 0.9229 (m110) REVERT: D 96 MET cc_start: 0.8187 (mmm) cc_final: 0.7783 (mmm) REVERT: D 131 LEU cc_start: 0.8971 (tt) cc_final: 0.8681 (tp) REVERT: D 149 ASP cc_start: 0.9019 (m-30) cc_final: 0.8772 (m-30) REVERT: D 168 PHE cc_start: 0.8638 (m-80) cc_final: 0.7730 (m-80) REVERT: D 169 TYR cc_start: 0.8080 (m-80) cc_final: 0.7515 (m-80) REVERT: D 174 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.7994 (t80) REVERT: D 242 TYR cc_start: 0.8782 (t80) cc_final: 0.8488 (t80) REVERT: D 268 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8436 (mt) outliers start: 70 outliers final: 44 residues processed: 743 average time/residue: 0.1266 time to fit residues: 141.7364 Evaluate side-chains 735 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 682 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 186 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.116913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.088234 restraints weight = 41069.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.091365 restraints weight = 21426.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.093505 restraints weight = 13649.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.095050 restraints weight = 9625.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.095642 restraints weight = 7377.352| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.7217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16386 Z= 0.196 Angle : 0.785 17.222 22134 Z= 0.397 Chirality : 0.049 0.253 2360 Planarity : 0.004 0.043 2818 Dihedral : 8.761 135.033 2294 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 20.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.55 % Allowed : 31.64 % Favored : 63.81 % 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: 0.77 (0.19), residues: 1932 helix: 0.99 (0.15), residues: 1130 sheet: -0.72 (0.40), residues: 144 loop : 0.20 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 225 TYR 0.027 0.002 TYR D 142 PHE 0.032 0.002 PHE C 168 TRP 0.015 0.002 TRP C 124 HIS 0.010 0.002 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (16386) covalent geometry : angle 0.78473 / 0.40 (22134) hydrogen bonds : bond 0.04250 / 2.65 ( 871) hydrogen bonds : angle 5.37119 / 3.78 ( 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 767 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 689 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: A 8 LYS cc_start: 0.9226 (tttt) cc_final: 0.8957 (tmtt) REVERT: A 15 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8441 (mt-10) REVERT: A 76 ASP cc_start: 0.8991 (m-30) cc_final: 0.8723 (m-30) REVERT: A 82 LYS cc_start: 0.9524 (mttm) cc_final: 0.9231 (mmmt) REVERT: A 95 MET cc_start: 0.8871 (mmm) cc_final: 0.8657 (tpp) REVERT: A 138 LYS cc_start: 0.9300 (mmtt) cc_final: 0.9030 (mmtt) REVERT: A 147 GLN cc_start: 0.9130 (mt0) cc_final: 0.8847 (mt0) REVERT: A 161 ARG cc_start: 0.8516 (ttm110) cc_final: 0.7795 (ptp-170) REVERT: A 174 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7705 (mt-10) REVERT: A 178 SER cc_start: 0.8361 (OUTLIER) cc_final: 0.7847 (t) REVERT: A 221 LYS cc_start: 0.8921 (mttp) cc_final: 0.8608 (mttm) REVERT: A 255 HIS cc_start: 0.9012 (t-90) cc_final: 0.8687 (t-90) REVERT: A 266 LYS cc_start: 0.8710 (ptmm) cc_final: 0.8178 (ptmm) REVERT: A 290 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8714 (tm-30) REVERT: A 317 MET cc_start: 0.8726 (ptp) cc_final: 0.8439 (ptp) REVERT: A 375 LYS cc_start: 0.8897 (mmtm) cc_final: 0.8478 (mmtm) REVERT: A 403 ILE cc_start: 0.9174 (mm) cc_final: 0.8970 (mm) REVERT: A 413 SER cc_start: 0.9430 (m) cc_final: 0.9016 (t) REVERT: A 415 ASN cc_start: 0.9107 (t0) cc_final: 0.8183 (t0) REVERT: A 418 ASN cc_start: 0.9408 (m-40) cc_final: 0.8912 (m110) REVERT: A 443 THR cc_start: 0.8736 (t) cc_final: 0.8496 (t) REVERT: A 493 MET cc_start: 0.8849 (tmm) cc_final: 0.8378 (tmm) REVERT: A 494 MET cc_start: 0.9040 (mtp) cc_final: 0.8477 (mtp) REVERT: A 505 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8461 (mt-10) REVERT: A 515 ASP cc_start: 0.9145 (m-30) cc_final: 0.8859 (m-30) REVERT: A 590 SER cc_start: 0.9521 (t) cc_final: 0.9024 (p) REVERT: A 595 MET cc_start: 0.9200 (mmm) cc_final: 0.8744 (mmm) REVERT: A 599 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8371 (mt-10) REVERT: A 615 MET cc_start: 0.9139 (mmm) cc_final: 0.8651 (mmm) REVERT: A 639 ASP cc_start: 0.8789 (m-30) cc_final: 0.8315 (m-30) REVERT: A 640 MET cc_start: 0.9492 (tpp) cc_final: 