Starting phenix.real_space_refine on Thu Aug 6 15:18:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byv_45045/08_2026/9byv_45045_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byv_45045/08_2026/9byv_45045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9byv_45045/08_2026/9byv_45045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byv_45045/08_2026/9byv_45045.map" model { file = "/net/cci-nas-00/data/ceres_data/9byv_45045/08_2026/9byv_45045_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byv_45045/08_2026/9byv_45045_neut.cif" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.18, per 1000 atoms: 0.20 Number of scatterers: 16038 At special positions: 0 Unit cell: (100.683, 122.04, 132.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 737.4 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: 0.49 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: 4.095A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.516A 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: 3.985A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.569A 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: 3.665A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.694A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.628A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.074A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.579A 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: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.645A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.729A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.027A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.069A 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: 3.514A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.936A 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: 3.669A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.359A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.478A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.394A 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: 7.501A 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: 5.661A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.228A 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: 4.049A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.749A 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: 2.98 Time building geometry restraints manager: 1.23 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: 4719 1.34 - 1.46: 3125 1.46 - 1.58: 8361 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" O3B TTP B 801 " pdb=" PG TTP B 801 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" O3B TTP A 803 " pdb=" PG TTP A 803 " ideal model delta sigma weight residual 1.748 1.610 0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.600 -0.060 1.25e-02 6.40e+03 2.30e+01 bond pdb=" O3A TTP A 803 " pdb=" PB TTP A 803 " ideal model delta sigma weight residual 1.675 1.605 0.070 2.00e-02 2.50e+03 1.21e+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 1.15e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21523 2.09 - 4.18: 529 4.18 - 6.27: 65 6.27 - 8.36: 8 8.36 - 10.45: 9 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.64 -6.10 1.36e+00 5.41e-01 2.01e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.17 -4.46 1.15e+00 7.56e-01 1.51e+01 angle pdb=" N SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.26 -3.98 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 113.50 117.80 -4.30 1.23e+00 6.61e-01 1.22e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.51 3.68 1.06e+00 8.90e-01 1.20e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.06: 9090 25.06 - 50.11: 653 50.11 - 75.17: 127 75.17 - 100.22: 26 100.22 - 125.28: 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 -98.26 125.28 1 2.00e+01 2.50e-03 3.79e+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 -95.57 122.59 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 -134.31 12.31 0 2.50e+00 1.60e-01 2.43e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2142 0.094 - 0.187: 185 0.187 - 0.281: 28 0.281 - 0.375: 3 0.375 - 0.468: 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 5.48e+00 chirality pdb=" CA TYR C 169 " pdb=" N TYR C 169 " pdb=" C TYR C 169 " pdb=" CB TYR C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " 0.017 2.00e-02 2.50e+03 1.10e-02 2.13e+00 pdb=" CG PHE D 92 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 35 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.91e+00 pdb=" C SER B 35 " -0.024 