Starting phenix.real_space_refine on Fri Jul 3 19:42:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzi_45068/07_2026/9bzi_45068_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzi_45068/07_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_45068/07_2026/9bzi_45068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzi_45068/07_2026/9bzi_45068.map" model { file = "/net/cci-nas-00/data/ceres_data/9bzi_45068/07_2026/9bzi_45068_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzi_45068/07_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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 2.82, per 1000 atoms: 0.18 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: 1.22 Conformation dependent library (CDL) restraints added in 608.5 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: 0.41 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: 2.69 Time building geometry restraints manager: 1.65 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 3.060 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 3.060 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 3.060 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 3.060 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.400 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.080 ------------------------------------------------------------------------------- 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 : 0.449 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: 0.8145 (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: 0.8201 (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: 0.8563 (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: 0.7009 (t80) REVERT: B 122 ILE cc_start: 0.8631 (mt) cc_final: 0.8429 (mt) REVERT: B 191 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8223 (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: 0.8148 (t) REVERT: B 226 VAL cc_start: 0.8791 (t) cc_final: 0.8583 (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: 0.8720 (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: 0.8116 (p90) REVERT: B 384 GLU cc_start: 0.8921 (pm20) cc_final: 0.8627 (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: 0.7849 (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: 0.7985 (tp40) REVERT: B 650 GLN cc_start: 0.8332 (mt0) cc_final: 0.7616 (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: 0.4535 (tmm) REVERT: C 131 LEU cc_start: 0.5653 (OUTLIER) cc_final: 0.5421 (tp) REVERT: C 153 LEU cc_start: 0.6621 (tp) cc_final: 0.6016 (tp) REVERT: C 155 LYS cc_start: 0.7675 (mttt) cc_final: 0.7441 (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: 0.6077 (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: 0.6644 (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: 0.3796 (m110) outliers start: 23 outliers final: 7 residues processed: 1094 average time/residue: 0.1293 time to fit residues: 204.3476 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 : 0.421 ------------------------------------------------------------------------------- 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 127 GLN C 234 GLN C 263 ASN D 71 ASN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 181 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.119932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.090312 restraints weight = 41165.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.093712 restraints weight = 20755.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.096060 restraints weight = 12872.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.097880 restraints weight = 9028.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.099053 restraints weight = 6708.534| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- 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 = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (16 function evaluations) r_final: 0.3216 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16386 Z= 0.178 Angle : 0.736 14.304 22134 Z= 0.387 Chirality : 0.047 0.180 2360 Planarity : 0.004 0.049 2818 Dihedral : 9.856 127.918 2306 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 4.31 % Allowed : 21.39 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.19), residues: 1932 helix: 1.21 (0.15), residues: 1126 sheet: 0.21 (0.42), residues: 126 loop : 0.42 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 243 TYR 0.022 0.002 TYR B 527 PHE 0.037 0.003 PHE D 172 TRP 0.021 0.002 TRP C 30 HIS 0.008 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (16386) covalent geometry : angle 0.73623 / 0.39 (22134) hydrogen bonds : bond 0.05033 / 3.21 ( 871) hydrogen bonds : angle 5.29192 / 3.79 ( 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 864 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 790 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8822 (tppt) cc_final: 0.8409 (tppt) REVERT: A 76 ASP cc_start: 0.9048 (m-30) cc_final: 0.8416 (m-30) REVERT: A 156 PHE cc_start: 0.9304 (t80) cc_final: 0.9057 (t80) REVERT: A 174 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7331 (mt-10) REVERT: A 191 GLN cc_start: 0.8514 (mm-40) cc_final: 0.8268 (mm-40) REVERT: A 232 ASN cc_start: 0.9367 (OUTLIER) cc_final: 0.8925 (m-40) REVERT: A 250 TYR cc_start: 0.8735 (m-80) cc_final: 0.8361 (m-80) REVERT: A 257 ASP cc_start: 0.9251 (m-30) cc_final: 0.9048 (m-30) REVERT: A 291 LEU cc_start: 0.9570 (mt) cc_final: 0.9302 (mt) REVERT: A 335 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7909 (mt-10) REVERT: A 378 PHE cc_start: 0.8939 (p90) cc_final: 0.8588 (p90) REVERT: A 415 ASN cc_start: 0.9215 (t0) cc_final: 0.8818 (t0) REVERT: A 436 LEU cc_start: 0.9382 (mt) cc_final: 0.8981 (mt) REVERT: A 447 ASN cc_start: 0.8418 (m-40) cc_final: 0.7767 (t0) REVERT: A 471 TYR cc_start: 0.8903 (t80) cc_final: 0.8442 (t80) REVERT: A 505 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8586 (pt0) REVERT: A 515 ASP cc_start: 0.9010 (m-30) cc_final: 0.8566 (m-30) REVERT: A 516 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8322 (tp-100) REVERT: A 546 LEU cc_start: 0.9747 (mt) cc_final: 0.9391 (mt) REVERT: A 550 MET cc_start: 0.6597 (mtm) cc_final: 0.5830 (mtm) REVERT: A 595 MET cc_start: 0.9274 (mmp) cc_final: 0.9007 (mmp) REVERT: A 615 MET cc_start: 0.9227 (mmt) cc_final: 0.8856 (mmm) REVERT: A 645 GLN cc_start: 0.8538 (tp40) cc_final: 0.8214 (tp-100) REVERT: A 648 ILE cc_start: 0.9575 (mm) cc_final: 0.9182 (mm) REVERT: A 669 ARG cc_start: 0.9221 (tpp-160) cc_final: 0.8841 (tpp-160) REVERT: B 16 ILE cc_start: 0.9477 (pt) cc_final: 0.9276 (pt) REVERT: B 18 ILE cc_start: 0.9615 (mp) cc_final: 0.9338 (pt) REVERT: B 95 MET cc_start: 0.9058 (tpt) cc_final: 0.8727 (tpp) REVERT: B 99 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8998 (tptp) REVERT: B 102 ASN cc_start: 0.9414 (m110) cc_final: 0.9086 (m110) REVERT: B 107 LYS cc_start: 0.9339 (mttt) cc_final: 0.9104 (mmmm) REVERT: B 112 LYS cc_start: 0.9178 (pptt) cc_final: 0.8876 (pttm) REVERT: B 181 ASP cc_start: 0.8761 (m-30) cc_final: 0.8523 (m-30) REVERT: B 184 ARG cc_start: 0.9425 (tpp80) cc_final: 0.9010 (tpp80) REVERT: B 227 MET cc_start: 0.9252 (mtt) cc_final: 0.8979 (mtt) REVERT: B 250 TYR cc_start: 0.8945 (m-80) cc_final: 0.8740 (m-80) REVERT: B 322 MET cc_start: 0.9164 (mmm) cc_final: 0.8774 (mmt) REVERT: B 378 PHE cc_start: 0.9150 (p90) cc_final: 0.8848 (p90) REVERT: B 393 SER cc_start: 0.9304 (m) cc_final: 0.8782 (p) REVERT: B 399 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8610 (mm-30) REVERT: B 402 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7534 (tm-30) REVERT: B 471 TYR cc_start: 0.9299 (t80) cc_final: 0.8527 (t80) REVERT: B 475 ASN cc_start: 0.9110 (m-40) cc_final: 0.8557 (m-40) REVERT: B 515 ASP cc_start: 0.9232 (m-30) cc_final: 0.8816 (m-30) REVERT: B 558 TRP cc_start: 0.9251 (m100) cc_final: 0.8765 (m100) REVERT: B 570 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7951 (mtm) REVERT: B 583 SER cc_start: 0.8764 (m) cc_final: 0.8182 (t) REVERT: B 645 GLN cc_start: 0.9236 (tp-100) cc_final: 0.8769 (tp-100) REVERT: C 21 PHE cc_start: 0.9313 (m-80) cc_final: 0.8962 (m-80) REVERT: C 30 TRP cc_start: 0.7528 (p-90) cc_final: 0.6914 (t60) REVERT: C 74 MET cc_start: 0.9440 (mmm) cc_final: 0.9095 (mmm) REVERT: C 90 LEU cc_start: 0.8997 (mt) cc_final: 0.8636 (mt) REVERT: C 92 PHE cc_start: 0.9425 (t80) cc_final: 0.8558 (t80) REVERT: C 93 MET cc_start: 0.9444 (mtt) cc_final: 0.9140 (mtt) REVERT: C 95 MET cc_start: 0.9063 (tmm) cc_final: 0.8585 (tmm) REVERT: C 96 MET cc_start: 0.9090 (mmm) cc_final: 0.8097 (mmm) REVERT: C 109 PHE cc_start: 0.8378 (m-10) cc_final: 0.8117 (m-10) REVERT: C 130 TYR cc_start: 0.9633 (m-80) cc_final: 0.9373 (m-10) REVERT: C 145 ILE cc_start: 0.7461 (tp) cc_final: 0.6835 (tp) REVERT: C 155 LYS cc_start: 0.8671 (mttt) cc_final: 0.8235 (mmtt) REVERT: C 157 MET cc_start: 0.9283 (mtt) cc_final: 0.9004 (mtt) REVERT: C 173 TYR cc_start: 0.8398 (t80) cc_final: 0.7883 (t80) REVERT: C 174 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.7731 (t80) REVERT: C 197 ASP cc_start: 0.9608 (m-30) cc_final: 0.9259 (m-30) REVERT: C 201 HIS cc_start: 0.8892 (m90) cc_final: 0.8647 (m90) REVERT: C 224 LEU cc_start: 0.9109 (mt) cc_final: 0.8817 (mt) REVERT: C 241 GLU cc_start: 0.9599 (mp0) cc_final: 0.9156 (mp0) REVERT: C 242 TYR cc_start: 0.9336 (t80) cc_final: 0.8760 (t80) REVERT: C 259 PHE cc_start: 0.8866 (t80) cc_final: 0.7741 (t80) REVERT: C 263 ASN cc_start: 0.9597 (OUTLIER) cc_final: 0.8434 (p0) REVERT: D 30 TRP cc_start: 0.8021 (p-90) cc_final: 0.7802 (p-90) REVERT: D 50 ASN cc_start: 0.8974 (m-40) cc_final: 0.8471 (p0) REVERT: D 63 THR cc_start: 0.9313 (m) cc_final: 0.9103 (p) REVERT: D 96 MET cc_start: 0.8347 (mmm) cc_final: 0.8142 (mmt) REVERT: D 131 LEU cc_start: 0.8526 (tt) cc_final: 0.8110 (tp) REVERT: D 164 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8035 (mm-30) REVERT: D 167 LEU cc_start: 0.9725 (mt) cc_final: 0.9306 (mt) REVERT: D 168 PHE cc_start: 0.8453 (m-80) cc_final: 0.7602 (m-80) REVERT: D 174 TYR cc_start: 0.8724 (t80) cc_final: 0.8271 (t80) REVERT: D 198 GLU cc_start: 0.8517 (pp20) cc_final: 0.8000 (pp20) REVERT: D 254 HIS cc_start: 0.8960 (m90) cc_final: 0.8733 (m-70) outliers start: 74 outliers final: 33 residues processed: 821 average time/residue: 0.1137 time to fit residues: 140.1383 Evaluate side-chains 735 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 696 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 27 ASP Chi-restraints excluded: chain B residue 99 LYS 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 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 399 GLU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 427 LYS Chi-restraints excluded: chain B residue 570 MET 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 25 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: 0.7980 chunk 131 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 182 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 158 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 410 ASN ** 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 338 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** B 645 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 HIS C 127 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.117406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.088475 restraints weight = 41170.