0.9238 (tpp) REVERT: A 645 GLN cc_start: 0.9098 (tp40) cc_final: 0.8804 (tp40) REVERT: B 8 LYS cc_start: 0.9285 (tptm) cc_final: 0.8915 (tppt) REVERT: B 82 LYS cc_start: 0.9546 (mtpp) cc_final: 0.9132 (ptpp) REVERT: B 95 MET cc_start: 0.9071 (tpt) cc_final: 0.8474 (tpp) REVERT: B 99 LYS cc_start: 0.9318 (tptp) cc_final: 0.8746 (tptp) REVERT: B 102 ASN cc_start: 0.9479 (m110) cc_final: 0.9275 (m110) REVERT: B 112 LYS cc_start: 0.9196 (pptt) cc_final: 0.8883 (pttm) REVERT: B 117 ARG cc_start: 0.8981 (mtp85) cc_final: 0.8781 (mtp85) REVERT: B 119 GLU cc_start: 0.9105 (mp0) cc_final: 0.8544 (mp0) REVERT: B 168 VAL cc_start: 0.9344 (t) cc_final: 0.9131 (m) REVERT: B 181 ASP cc_start: 0.8815 (m-30) cc_final: 0.8437 (m-30) REVERT: B 191 GLN cc_start: 0.9137 (mm-40) cc_final: 0.8840 (mm-40) REVERT: B 235 ARG cc_start: 0.9086 (mtm180) cc_final: 0.8839 (ptp-110) REVERT: B 263 ASP cc_start: 0.9112 (m-30) cc_final: 0.8687 (m-30) REVERT: B 266 LYS cc_start: 0.9176 (mtpp) cc_final: 0.8588 (mttm) REVERT: B 274 ARG cc_start: 0.8660 (ttm110) cc_final: 0.8360 (ttm170) REVERT: B 322 MET cc_start: 0.9316 (mmm) cc_final: 0.8960 (mmt) REVERT: B 341 LYS cc_start: 0.9645 (mmtm) cc_final: 0.9261 (mmmt) REVERT: B 344 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8593 (pt0) REVERT: B 348 MET cc_start: 0.8791 (tmm) cc_final: 0.8372 (tpt) REVERT: B 358 ILE cc_start: 0.9666 (mm) cc_final: 0.9235 (tp) REVERT: B 362 ASP cc_start: 0.8548 (m-30) cc_final: 0.8280 (m-30) REVERT: B 387 GLN cc_start: 0.8483 (mp10) cc_final: 0.7637 (mp10) REVERT: B 393 SER cc_start: 0.9265 (m) cc_final: 0.8902 (p) REVERT: B 399 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8629 (mp0) REVERT: B 402 GLU cc_start: 0.8534 (tm-30) cc_final: 0.7842 (tm-30) REVERT: B 475 ASN cc_start: 0.9292 (m-40) cc_final: 0.8967 (m110) REVERT: B 483 GLU cc_start: 0.9442 (mp0) cc_final: 0.9212 (mp0) REVERT: B 515 ASP cc_start: 0.9145 (m-30) cc_final: 0.8692 (m-30) REVERT: B 548 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7765 (mm-30) REVERT: B 583 SER cc_start: 0.9068 (m) cc_final: 0.8563 (p) REVERT: B 595 MET cc_start: 0.9348 (mmm) cc_final: 0.8905 (mmm) REVERT: B 602 GLU cc_start: 0.8550 (pt0) cc_final: 0.7851 (pt0) REVERT: B 610 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8578 (ptmm) REVERT: B 632 MET cc_start: 0.8045 (mtm) cc_final: 0.7644 (mtt) REVERT: B 645 GLN cc_start: 0.9396 (tp40) cc_final: 0.8975 (tp40) REVERT: B 650 GLN cc_start: 0.8063 (mt0) cc_final: 0.7681 (mt0) REVERT: B 668 ASN cc_start: 0.9061 (m110) cc_final: 0.8504 (m110) REVERT: C 20 MET cc_start: 0.9480 (tmm) cc_final: 0.9146 (tmm) REVERT: C 21 PHE cc_start: 0.9548 (m-80) cc_final: 0.8736 (m-80) REVERT: C 74 MET cc_start: 0.8939 (mtt) cc_final: 0.8585 (mtt) REVERT: C 90 LEU cc_start: 0.9068 (mt) cc_final: 0.8834 (mt) REVERT: C 92 PHE cc_start: 0.9630 (t80) cc_final: 0.9130 (t80) REVERT: C 96 MET cc_start: 0.8985 (mmm) cc_final: 0.8594 (mmm) REVERT: C 109 PHE cc_start: 0.8189 (m-10) cc_final: 0.7806 (m-80) REVERT: C 110 MET cc_start: 0.7694 (mpp) cc_final: 0.7390 (mtt) REVERT: C 130 TYR cc_start: 0.9548 (m-80) cc_final: 0.9190 (m-10) REVERT: C 155 LYS cc_start: 0.9320 (mttt) cc_final: 0.8998 (mmtt) REVERT: C 174 TYR cc_start: 0.8066 (OUTLIER) cc_final: 0.7781 (t80) REVERT: C 185 MET cc_start: 0.8287 (mmm) cc_final: 0.7616 (mmm) REVERT: C 189 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8275 (mm-30) REVERT: C 242 TYR cc_start: 0.9469 (t80) cc_final: 0.9167 (t80) REVERT: C 259 PHE cc_start: 0.9285 (t80) cc_final: 0.8586 (t80) REVERT: C 269 MET cc_start: 0.9532 (OUTLIER) cc_final: 0.9135 (mmp) REVERT: D 30 TRP cc_start: 0.8234 (p-90) cc_final: 0.7715 (p-90) REVERT: D 46 TYR cc_start: 0.8830 (m-10) cc_final: 0.8624 (m-10) REVERT: D 96 MET cc_start: 0.8297 (mmm) cc_final: 0.7991 (mmm) REVERT: D 131 LEU cc_start: 0.9007 (tt) cc_final: 0.8726 (tp) REVERT: D 137 MET cc_start: 0.8431 (mmt) cc_final: 0.7953 (mpp) REVERT: D 148 ASP cc_start: 0.8590 (t70) cc_final: 0.8332 (t70) REVERT: D 168 PHE cc_start: 0.8734 (m-80) cc_final: 0.7713 (m-80) REVERT: D 169 TYR cc_start: 0.8292 (m-80) cc_final: 0.7571 (m-80) REVERT: D 174 TYR cc_start: 0.8901 (OUTLIER) cc_final: 0.8117 (t80) REVERT: D 242 TYR cc_start: 0.8894 (t80) cc_final: 0.8529 (t80) REVERT: D 268 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8392 (mt) outliers start: 78 outliers final: 53 residues processed: 718 average time/residue: 0.1153 time to fit residues: 125.9618 Evaluate side-chains 719 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 659 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 254 HIS Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 312 VAL 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: 8.9990 chunk 61 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 153 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 158 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 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 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.118696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.089619 restraints weight = 40937.