2.00e-02 2.50e+03 pdb=" O SER B 35 " 0.009 2.00e-02 2.50e+03 pdb=" N TYR B 36 " 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: 11557 3.11 - 3.70: 27043 3.70 - 4.30: 41579 4.30 - 4.90: 65483 Nonbonded interactions: 145791 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.911 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.991 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.013 3.040 ... (remaining 145786 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: 1.450 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.630 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 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 10.454 22134 Z= 0.472 Chirality : 0.058 0.468 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.675 125.279 6202 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.40 % Allowed : 15.27 % Favored : 83.33 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.18), residues: 1932 helix: 0.58 (0.14), residues: 1151 sheet: 0.46 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 196 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE C 168 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 0.78779 / 0.47 (22134) hydrogen bonds : bond 0.15422 / 9.51 ( 871) hydrogen bonds : angle 6.51813 / 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 888 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 864 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8484 (m) REVERT: A 116 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7111 (mt-10) REVERT: A 179 LEU cc_start: 0.9121 (tp) cc_final: 0.8784 (tp) REVERT: A 232 ASN cc_start: 0.8164 (OUTLIER) cc_final: 0.7964 (m-40) REVERT: A 362 ASP cc_start: 0.6467 (m-30) cc_final: 0.6136 (m-30) REVERT: A 490 THR cc_start: 0.8604 (m) cc_final: 0.8295 (m) REVERT: A 576 LEU cc_start: 0.8938 (mt) cc_final: 0.8557 (mt) REVERT: A 606 TYR cc_start: 0.7504 (m-80) cc_final: 0.7289 (m-10) REVERT: B 81 PHE cc_start: 0.7719 (m-80) cc_final: 0.7493 (m-80) REVERT: B 179 LEU cc_start: 0.8956 (tp) cc_final: 0.8687 (tp) REVERT: B 186 ILE cc_start: 0.9326 (mt) cc_final: 0.8995 (mt) REVERT: B 190 MET cc_start: 0.8126 (mtm) cc_final: 0.7906 (mtm) REVERT: B 288 PHE cc_start: 0.8003 (t80) cc_final: 0.7671 (t80) REVERT: B 362 ASP cc_start: 0.7308 (m-30) cc_final: 0.6983 (m-30) REVERT: B 373 ILE cc_start: 0.9064 (mt) cc_final: 0.8800 (mt) REVERT: B 420 MET cc_start: 0.7976 (mmm) cc_final: 0.7741 (mmm) REVERT: B 436 LEU cc_start: 0.9237 (mt) cc_final: 0.8922 (mt) REVERT: B 460 SER cc_start: 0.9036 (t) cc_final: 0.8771 (p) REVERT: B 471 TYR cc_start: 0.8196 (t80) cc_final: 0.7492 (t80) REVERT: B 546 LEU cc_start: 0.8958 (mt) cc_final: 0.8449 (mt) REVERT: B 550 MET cc_start: 0.8033 (mtm) cc_final: 0.7706 (mtp) REVERT: B 584 ILE cc_start: 0.8946 (tp) cc_final: 0.8730 (tp) REVERT: B 612 TYR cc_start: 0.7224 (m-80) cc_final: 0.6873 (m-80) REVERT: C 286 VAL cc_start: 0.4799 (t) cc_final: 0.4033 (p) REVERT: D 89 VAL cc_start: 0.5044 (t) cc_final: 0.4267 (t) REVERT: D 126 LYS cc_start: 0.3277 (OUTLIER) cc_final: 0.2610 (tttt) REVERT: D 246 LEU cc_start: 0.5231 (mt) cc_final: 0.4712 (tp) REVERT: D 287 LEU cc_start: 0.4919 (mt) cc_final: 0.4463 (tp) outliers start: 24 outliers final: 9 residues processed: 877 average time/residue: 0.1337 time to fit residues: 173.1800 Evaluate side-chains 624 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 612 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 126 LYS Chi-restraints excluded: chain D residue 127 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN A 312 GLN A 365 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN B 312 GLN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN B 338 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN C 107 ASN C 127 GLN D 71 ASN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN D 181 GLN D 186 GLN D 210 GLN D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.146032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.101691 restraints weight = 31462.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.105447 restraints weight = 14875.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.107837 restraints weight = 8746.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.109249 restraints weight = 6097.