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.091665 restraints weight = 21197.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.093868 restraints weight = 13318.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.095506 restraints weight = 9351.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.096723 restraints weight = 7068.386| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.5618 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= 0.177 Angle : 0.723 14.620 22134 Z= 0.374 Chirality : 0.047 0.260 2360 Planarity : 0.004 0.039 2818 Dihedral : 9.324 130.713 2298 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.31 % Allowed : 24.53 % Favored : 71.15 % 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: 1.06 (0.18), residues: 1932 helix: 1.17 (0.15), residues: 1105 sheet: 0.70 (0.46), residues: 114 loop : 0.12 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 243 TYR 0.034 0.002 TYR D 142 PHE 0.037 0.002 PHE C 168 TRP 0.015 0.002 TRP C 44 HIS 0.008 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (16386) covalent geometry : angle 0.72320 / 0.37 (22134) hydrogen bonds : bond 0.04628 / 2.94 ( 871) hydrogen bonds : angle 5.26142 / 3.75 ( 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 852 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 778 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8898 (tppt) cc_final: 0.8681 (tppt) REVERT: A 31 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8755 (pm20) REVERT: A 76 ASP cc_start: 0.8920 (m-30) cc_final: 0.8616 (m-30) REVERT: A 138 LYS cc_start: 0.9215 (mmtt) cc_final: 0.8952 (mmtp) REVERT: A 147 GLN cc_start: 0.9124 (mt0) cc_final: 0.8616 (mt0) REVERT: A 161 ARG cc_start: 0.8439 (ttm110) cc_final: 0.8014 (ptm160) REVERT: A 174 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7604 (mt-10) REVERT: A 211 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7936 (mm-30) REVERT: A 221 LYS cc_start: 0.8926 (mttp) cc_final: 0.8567 (mttm) REVERT: A 250 TYR cc_start: 0.8825 (m-80) cc_final: 0.8582 (m-80) REVERT: A 255 HIS cc_start: 0.8745 (t-90) cc_final: 0.8180 (t-90) REVERT: A 325 LYS cc_start: 0.9586 (mmmt) cc_final: 0.9126 (mmtp) REVERT: A 335 GLU cc_start: 0.8224 (mt-10) cc_final: 0.8021 (mt-10) REVERT: A 360 PHE cc_start: 0.9082 (m-80) cc_final: 0.8859 (m-80) REVERT: A 436 LEU cc_start: 0.9411 (mt) cc_final: 0.9208 (mt) REVERT: A 447 ASN cc_start: 0.8301 (m-40) cc_final: 0.7624 (t0) REVERT: A 471 TYR cc_start: 0.9015 (t80) cc_final: 0.8666 (t80) REVERT: A 474 GLN cc_start: 0.9099 (mt0) cc_final: 0.8868 (mt0) REVERT: A 505 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8643 (mt-10) REVERT: A 509 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8395 (tm-30) REVERT: A 510 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8660 (mtpt) REVERT: A 515 ASP cc_start: 0.9086 (m-30) cc_final: 0.8767 (m-30) REVERT: A 516 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8437 (tp40) REVERT: A 546 LEU cc_start: 0.9708 (mt) cc_final: 0.9471 (mt) REVERT: A 590 SER cc_start: 0.9660 (t) cc_final: 0.9029 (p) REVERT: A 595 MET cc_start: 0.9198 (mmp) cc_final: 0.8879 (mmp) REVERT: A 600 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7845 (mtt-85) REVERT: A 615 MET cc_start: 0.9194 (mmt) cc_final: 0.8968 (mmm) REVERT: A 645 GLN cc_start: 0.8998 (tp40) cc_final: 0.8518 (tp-100) REVERT: A 647 HIS cc_start: 0.8814 (m-70) cc_final: 0.8091 (m90) REVERT: A 648 ILE cc_start: 0.9551 (mm) cc_final: 0.9290 (mm) REVERT: A 650 GLN cc_start: 0.8817 (mt0) cc_final: 0.8308 (mm-40) REVERT: B 8 LYS cc_start: 0.9213 (tptm) cc_final: 0.8930 (tptm) REVERT: B 18 ILE cc_start: 0.9638 (mp) cc_final: 0.9346 (pt) REVERT: B 54 LYS cc_start: 0.9600 (tttt) cc_final: 0.9289 (tttt) REVERT: B 82 LYS cc_start: 0.9586 (mtpp) cc_final: 0.9121 (ptpp) REVERT: B 95 MET cc_start: 0.9086 (tpt) cc_final: 0.8553 (tpp) REVERT: B 99 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.8589 (tptp) REVERT: B 102 ASN cc_start: 0.9496 (m110) cc_final: 0.9209 (m110) REVERT: B 181 ASP cc_start: 0.8831 (m-30) cc_final: 0.8586 (m-30) REVERT: B 250 TYR cc_start: 0.8965 (m-80) cc_final: 0.8751 (m-80) REVERT: B 263 ASP cc_start: 0.9215 (m-30) cc_final: 0.8855 (m-30) REVERT: B 266 LYS cc_start: 0.9057 (mtpp) cc_final: 0.8211 (mttp) REVERT: B 274 ARG cc_start: 0.8573 (ttm110) cc_final: 0.8211 (ttm110) REVERT: B 322 MET cc_start: 0.9182 (mmm) cc_final: 0.8831 (mmt) REVERT: B 341 LYS cc_start: 0.9589 (mmtm) cc_final: 0.9236 (mmmt) REVERT: B 344 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8751 (pt0) REVERT: B 348 MET cc_start: 0.8662 (tmm) cc_final: 0.8282 (tpt) REVERT: B 362 ASP cc_start: 0.8450 (m-30) cc_final: 0.8100 (m-30) REVERT: B 393 SER cc_start: 0.9335 (m) cc_final: 0.9051 (p) REVERT: B 396 ASP cc_start: 0.8879 (p0) cc_final: 0.8506 (p0) REVERT: B 399 GLU cc_start: 0.8994 (tp30) cc_final: 0.8583 (mm-30) REVERT: B 402 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7575 (tm-30) REVERT: B 471 TYR cc_start: 0.9140 (t80) cc_final: 0.8767 (t80) REVERT: B 475 ASN cc_start: 0.9043 (m-40) cc_final: 0.8669 (m110) REVERT: B 515 ASP cc_start: 0.9173 (m-30) cc_final: 0.8672 (m-30) REVERT: B 546 LEU cc_start: 0.9613 (mt) cc_final: 0.9236 (mt) REVERT: B 548 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7562 (mm-30) REVERT: B 550 MET cc_start: 0.8194 (mtp) cc_final: 0.7772 (mtp) REVERT: B 558 TRP cc_start: 0.9468 (m100) cc_final: 0.8712 (m100) REVERT: B 583 SER cc_start: 0.8955 (m) cc_final: 0.8426 (p) REVERT: B 645 GLN cc_start: 0.9360 (tp40) cc_final: 0.8906 (tp40) REVERT: B 668 ASN cc_start: 0.8995 (m110) cc_final: 0.8481 (m-40) REVERT: C 20 MET cc_start: 0.9424 (tmm) cc_final: 0.9150 (tmm) REVERT: C 21 PHE cc_start: 0.9456 (m-80) cc_final: 0.8682 (m-80) REVERT: C 55 TYR cc_start: 0.8844 (t80) cc_final: 0.8614 (m-80) REVERT: C 74 MET cc_start: 0.9349 (mmm) cc_final: 0.8604 (tpt) REVERT: C 79 GLU cc_start: 0.8810 (pt0) cc_final: 0.8510 (pt0) REVERT: C 89 VAL cc_start: 0.8607 (t) cc_final: 0.8403 (t) REVERT: C 90 LEU cc_start: 0.9171 (mt) cc_final: 0.8875 (mt) REVERT: C 92 PHE cc_start: 0.9511 (t80) cc_final: 0.8499 (t80) REVERT: C 93 MET cc_start: 0.9416 (mtt) cc_final: 0.9003 (mtt) REVERT: C 95 MET cc_start: 0.8939 (tmm) cc_final: 0.8537 (tmm) REVERT: C 96 MET cc_start: 0.9293 (mmm) cc_final: 0.8245 (mmm) REVERT: C 101 HIS cc_start: 0.8020 (m170) cc_final: 0.7143 (m-70) REVERT: C 109 PHE cc_start: 0.8311 (m-10) cc_final: 0.8078 (m-10) REVERT: C 134 LYS cc_start: 0.9428 (pttm) cc_final: 0.9194 (pttm) REVERT: C 174 TYR cc_start: 0.8714 (OUTLIER) cc_final: 0.7330 (t80) REVERT: C 197 ASP cc_start: 0.9601 (m-30) cc_final: 0.9331 (m-30) REVERT: C 201 HIS cc_start: 0.9155 (m90) cc_final: 0.8783 (m90) REVERT: C 242 TYR cc_start: 0.9430 (t80) cc_final: 0.8815 (t80) REVERT: C 259 PHE cc_start: 0.9025 (t80) cc_final: 0.8485 (t80) REVERT: C 269 MET cc_start: 0.9650 (ptt) cc_final: 0.9092 (mmp) REVERT: C 270 ASN cc_start: 0.8705 (m110) cc_final: 0.8453 (m-40) REVERT: D 20 MET cc_start: 0.9202 (ppp) cc_final: 0.8936 (ppp) REVERT: D 30 TRP cc_start: 0.8420 (p-90) cc_final: 0.8066 (p-90) REVERT: D 96 MET cc_start: 0.8124 (mmm) cc_final: 0.7773 (mmm) REVERT: D 131 LEU cc_start: 0.8728 (tt) cc_final: 0.8367 (tp) REVERT: D 155 LYS cc_start: 0.8269 (mttt) cc_final: 0.7799 (mtmm) REVERT: D 168 PHE cc_start: 0.8493 (m-80) cc_final: 0.7912 (m-80) REVERT: D 172 PHE cc_start: 0.8772 (m-80) cc_final: 0.8422 (m-80) REVERT: D 174 TYR cc_start: 0.8589 (t80) cc_final: 0.8270 (t80) REVERT: D 212 ILE cc_start: 0.9367 (mt) cc_final: 0.9144 (mt) REVERT: D 254 HIS cc_start: 0.8938 (m90) cc_final: 0.8724 (m-70) REVERT: D 268 LEU cc_start: 0.8857 (mm) cc_final: 0.8621 (mt) REVERT: D 282 ILE cc_start: 0.7676 (OUTLIER) cc_final: 0.7169 (pt) outliers start: 74 outliers final: 39 residues processed: 806 average time/residue: 0.1086 time to fit residues: 130.8275 Evaluate side-chains 752 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 707 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU 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 220 THR 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 437 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 27 ASP 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 239 GLN Chi-restraints excluded: chain B residue 267 ILE 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 460 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 626 TYR 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 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 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 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: 3.9990 chunk 157 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 127 optimal weight: 0.0370 chunk 60 optimal weight: 0.0000 chunk 185 optimal weight: 0.9980 chunk 191 optimal weight: 0.0570 chunk 159 optimal weight: 20.0000 chunk 182 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 313 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 GLN ** B 158 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 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 23 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.120772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.091275 restraints weight = 40900.