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.092913 restraints weight = 20874.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.095226 restraints weight = 13133.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.096820 restraints weight = 9130.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.098044 restraints weight = 6936.324| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3216 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3216 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.7447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16386 Z= 0.161 Angle : 0.800 15.113 22134 Z= 0.399 Chirality : 0.049 0.264 2360 Planarity : 0.004 0.038 2818 Dihedral : 8.682 135.012 2294 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.85 % Allowed : 32.93 % Favored : 63.23 % 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: 0.94 (0.15), residues: 1122 sheet: -0.46 (0.42), residues: 138 loop : 0.00 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 164 TYR 0.021 0.001 TYR D 142 PHE 0.036 0.002 PHE C 29 TRP 0.009 0.001 TRP B 9 HIS 0.011 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (16386) covalent geometry : angle 0.80006 / 0.40 (22134) hydrogen bonds : bond 0.04231 / 2.66 ( 871) hydrogen bonds : angle 5.34259 / 3.76 ( 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 749 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 683 time to evaluate : 0.618 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 18 ILE cc_start: 0.9296 (pt) cc_final: 0.8154 (pt) REVERT: A 56 ASP cc_start: 0.9101 (m-30) cc_final: 0.8650 (m-30) REVERT: A 76 ASP cc_start: 0.8996 (m-30) cc_final: 0.8730 (m-30) REVERT: A 82 LYS cc_start: 0.9518 (mttm) cc_final: 0.9190 (mmmt) REVERT: A 138 LYS cc_start: 0.9281 (mmtt) cc_final: 0.9010 (mmtt) REVERT: A 144 MET cc_start: 0.8443 (mmp) cc_final: 0.8184 (mmm) REVERT: A 161 ARG cc_start: 0.8538 (ttm110) cc_final: 0.7792 (ptp-170) REVERT: A 174 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7724 (mt-10) REVERT: A 178 SER cc_start: 0.8287 (OUTLIER) cc_final: 0.7804 (t) REVERT: A 221 LYS cc_start: 0.8960 (mttp) cc_final: 0.8619 (mttm) REVERT: A 255 HIS cc_start: 0.8919 (t-90) cc_final: 0.8610 (t-90) REVERT: A 290 GLU cc_start: 0.9160 (tm-30) cc_final: 0.8747 (tm-30) REVERT: A 301 PHE cc_start: 0.9041 (m-10) cc_final: 0.8805 (m-10) REVERT: A 375 LYS cc_start: 0.8871 (mmtm) cc_final: 0.8462 (mmtm) REVERT: A 403 ILE cc_start: 0.9145 (mm) cc_final: 0.8937 (mm) REVERT: A 413 SER cc_start: 0.9475 (m) cc_final: 0.8991 (t) REVERT: A 493 MET cc_start: 0.8758 (tmm) cc_final: 0.8313 (tmm) REVERT: A 505 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8485 (mt-10) REVERT: A 515 ASP cc_start: 0.9172 (m-30) cc_final: 0.8834 (m-30) REVERT: A 590 SER cc_start: 0.9480 (t) cc_final: 0.8936 (p) REVERT: A 595 MET cc_start: 0.9227 (mmm) cc_final: 0.8819 (mmm) REVERT: A 600 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8083 (mtt180) REVERT: A 639 ASP cc_start: 0.8768 (m-30) cc_final: 0.8264 (m-30) REVERT: A 640 MET cc_start: 0.9515 (tpp) cc_final: 0.9286 (tpp) REVERT: A 645 GLN cc_start: 0.9039 (tp40) cc_final: 0.8785 (tp40) REVERT: B 8 LYS cc_start: 0.9301 (tptm) cc_final: 0.9093 (tptm) REVERT: B 75 GLU cc_start: 0.9163 (mp0) cc_final: 0.8907 (pm20) REVERT: B 82 LYS cc_start: 0.9538 (mtpp) cc_final: 0.9131 (mmtm) REVERT: B 95 MET cc_start: 0.9054 (tpt) cc_final: 0.8423 (tpp) REVERT: B 99 LYS cc_start: 0.9291 (tptp) cc_final: 0.8736 (tptp) REVERT: B 112 LYS cc_start: 0.9213 (pptt) cc_final: 0.8933 (pttm) REVERT: B 117 ARG cc_start: 0.8911 (mtp85) cc_final: 0.8685 (mtp85) REVERT: B 119 GLU cc_start: 0.9094 (mp0) cc_final: 0.8523 (mp0) REVERT: B 168 VAL cc_start: 0.9332 (t) cc_final: 0.9116 (m) REVERT: B 181 ASP cc_start: 0.8749 (m-30) cc_final: 0.8372 (m-30) REVERT: B 235 ARG cc_start: 0.9046 (mtm180) cc_final: 