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.109902 restraints weight = 4769.994| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (15 function evaluations) r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 16386 Z= 0.220 Angle : 0.675 9.667 22134 Z= 0.353 Chirality : 0.046 0.304 2360 Planarity : 0.004 0.048 2818 Dihedral : 9.867 132.244 2311 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 4.66 % Allowed : 19.41 % Favored : 75.93 % 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: 1.38 (0.19), residues: 1932 helix: 1.40 (0.15), residues: 1132 sheet: -0.40 (0.46), residues: 114 loop : 0.53 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 686 TYR 0.021 0.002 TYR C 247 PHE 0.037 0.002 PHE D 168 TRP 0.013 0.002 TRP C 44 HIS 0.022 0.002 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.22 (16386) covalent geometry : angle 0.67527 / 0.35 (22134) hydrogen bonds : bond 0.04715 / 2.90 ( 871) hydrogen bonds : angle 5.13236 / 3.65 ( 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 719 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 639 time to evaluate : 0.629 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: A 8 LYS cc_start: 0.8824 (tptp) cc_final: 0.8393 (tppt) REVERT: A 40 TYR cc_start: 0.8923 (t80) cc_final: 0.8678 (t80) REVERT: A 76 ASP cc_start: 0.8470 (m-30) cc_final: 0.8136 (m-30) REVERT: A 119 GLU cc_start: 0.8493 (mp0) cc_final: 0.8283 (mp0) REVERT: A 194 LYS cc_start: 0.9018 (tttt) cc_final: 0.8786 (tttt) REVERT: A 200 SER cc_start: 0.9095 (t) cc_final: 0.8890 (t) REVERT: A 232 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.8196 (m-40) REVERT: A 250 TYR cc_start: 0.8720 (m-80) cc_final: 0.8017 (m-80) REVERT: A 263 ASP cc_start: 0.7808 (m-30) cc_final: 0.7497 (m-30) REVERT: A 290 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8209 (mt-10) REVERT: A 317 MET cc_start: 0.8794 (ptp) cc_final: 0.8456 (ptp) REVERT: A 348 MET cc_start: 0.8257 (tmm) cc_final: 0.7893 (tmm) REVERT: A 384 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7607 (pm20) REVERT: A 394 TYR cc_start: 0.8852 (m-80) cc_final: 0.8633 (m-80) REVERT: A 406 ASP cc_start: 0.8286 (m-30) cc_final: 0.8036 (t0) REVERT: A 446 ARG cc_start: 0.7543 (mmm160) cc_final: 0.6876 (mmm160) REVERT: A 452 ARG cc_start: 0.9013 (ttp80) cc_final: 0.8727 (ttt-90) REVERT: A 583 SER cc_start: 0.8963 (m) cc_final: 0.8729 (t) REVERT: A 590 SER cc_start: 0.9262 (t) cc_final: 0.8552 (p) REVERT: A 606 TYR cc_start: 0.8486 (m-80) cc_final: 0.8210 (m-10) REVERT: A 640 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.8882 (tpp) REVERT: A 667 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8818 (tt) REVERT: B 72 TYR cc_start: 0.8131 (m-80) cc_final: 0.7924 (m-10) REVERT: B 136 LYS cc_start: 0.9164 (mmmm) cc_final: 0.8721 (mmtt) REVERT: B 182 ILE cc_start: 0.9513 (mt) cc_final: 0.9306 (mp) REVERT: B 218 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8505 (t0) REVERT: B 221 LYS cc_start: 0.9196 (mttm) cc_final: 0.8916 (mmtm) REVERT: B 236 TYR cc_start: 0.9106 (t80) cc_final: 0.8872 (t80) REVERT: B 274 ARG cc_start: 0.8235 (ttm-80) cc_final: 0.7670 (ttm-80) REVERT: B 308 LYS cc_start: 0.9090 (mtpt) cc_final: 0.8730 (mtmm) REVERT: B 322 MET cc_start: 0.9182 (tpp) cc_final: 0.8744 (tpp) REVERT: B 348 MET cc_start: 0.7891 (tpp) cc_final: 0.7539 (tpp) REVERT: B 352 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7498 (mt-10) REVERT: B 420 MET cc_start: 0.8943 (mmm) cc_final: 0.8693 (mmm) REVERT: B 471 TYR cc_start: 0.9057 (t80) cc_final: 0.8316 (t80) REVERT: B 546 LEU cc_start: 0.9534 (mt) cc_final: 0.9126 (mt) REVERT: B 627 LYS cc_start: 0.8939 (tttt) cc_final: 0.8523 (ttpt) REVERT: C 43 THR cc_start: 0.6751 (OUTLIER) cc_final: 0.6429 (p) REVERT: C 44 TRP cc_start: 0.8386 (t-100) cc_final: 0.8099 (t-100) REVERT: C 68 GLU cc_start: 0.8678 (mp0) cc_final: 0.7752 (tm-30) REVERT: C 72 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8845 (t) REVERT: C 76 ILE cc_start: 0.9128 (mt) cc_final: 0.8915 (pt) REVERT: C 93 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.6680 (tmm) REVERT: C 124 TRP cc_start: 0.8374 (t60) cc_final: 0.8112 (t60) REVERT: C 154 PHE cc_start: 0.8813 (t80) cc_final: 0.8583 (t80) REVERT: C 269 MET cc_start: 0.8753 (tpt) cc_final: 0.8440 (tmm) REVERT: D 47 LEU cc_start: 0.4813 (mt) cc_final: 0.4283 (tp) REVERT: D 59 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7584 (tt) REVERT: D 174 TYR cc_start: 0.7568 (t80) cc_final: 0.6712 (t80) REVERT: D 185 MET cc_start: 0.0296 (ptt) cc_final: -0.0062 (ptt) REVERT: D 198 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8174 (mm-30) REVERT: D 219 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7012 (pm20) REVERT: D 260 ILE cc_start: 0.7968 (mt) cc_final: 0.7717 (pt) outliers start: 80 outliers final: 32 residues processed: 674 average time/residue: 0.1239 time to fit residues: 126.8962 Evaluate side-chains 591 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 549 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 240 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 chunk 164 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 147 GLN B 312 GLN B 320 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 249 GLN D 91 ASN D 181 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.146193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.101858 restraints weight = 31914.