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.094636 restraints weight = 21315.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.096910 restraints weight = 13294.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.098631 restraints weight = 9293.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.099773 restraints weight = 7049.096| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.6225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16386 Z= 0.146 Angle : 0.738 19.818 22134 Z= 0.374 Chirality : 0.047 0.253 2360 Planarity : 0.004 0.040 2818 Dihedral : 9.003 132.004 2296 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.73 % Allowed : 26.46 % Favored : 69.81 % 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: 0.96 (0.18), residues: 1932 helix: 1.10 (0.15), residues: 1104 sheet: 0.34 (0.44), residues: 118 loop : 0.12 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 243 TYR 0.031 0.001 TYR D 142 PHE 0.038 0.002 PHE C 168 TRP 0.008 0.002 TRP C 44 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (16386) covalent geometry : angle 0.73798 / 0.37 (22134) hydrogen bonds : bond 0.04375 / 2.79 ( 871) hydrogen bonds : angle 5.19750 / 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 803 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 739 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8994 (tppt) cc_final: 0.8664 (tppt) REVERT: A 30 LYS cc_start: 0.9015 (tptp) cc_final: 0.8771 (tptp) REVERT: A 31 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8716 (pm20) REVERT: A 76 ASP cc_start: 0.9014 (m-30) cc_final: 0.8655 (m-30) REVERT: A 82 LYS cc_start: 0.9509 (mttm) cc_final: 0.9291 (mmtm) REVERT: A 144 MET cc_start: 0.8379 (mmp) cc_final: 0.8173 (mmp) REVERT: A 147 GLN cc_start: 0.8977 (mt0) cc_final: 0.8328 (mm-40) REVERT: A 161 ARG cc_start: 0.8379 (ttm110) cc_final: 0.7733 (ptp-170) REVERT: A 202 ASN cc_start: 0.9489 (t0) cc_final: 0.9246 (t0) REVERT: A 205 LYS cc_start: 0.8676 (mttm) cc_final: 0.8308 (mtpt) REVERT: A 211 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7693 (mt-10) REVERT: A 221 LYS cc_start: 0.8932 (mttp) cc_final: 0.8619 (mttm) REVERT: A 295 ASP cc_start: 0.9203 (t0) cc_final: 0.8971 (t70) REVERT: A 325 LYS cc_start: 0.9568 (mmmt) cc_final: 0.9367 (mmtp) REVERT: A 335 GLU cc_start: 0.8232 (mt-10) cc_final: 0.8002 (mt-10) REVERT: A 447 ASN cc_start: 0.8238 (m-40) cc_final: 0.7466 (t0) REVERT: A 456 LYS cc_start: 0.9286 (ptpp) cc_final: 0.9017 (ptpp) REVERT: A 471 TYR cc_start: 0.8907 (t80) cc_final: 0.8513 (t80) REVERT: A 493 MET cc_start: 0.8964 (tmm) cc_final: 0.8587 (tmm) REVERT: A 505 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8518 (mt-10) REVERT: A 515 ASP cc_start: 0.9137 (m-30) cc_final: 0.8783 (m-30) REVERT: A 516 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8450 (tp40) REVERT: A 546 LEU cc_start: 0.9671 (mt) cc_final: 0.9400 (mt) REVERT: A 590 SER cc_start: 0.9564 (t) cc_final: 0.9049 (p) REVERT: A 595 MET cc_start: 0.9161 (mmp) cc_final: 0.8787 (mmp) REVERT: A 599 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8227 (mm-30) REVERT: A 639 ASP cc_start: 0.8779 (m-30) cc_final: 0.8389 (m-30) REVERT: A 645 GLN cc_start: 0.8809 (tp40) cc_final: 0.8423 (tp-100) REVERT: A 665 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8803 (ttt-90) REVERT: B 8 LYS cc_start: 0.9259 (tptm) cc_final: 0.9014 (tptm) REVERT: B 18 ILE cc_start: 0.9634 (mp) cc_final: 0.9319 (pt) REVERT: B 82 LYS cc_start: 0.9586 (mtpp) cc_final: 0.9118 (ptpp) REVERT: B 95 MET cc_start: 0.9055 (tpt) cc_final: 0.8486 (tpp) REVERT: B 99 LYS cc_start: 0.9336 (tptp) cc_final: 0.8682 (tptp) REVERT: B 102 ASN cc_start: 0.9486 (m110) cc_final: 0.9244 (m110) REVERT: B 107 LYS cc_start: 0.9371 (mmtp) cc_final: 0.9159 (mmmm) REVERT: B 112 LYS cc_start: 0.9179 (pptt) cc_final: 0.8835 (pttm) REVERT: B 168 VAL cc_start: 0.9239 (t) cc_final: 0.8952 (m) REVERT: B 181 ASP cc_start: 0.8814 (m-30) cc_final: 0.8474 (m-30) REVERT: B 250 TYR cc_start: 0.8996 (m-80) cc_final: 0.8726 (m-80) REVERT: B 263 ASP cc_start: 0.9173 (m-30) cc_final: 0.8704 (m-30) REVERT: B 266 LYS cc_start: 0.9044 (mtpp) cc_final: 0.8801 (mttm) REVERT: B 322 MET cc_start: 0.9275 (mmm) cc_final: 0.8929 (mmt) REVERT: B 333 LYS cc_start: 0.9110 (tttm) cc_final: 0.8772 (tttm) REVERT: B 341 LYS cc_start: 0.9614 (mmtm) cc_final: 0.8901 (mmmt) REVERT: B 348 MET cc_start: 0.8739 (tmm) cc_final: 0.8491 (tpt) REVERT: B 362 ASP cc_start: 0.8566 (m-30) cc_final: 0.8143 (m-30) REVERT: B 375 LYS cc_start: 0.9065 (mmmm) cc_final: 0.8580 (mmmm) REVERT: B 396 ASP cc_start: 0.8841 (p0) cc_final: 0.7994 (p0) REVERT: B 399 GLU cc_start: 0.8938 (tp30) cc_final: 0.8559 (mp0) REVERT: B 402 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7712 (tm-30) REVERT: B 475 ASN cc_start: 0.9145 (m-40) cc_final: 0.8690 (m110) REVERT: B 483 GLU cc_start: 0.9444 (mp0) cc_final: 0.9120 (mp0) REVERT: B 515 ASP cc_start: 0.9155 (m-30) cc_final: 0.8625 (m-30) REVERT: B 522 TYR cc_start: 0.8716 (m-10) cc_final: 0.8319 (m-10) REVERT: B 548 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7682 (mm-30) REVERT: B 550 MET cc_start: 0.8083 (mtp) cc_final: 0.7737 (mtp) REVERT: B 558 TRP cc_start: 0.9506 (m100) cc_final: 0.8738 (m100) REVERT: B 571 TYR cc_start: 0.8678 (t80) cc_final: 0.8423 (t80) REVERT: B 583 SER cc_start: 0.8966 (m) cc_final: 0.8403 (p) REVERT: B 602 GLU cc_start: 0.8353 (pt0) cc_final: 0.7987 (pt0) REVERT: B 645 GLN cc_start: 0.9308 (tp40) cc_final: 0.8957 (tp-100) REVERT: B 668 ASN cc_start: 0.9081 (m110) cc_final: 0.8560 (m110) REVERT: B 686 ARG cc_start: 0.8339 (ttm170) cc_final: 0.8036 (mpt-90) REVERT: C 20 MET cc_start: 0.9449 (tmm) cc_final: 0.9172 (tmm) REVERT: C 21 PHE cc_start: 0.9494 (m-80) cc_final: 0.8712 (m-80) REVERT: C 55 TYR cc_start: 0.8805 (t80) cc_final: 0.8329 (m-80) REVERT: C 74 MET cc_start: 0.9302 (mmm) cc_final: 0.8785 (tpp) REVERT: C 79 GLU cc_start: 0.8801 (pt0) cc_final: 0.8405 (pt0) REVERT: C 89 VAL cc_start: 0.8689 (t) cc_final: 0.8344 (t) REVERT: C 90 LEU cc_start: 0.9191 (mt) cc_final: 0.8989 (mt) REVERT: C 92 PHE cc_start: 0.9569 (t80) cc_final: 0.9301 (t80) REVERT: C 93 MET cc_start: 0.9418 (mtt) cc_final: 0.8980 (mtt) REVERT: C 101 HIS cc_start: 0.7885 (m170) cc_final: 0.7272 (m-70) REVERT: C 109 PHE cc_start: 0.8225 (m-10) cc_final: 0.8011 (m-10) REVERT: C 130 TYR cc_start: 0.9605 (m-80) cc_final: 0.9283 (m-10) REVERT: C 134 LYS cc_start: 0.9443 (pttm) cc_final: 0.9200 (pttm) REVERT: C 174 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.6976 (t80) REVERT: C 185 MET cc_start: 0.8175 (mmm) cc_final: 0.7680 (mmm) REVERT: C 189 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8120 (mm-30) REVERT: C 197 ASP cc_start: 0.9647 (m-30) cc_final: 0.9410 (m-30) REVERT: C 198 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8953 (mm-30) REVERT: C 201 HIS cc_start: 0.9115 (m90) cc_final: 0.8805 (m90) REVERT: C 242 TYR cc_start: 0.9477 (t80) cc_final: 0.8809 (t80) REVERT: C 259 PHE cc_start: 0.8980 (t80) cc_final: 0.8335 (t80) REVERT: C 269 MET cc_start: 0.9583 (ptt) cc_final: 0.9166 (mmp) REVERT: C 270 ASN cc_start: 0.8609 (m110) cc_final: 0.8305 (m110) REVERT: D 20 MET cc_start: 0.9426 (ppp) cc_final: 0.9216 (ppp) REVERT: D 96 MET cc_start: 0.8118 (mmm) cc_final: 0.7822 (mmm) REVERT: D 131 LEU cc_start: 0.8851 (tt) cc_final: 0.8590 (tp) REVERT: D 149 ASP cc_start: 0.9002 (m-30) cc_final: 0.8794 (p0) REVERT: D 168 PHE cc_start: 0.8521 (m-80) cc_final: 0.7502 (m-80) REVERT: D 169 TYR cc_start: 0.8186 (m-80) cc_final: 0.7702 (m-80) REVERT: D 173 TYR cc_start: 0.8793 (t80) cc_final: 0.8476 (t80) REVERT: D 242 TYR cc_start: 0.8730 (t80) cc_final: 0.8502 (t80) REVERT: D 268 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8483 (mt) outliers start: 64 outliers final: 40 residues processed: 764 average time/residue: 0.1277 time to fit residues: 146.9182 Evaluate side-chains 734 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 690 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU 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 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 408 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 667 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 223 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 565 VAL 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 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 312 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 153 LEU 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 312 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 126 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 168 optimal weight: 10.0000 chunk 157 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 370 ASN ** B 387 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 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN C 263 ASN D 23 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 210 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.115507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.086987 restraints weight = 40608.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.090113 restraints weight = 21543.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.092297 restraints weight = 13844.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.093817 restraints weight = 9866.