0.8835 (mtm-85) REVERT: B 243 ARG cc_start: 0.6543 (OUTLIER) cc_final: 0.5229 (tmm-80) REVERT: B 250 TYR cc_start: 0.8755 (m-10) cc_final: 0.8500 (m-10) REVERT: B 256 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8496 (ttp80) REVERT: B 263 ASP cc_start: 0.9047 (m-30) cc_final: 0.8633 (m-30) REVERT: B 266 LYS cc_start: 0.9223 (mtpp) cc_final: 0.8568 (mttm) REVERT: B 274 ARG cc_start: 0.8684 (ttm110) cc_final: 0.8354 (ttm170) REVERT: B 322 MET cc_start: 0.9323 (mmm) cc_final: 0.8989 (mmt) REVERT: B 333 LYS cc_start: 0.9034 (tttm) cc_final: 0.8716 (tttm) REVERT: B 341 LYS cc_start: 0.9636 (mmtm) cc_final: 0.9254 (mmmt) REVERT: B 344 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8575 (pt0) REVERT: B 348 MET cc_start: 0.8837 (tmm) cc_final: 0.8459 (tpt) REVERT: B 362 ASP cc_start: 0.8578 (m-30) cc_final: 0.8291 (m-30) REVERT: B 387 GLN cc_start: 0.8438 (mp10) cc_final: 0.7571 (mp10) REVERT: B 393 SER cc_start: 0.9228 (m) cc_final: 0.8874 (p) REVERT: B 396 ASP cc_start: 0.8930 (p0) cc_final: 0.8514 (p0) REVERT: B 399 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8626 (mm-30) REVERT: B 402 GLU cc_start: 0.8589 (tm-30) cc_final: 0.7812 (tm-30) REVERT: B 475 ASN cc_start: 0.9279 (m-40) cc_final: 0.8914 (m110) REVERT: B 483 GLU cc_start: 0.9418 (mp0) cc_final: 0.9202 (mp0) REVERT: B 515 ASP cc_start: 0.9109 (m-30) cc_final: 0.8677 (m-30) REVERT: B 548 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7714 (mm-30) REVERT: B 558 TRP cc_start: 0.9407 (m100) cc_final: 0.8800 (m100) REVERT: B 583 SER cc_start: 0.9061 (m) cc_final: 0.8529 (p) REVERT: B 595 MET cc_start: 0.9305 (mmm) cc_final: 0.9001 (mmm) REVERT: B 602 GLU cc_start: 0.8555 (pt0) cc_final: 0.8155 (pt0) REVERT: B 610 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8332 (tttt) REVERT: B 632 MET cc_start: 0.7785 (mtm) cc_final: 0.7545 (mtt) REVERT: B 645 GLN cc_start: 0.9378 (tp40) cc_final: 0.8986 (tp40) REVERT: B 650 GLN cc_start: 0.8014 (mt0) cc_final: 0.7682 (mt0) REVERT: B 657 PHE cc_start: 0.8723 (m-80) cc_final: 0.8519 (m-80) REVERT: B 668 ASN cc_start: 0.9110 (m110) cc_final: 0.8630 (m-40) REVERT: B 686 ARG cc_start: 0.8393 (mpt180) cc_final: 0.8179 (mmt180) REVERT: C 20 MET cc_start: 0.9498 (tmm) cc_final: 0.9180 (tmm) REVERT: C 21 PHE cc_start: 0.9571 (m-80) cc_final: 0.8792 (m-80) REVERT: C 74 MET cc_start: 0.8993 (mtt) cc_final: 0.8532 (mtt) REVERT: C 92 PHE cc_start: 0.9634 (t80) cc_final: 0.9172 (t80) REVERT: C 96 MET cc_start: 0.9020 (mmm) cc_final: 0.8541 (mmm) REVERT: C 109 PHE cc_start: 0.8154 (m-10) cc_final: 0.7760 (m-80) REVERT: C 110 MET cc_start: 0.7629 (mpp) cc_final: 0.7370 (mtt) REVERT: C 155 LYS cc_start: 0.9372 (mttt) cc_final: 0.9035 (mmtt) REVERT: C 173 TYR cc_start: 0.9080 (t80) cc_final: 0.8879 (t80) REVERT: C 185 MET cc_start: 0.8403 (mmm) cc_final: 0.7731 (mmm) REVERT: C 189 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8143 (mm-30) REVERT: C 242 TYR cc_start: 0.9456 (t80) cc_final: 0.9128 (t80) REVERT: C 259 PHE cc_start: 0.9262 (t80) cc_final: 0.8747 (t80) REVERT: C 269 MET cc_start: 0.9563 (OUTLIER) cc_final: 0.9101 (mmp) REVERT: D 30 TRP cc_start: 0.8082 (p-90) cc_final: 0.7505 (p-90) REVERT: D 33 GLU cc_start: 0.9089 (mp0) cc_final: 0.8363 (pp20) REVERT: D 96 MET cc_start: 0.8313 (mmm) cc_final: 0.7968 (mmm) REVERT: D 131 LEU cc_start: 0.9041 (tt) cc_final: 0.8787 (tp) REVERT: D 137 MET cc_start: 0.8352 (mmt) cc_final: 0.7907 (mpp) REVERT: D 168 PHE cc_start: 0.8720 (m-80) cc_final: 0.7588 (m-80) REVERT: D 169 TYR cc_start: 0.8096 (m-80) cc_final: 0.7434 (m-80) REVERT: D 172 PHE cc_start: 0.8808 (m-80) cc_final: 0.8573 (t80) REVERT: D 174 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.8126 (t80) REVERT: D 185 MET cc_start: 0.6822 (mmm) cc_final: 0.6177 (ttt) REVERT: D 242 TYR cc_start: 0.8915 (t80) cc_final: 0.8572 (t80) outliers start: 66 outliers final: 51 residues processed: 709 average time/residue: 0.1190 time to fit residues: 126.9520 Evaluate side-chains 719 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 660 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 0.0060 chunk 133 optimal weight: 9.9990 chunk 149 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 365 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.121523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.092792 restraints weight = 41013.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.096026 restraints weight = 20736.