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.105510 restraints weight = 15064.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.107839 restraints weight = 8853.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.109273 restraints weight = 6188.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110178 restraints weight = 4859.629| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16386 Z= 0.169 Angle : 0.639 12.304 22134 Z= 0.333 Chirality : 0.045 0.358 2360 Planarity : 0.003 0.039 2818 Dihedral : 9.292 134.470 2300 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 4.31 % Allowed : 21.91 % Favored : 73.78 % 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: 1.37 (0.19), residues: 1932 helix: 1.40 (0.15), residues: 1132 sheet: -0.42 (0.45), residues: 114 loop : 0.50 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 196 TYR 0.030 0.001 TYR C 142 PHE 0.042 0.002 PHE D 168 TRP 0.008 0.001 TRP C 124 HIS 0.010 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (16386) covalent geometry : angle 0.63880 / 0.33 (22134) hydrogen bonds : bond 0.04216 / 2.59 ( 871) hydrogen bonds : angle 4.98580 / 3.54 ( 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 668 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 594 time to evaluate : 0.628 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: A 8 LYS cc_start: 0.8767 (tptp) cc_final: 0.8336 (tppt) REVERT: A 40 TYR cc_start: 0.8900 (t80) cc_final: 0.8535 (t80) REVERT: A 76 ASP cc_start: 0.8401 (m-30) cc_final: 0.8133 (m-30) REVERT: A 119 GLU cc_start: 0.8470 (mp0) cc_final: 0.8180 (mp0) REVERT: A 200 SER cc_start: 0.9088 (t) cc_final: 0.8881 (t) REVERT: A 214 LYS cc_start: 0.8093 (mmtt) cc_final: 0.7886 (mmtt) REVERT: A 232 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8156 (m-40) REVERT: A 250 TYR cc_start: 0.8673 (m-80) cc_final: 0.8284 (m-80) REVERT: A 263 ASP cc_start: 0.8066 (m-30) cc_final: 0.7802 (m-30) REVERT: A 290 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8236 (mt-10) REVERT: A 348 MET cc_start: 0.8212 (tmm) cc_final: 0.7749 (tmm) REVERT: A 361 GLN cc_start: 0.8751 (tt0) cc_final: 0.8378 (tp40) REVERT: A 362 ASP cc_start: 0.8367 (m-30) cc_final: 0.7854 (m-30) REVERT: A 384 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7381 (pm20) REVERT: A 394 TYR cc_start: 0.8892 (m-80) cc_final: 0.8546 (m-80) REVERT: A 406 ASP cc_start: 0.8302 (m-30) cc_final: 0.8017 (t0) REVERT: A 446 ARG cc_start: 0.7485 (mmm160) cc_final: 0.6869 (mmm160) REVERT: A 452 ARG cc_start: 0.9020 (ttp80) cc_final: 0.8741 (ttt-90) REVERT: A 590 SER cc_start: 0.9035 (t) cc_final: 0.8828 (t) REVERT: A 598 MET cc_start: 0.8448 (mtm) cc_final: 0.8227 (mtm) REVERT: A 640 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8830 (tpp) REVERT: A 646 GLN cc_start: 0.8806 (pt0) cc_final: 0.8263 (pm20) REVERT: A 654 PHE cc_start: 0.9261 (t80) cc_final: 0.9043 (t80) REVERT: B 72 TYR cc_start: 0.7964 (m-80) cc_final: 0.7695 (m-10) REVERT: B 82 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8913 (mttp) REVERT: B 136 LYS cc_start: 0.9182 (mmmm) cc_final: 0.8700 (mmtt) REVERT: B 174 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7575 (tt0) REVERT: B 218 ASN cc_start: 0.8967 (m110) cc_final: 0.8526 (t0) REVERT: B 221 LYS cc_start: 0.9047 (mttm) cc_final: 0.8785 (mmtm) REVERT: B 236 TYR cc_start: 0.9030 (t80) cc_final: 0.8783 (t80) REVERT: B 296 LYS cc_start: 0.8541 (mmmt) cc_final: 0.8297 (mmmt) REVERT: B 308 LYS cc_start: 0.9147 (mtpt) cc_final: 0.8940 (ptpt) REVERT: B 434 ASP cc_start: 0.8602 (m-30) cc_final: 0.8247 (m-30) REVERT: B 471 TYR cc_start: 0.9066 (t80) cc_final: 0.8448 (t80) REVERT: B 493 MET cc_start: 0.9621 (tmm) cc_final: 0.9312 (tmm) REVERT: B 546 LEU cc_start: 0.9520 (mt) cc_final: 0.9167 (mt) REVERT: B 586 TYR cc_start: 0.9102 (m-80) cc_final: 0.8534 (m-80) REVERT: B 602 GLU cc_start: 0.7898 (pp20) cc_final: 0.7573 (pp20) REVERT: B 627 LYS cc_start: 0.8888 (tttt) cc_final: 0.8497 (ttpt) REVERT: B 628 GLU cc_start: 0.8473 (mt-10) cc_final: 0.7979 (mp0) REVERT: C 55 TYR cc_start: 0.6080 (t80) cc_final: 0.5515 (t80) REVERT: C 68 GLU cc_start: 0.8825 (mp0) cc_final: 0.8097 (tm-30) REVERT: C 124 TRP cc_start: 0.8211 (t60) cc_final: 0.7973 (t60) REVERT: C 137 MET cc_start: 0.6838 (mpp) cc_final: 0.6565 (mpp) REVERT: C 154 PHE cc_start: 0.8943 (t80) cc_final: 0.8616 (t80) REVERT: C 178 PHE cc_start: 0.8505 (m-10) cc_final: 0.8201 (m-10) REVERT: C 184 LEU cc_start: 0.7092 (mt) cc_final: 0.6438 (tt) REVERT: C 240 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8767 (mm) REVERT: C 269 MET cc_start: 0.8676 (tpt) cc_final: 0.8332 (tmm) REVERT: C 285 ILE cc_start: 0.8881 (mp) cc_final: 0.8678 (tp) REVERT: D 47 LEU cc_start: 0.5203 (mt) cc_final: 0.4806 (tp) REVERT: D 59 LEU cc_start: 0.6912 (pp) cc_final: 0.5906 (tt) REVERT: D 76 ILE cc_start: 0.7763 (tp) cc_final: 0.7495 (tp) REVERT: D 80 HIS cc_start: 0.7282 (m-70) cc_final: 0.6989 (m-70) REVERT: D 112 LEU cc_start: 0.4583 (tp) cc_final: 0.4298 (tt) REVERT: D 174 TYR cc_start: 0.7405 (t80) cc_final: 0.6534 (t80) REVERT: D 198 GLU cc_start: 0.8392 (mm-30) cc_final: 0.6774 (tp30) REVERT: D 219 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7027 (pm20) REVERT: D 266 LYS cc_start: 0.7409 (mtpt) cc_final: 0.7198 (mmtt) outliers start: 74 outliers final: 44 residues processed: 631 average time/residue: 0.1260 time to fit residues: 120.8143 Evaluate side-chains 587 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 537 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 262 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 0.5980 chunk 157 optimal weight: 0.9990 chunk 168 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 159 optimal weight: 30.0000 chunk 182 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN B 147 GLN B 312 GLN B 320 ASN B 387 GLN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 127 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.140002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.096846 restraints weight = 32529.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.100308 restraints weight = 15516.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.102458 restraints weight = 9212.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.103836 restraints weight = 6484.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.104590 restraints weight = 5129.025| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 16386 Z= 0.233 Angle : 0.655 9.243 22134 Z= 0.341 Chirality : 0.046 0.383 2360 Planarity : 0.004 0.052 2818 Dihedral : 9.075 139.234 2300 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 5.19 % Allowed : 21.62 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.19), residues: 1932 helix: 1.33 (0.15), residues: 1135 sheet: -0.79 (0.45), residues: 118 loop : 0.44 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 274 TYR 0.021 0.002 TYR A 606 PHE 0.040 0.002 PHE D 168 TRP 0.012 0.001 TRP A 623 HIS 0.009 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.23 (16386) covalent geometry : angle 0.65520 / 0.34 (22134) hydrogen bonds : bond 0.04176 / 2.59 ( 871) hydrogen bonds : angle 5.00699 / 3.56 ( 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 634 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 545 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8781 (tptp) cc_final: 0.8412 (tppt) REVERT: A 40 TYR cc_start: 0.8947 (t80) cc_final: 0.8540 (t80) REVERT: A 119 GLU cc_start: 0.8579 (mp0) cc_final: 0.8301 (mp0) REVERT: A 214 LYS cc_start: 0.8256 (mmtt) cc_final: 0.7985 (mmtt) REVERT: A 232 ASN cc_start: 0.8886 (OUTLIER) cc_final: 0.8094 (m-40) REVERT: A 250 TYR cc_start: 0.8696 (m-80) cc_final: 0.8365 (m-80) REVERT: A 263 ASP cc_start: 0.8086 (m-30) cc_final: 0.7866 (m-30) REVERT: A 290 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8245 (mt-10) REVERT: A 348 MET cc_start: 0.8259 (tmm) cc_final: 0.7213 (tmm) REVERT: A 352 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7253 (mt-10) REVERT: A 362 ASP cc_start: 0.8235 (m-30) cc_final: 0.7978 (m-30) REVERT: A 384 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.6932 (pm20) REVERT: A 427 LYS cc_start: 0.9078 (tppp) cc_final: 0.8692 (tppp) REVERT: A 446 ARG cc_start: 0.7709 (mmm160) cc_final: 0.7250 (mmm160) REVERT: A 640 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8941 (tpp) REVERT: A 684 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.7950 (m-80) REVERT: B 27 ASP cc_start: 0.9100 (p0) cc_final: 0.8892 (p0) REVERT: B 72 