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.094953 restraints weight = 7552.526| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.6597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16386 Z= 0.156 Angle : 0.718 15.981 22134 Z= 0.368 Chirality : 0.047 0.258 2360 Planarity : 0.004 0.047 2818 Dihedral : 8.931 132.316 2296 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.55 % Allowed : 26.57 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.18), residues: 1932 helix: 1.05 (0.15), residues: 1121 sheet: 0.17 (0.44), residues: 114 loop : 0.08 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 686 TYR 0.047 0.002 TYR D 142 PHE 0.034 0.002 PHE C 168 TRP 0.025 0.002 TRP D 30 HIS 0.008 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (16386) covalent geometry : angle 0.71785 / 0.37 (22134) hydrogen bonds : bond 0.04298 / 2.74 ( 871) hydrogen bonds : angle 5.21632 / 3.67 ( 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 788 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 710 time to evaluate : 0.449 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 8 LYS cc_start: 0.9105 (tppt) cc_final: 0.8826 (tppt) REVERT: A 12 LEU cc_start: 0.9582 (mp) cc_final: 0.9335 (mp) REVERT: A 31 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8701 (pm20) REVERT: A 76 ASP cc_start: 0.9062 (m-30) cc_final: 0.8682 (m-30) REVERT: A 82 LYS cc_start: 0.9525 (mttm) cc_final: 0.9258 (mmtt) REVERT: A 147 GLN cc_start: 0.9120 (mt0) cc_final: 0.8552 (mt0) REVERT: A 161 ARG cc_start: 0.8455 (ttm110) cc_final: 0.7865 (ptp-170) REVERT: A 166 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7363 (mm-30) REVERT: A 205 LYS cc_start: 0.8743 (mttm) cc_final: 0.8338 (mtpp) REVERT: A 221 LYS cc_start: 0.8879 (mttp) cc_final: 0.8580 (mttm) REVERT: A 250 TYR cc_start: 0.8712 (m-80) cc_final: 0.8497 (m-10) REVERT: A 255 HIS cc_start: 0.8645 (t-90) cc_final: 0.8385 (t-90) REVERT: A 325 LYS cc_start: 0.9659 (mmmt) cc_final: 0.9392 (mmtp) REVERT: A 335 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7988 (mt-10) REVERT: A 362 ASP cc_start: 0.8224 (m-30) cc_final: 0.7887 (m-30) REVERT: A 420 MET cc_start: 0.9079 (mmm) cc_final: 0.8661 (mmm) REVERT: A 443 THR cc_start: 0.8495 (t) cc_final: 0.8238 (t) REVERT: A 471 TYR cc_start: 0.9062 (t80) cc_final: 0.8692 (t80) REVERT: A 493 MET cc_start: 0.8919 (tmm) cc_final: 0.8500 (tmm) REVERT: A 505 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8248 (mt-10) REVERT: A 515 ASP cc_start: 0.9124 (m-30) cc_final: 0.8793 (m-30) REVERT: A 516 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8379 (tp40) REVERT: A 546 LEU cc_start: 0.9684 (mt) cc_final: 0.9440 (mt) REVERT: A 590 SER cc_start: 0.9541 (t) cc_final: 0.8980 (p) REVERT: A 600 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7727 (mtt-85) REVERT: A 615 MET cc_start: 0.9155 (mmm) cc_final: 0.8792 (mmm) REVERT: A 628 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8591 (mm-30) REVERT: A 639 ASP cc_start: 0.8712 (m-30) cc_final: 0.8300 (m-30) REVERT: A 640 MET cc_start: 0.9483 (tpp) cc_final: 0.9098 (tpp) REVERT: A 645 GLN cc_start: 0.8901 (tp40) cc_final: 0.8459 (tp-100) REVERT: A 665 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8824 (ttt-90) REVERT: B 8 LYS cc_start: 0.9278 (tptm) cc_final: 0.9055 (tptm) REVERT: B 82 LYS cc_start: 0.9580 (mtpp) cc_final: 0.9105 (ptpp) REVERT: B 95 MET cc_start: 0.9064 (tpt) cc_final: 0.8489 (tpp) REVERT: B 99 LYS cc_start: 0.9357 (tptp) cc_final: 0.8762 (tptp) REVERT: B 102 ASN cc_start: 0.9473 (m110) cc_final: 0.9246 (m110) REVERT: B 107 LYS cc_start: 0.9356 (mmtp) cc_final: 0.9095 (mmmm) REVERT: B 168 VAL cc_start: 0.9305 (t) cc_final: 0.9028 (m) REVERT: B 181 ASP cc_start: 0.8765 (m-30) cc_final: 0.8414 (m-30) REVERT: B 235 ARG cc_start: 0.9081 (ptp-110) cc_final: 0.8724 (mtm-85) REVERT: B 250 TYR cc_start: 0.8886 (m-80) cc_final: 0.8632 (m-80) REVERT: B 256 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8267 (tpt90) REVERT: B 263 ASP cc_start: 0.9213 (m-30) cc_final: 0.8797 (m-30) REVERT: B 266 LYS cc_start: 0.9081 (mtpp) cc_final: 0.8852 (mttm) REVERT: B 322 MET cc_start: 0.9280 (mmm) cc_final: 0.8926 (mmt) REVERT: B 333 LYS cc_start: 0.9153 (tttm) cc_final: 0.8855 (tttm) REVERT: B 348 MET cc_start: 0.8816 (tmm) cc_final: 0.8397 (tpt) REVERT: B 362 ASP cc_start: 0.8592 (m-30) cc_final: 0.8335 (m-30) REVERT: B 375 LYS cc_start: 0.9124 (mmmm) cc_final: 0.8514 (mmmm) REVERT: B 396 ASP cc_start: 0.8850 (p0) cc_final: 0.8442 (p0) REVERT: B 399 GLU cc_start: 0.9011 (tp30) cc_final: 0.8600 (mm-30) REVERT: B 402 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7880 (tm-30) REVERT: B 475 ASN cc_start: 0.9273 (m-40) cc_final: 0.8988 (m110) REVERT: B 515 ASP cc_start: 0.9171 (m-30) cc_final: 0.8674 (m-30) REVERT: B 548 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7622 (mm-30) REVERT: B 550 MET cc_start: 0.7978 (mtp) cc_final: 0.7766 (mtp) REVERT: B 558 TRP cc_start: 0.9505 (m100) cc_final: 0.8769 (m100) REVERT: B 583 SER cc_start: 0.9055 (m) cc_final: 0.8482 (p) REVERT: B 602 GLU cc_start: 0.8406 (pt0) cc_final: 0.8060 (pt0) REVERT: B 645 GLN cc_start: 0.9363 (tp40) cc_final: 0.9005 (tp40) REVERT: B 650 GLN cc_start: 0.8547 (mt0) cc_final: 0.8200 (mt0) REVERT: B 668 ASN cc_start: 0.9118 (m110) cc_final: 0.8587 (m110) REVERT: B 686 ARG cc_start: 0.8354 (ttm170) cc_final: 0.8050 (mpt-90) REVERT: C 20 MET cc_start: 0.9513 (tmm) cc_final: 0.9234 (tmm) REVERT: C 21 PHE cc_start: 0.9523 (m-80) cc_final: 0.8749 (m-80) REVERT: C 55 TYR cc_start: 0.8880 (t80) cc_final: 0.8329 (m-80) REVERT: C 74 MET cc_start: 0.9366 (mmm) cc_final: 0.8875 (tpp) REVERT: C 89 VAL cc_start: 0.8779 (t) cc_final: 0.8431 (t) REVERT: C 92 PHE cc_start: 0.9557 (t80) cc_final: 0.8974 (t80) REVERT: C 93 MET cc_start: 0.9447 (mtt) cc_final: 0.9053 (mtt) REVERT: C 96 MET cc_start: 0.9083 (mmm) cc_final: 0.8443 (mmm) REVERT: C 101 HIS cc_start: 0.8163 (m170) cc_final: 0.7372 (m-70) REVERT: C 109 PHE cc_start: 0.8276 (m-10) cc_final: 0.7889 (m-10) REVERT: C 134 LYS cc_start: 0.9444 (pttm) cc_final: 0.9103 (pttt) REVERT: C 174 TYR cc_start: 0.7871 (OUTLIER) cc_final: 0.6873 (t80) REVERT: C 198 GLU cc_start: 0.9230 (mm-30) cc_final: 0.8922 (mm-30) REVERT: C 201 HIS cc_start: 0.9141 (m90) cc_final: 0.8756 (m90) REVERT: C 252 LEU cc_start: 0.8386 (pp) cc_final: 0.7813 (tt) REVERT: C 259 PHE cc_start: 0.9099 (t80) cc_final: 0.8328 (t80) REVERT: C 263 ASN cc_start: 0.9673 (m-40) cc_final: 0.9356 (p0) REVERT: C 269 MET cc_start: 0.9495 (OUTLIER) cc_final: 0.9132 (mmp) REVERT: C 270 ASN cc_start: 0.8679 (m110) cc_final: 0.8456 (m110) REVERT: D 96 MET cc_start: 0.8116 (mmm) cc_final: 0.7903 (mmt) REVERT: D 131 LEU cc_start: 0.8925 (tt) cc_final: 0.8604 (tp) REVERT: D 168 PHE cc_start: 0.8660 (m-80) cc_final: 0.7589 (m-80) REVERT: D 169 TYR cc_start: 0.8332 (m-80) cc_final: 0.7886 (m-80) REVERT: D 174 TYR cc_start: 0.8875 (t80) cc_final: 0.8218 (t80) REVERT: D 242 TYR cc_start: 0.8709 (t80) cc_final: 0.8289 (t80) REVERT: D 268 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8508 (mt) outliers start: 78 outliers final: 52 residues processed: 743 average time/residue: 0.1293 time to fit residues: 145.1361 Evaluate side-chains 723 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 664 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 31 GLU 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 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 411 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 445 ILE 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 600 ARG Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 THR 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 239 GLN 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 342 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 410 ASN 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 573 SER 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 216 GLN 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 47 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 203 VAL 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: 0.9990 chunk 183 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 136 optimal weight: 0.0570 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 ASN ** 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 101 HIS D 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.113659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.086109 restraints weight = 40919.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.089226 restraints weight = 21523.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.091468 restraints weight = 13590.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.092985 restraints weight = 9574.