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.098340 restraints weight = 12948.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.099960 restraints weight = 8996.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.101157 restraints weight = 6824.942| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 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 = 0.3238 r_free = 0.3238 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 (9 function evaluations) r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.7714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16386 Z= 0.157 Angle : 0.841 14.759 22134 Z= 0.416 Chirality : 0.049 0.279 2360 Planarity : 0.004 0.040 2818 Dihedral : 8.551 134.853 2291 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.32 % Allowed : 33.74 % Favored : 62.94 % 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: 0.46 (0.19), residues: 1932 helix: 0.82 (0.15), residues: 1121 sheet: -0.96 (0.40), residues: 158 loop : -0.03 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 604 TYR 0.026 0.002 TYR C 177 PHE 0.035 0.002 PHE C 172 TRP 0.012 0.001 TRP D 124 HIS 0.012 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (16386) covalent geometry : angle 0.84087 / 0.42 (22134) hydrogen bonds : bond 0.04305 / 2.71 ( 871) hydrogen bonds : angle 5.40878 / 3.82 ( 2571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 685 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8678 (pm20) REVERT: A 56 ASP cc_start: 0.9066 (m-30) cc_final: 0.8600 (m-30) REVERT: A 76 ASP cc_start: 0.8970 (m-30) cc_final: 0.8700 (m-30) REVERT: A 82 LYS cc_start: 0.9496 (mttm) cc_final: 0.9157 (mmmt) REVERT: A 138 LYS cc_start: 0.9296 (mmtt) cc_final: 0.9090 (mmtt) REVERT: A 144 MET cc_start: 0.8458 (mmp) cc_final: 0.8255 (mmp) REVERT: A 161 ARG cc_start: 0.8531 (ttm110) cc_final: 0.7805 (ptp-170) REVERT: A 174 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7720 (mt-10) REVERT: A 178 SER cc_start: 0.8220 (OUTLIER) cc_final: 0.7758 (t) REVERT: A 221 LYS cc_start: 0.8955 (mttp) cc_final: 0.8708 (mttm) REVERT: A 266 LYS cc_start: 0.8678 (ptmm) cc_final: 0.8168 (ptmm) REVERT: A 290 GLU cc_start: 0.9173 (tm-30) cc_final: 0.8760 (tm-30) REVERT: A 295 ASP cc_start: 0.9306 (t0) cc_final: 0.8847 (t0) REVERT: A 301 PHE cc_start: 0.8978 (m-10) cc_final: 0.8764 (m-10) REVERT: A 375 LYS cc_start: 0.8939 (mmtm) cc_final: 0.8540 (mmtm) REVERT: A 403 ILE cc_start: 0.9142 (mm) cc_final: 0.8909 (mm) REVERT: A 441 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8950 (mm-30) REVERT: A 447 ASN cc_start: 0.7924 (t0) cc_final: 0.6634 (t0) REVERT: A 456 LYS cc_start: 0.9245 (ptpp) cc_final: 0.8802 (mtmm) REVERT: A 475 ASN cc_start: 0.9047 (m-40) cc_final: 0.8593 (m110) REVERT: A 493 MET cc_start: 0.8839 (tmm) cc_final: 0.8411 (tmm) REVERT: A 505 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8511 (mt-10) REVERT: A 515 ASP cc_start: 0.9142 (m-30) cc_final: 0.8830 (m-30) REVERT: A 639 ASP cc_start: 0.8713 (m-30) cc_final: 0.8182 (m-30) REVERT: A 640 MET cc_start: 0.9525 (tpp) cc_final: 0.9243 (tpp) REVERT: A 645 GLN cc_start: 0.9014 (tp40) cc_final: 0.8539 (tp-100) REVERT: A 683 TYR cc_start: 0.8591 (t80) cc_final: 0.8263 (t80) REVERT: A 686 ARG cc_start: 0.8347 (ttm-80) cc_final: 0.7721 (mtp-110) REVERT: B 8 LYS cc_start: 0.9292 (tptm) cc_final: 0.9075 (tptm) REVERT: B 82 LYS cc_start: 0.9509 (mtpp) cc_final: 0.9080 (mmtm) REVERT: B 95 MET cc_start: 0.8989 (tpt) cc_final: 0.8388 (tpp) REVERT: B 99 LYS cc_start: 0.9307 (tptp) cc_final: 0.8833 (tptp) REVERT: B 112 LYS cc_start: 0.9188 (pptt) cc_final: 0.8896 (pttm) REVERT: B 117 ARG cc_start: 0.8928 (mtp85) cc_final: 0.8724 (mtp85) REVERT: B 119 GLU cc_start: 0.9078 (mp0) cc_final: 0.8534 (mp0) REVERT: B 168 VAL cc_start: 0.9313 (t) cc_final: 0.9097 (m) REVERT: B 180 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8638 (m-40) REVERT: B 181 ASP cc_start: 0.8737 (m-30) cc_final: 0.8339 (m-30) REVERT: B 232 ASN cc_start: 0.9009 (m-40) cc_final: 0.7677 (m-40) REVERT: B 243 ARG cc_start: 0.6394 (OUTLIER) cc_final: 0.5105 (tmm-80) REVERT: B 250 TYR cc_start: 0.8894 (m-10) cc_final: 0.8452 (m-10) REVERT: B 256 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8466 (ttp80) REVERT: B 263 ASP cc_start: 0.9019 (m-30) cc_final: 0.8600 (m-30) REVERT: B 266 LYS cc_start: 0.9233 (mtpp) cc_final: 0.8573 (mttm) REVERT: B 274 ARG cc_start: 0.8720 (ttm110) cc_final: 0.8376 (ttm170) REVERT: B 322 MET cc_start: 0.9318 (mmm) cc_final: 0.8989 (mmt) REVERT: B 333 LYS