TYR cc_start: 0.8007 (m-80) cc_final: 0.7677 (m-10) REVERT: B 82 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8962 (mttp) REVERT: B 108 THR cc_start: 0.9131 (OUTLIER) cc_final: 0.8927 (p) REVERT: B 136 LYS cc_start: 0.9266 (mmmm) cc_final: 0.8764 (mmtt) REVERT: B 174 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7542 (tt0) REVERT: B 218 ASN cc_start: 0.8991 (m110) cc_final: 0.8524 (t0) REVERT: B 236 TYR cc_start: 0.9160 (t80) cc_final: 0.8877 (t80) REVERT: B 308 LYS cc_start: 0.9202 (mtpt) cc_final: 0.8956 (ptpt) REVERT: B 374 SER cc_start: 0.9504 (t) cc_final: 0.9191 (t) REVERT: B 394 TYR cc_start: 0.9188 (m-80) cc_final: 0.8813 (m-80) REVERT: B 417 LEU cc_start: 0.9604 (tt) cc_final: 0.9392 (tp) REVERT: B 434 ASP cc_start: 0.8565 (m-30) cc_final: 0.8226 (m-30) REVERT: B 493 MET cc_start: 0.9624 (tmm) cc_final: 0.9233 (tmm) REVERT: B 546 LEU cc_start: 0.9538 (mt) cc_final: 0.9287 (mt) REVERT: B 586 TYR cc_start: 0.9141 (m-80) cc_final: 0.8569 (m-80) REVERT: B 602 GLU cc_start: 0.8037 (pp20) cc_final: 0.7256 (pp20) REVERT: B 627 LYS cc_start: 0.8867 (tttt) cc_final: 0.8273 (ttpp) REVERT: B 628 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8019 (mp0) REVERT: C 21 PHE cc_start: 0.8387 (m-80) cc_final: 0.8112 (t80) REVERT: C 103 LYS cc_start: 0.8149 (tppt) cc_final: 0.7788 (tppt) REVERT: C 124 TRP cc_start: 0.8262 (t60) cc_final: 0.8045 (t60) REVERT: C 154 PHE cc_start: 0.9088 (t80) cc_final: 0.8720 (t80) REVERT: C 174 TYR cc_start: 0.7190 (OUTLIER) cc_final: 0.6578 (t80) REVERT: C 186 GLN cc_start: 0.7516 (mp10) cc_final: 0.6974 (mp10) REVERT: C 269 MET cc_start: 0.8691 (tpt) cc_final: 0.8393 (tmm) REVERT: C 274 ASP cc_start: 0.8139 (p0) cc_final: 0.7750 (p0) REVERT: D 59 LEU cc_start: 0.7072 (pp) cc_final: 0.6178 (tt) REVERT: D 80 HIS cc_start: 0.7205 (m-70) cc_final: 0.6924 (m90) REVERT: D 116 GLU cc_start: 0.9127 (tp30) cc_final: 0.8756 (tp30) REVERT: D 157 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8738 (ttm) REVERT: D 174 TYR cc_start: 0.7693 (t80) cc_final: 0.6917 (t80) REVERT: D 236 TYR cc_start: 0.7068 (t80) cc_final: 0.6732 (m-10) REVERT: D 240 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7930 (mm) outliers start: 89 outliers final: 54 residues processed: 586 average time/residue: 0.1194 time to fit residues: 106.8457 Evaluate side-chains 543 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 480 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 240 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 168 optimal weight: 6.9990 chunk 157 optimal weight: 0.6980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 312 GLN B 320 ASN B 387 GLN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 127 GLN C 132 GLN C 234 GLN D 91 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.142153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.098525 restraints weight = 32755.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.102040 restraints weight = 15567.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.104236 restraints weight = 9239.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.105688 restraints weight = 6476.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.106501 restraints weight = 5102.372| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16386 Z= 0.218 Angle : 0.662 10.323 22134 Z= 0.341 Chirality : 0.045 0.448 2360 Planarity : 0.004 0.055 2818 Dihedral : 8.704 140.129 2300 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 5.13 % Allowed : 23.43 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.19), residues: 1932 helix: 1.34 (0.15), residues: 1133 sheet: -0.83 (0.45), residues: 114 loop : 0.43 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 686 TYR 0.015 0.002 TYR A 626 PHE 0.041 0.002 PHE D 168 TRP 0.008 0.001 TRP A 623 HIS 0.006 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 (16386) covalent geometry : angle 0.66194 / 0.34 (22134) hydrogen bonds : bond 0.04046 / 2.53 ( 871) hydrogen bonds : angle 4.93718 / 3.52 ( 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 587 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 499 time to evaluate : 0.630 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: A 8 LYS cc_start: 0.8837 (tptp) cc_final: 0.8566 (tppt) REVERT: A 40 TYR cc_start: 0.8966 (t80) cc_final: 0.8479 (t80) REVERT: A 119 GLU cc_start: 0.8585 (mp0) cc_final: 0.8315 (mp0) REVERT: A 144 MET cc_start: 0.8693 (mtm) cc_final: 0.8390 (mtm) REVERT: A 214 LYS cc_start: 0.8259 (mmtt) cc_final: 0.7966 (mmtt) REVERT: A 232 ASN