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.094084 restraints weight = 7244.189| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 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 = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.6932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16386 Z= 0.147 Angle : 0.753 19.035 22134 Z= 0.377 Chirality : 0.047 0.262 2360 Planarity : 0.004 0.039 2818 Dihedral : 8.803 132.970 2296 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.73 % Allowed : 29.25 % Favored : 67.02 % 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: 0.74 (0.18), residues: 1932 helix: 0.98 (0.15), residues: 1115 sheet: -0.76 (0.40), residues: 148 loop : 0.19 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 350 TYR 0.035 0.002 TYR C 46 PHE 0.038 0.002 PHE C 172 TRP 0.020 0.002 TRP D 30 HIS 0.007 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (16386) covalent geometry : angle 0.75345 / 0.38 (22134) hydrogen bonds : bond 0.04201 / 2.67 ( 871) hydrogen bonds : angle 5.23849 / 3.67 ( 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 778 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 714 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9093 (tppt) cc_final: 0.8825 (tppt) REVERT: A 31 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8727 (pm20) REVERT: A 56 ASP cc_start: 0.8856 (m-30) cc_final: 0.8433 (m-30) REVERT: A 76 ASP cc_start: 0.9043 (m-30) cc_final: 0.8654 (m-30) REVERT: A 82 LYS cc_start: 0.9506 (mttm) cc_final: 0.9203 (mmmt) REVERT: A 144 MET cc_start: 0.8503 (mmp) cc_final: 0.8275 (mmp) REVERT: A 147 GLN cc_start: 0.9084 (mt0) cc_final: 0.8448 (mm-40) REVERT: A 150 GLN cc_start: 0.9483 (tp40) cc_final: 0.9082 (tp40) REVERT: A 161 ARG cc_start: 0.8463 (ttm110) cc_final: 0.7730 (ptp-170) REVERT: A 205 LYS cc_start: 0.8663 (mttm) cc_final: 0.8221 (mtpp) REVERT: A 250 TYR cc_start: 0.8791 (m-80) cc_final: 0.8546 (m-10) REVERT: A 255 HIS cc_start: 0.8614 (t-90) cc_final: 0.8361 (t-90) REVERT: A 290 GLU cc_start: 0.9052 (tm-30) cc_final: 0.8645 (tm-30) REVERT: A 325 LYS cc_start: 0.9635 (mmmt) cc_final: 0.9401 (mmtp) REVERT: A 420 MET cc_start: 0.9062 (mmm) cc_final: 0.8638 (mmm) REVERT: A 443 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.8110 (t) REVERT: A 456 LYS cc_start: 0.9270 (ptpp) cc_final: 0.8984 (ptpp) REVERT: A 471 TYR cc_start: 0.9050 (t80) cc_final: 0.8741 (t80) REVERT: A 493 MET cc_start: 0.8859 (tmm) cc_final: 0.8461 (tmm) REVERT: A 494 MET cc_start: 0.9104 (mtp) cc_final: 0.8877 (mtp) REVERT: A 505 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8265 (mt-10) REVERT: A 515 ASP cc_start: 0.9123 (m-30) cc_final: 0.8766 (m-30) REVERT: A 516 GLN cc_start: 0.8926 (mm-40) cc_final: 0.8378 (tp40) REVERT: A 546 LEU cc_start: 0.9668 (mt) cc_final: 0.9435 (mt) REVERT: A 590 SER cc_start: 0.9486 (t) cc_final: 0.8952 (p) REVERT: A 600 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7697 (mtt-85) REVERT: A 606 TYR cc_start: 0.8025 (m-80) cc_final: 0.7599 (m-80) REVERT: A 615 MET cc_start: 0.9182 (mmm) cc_final: 0.8805 (mmm) REVERT: A 639 ASP cc_start: 0.8680 (m-30) cc_final: 0.8243 (m-30) REVERT: A 645 GLN cc_start: 0.8879 (tp40) cc_final: 0.8484 (tp-100) REVERT: B 8 LYS cc_start: 0.9266 (tptm) cc_final: 0.9043 (tptm) REVERT: B 82 LYS cc_start: 0.9583 (mtpp) cc_final: 0.9220 (mmtm) REVERT: B 95 MET cc_start: 0.9025 (tpt) cc_final: 0.8212 (tpp) REVERT: B 99 LYS cc_start: 0.9322 (tptp) cc_final: 0.8760 (tptp) REVERT: B 102 ASN cc_start: 0.9494 (m110) cc_final: 0.9276 (m110) REVERT: B 107 LYS cc_start: 0.9374 (mmtp) cc_final: 0.9101 (mmmm) REVERT: B 110 ASP cc_start: 0.9188 (p0) cc_final: 0.8970 (p0) REVERT: B 112 LYS cc_start: 0.9154 (pptt) cc_final: 0.8873 (pttm) REVERT: B 119 GLU cc_start: 0.9024 (mp0) cc_final: 0.8525 (mp0) REVERT: B 168 VAL cc_start: 0.9306 (t) cc_final: 0.8994 (m) REVERT: B 181 ASP cc_start: 0.8767 (m-30) cc_final: 0.8504 (m-30) REVERT: B 256 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8074 (tpt90) REVERT: B 263 ASP cc_start: 0.9155 (m-30) cc_final: 0.8775 (m-30) REVERT: B 266 LYS cc_start: 0.9122 (mtpp) cc_final: 0.8896 (mttm) REVERT: B 322 MET cc_start: 0.9301 (mmm) cc_final: 0.8935 (mmt) REVERT: B 333 LYS cc_start: 0.9107 (tttm) cc_final: 0.8767 (tttm) REVERT: B 348 MET cc_start: 0.8800 (tmm) cc_final: 0.8421 (tpt) REVERT: B 358 ILE cc_start: 0.9536 (mm) cc_final: 0.9074 (tp) REVERT: B 362 ASP cc_start: 0.8636 (m-30) cc_final: 0.8088 (m-30) REVERT: B 396 ASP cc_start: 0.8780 (p0) cc_final: 0.8570 (p0) REVERT: B 399 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8617 (mm-30) REVERT: B 402 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7910 (tm-30) REVERT: B 475 ASN cc_start: 0.9338 (m-40) cc_final: 0.9063 (m110) REVERT: B 515 ASP cc_start: 0.9096 (m-30) cc_final: 0.8621 (m-30) REVERT: B 548 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7647 (mm-30) REVERT: B 558 TRP cc_start: 0.9471 (m100) cc_final: 0.8768 (m100) REVERT: B 583 SER cc_start: 0.9015 (m) cc_final: 0.8464 (p) REVERT: B 586 TYR cc_start: 0.9265 (m-80) cc_final: 0.8623 (m-80) REVERT: B 595 MET cc_start: 0.9155 (mmm) cc_final: 0.8785 (mmm) REVERT: B 602 GLU cc_start: 0.8428 (pt0) cc_final: 0.5040 (pt0) REVERT: B 645 GLN cc_start: 0.9300 (tp40) cc_final: 0.9008 (tp-100) REVERT: B 650 GLN cc_start: 0.8410 (mt0) cc_final: 0.8145 (mt0) REVERT: B 668 ASN cc_start: 0.9099 (m110) cc_final: 0.8544 (m110) REVERT: B 683 TYR cc_start: 0.8818 (t80) cc_final: 0.8404 (t80) REVERT: B 686 ARG cc_start: 0.8359 (ttm170) cc_final: 0.7987 (mpt-90) REVERT: C 20 MET cc_start: 0.9538 (tmm) cc_final: 0.9253 (tmm) REVERT: C 21 PHE cc_start: 0.9535 (m-80) cc_final: 0.8785 (m-80) REVERT: C 30 TRP cc_start: 0.7435 (t60) cc_final: 0.7075 (t60) REVERT: C 55 TYR cc_start: 0.8971 (t80) cc_final: 0.8334 (m-80) REVERT: C 92 PHE cc_start: 0.9587 (t80) cc_final: 0.8711 (t80) REVERT: C 96 MET cc_start: 0.9074 (mmm) cc_final: 0.8408 (mmm) REVERT: C 109 PHE cc_start: 0.7998 (m-10) cc_final: 0.7756 (m-10) REVERT: C 174 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.7075 (t80) REVERT: C 198 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8920 (mm-30) REVERT: C 201 HIS cc_start: 0.9083 (m90) cc_final: 0.8842 (m90) REVERT: C 242 TYR cc_start: 0.9504 (t80) cc_final: 0.9090 (t80) REVERT: C 259 PHE cc_start: 0.9269 (t80) cc_final: 0.8539 (t80) REVERT: C 260 ILE cc_start: 0.9037 (pt) cc_final: 0.8524 (pp) REVERT: C 263 ASN cc_start: 0.9607 (m-40) cc_final: 0.9397 (p0) REVERT: C 269 MET cc_start: 0.9579 (OUTLIER) cc_final: 0.9025 (mmp) REVERT: D 30 TRP cc_start: 0.8228 (p-90) cc_final: 0.7675 (p-90) REVERT: D 131 LEU cc_start: 0.8967 (tt) cc_final: 0.8666 (tp) REVERT: D 137 MET cc_start: 0.8403 (mmt) cc_final: 0.7875 (mpp) REVERT: D 168 PHE cc_start: 0.8710 (m-80) cc_final: 0.7623 (m-80) REVERT: D 169 TYR cc_start: 0.8228 (m-80) cc_final: 0.7830 (m-80) REVERT: D 174 TYR cc_start: 0.8934 (OUTLIER) cc_final: 0.8267 (t80) REVERT: D 242 TYR cc_start: 0.8849 (t80) cc_final: 0.8478 (t80) REVERT: D 268 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8449 (mt) outliers start: 64 outliers final: 42 residues processed: 739 average time/residue: 0.1310 time to fit residues: 145.3151 Evaluate side-chains 712 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 661 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 58 LEU 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 183 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 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 239 GLN 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 284 ILE Chi-restraints excluded: chain B residue 342 LEU 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 460 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 565 VAL 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 255 ASP Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 58 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: 1.9990 chunk 51 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 186 optimal weight: 9.9990 chunk 140 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.120126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.090691 restraints weight = 40530.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.093912 restraints weight = 21374.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.096229 restraints weight = 13613.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.097828 restraints weight = 9624.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.099030 restraints weight = 7379.157| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (15 function evaluations) r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.7195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16386 Z= 0.148 Angle : 0.776 16.731 22134 Z= 0.389 Chirality : 0.048 0.263 2360 Planarity : 0.004 0.052 2818 Dihedral : 8.739 133.730 2294 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.73 % Allowed : 31.59 % Favored : 64.69 % 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: 0.54 (0.18), residues: 1932 helix: 0.78 (0.15), residues: 1123 sheet: -0.79 (0.39), residues: 158 loop : 0.14 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 686 TYR 0.032 0.002 TYR C 46 PHE 0.035 0.002 PHE B 261 TRP 0.016 0.002 TRP D 30 HIS 0.005 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (16386) covalent geometry : angle 0.77595 / 0.39 (22134) hydrogen bonds : bond 0.04200 / 2.66 ( 871) hydrogen bonds : angle 5.25398 / 3.70 ( 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 774 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 710 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8668 (pm20) REVERT: A 56 ASP cc_start: 0.8791 (m-30) cc_final: 0.8345 (m-30) REVERT: A 76 ASP cc_start: 0.8998 (m-30) cc_final: 0.8719 (m-30) REVERT: A 82 LYS cc_start: 0.9483 (mttm) cc_final: 0.9199 (mmmt) REVERT: A 87 LYS cc_start: 0.9031 (tptm) cc_final: 0.8717 (tttt) REVERT: A 147 GLN cc_start: 0.9073 (mt0) cc_final: 0.8516 (mt0) REVERT: A 150 GLN cc_start: 0.9469 (tp40) cc_final: 0.9085 (tp40) REVERT: A 161 ARG cc_start: 0.8304 (ttm110) cc_final: 0.7679 (ptp-170) REVERT: A 178 SER cc_start: 0.8231 (OUTLIER) cc_final: 0.7564 (t) REVERT: A 205 LYS cc_start: 0.8656 (mttm) cc_final: 0.8200 (mtpp) REVERT: A 266 LYS cc_start: 0.8695 (ptmm) cc_final: 0.8214 (ptmm) REVERT: A 290 GLU cc_start: 0.9045 (tm-30) cc_final: 0.8599 (tm-30) REVERT: A 413 SER cc_start: 0.9442 (m) cc_final: 0.8972 (t) REVERT: A 443 THR cc_start: 0.8334 (OUTLIER) cc_final: 0.7754 (t) REVERT: A 447 ASN cc_start: 0.7438 (t0) cc_final: 0.6674 (t0) REVERT: A 456 LYS cc_start: 0.9267 (ptpp) cc_final: 0.8966 (ptpp) REVERT: A 471 TYR cc_start: 0.9075 (t80) cc_final: 0.8800 (t80) REVERT: A 493 MET cc_start: 0.8871 (tmm) cc_final: 0.8463 (tmm) REVERT: A 505 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8235 (mt-10) REVERT: A 515 ASP cc_start: 0.9078 (m-30) cc_final: 0.8780 (m-30) REVERT: A 516 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8384 (tp40) REVERT: A 546 LEU cc_start: 0.9625 (mt) cc_final: 0.9422 (mt) REVERT: A 590 SER cc_start: 0.9509 (t) cc_final: 0.8951 (p) REVERT: A 595 MET cc_start: 0.8936 (mmm) cc_final: 0.8722 (mmt) REVERT: A 600 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8267 (mtt-85) REVERT: A 606 TYR cc_start: 0.8133 (m-80) cc_final: 0.7627 (m-80) REVERT: A 639 ASP cc_start: 