cc_start: 0.9008 (tttm) cc_final: 0.8692 (tttm) REVERT: B 341 LYS cc_start: 0.9635 (mmtm) cc_final: 0.9237 (mmmt) REVERT: B 344 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8556 (pt0) REVERT: B 348 MET cc_start: 0.8826 (tmm) cc_final: 0.8489 (tpt) REVERT: B 362 ASP cc_start: 0.8543 (m-30) cc_final: 0.8251 (m-30) REVERT: B 387 GLN cc_start: 0.8411 (mp10) cc_final: 0.7609 (mp10) REVERT: B 393 SER cc_start: 0.9233 (m) cc_final: 0.8933 (p) REVERT: B 396 ASP cc_start: 0.8912 (p0) cc_final: 0.8514 (p0) REVERT: B 399 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8564 (mm-30) REVERT: B 402 GLU cc_start: 0.8703 (tm-30) cc_final: 0.7942 (tm-30) REVERT: B 475 ASN cc_start: 0.9296 (m-40) cc_final: 0.8955 (m110) REVERT: B 483 GLU cc_start: 0.9397 (mp0) cc_final: 0.9190 (mp0) REVERT: B 515 ASP cc_start: 0.9045 (m-30) cc_final: 0.8614 (m-30) REVERT: B 548 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7767 (mm-30) REVERT: B 558 TRP cc_start: 0.9334 (m100) cc_final: 0.8782 (m100) REVERT: B 583 SER cc_start: 0.9056 (m) cc_final: 0.8627 (p) REVERT: B 588 GLN cc_start: 0.9338 (mm110) cc_final: 0.9094 (mm-40) REVERT: B 595 MET cc_start: 0.9266 (mmm) cc_final: 0.8821 (mmm) REVERT: B 602 GLU cc_start: 0.8439 (pt0) cc_final: 0.7830 (pt0) REVERT: B 610 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8526 (ptmm) REVERT: B 645 GLN cc_start: 0.9371 (tp40) cc_final: 0.8983 (tp40) REVERT: B 650 GLN cc_start: 0.8095 (mt0) cc_final: 0.7390 (mt0) REVERT: B 668 ASN cc_start: 0.9101 (m110) cc_final: 0.8604 (m-40) REVERT: C 20 MET cc_start: 0.9495 (tmm) cc_final: 0.9165 (tmm) REVERT: C 21 PHE cc_start: 0.9562 (m-80) cc_final: 0.8764 (m-80) REVERT: C 74 MET cc_start: 0.8966 (mtt) cc_final: 0.8517 (mtt) REVERT: C 92 PHE cc_start: 0.9600 (t80) cc_final: 0.9156 (t80) REVERT: C 96 MET cc_start: 0.9021 (mmm) cc_final: 0.8530 (mmm) REVERT: C 109 PHE cc_start: 0.8163 (m-10) cc_final: 0.7689 (m-80) REVERT: C 110 MET cc_start: 0.7490 (mpp) cc_final: 0.7232 (mtt) REVERT: C 155 LYS cc_start: 0.9421 (mttt) cc_final: 0.9081 (mmtt) REVERT: C 218 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8908 (pm20) REVERT: C 242 TYR cc_start: 0.9429 (t80) cc_final: 0.9118 (t80) REVERT: C 259 PHE cc_start: 0.9321 (t80) cc_final: 0.8627 (t80) REVERT: C 269 MET cc_start: 0.9543 (ptt) cc_final: 0.9078 (mmp) REVERT: C 278 GLU cc_start: 0.8149 (tp30) cc_final: 0.7824 (tm-30) REVERT: D 30 TRP cc_start: 0.7926 (p-90) cc_final: 0.7254 (p-90) REVERT: D 33 GLU cc_start: 0.9112 (mp0) cc_final: 0.8339 (pp20) REVERT: D 96 MET cc_start: 0.8268 (mmm) cc_final: 0.7899 (mmm) REVERT: D 137 MET cc_start: 0.8301 (mmt) cc_final: 0.7859 (mpp) REVERT: D 168 PHE cc_start: 0.8701 (m-80) cc_final: 0.7588 (m-80) REVERT: D 169 TYR cc_start: 0.8007 (m-80) cc_final: 0.7380 (m-80) REVERT: D 172 PHE cc_start: 0.8760 (m-80) cc_final: 0.8470 (t80) REVERT: D 174 TYR cc_start: 0.8902 (OUTLIER) cc_final: 0.8234 (t80) REVERT: D 242 TYR cc_start: 0.8954 (t80) cc_final: 0.8629 (t80) outliers start: 57 outliers final: 40 residues processed: 705 average time/residue: 0.1254 time to fit residues: 133.7098 Evaluate side-chains 707 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 659 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 189 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 165 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 HIS ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.116087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.088777 restraints weight = 41547.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.091842 restraints weight = 21585.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.094000 restraints weight = 13735.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.095560 restraints weight = 9590.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.096693 restraints weight = 7269.296| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 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 = 0.3237 r_free = 0.3237 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 (9 function evaluations) r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.7880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16386 Z= 0.167 Angle : 0.880 16.358 22134 Z= 0.438 Chirality : 0.050 0.307 2360 Planarity : 0.004 0.041 2818 Dihedral : 8.539 134.966 2291 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 19.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.09 % Allowed : 35.31 % Favored : 61.