cc_start: 0.8779 (OUTLIER) cc_final: 0.7997 (m-40) REVERT: A 250 TYR cc_start: 0.8703 (m-80) cc_final: 0.8344 (m-80) REVERT: A 263 ASP cc_start: 0.8109 (m-30) cc_final: 0.7839 (m-30) REVERT: A 290 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8271 (mt-10) REVERT: A 348 MET cc_start: 0.8275 (tmm) cc_final: 0.7155 (tmm) REVERT: A 352 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7272 (mt-10) REVERT: A 379 SER cc_start: 0.9161 (t) cc_final: 0.8841 (t) REVERT: A 381 LEU cc_start: 0.9314 (tp) cc_final: 0.9086 (tp) REVERT: A 384 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7647 (pm20) REVERT: A 389 SER cc_start: 0.9352 (OUTLIER) cc_final: 0.8932 (p) REVERT: A 427 LYS cc_start: 0.9067 (tppp) cc_final: 0.8607 (tppp) REVERT: A 446 ARG cc_start: 0.7625 (mmm160) cc_final: 0.7166 (mmm160) REVERT: A 590 SER cc_start: 0.8924 (t) cc_final: 0.8654 (p) REVERT: A 640 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.8904 (tpp) REVERT: A 684 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.8071 (m-80) REVERT: B 27 ASP cc_start: 0.9129 (p0) cc_final: 0.8837 (p0) REVERT: B 65 GLU cc_start: 0.8458 (mm-30) cc_final: 0.7628 (mp0) REVERT: B 82 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8922 (mttp) REVERT: B 174 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7498 (tt0) REVERT: B 236 TYR cc_start: 0.9166 (t80) cc_final: 0.8919 (t80) REVERT: B 374 SER cc_start: 0.9506 (t) cc_final: 0.9195 (t) REVERT: B 434 ASP cc_start: 0.8640 (m-30) cc_final: 0.8238 (m-30) REVERT: B 467 ASN cc_start: 0.9019 (t0) cc_final: 0.8600 (t0) REVERT: B 493 MET cc_start: 0.9579 (tmm) cc_final: 0.9140 (tmm) REVERT: B 586 TYR cc_start: 0.9152 (m-80) cc_final: 0.8544 (m-80) REVERT: B 595 MET cc_start: 0.8637 (mmm) cc_final: 0.8150 (mmm) REVERT: B 602 GLU cc_start: 0.8043 (pp20) cc_final: 0.7379 (pp20) REVERT: B 627 LYS cc_start: 0.8914 (tttt) cc_final: 0.8350 (tttm) REVERT: B 628 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8002 (mp0) REVERT: C 21 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.8145 (t80) REVERT: C 55 TYR cc_start: 0.6208 (t80) cc_final: 0.5696 (t80) REVERT: C 68 GLU cc_start: 0.8478 (mm-30) cc_final: 0.7671 (tm-30) REVERT: C 103 LYS cc_start: 0.8295 (tppt) cc_final: 0.7978 (tppt) REVERT: C 105 TYR cc_start: 0.8748 (m-80) cc_final: 0.8530 (m-80) REVERT: C 107 ASN cc_start: 0.9041 (m-40) cc_final: 0.8624 (m-40) REVERT: C 124 TRP cc_start: 0.8269 (t60) cc_final: 0.8022 (t60) REVERT: C 137 MET cc_start: 0.7199 (OUTLIER) cc_final: 0.6890 (mpp) REVERT: C 154 PHE cc_start: 0.9168 (t80) cc_final: 0.8706 (t80) REVERT: C 174 TYR cc_start: 0.7245 (OUTLIER) cc_final: 0.6552 (t80) REVERT: C 238 ASN cc_start: 0.7669 (t0) cc_final: 0.7130 (t0) REVERT: C 261 ARG cc_start: 0.7488 (mtm-85) cc_final: 0.7274 (mtm110) REVERT: C 269 MET cc_start: 0.8734 (tpt) cc_final: 0.8351 (tmm) REVERT: C 285 ILE cc_start: 0.8895 (mp) cc_final: 0.8627 (tp) REVERT: D 29 PHE cc_start: 0.7122 (t80) cc_final: 0.6217 (t80) REVERT: D 59 LEU cc_start: 0.6893 (pp) cc_final: 0.6017 (tt) REVERT: D 80 HIS cc_start: 0.7343 (m-70) cc_final: 0.6998 (m90) REVERT: D 116 GLU cc_start: 0.9127 (tp30) cc_final: 0.8773 (tp30) REVERT: D 178 PHE cc_start: 0.8727 (m-10) cc_final: 0.8392 (m-80) REVERT: D 219 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7033 (pm20) REVERT: D 242 TYR cc_start: 0.6695 (t80) cc_final: 0.5786 (m-80) outliers start: 88 outliers final: 59 residues processed: 543 average time/residue: 0.1232 time to fit residues: 102.8629 Evaluate side-chains 550 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 481 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 82 LYS 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 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 230 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 4.9990 chunk 183 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 172 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 312 GLN B 320 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS C 127 GLN C 136 GLN C 234 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.143878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.101300 restraints weight = 32589.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.104744 restraints weight = 15597.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.106968 restraints weight = 9228.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.108350 restraints weight = 6416.