0.8587 (m-30) cc_final: 0.8136 (m-30) REVERT: A 645 GLN cc_start: 0.8974 (tp40) cc_final: 0.8513 (tp-100) REVERT: A 686 ARG cc_start: 0.8215 (ttm110) cc_final: 0.7555 (mtp-110) REVERT: B 8 LYS cc_start: 0.9256 (tptm) cc_final: 0.9038 (tptm) REVERT: B 82 LYS cc_start: 0.9562 (mtpp) cc_final: 0.9225 (ptpp) REVERT: B 95 MET cc_start: 0.8992 (tpt) cc_final: 0.8371 (tpp) REVERT: B 99 LYS cc_start: 0.9340 (tptp) cc_final: 0.8789 (tptp) REVERT: B 107 LYS cc_start: 0.9357 (mmtp) cc_final: 0.9052 (mmmm) REVERT: B 110 ASP cc_start: 0.9082 (p0) cc_final: 0.8854 (p0) REVERT: B 117 ARG cc_start: 0.8906 (mtp85) cc_final: 0.8685 (mtp85) REVERT: B 119 GLU cc_start: 0.8993 (mp0) cc_final: 0.8492 (mp0) REVERT: B 168 VAL cc_start: 0.9307 (t) cc_final: 0.9040 (m) REVERT: B 181 ASP cc_start: 0.8822 (m-30) cc_final: 0.8124 (m-30) REVERT: B 191 GLN cc_start: 0.9044 (mm-40) cc_final: 0.8664 (mm-40) REVERT: B 235 ARG cc_start: 0.9098 (ptp-110) cc_final: 0.8862 (mtm-85) REVERT: B 256 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8440 (ttp80) REVERT: B 263 ASP cc_start: 0.9063 (m-30) cc_final: 0.8687 (m-30) REVERT: B 322 MET cc_start: 0.9269 (mmm) cc_final: 0.8888 (mmt) REVERT: B 333 LYS cc_start: 0.9069 (tttm) cc_final: 0.8718 (tttm) REVERT: B 348 MET cc_start: 0.8736 (tmm) cc_final: 0.8420 (tpt) REVERT: B 358 ILE cc_start: 0.9607 (mm) cc_final: 0.9089 (tp) REVERT: B 362 ASP cc_start: 0.8530 (m-30) cc_final: 0.8279 (m-30) REVERT: B 396 ASP cc_start: 0.8789 (p0) cc_final: 0.8105 (p0) REVERT: B 399 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8500 (mm-30) REVERT: B 402 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7891 (tm-30) REVERT: B 475 ASN cc_start: 0.9245 (m-40) cc_final: 0.8992 (m110) REVERT: B 515 ASP cc_start: 0.8999 (m-30) cc_final: 0.8559 (m-30) REVERT: B 548 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7655 (mm-30) REVERT: B 558 TRP cc_start: 0.9439 (m100) cc_final: 0.8787 (m100) REVERT: B 583 SER cc_start: 0.8888 (m) cc_final: 0.8341 (p) REVERT: B 595 MET cc_start: 0.9189 (mmm) cc_final: 0.8824 (mmm) REVERT: B 599 GLU cc_start: 0.8774 (pm20) cc_final: 0.8483 (pm20) REVERT: B 602 GLU cc_start: 0.8281 (pt0) cc_final: 0.8069 (pt0) REVERT: B 645 GLN cc_start: 0.9289 (tp40) cc_final: 0.9040 (tp-100) REVERT: B 668 ASN cc_start: 0.9057 (m110) cc_final: 0.8491 (m110) REVERT: B 683 TYR cc_start: 0.8821 (t80) cc_final: 0.8079 (t80) REVERT: B 684 TYR cc_start: 0.7600 (OUTLIER) cc_final: 0.7142 (m-80) REVERT: C 20 MET cc_start: 0.9518 (tmm) cc_final: 0.9232 (tmm) REVERT: C 21 PHE cc_start: 0.9513 (m-80) cc_final: 0.8831 (m-80) REVERT: C 55 TYR cc_start: 0.8825 (t80) cc_final: 0.8245 (m-80) REVERT: C 92 PHE cc_start: 0.9579 (t80) cc_final: 0.8726 (t80) REVERT: C 96 MET cc_start: 0.9053 (mmm) cc_final: 0.8422 (mmm) REVERT: C 174 TYR cc_start: 0.8046 (OUTLIER) cc_final: 0.7509 (t80) REVERT: C 197 ASP cc_start: 0.9651 (m-30) cc_final: 0.9430 (m-30) REVERT: C 198 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8890 (mm-30) REVERT: C 204 TYR cc_start: 0.8922 (t80) cc_final: 0.8650 (t80) REVERT: C 242 TYR cc_start: 0.9396 (t80) cc_final: 0.8978 (t80) REVERT: C 259 PHE cc_start: 0.9228 (t80) cc_final: 0.8541 (t80) REVERT: C 260 ILE cc_start: 0.8865 (pt) cc_final: 0.8394 (pp) REVERT: C 269 MET cc_start: 0.9579 (ptt) cc_final: 0.9044 (mmp) REVERT: C 317 ASP cc_start: 0.9123 (p0) cc_final: 0.8733 (t0) REVERT: D 30 TRP cc_start: 0.8027 (p-90) cc_final: 0.7408 (p-90) REVERT: D 96 MET cc_start: 0.7814 (mmm) cc_final: 0.7447 (mmm) REVERT: D 131 LEU cc_start: 0.8992 (tt) cc_final: 0.8691 (tp) REVERT: D 168 PHE cc_start: 0.8509 (m-80) cc_final: 0.7534 (m-80) REVERT: D 169 TYR cc_start: 0.8121 (m-80) cc_final: 0.7670 (m-80) REVERT: D 174 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.8215 (t80) REVERT: D 242 TYR cc_start: 0.8837 (t80) cc_final: 0.8500 (t80) REVERT: D 268 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8359 (mt) outliers start: 64 outliers final: 40 residues processed: 735 average time/residue: 0.1274 time to fit residues: 141.1860 Evaluate side-chains 709 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 659 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 58 LEU 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 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 443 THR 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 600 ARG Chi-restraints excluded: chain A residue 602 GLU 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 224 VAL 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 399 GLU Chi-restraints excluded: chain B residue 410 ASN 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 640 MET 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 255 ASP Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 58 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 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: 2.9990 chunk 99 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 153 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN B 102 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** 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 210 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.112367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.084541 restraints weight = 42257.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.087773 restraints weight = 21503.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.089963 restraints weight = 13367.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.091513 restraints weight = 9315.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.092627 restraints weight = 7071.162| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.7418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16386 Z= 0.202 Angle : 0.824 18.684 22134 Z= 0.418 Chirality : 0.050 0.269 2360 Planarity : 0.004 0.042 2818 Dihedral : 8.804 135.494 2294 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.73 % Allowed : 32.46 % 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: 0.52 (0.19), residues: 1932 helix: 0.78 (0.15), residues: 1123 sheet: -0.82 (0.42), residues: 138 loop : 0.08 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 686 TYR 0.031 0.002 TYR D 262 PHE 0.035 0.002 PHE C 172 TRP 0.059 0.003 TRP C 30 HIS 0.012 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (16386) covalent geometry : angle 0.82411 / 0.42 (22134) hydrogen bonds : bond 0.04458 / 2.82 ( 871) hydrogen bonds : angle 5.46223 / 3.85 ( 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 755 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 691 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8684 (pm20) REVERT: A 82 LYS cc_start: 0.9501 (mttm) cc_final: 0.9164 (mmmt) REVERT: A 87 LYS cc_start: 0.9141 (tptm) cc_final: 0.8845 (tttt) REVERT: A 139 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8738 (mp0) REVERT: A 147 GLN cc_start: 0.9157 (mt0) cc_final: 0.8671 (mt0) REVERT: A 150 GLN cc_start: 0.9513 (tp40) cc_final: 0.9162 (tp40) REVERT: A 161 ARG cc_start: 0.8482 (ttm110) cc_final: 0.7658 (ptp-170) REVERT: A 174 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7674 (mt-10) REVERT: A 178 SER cc_start: 0.8292 (OUTLIER) cc_final: 0.7781 (t) REVERT: A 205 LYS cc_start: 0.8770 (mttm) cc_final: 0.8307 (mtpp) REVERT: A 266 LYS cc_start: 0.8729 (ptmm) cc_final: 0.8199 (ptmm) REVERT: A 290 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8769 (tm-30) REVERT: A 350 ARG cc_start: 0.9338 (mtp85) cc_final: 0.9022 (mtp-110) REVERT: A 375 LYS cc_start: 0.8849 (mmtp) cc_final: 0.8050 (mmtm) REVERT: A 413 SER cc_start: 0.9434 (m) cc_final: 0.8979 (t) REVERT: A 445 ILE cc_start: 0.8848 (mm) cc_final: 0.8610 (mm) REVERT: A 471 TYR cc_start: 0.9210 (t80) cc_final: 0.8997 (t80) REVERT: A 493 MET cc_start: 0.8869 (tmm) cc_final: 0.8441 (tmm) REVERT: A 505 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8437 (mt-10) REVERT: A 515 ASP cc_start: 0.9170 (m-30) cc_final: 0.8926 (m-30) REVERT: A 606 TYR cc_start: 0.8007 (m-80) cc_final: 0.7655 (m-80) REVERT: A 639 ASP cc_start: 0.8700 (m-30) cc_final: 0.8257 (m-30) REVERT: A 645 GLN cc_start: 0.9107 (tp40) cc_final: 0.8826 (tp40) REVERT: A 686 ARG cc_start: 0.8293 (ttm110) cc_final: 0.7525 (mtp-110) REVERT: B 8 LYS cc_start: 0.9291 (tptm) cc_final: 0.9072 (tptm) REVERT: B 82 LYS cc_start: 0.9548 (mtpp) cc_final: 0.9150 (mmtm) REVERT: B 95 MET cc_start: 0.9018 (tpt) cc_final: 0.8437 (tpp) REVERT: B 99 LYS cc_start: 0.9357 (tptp) cc_final: 0.8823 (tptp) REVERT: B 107 LYS cc_start: 0.9422 (mmtp) cc_final: 0.9164 (mmmm) REVERT: B 117 ARG cc_start: 0.9054 (mtp85) cc_final: 0.8843 (mtp85) REVERT: B 119 GLU cc_start: 0.9096 (mp0) cc_final: 0.8578 (mp0) REVERT: B 128 PHE cc_start: 0.9724 (t80) cc_final: 0.9440 (t80) REVERT: B 250 TYR cc_start: 0.9029 (m-10) cc_final: 0.8793 (m-10) REVERT: B 256 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8447 (ttp80) REVERT: B 274 ARG cc_start: 0.8711 (ttm110) cc_final: 0.8336 (ttm170) REVERT: B 322 MET cc_start: 0.9317 (mmm) cc_final: 0.8972 (mmt) REVERT: B 333 LYS cc_start: 0.9009 (tttm) cc_final: 0.8709 (tttm) REVERT: B 348 MET cc_start: 0.8836 (tmm) cc_final: 0.8423 (tpt) REVERT: B 358 ILE cc_start: 0.9605 (mm) cc_final: 0.9103 (tp) REVERT: B 362 ASP cc_start: 0.8603 (m-30) cc_final: 0.8308 (m-30) REVERT: B 396 ASP cc_start: 0.9018 (p0) cc_final: 0.8351 (p0) REVERT: B 399 GLU cc_start: 0.8945 (tp30) cc_final: 0.8575 (mp0) REVERT: B 402 GLU cc_start: 0.8505 (tm-30) cc_final: 0.7986 (tm-30) REVERT: B 475 ASN cc_start: 0.9286 (m-40) cc_final: 0.8964 (m110) REVERT: B 515 ASP cc_start: 0.9100 (m-30) cc_final: 0.8614 (m-30) REVERT: B 546 LEU cc_start: 0.9599 (mm) cc_final: 0.9391 (tp) REVERT: B 548 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7656 (mm-30) REVERT: B 558 TRP cc_start: 0.9460 (m100) cc_final: 0.8821 (m100) REVERT: B 583 SER cc_start: 0.9094 (m) cc_final: 0.8592 (p) REVERT: B 595 MET cc_start: 0.9286 (mmm) cc_final: 0.8914 (mmm) REVERT: B 599 GLU cc_start: 0.8809 (pm20) cc_final: 0.8474 (pm20) REVERT: B 