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.19), residues: 1932 helix: 0.74 (0.15), residues: 1125 sheet: -1.08 (0.40), residues: 158 loop : 0.04 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 604 TYR 0.028 0.002 TYR C 177 PHE 0.034 0.002 PHE C 172 TRP 0.014 0.001 TRP D 124 HIS 0.021 0.002 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (16386) covalent geometry : angle 0.88024 / 0.44 (22134) hydrogen bonds : bond 0.04339 / 2.74 ( 871) hydrogen bonds : angle 5.51268 / 3.89 ( 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 721 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 668 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ASP cc_start: 0.9067 (m-30) cc_final: 0.8590 (m-30) REVERT: A 82 LYS cc_start: 0.9490 (mttm) cc_final: 0.9147 (mmmt) REVERT: A 138 LYS cc_start: 0.9313 (mmtt) cc_final: 0.9099 (mmtt) REVERT: A 144 MET cc_start: 0.8436 (mmp) cc_final: 0.8194 (mmm) REVERT: A 161 ARG cc_start: 0.8543 (ttm110) cc_final: 0.8086 (ptp-170) REVERT: A 174 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7790 (mt-10) REVERT: A 178 SER cc_start: 0.8274 (OUTLIER) cc_final: 0.7821 (t) REVERT: A 290 GLU cc_start: 0.9183 (tm-30) cc_final: 0.8759 (tm-30) REVERT: A 301 PHE cc_start: 0.9014 (m-10) cc_final: 0.8765 (m-10) REVERT: A 375 LYS cc_start: 0.8951 (mmtm) cc_final: 0.8555 (mmtm) REVERT: A 441 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8945 (mm-30) REVERT: A 456 LYS cc_start: 0.9216 (ptpp) cc_final: 0.8817 (mtmm) REVERT: A 475 ASN cc_start: 0.9030 (m-40) cc_final: 0.8627 (m110) REVERT: A 493 MET cc_start: 0.8876 (tmm) cc_final: 0.8305 (tmm) REVERT: A 494 MET cc_start: 0.9143 (mtp) cc_final: 0.8858 (mmm) REVERT: A 505 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8465 (mt-10) REVERT: A 515 ASP cc_start: 0.9180 (m-30) cc_final: 0.8848 (m-30) REVERT: A 590 SER cc_start: 0.9519 (t) cc_final: 0.8850 (p) REVERT: A 639 ASP cc_start: 0.8722 (m-30) cc_final: 0.8252 (m-30) REVERT: A 640 MET cc_start: 0.9503 (tpp) cc_final: 0.9157 (tpp) REVERT: A 645 GLN cc_start: 0.8995 (tp40) cc_final: 0.8521 (tp-100) REVERT: A 686 ARG cc_start: 0.8318 (ttm-80) cc_final: 0.7693 (mtp-110) REVERT: B 8 LYS cc_start: 0.9275 (tptm) cc_final: 0.9070 (tptm) REVERT: B 82 LYS cc_start: 0.9497 (mtpp) cc_final: 0.9099 (mmtp) REVERT: B 95 MET cc_start: 0.8962 (tpt) cc_final: 0.8618 (tpp) REVERT: B 99 LYS cc_start: 0.9304 (tptp) cc_final: 0.8917 (tptp) REVERT: B 112 LYS cc_start: 0.9167 (pptt) cc_final: 0.8891 (pttm) REVERT: B 117 ARG cc_start: 0.8915 (mtp85) cc_final: 0.8712 (mtp85) REVERT: B 119 GLU cc_start: 0.9078 (mp0) cc_final: 0.8563 (mp0) REVERT: B 168 VAL cc_start: 0.9324 (t) cc_final: 0.9077 (m) REVERT: B 180 ASN cc_start: 0.8919 (OUTLIER) cc_final: 0.8505 (m-40) REVERT: B 181 ASP cc_start: 0.8760 (m-30) cc_final: 0.8341 (m-30) REVERT: B 232 ASN cc_start: 0.9167 (m-40) cc_final: 0.8149 (m110) REVERT: B 235 ARG cc_start: 0.9120 (mtm-85) cc_final: 0.8343 (mtm-85) REVERT: B 243 ARG cc_start: 0.6489 (OUTLIER) cc_final: 0.5192 (tmm-80) REVERT: B 250 TYR cc_start: 0.8960 (m-10) cc_final: 0.8430 (m-10) REVERT: B 256 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8453 (ttp80) REVERT: B 263 ASP cc_start: 0.9015 (m-30) cc_final: 0.8582 (m-30) REVERT: B 266 LYS cc_start: 0.9265 (mtpp) cc_final: 0.8627 (mttm) REVERT: B 274 ARG cc_start: 0.8725 (ttm110) cc_final: 0.8365 (ttm170) REVERT: B 322 MET cc_start: 0.9309 (mmm) cc_final: 0.8937 (mmt) REVERT: B 333 LYS cc_start: 0.8996 (tttm) cc_final: 0.8742 (tttm) REVERT: B 341 LYS cc_start: 0.9630 (mmtm) cc_final: 0.9226 (mmmt) REVERT: B 344 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8538 (pt0) REVERT: B 348 MET cc_start: 0.8838 (tmm) cc_final: 0.8523 (tpt) REVERT: B 357 TYR cc_start: 0.7966 (m-10) cc_final: 0.7739 (m-10) REVERT: B 362 ASP cc_start: 0.8562 (m-30) cc_final: 0.8249 (m-30) REVERT: B 375 LYS cc_start: 0.9164 (mmmm) cc_final: 0.8566 (mmmm) REVERT: B 387 GLN cc_start: 0.8369 (mp10) cc_final: 0.7527 (mp10) REVERT: B 393 SER cc_start: 0.9235 (m) cc_final: 0.8882 (p) REVERT: B 396 ASP cc_start: 0.8935 (p0) cc_final: 0.8282 (p0) REVERT: B 399 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8647 (mp0) REVERT: B 402 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8028 (tm-30) REVERT: B 475 ASN cc_start: 0.9300 (m-40) cc_final: 0.8987 (m110) REVERT: B 483 GLU cc_start: 0.9393 (mp0) cc_final: 0.9183 (mp0) REVERT: B 494 MET cc_start: 0.9081 (ttt) cc_final: 0.8577 (ttm) REVERT: B 515 ASP cc_start: 