645 GLN cc_start: 0.9369 (tp40) cc_final: 0.9016 (tp40) REVERT: B 668 ASN cc_start: 0.9110 (m110) cc_final: 0.8559 (m110) REVERT: B 683 TYR cc_start: 0.8898 (t80) cc_final: 0.8360 (t80) REVERT: B 686 ARG cc_start: 0.8190 (mmt180) cc_final: 0.7846 (mmt180) REVERT: C 20 MET cc_start: 0.9571 (tmm) cc_final: 0.9219 (tmm) REVERT: C 21 PHE cc_start: 0.9556 (m-80) cc_final: 0.8748 (m-80) REVERT: C 30 TRP cc_start: 0.7028 (m100) cc_final: 0.6798 (m100) REVERT: C 90 LEU cc_start: 0.9203 (mt) cc_final: 0.8962 (tp) REVERT: C 92 PHE cc_start: 0.9589 (t80) cc_final: 0.9031 (t80) REVERT: C 93 MET cc_start: 0.9492 (mtt) cc_final: 0.9149 (mtt) REVERT: C 96 MET cc_start: 0.9011 (mmm) cc_final: 0.8617 (mmm) REVERT: C 110 MET cc_start: 0.7521 (mpp) cc_final: 0.7213 (mtt) REVERT: C 174 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7894 (t80) REVERT: C 185 MET cc_start: 0.8439 (mmm) cc_final: 0.8197 (mmm) REVERT: C 198 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8863 (mm-30) REVERT: C 204 TYR cc_start: 0.9003 (t80) cc_final: 0.8795 (t80) REVERT: C 218 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8866 (pm20) REVERT: C 259 PHE cc_start: 0.9302 (t80) cc_final: 0.8980 (t80) REVERT: C 269 MET cc_start: 0.9617 (OUTLIER) cc_final: 0.9006 (mmp) REVERT: C 274 ASP cc_start: 0.8415 (p0) cc_final: 0.7942 (p0) REVERT: D 30 TRP cc_start: 0.8180 (p-90) cc_final: 0.7542 (p-90) REVERT: D 96 MET cc_start: 0.7938 (mmm) cc_final: 0.7448 (mmm) REVERT: D 168 PHE cc_start: 0.8632 (m-80) cc_final: 0.7449 (m-80) REVERT: D 169 TYR cc_start: 0.8368 (m-80) cc_final: 0.7726 (m-80) REVERT: D 174 TYR cc_start: 0.9017 (OUTLIER) cc_final: 0.8350 (t80) REVERT: D 185 MET cc_start: 0.6796 (mmp) cc_final: 0.6184 (ttt) REVERT: D 225 ARG cc_start: 0.8797 (mtt180) cc_final: 0.8387 (mtt180) REVERT: D 268 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8314 (mt) outliers start: 64 outliers final: 44 residues processed: 718 average time/residue: 0.1272 time to fit residues: 137.8218 Evaluate side-chains 699 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 648 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 58 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 306 ILE Chi-restraints excluded: chain A residue 358 ILE 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 441 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 583 SER 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 224 VAL Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 260 ASP 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 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 255 ASP Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 268 LEU 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: 8.9990 chunk 133 optimal weight: 0.8980 chunk 149 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 127 GLN ** C 216 GLN ** 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 = 0.3600 r_free = 0.3600 target = 0.115948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.088045 restraints weight = 40993.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.091232 restraints weight = 21599.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.093143 restraints weight = 13846.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.094770 restraints weight = 10103.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.095998 restraints weight = 7703.360| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.7705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16386 Z= 0.159 Angle : 0.854 17.015 22134 Z= 0.429 Chirality : 0.050 0.291 2360 Planarity : 0.004 0.037 2818 Dihedral : 8.720 135.167 2294 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.21 % Allowed : 33.92 % Favored : 62.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.39 (0.19), residues: 1932 helix: 0.69 (0.15), residues: 1120 sheet: -0.83 (0.42), residues: 138 loop : -0.00 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 686 TYR 0.042 0.002 TYR C 242 PHE 0.055 0.002 PHE C 178 TRP 0.041 0.002 TRP C 30 HIS 0.009 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (16386) covalent geometry : angle 0.85376 / 0.43 (22134) hydrogen bonds : bond 0.04425 / 2.79 ( 871) hydrogen bonds : angle 5.51130 / 3.88 ( 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 753 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 698 time to evaluate : 0.617 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: A 31 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8527 (pm20) REVERT: A 56 ASP cc_start: 0.8850 (m-30) cc_final: 0.8397 (m-30) REVERT: A 82 LYS cc_start: 0.9503 (mttm) cc_final: 0.9181 (mmmt) REVERT: A 95 MET cc_start: 0.8929 (mmm) cc_final: 0.8303 (tpp) REVERT: A 147 GLN cc_start: 0.9096 (mt0) cc_final: 0.8573 (mt0) REVERT: A 150 GLN cc_start: 0.9494 (tp40) cc_final: 0.9142 (tp40) REVERT: A 161 ARG cc_start: 0.8472 (ttm110) cc_final: 0.7642 (ptp-170) REVERT: A 162 LYS cc_start: 0.9242 (tmmt) cc_final: 0.8928 (ttpp) REVERT: A 178 SER cc_start: 0.8258 (OUTLIER) cc_final: 0.7774 (t) REVERT: A 205 LYS cc_start: 0.8737 (mttm) cc_final: 0.8386 (mtpp) REVERT: A 290 GLU cc_start: 0.9154 (tm-30) cc_final: 0.8725 (tm-30) REVERT: A 301 PHE cc_start: 0.8988 (m-10) cc_final: 0.8730 (m-10) REVERT: A 350 ARG cc_start: 0.9277 (mtp85) cc_final: 0.9028 (mtp-110) REVERT: A 375 LYS cc_start: 0.8849 (mmtp) cc_final: 0.8363 (mmtm) REVERT: A 413 SER cc_start: 0.9432 (m) cc_final: 0.8931 (t) REVERT: A 444 ASP cc_start: 0.8367 (t0) cc_final: 0.7756 (p0) REVERT: A 446 ARG cc_start: 0.7800 (mtm-85) cc_final: 0.7577 (mmm160) REVERT: A 456 LYS cc_start: 0.9302 (ptpp) cc_final: 0.8983 (ptpp) REVERT: A 493 MET cc_start: 0.8771 (tmm) cc_final: 0.8355 (tmm) REVERT: A 505 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8274 (mt-10) REVERT: A 515 ASP cc_start: 0.9183 (m-30) cc_final: 0.8875 (m-30) REVERT: A 590 SER cc_start: 0.9578 (t) cc_final: 0.8933 (p) REVERT: A 606 TYR cc_start: 0.8113 (m-80) cc_final: 0.7652 (m-80) REVERT: A 639 ASP cc_start: 0.8624 (m-30) cc_final: 0.8160 (m-30) REVERT: A 645 GLN cc_start: 0.9028 (tp40) cc_final: 0.8799 (tp40) REVERT: A 686 ARG cc_start: 0.8232 (ttm110) cc_final: 0.7615 (mtp-110) REVERT: B 82 LYS cc_start: 0.9525 (mtpp) cc_final: 0.9108 (mmtm) REVERT: B 95 MET cc_start: 0.8967 (tpt) cc_final: 0.8153 (tpp) REVERT: B 99 LYS cc_start: 0.9345 (tptp) cc_final: 0.8886 (tptp) REVERT: B 107 LYS cc_start: 0.9409 (mmtp) cc_final: 0.9181 (mmmm) REVERT: B 119 GLU cc_start: 0.9080 (mp0) cc_final: 0.8594 (mp0) REVERT: B 168 VAL cc_start: 0.9294 (t) cc_final: 0.9041 (m) REVERT: B 191 GLN cc_start: 0.9122 (mm-40) cc_final: 0.8865 (mm-40) REVERT: B 250 TYR cc_start: 0.8920 (m-10) cc_final: 0.8573 (m-10) REVERT: B 256 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8405 (ttp80) REVERT: B 274 ARG cc_start: 0.8695 (ttm110) cc_final: 0.8274 (ttm170) REVERT: B 322 MET cc_start: 0.9326 (mmm) cc_final: 0.9005 (mmt) REVERT: B 333 LYS cc_start: 0.9022 (tttm) cc_final: 0.8722 (tttm) REVERT: B 348 MET cc_start: 0.8868 (tmm) cc_final: 0.8437 (tpt) REVERT: B 358 ILE cc_start: 0.9629 (mm) cc_final: 0.9157 (tp) REVERT: B 362 ASP cc_start: 0.8597 (m-30) cc_final: 0.8317 (m-30) REVERT: B 396 ASP cc_start: 0.8891 (p0) cc_final: 0.8296 (p0) REVERT: B 399 GLU cc_start: 0.8846 (tp30) cc_final: 0.8468 (mp0) REVERT: B 402 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8066 (tm-30) REVERT: B 475 ASN cc_start: 0.9249 (m-40) cc_final: 0.8937 (m110) REVERT: B 515 ASP cc_start: 0.9042 (m-30) cc_final: 0.8615 (m-30) REVERT: B 548 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7683 (mm-30) REVERT: B 558 TRP cc_start: 0.9423 (m100) cc_final: 0.8719 (m100) REVERT: B 586 TYR cc_start: 0.9210 (m-80) cc_final: 0.8562 (m-80) REVERT: B 595 MET cc_start: 0.9216 (mmm) cc_final: 0.8855 (mmm) REVERT: B 599 GLU cc_start: 0.8721 (pm20) cc_final: 0.8398 (pm20) REVERT: B 645 GLN cc_start: 0.9341 (tp40) cc_final: 0.9049 (tp-100) REVERT: B 650 GLN cc_start: 0.8310 (mt0) cc_final: 0.7999 (mt0) REVERT: B 668 ASN cc_start: 0.9088 (m110) cc_final: 0.8672 (m110) REVERT: C 20 MET cc_start: 0.9582 (tmm) cc_final: 0.9230 (tmm) REVERT: C 21 PHE cc_start: 0.9559 (m-80) cc_final: 0.8748 (m-80) REVERT: C 30 TRP cc_start: 0.6998 (m100) cc_final: 0.6796 (m100) REVERT: C 74 MET cc_start: 0.8745 (mtt) cc_final: 0.8536 (mtm) REVERT: C 92 PHE cc_start: 0.9574 (t80) cc_final: 0.9021 (t80) REVERT: C 96 MET cc_start: 0.8983 (mmm) cc_final: 0.8547 (mmm) REVERT: C 110 MET cc_start: 0.7352 (mpp) cc_final: 0.6993 (mtt) REVERT: C 198 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8700 (mm-30) REVERT: C 204 TYR cc_start: 0.8970 (t80) cc_final: 0.8760 (t80) REVERT: C 223 GLU cc_start: 0.9343 (tm-30) cc_final: 0.8721 (pt0) REVERT: C 259 PHE cc_start: 0.9290 (t80) cc_final: 0.8673 (t80) REVERT: C 269 MET cc_start: 0.9548 (OUTLIER) cc_final: 0.8973 (mmp) REVERT: C 274 ASP cc_start: 0.8156 (p0) cc_final: 0.7708 (p0) REVERT: C 317 ASP cc_start: 0.9148 (p0) cc_final: 0.8763 (t0) REVERT: D 33 GLU cc_start: 0.9117 (mp0) cc_final: 0.8346 (pp20) REVERT: D 96 MET cc_start: 0.7827 (mmm) cc_final: 0.7408 (mmm) REVERT: D 168 PHE cc_start: 0.8536 (m-80) cc_final: 0.7508 (m-80) REVERT: D 169 TYR cc_start: 0.8015 (m-80) cc_final: 0.7580 (m-80) REVERT: D 174 TYR cc_start: 0.8943 (OUTLIER) cc_final: 0.8301 (t80) REVERT: D 185 MET cc_start: 0.6775 (mmp) cc_final: 0.6178 (ttt) REVERT: D 225 ARG cc_start: 0.8857 (mtt180) cc_final: 0.8567 (mtt180) REVERT: D 266 LYS cc_start: 0.8601 (mtmm) cc_final: 0.8383 (mtmm) REVERT: D 268 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8151 (mt) outliers start: 55 outliers final: 40 residues processed: 721 average time/residue: 0.1284 time to fit residues: 139.9209 Evaluate side-chains 704 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 658 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 141 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 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 583 SER 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 256 ARG Chi-restraints excluded: chain B residue 260 ASP 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 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 255 ASP Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 268 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 189 optimal weight: 0.7980 chunk 181 optimal weight: 0.9980 chunk 165 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 132 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 ASN ** 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 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.116987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.089103 restraints weight = 41630.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.092446 restraints weight = 21172.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.094700 restraints weight = 13077.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.096287 restraints weight = 9085.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.097454 restraints weight = 6850.006| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.7924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16386 Z= 0.168 Angle : 0.893 17.252 22134 Z= 0.452 Chirality : 0.051 0.294 2360 Planarity : 0.004 0.037 2818 Dihedral : 8.664 135.235 2292 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 21.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.62 % Allowed : 35.72 % Favored : 61.66 % 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: 0.23 (0.19), residues: 1932 helix: 0.55 (0.15), residues: 1113 sheet: -0.85 (0.43), residues: 138 loop : -0.06 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 686 TYR 0.040 0.002 TYR C 242 PHE 0.067 0.003 PHE C 178 TRP 0.035 0.002 TRP C 30 HIS 0.017 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (16386) covalent geometry : angle 0.89342 / 0.45 (22134) hydrogen bonds : bond 0.04499 / 2.84 ( 871) hydrogen bonds : angle 5.63167 / 3.97 ( 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 732 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 687 time to evaluate : 0.692 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 31 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8557 (pm20) REVERT: A 56 ASP cc_start: 0.8823 (m-30) cc_final: 0.8366 (m-30) REVERT: A 82 LYS cc_start: 0.9493 (mttm) cc_final: 0.9172 (mmmt) REVERT: A 95 MET cc_start: 0.8913 (mmm) cc_final: 0.8246 (tpp) REVERT: A 147 GLN cc_start: 0.9084 (mt0) cc_final: 0.8572 (mt0) REVERT: A 150 GLN cc_start: 0.9498 (tp40) cc_final: 0.9088 (tp40) REVERT: A 161 ARG cc_start: 0.8479 (ttm110) cc_final: 0.7730 (ptp-170) REVERT: A 162 LYS cc_start: 0.9230 (tmmt) cc_final: 0.8939 (ttpp) REVERT: A 178 SER cc_start: 0.8240 (OUTLIER) cc_final: 0.7763 (t) REVERT: A 205 LYS cc_start: 0.8732 (mttm) cc_final: 0.8371 (mtpp) REVERT: A 266 LYS cc_start: 0.8768 (ptmm) cc_final: 0.8357 (ptmm) REVERT: A 290 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8726 (tm-30) REVERT: A 301 PHE cc_start: 0.9051 (m-10) cc_final: 0.8796 (m-10) REVERT: A 350 ARG cc_start: 0.9274 (mtp85) cc_final: 0.9022 (mtp-110) REVERT: A 375 LYS cc_start: 0.8818 (mmtp) cc_final: 0.8391 (mmtm) REVERT: A 413 SER cc_start: 0.9443 (m) cc_final: 0.8968 (t) REVERT: A 493 MET cc_start: 0.8778 (tmm) cc_final: 0.8395 (tmm) REVERT: A 505 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8272 (mt-10) REVERT: A 515 ASP cc_start: 0.9170 (m-30) cc_final: 0.8938 (m-30) REVERT: A 546 LEU cc_start: 0.9572 (mp) cc_final: 0.9346 (tp) REVERT: A 590 SER cc_start: 0.9581 (t) cc_final: 0.8896 (p) REVERT: A 606 TYR cc_start: 0.8163 (m-80) cc_final: 0.7716 (m-80) REVERT: A 639 ASP cc_start: 0.8625 (m-30) cc_final: 0.8141 (m-30) REVERT: A 645 GLN cc_start: 0.9010 (tp40) cc_final: 0.8776 (tp40) REVERT: A 686 ARG cc_start: 0.8285 (ttm110) cc_final: 0.7666 (mtp-110) REVERT: B 82 LYS cc_start: 0.9503 (mtpp) cc_final: 0.9090 (mmtm) REVERT: B 95 MET cc_start: 0.8957 (tpt) cc_final: 0.8120 (tpp) REVERT: B 99 LYS cc_start: 0.9316 (tptp) cc_final: 0.8828 (tptp) REVERT: B 107 LYS cc_start: 0.9391 (mmtp) cc_final: 0.9168 (mmmm) REVERT: B 119 GLU cc_start: 0.9076 (mp0) cc_final: 0.8648 (mp0) REVERT: B 168 VAL cc_start: 0.9297 (t) cc_final: 0.9054 (m) REVERT: B 191 GLN cc_start: 0.9118 (mm-40) cc_final: 0.8896 (mm-40) REVERT: B 250 TYR cc_start: 0.9043 (m-10) cc_final: 0.8560 (m-10) REVERT: B 256 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8404 (ttp80) REVERT: B 322 MET cc_start: 0.9313 (mmm) cc_final: 0.8949 (mmt) REVERT: B 333 LYS cc_start: 0.9050 (tttm) cc_final: 0.8755 (tttm) REVERT: B 348 MET cc_start: 0.8865 (tmm) cc_final: 0.8433 (tpt) REVERT: B 357 TYR cc_start: 0.8187 (m-10) cc_final: 0.7952 (m-10) REVERT: B 358 ILE cc_start: 0.9619 (mm) cc_final: 0.9169 (tp) REVERT: B 362 ASP cc_start: 0.8622 (m-30) cc_final: 0.8331 (m-30) REVERT: B 396 ASP cc_start: 0.8880 (p0) cc_final: 0.8297 (p0) REVERT: B 399 GLU cc_start: 0.8764 (tp30) cc_final: 0.8444 (mp0) REVERT: B 402 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8127 (tm-30) REVERT: B 430 LYS cc_start: 0.9488 (mttt) cc_final: 0.9242 (mttm) REVERT: B 475 ASN cc_start: 0.9257 (m-40) cc_final: 0.8995 (m110) REVERT: B 515 ASP cc_start: 0.9008 (m-30) cc_final: 0.8573 (m-30) REVERT: B 548 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7704 (mm-30) REVERT: B 558 TRP cc_start: 0.9416 (m100) cc_final: 0.8826 (m100) REVERT: B 583 SER cc_start: 0.9085 (m) cc_final: 0.8339 (t) REVERT: B 586 TYR cc_start: 0.9212 (m-80) cc_final: 0.8661 (m-80) REVERT: B 595 MET cc_start: 0.9206 (mmm) cc_final: 0.8945 (mmm) REVERT: B 613 TYR cc_start: 0.8804 (t80) cc_final: 0.8332 (t80) REVERT: B 645 GLN cc_start: 0.9353 (tp40) cc_final: 0.9055 (tp-100) REVERT: B 668 ASN cc_start: 0.9147 (m110) cc_final: 0.8672 (m110) REVERT: C 20 MET cc_start: 0.9585 (tmm) cc_final: 0.9232 (tmm) REVERT: C 21 PHE cc_start: 0.9558 (m-80) cc_final: 0.8769 (m-80) REVERT: C 30 TRP cc_start: 0.6928 (m100) cc_final: 0.6390 (m100) REVERT: C 85 GLN cc_start: 0.8157 (mt0) cc_final: 0.7497 (mm-40) REVERT: C 92 PHE cc_start: 0.9616 (t80) cc_final: 0.9084 (t80) REVERT: C 96 MET cc_start: 0.8945 (mmm) cc_final: 0.8485 (mmm) REVERT: C 110 MET cc_start: 0.7234 (mpp) cc_final: 0.6889 (mtt) REVERT: C 198 GLU cc_start: 0.9291 (mm-30) cc_final: 0.8787 (mm-30) REVERT: C 218 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8800 (pm20) REVERT: C 223 GLU cc_start: 0.9360 (tm-30) cc_final: 0.8769 (pt0) REVERT: C 259 PHE cc_start: 0.9305 (t80) cc_final: 0.8702 (t80) REVERT: C 269 MET cc_start: 0.9540 (OUTLIER) cc_final: 0.8939 (mmp) REVERT: C 274 ASP cc_start: 0.8156 (p0) cc_final: 0.7710 (p0) REVERT: C 317 ASP cc_start: 0.9163 (p0) cc_final: 0.8771 (t0) REVERT: D 33 GLU cc_start: 0.9122 (mp0) cc_final: 0.8338 (pp20) REVERT: D 51 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7622 (mm-30) REVERT: D 96 MET cc_start: 0.7919 (mmm) cc_final: 0.7530 (mmm) REVERT: D 168 PHE cc_start: 0.8451 (m-80) cc_final: 0.7591 (m-80) REVERT: D 169 TYR cc_start: 0.7807 (m-80) cc_final: 0.7500 (m-80) REVERT: D 174 TYR cc_start: 0.9051 (OUTLIER) cc_final: 0.8437 (t80) REVERT: D 185 MET cc_start: 0.6569 (mmp) cc_final: 0.6043 (ttt) REVERT: D 198 GLU cc_start: 0.8427 (pp20) cc_final: 0.8214 (pp20) REVERT: D 225 ARG cc_start: 0.8845 (mtt180) cc_final: 0.8556 (mtt180) outliers start: 45 outliers final: 37 residues processed: 704 average time/residue: 0.1257 time to fit residues: 134.5309 Evaluate side-chains 715 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 673 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 58 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 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 583 SER 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 256 ARG Chi-restraints excluded: chain B residue 410 ASN 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 591 THR 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 255 ASP Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 203 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 39 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 125 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 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** ** C 71 ASN ** 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 181 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 = 0.3602 r_free = 0.3602 target = 0.116815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.088722 restraints weight = 40981.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.092069 restraints weight = 21101.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.094345 restraints weight = 13134.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.095954 restraints weight = 9174.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.097149 restraints weight = 6921.308| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 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 = 0.3254 r_free = 0.3254 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 (32 function evaluations) r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.8113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16386 Z= 0.175 Angle : 0.907 18.317 22134 Z= 0.459 Chirality : 0.051 0.266 2360 Planarity : 0.004 0.037 2818 Dihedral : 8.648 135.385 2291 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 22.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.97 % Allowed : 36.36 % Favored : 60.66 % 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: 0.13 (0.19), residues: 1932 helix: 0.52 (0.15), residues: 1110 sheet: -0.90 (0.43), residues: 140 loop : -0.18 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 686 TYR 0.034 0.002 TYR C 242 PHE 0.068 0.003 PHE C 178 TRP 0.030 0.002 TRP C 30 HIS 0.015 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (16386) covalent geometry : angle 0.90702 / 0.46 (22134) hydrogen bonds : bond 0.04534 / 2.86 ( 871) hydrogen bonds : angle 5.68062 / 3.99 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3520.72 seconds wall clock time: 61 minutes 53.58 seconds (3713.58 seconds total)