0.9018 (m-30) cc_final: 0.8604 (m-30) REVERT: B 548 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7686 (mm-30) REVERT: B 583 SER cc_start: 0.9074 (m) cc_final: 0.8625 (p) REVERT: B 588 GLN cc_start: 0.9312 (mm110) cc_final: 0.9055 (mm-40) REVERT: B 595 MET cc_start: 0.9261 (mmm) cc_final: 0.8994 (mmm) REVERT: B 602 GLU cc_start: 0.8251 (pt0) cc_final: 0.7642 (pt0) REVERT: B 628 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8398 (mm-30) REVERT: B 634 MET cc_start: 0.8753 (mmm) cc_final: 0.8472 (tpp) REVERT: B 645 GLN cc_start: 0.9375 (tp40) cc_final: 0.8986 (tp40) REVERT: B 650 GLN cc_start: 0.8105 (mt0) cc_final: 0.7722 (mt0) REVERT: B 668 ASN cc_start: 0.9093 (m110) cc_final: 0.8599 (m-40) REVERT: B 686 ARG cc_start: 0.8357 (mpt180) cc_final: 0.8102 (mmt180) REVERT: C 20 MET cc_start: 0.9518 (tmm) cc_final: 0.9211 (tmm) REVERT: C 21 PHE cc_start: 0.9577 (m-80) cc_final: 0.8811 (m-80) REVERT: C 74 MET cc_start: 0.8938 (mtt) cc_final: 0.8522 (mtt) REVERT: C 92 PHE cc_start: 0.9596 (t80) cc_final: 0.9167 (t80) REVERT: C 96 MET cc_start: 0.9042 (mmm) cc_final: 0.8553 (mmm) REVERT: C 109 PHE cc_start: 0.8088 (m-10) cc_final: 0.7711 (m-80) REVERT: C 155 LYS cc_start: 0.9443 (mttt) cc_final: 0.9097 (mmtt) REVERT: C 218 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8920 (pm20) REVERT: C 242 TYR cc_start: 0.9474 (t80) cc_final: 0.9152 (t80) REVERT: C 259 PHE cc_start: 0.9287 (t80) cc_final: 0.8665 (t80) REVERT: C 269 MET cc_start: 0.9508 (ptt) cc_final: 0.9038 (mmp) REVERT: C 278 GLU cc_start: 0.8185 (tp30) cc_final: 0.7855 (pp20) REVERT: D 30 TRP cc_start: 0.8022 (p-90) cc_final: 0.7246 (p-90) REVERT: D 33 GLU cc_start: 0.9145 (mp0) cc_final: 0.8353 (pp20) REVERT: D 96 MET cc_start: 0.8250 (mmm) cc_final: 0.7988 (mmm) REVERT: D 137 MET cc_start: 0.8231 (mmt) cc_final: 0.7804 (mpp) REVERT: D 168 PHE cc_start: 0.8691 (m-80) cc_final: 0.7472 (m-80) REVERT: D 174 TYR cc_start: 0.8884 (OUTLIER) cc_final: 0.8232 (t80) REVERT: D 185 MET cc_start: 0.6432 (mmp) cc_final: 0.6092 (ttt) REVERT: D 242 TYR cc_start: 0.8995 (t80) cc_final: 0.8713 (t80) outliers start: 53 outliers final: 39 residues processed: 685 average time/residue: 0.1168 time to fit residues: 120.7508 Evaluate side-chains 690 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 645 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 259 ASN 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 431 LEU Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 254 HIS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 1.9990 chunk 1 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 148 optimal weight: 7.9990 chunk 125 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 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 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 210 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.117318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.090308 restraints weight = 41188.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.093527 restraints weight = 21402.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.095661 restraints weight = 13359.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.097232 restraints weight = 9395.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.098370 restraints weight = 7103.428| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 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 = 0.3264 r_free = 0.3264 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: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.8100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16386 Z= 0.162 Angle : 0.898 16.143 22134 Z= 0.445 Chirality : 0.051 0.287 2360 Planarity : 0.004 0.039 2818 Dihedral : 8.576 138.612 2291 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.97 % Allowed : 36.31 % Favored : 60.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.19), residues: 1932 helix: 0.71 (0.15), residues: 1125 sheet: -0.98 (0.41), residues: 154 loop : -0.04 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 604 TYR 0.027 0.002 TYR C 177 PHE 0.036 0.002 PHE A 378 TRP 0.015 0.001 TRP D 124 HIS 0.012 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (16386) covalent geometry : angle 0.89752 / 0.45 (22134) hydrogen bonds : bond 0.04400 / 2.77 ( 871) hydrogen bonds : angle 5.56902 / 3.94 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3415.63 seconds wall clock time: 59 minutes 55.99 seconds (3595.99 seconds total)