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.109241 restraints weight = 5030.679| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.104 | | 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) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16386 Z= 0.148 Angle : 0.636 10.471 22134 Z= 0.326 Chirality : 0.044 0.409 2360 Planarity : 0.004 0.050 2818 Dihedral : 8.371 139.711 2299 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.37 % Allowed : 25.06 % Favored : 70.57 % 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: 1.12 (0.19), residues: 1932 helix: 1.31 (0.15), residues: 1147 sheet: -0.99 (0.44), residues: 118 loop : 0.26 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 225 TYR 0.030 0.001 TYR C 173 PHE 0.042 0.002 PHE D 168 TRP 0.004 0.001 TRP A 623 HIS 0.016 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (16386) covalent geometry : angle 0.63616 / 0.33 (22134) hydrogen bonds : bond 0.03887 / 2.43 ( 871) hydrogen bonds : angle 4.85776 / 3.47 ( 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 600 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 525 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8840 (tptp) cc_final: 0.8568 (tppt) REVERT: A 40 TYR cc_start: 0.8913 (t80) cc_final: 0.8418 (t80) REVERT: A 119 GLU cc_start: 0.8519 (mp0) cc_final: 0.8241 (mp0) REVERT: A 144 MET cc_start: 0.8680 (mtm) cc_final: 0.8294 (mtm) REVERT: A 179 LEU cc_start: 0.9281 (tp) cc_final: 0.8996 (tp) REVERT: A 214 LYS cc_start: 0.8225 (mmtt) cc_final: 0.8020 (mmtt) REVERT: A 232 ASN cc_start: 0.8614 (OUTLIER) cc_final: 0.8060 (m-40) REVERT: A 263 ASP cc_start: 0.8129 (m-30) cc_final: 0.7919 (m-30) REVERT: A 290 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8257 (mt-10) REVERT: A 348 MET cc_start: 0.8314 (tmm) cc_final: 0.7133 (tmm) REVERT: A 352 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7206 (mt-10) REVERT: A 384 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7506 (pm20) REVERT: A 389 SER cc_start: 0.9317 (OUTLIER) cc_final: 0.8919 (p) REVERT: A 406 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8088 (t70) REVERT: A 410 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7765 (t160) REVERT: A 446 ARG cc_start: 0.7614 (mmm160) cc_final: 0.7221 (mmm160) REVERT: A 505 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8442 (mt-10) REVERT: A 590 SER cc_start: 0.8777 (t) cc_final: 0.8524 (p) REVERT: A 640 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8893 (tpp) REVERT: B 27 ASP cc_start: 0.9045 (p0) cc_final: 0.8677 (p0) REVERT: B 82 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8869 (mttp) REVERT: B 174 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7452 (tt0) REVERT: B 184 ARG cc_start: 0.8941 (tpp-160) cc_final: 0.8644 (mmm-85) REVERT: B 218 ASN cc_start: 0.8979 (m110) cc_final: 0.8498 (t0) REVERT: B 274 ARG cc_start: 0.8341 (tpp80) cc_final: 0.7958 (ttm-80) REVERT: B 287 LYS cc_start: 0.9200 (tptt) cc_final: 0.8965 (tppt) REVERT: B 374 SER cc_start: 0.9499 (t) cc_final: 0.9182 (t) REVERT: B 398 ASP cc_start: 0.8186 (t0) cc_final: 0.7900 (t0) REVERT: B 421 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7932 (pt0) REVERT: B 434 ASP cc_start: 0.8634 (m-30) cc_final: 0.8239 (m-30) REVERT: B 467 ASN cc_start: 0.9038 (t0) cc_final: 0.8585 (t0) REVERT: B 493 MET cc_start: 0.9573 (tmm) cc_final: 0.9139 (tmm) REVERT: B 571 TYR cc_start: 0.8724 (t80) cc_final: 0.8276 (t80) REVERT: B 586 TYR cc_start: 0.9090 (m-80) cc_final: 0.8474 (m-80) REVERT: B 595 MET cc_start: 0.8584 (mmm) cc_final: 0.8143 (mmm) REVERT: B 602 GLU cc_start: 0.8048 (pp20) cc_final: 0.7365 (pp20) REVERT: B 613 TYR cc_start: 0.8956 (t80) cc_final: 0.8725 (t80) REVERT: B 627 LYS cc_start: 0.8908 (tttt) cc_final: 0.8327 (tttm) REVERT: B 628 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8067 (mp0) REVERT: C 21 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.8063 (t80) REVERT: C 56 MET cc_start: 0.3297 (tpt) cc_final: 0.3061 (tpt) REVERT: C 82 ASP cc_start: 0.7744 (m-30) cc_final: 0.7187 (t0) REVERT: C 103 LYS cc_start: 0.8396 (tppt) cc_final: 0.8013 (tppt) REVERT: C 107 ASN cc_start: 0.9066 (m-40) cc_final: 0.8545 (m-40) REVERT: C 124 TRP cc_start: 0.8260 (t60) cc_final: 0.8002 (t60) REVERT: C 127 GLN cc_start: 0.9106 (tp40) cc_final: 0.8803 (mm110) REVERT: C 154 PHE cc_start: 0.9154 (t80) cc_final: 0.8686 (t80) REVERT: C 174 TYR cc_start: 0.7172 (OUTLIER) cc_final: 0.6484 (t80) REVERT: C 210 GLN cc_start: 0.4565 (mm110) cc_final: 0.4108 (mm110) REVERT: C 238 ASN cc_start: 0.7561 (t0) cc_final: 0.7292 (t0) REVERT: C 269 MET cc_start: 0.8836 (tpt) cc_final: 0.8475 (tmm) REVERT: C 282 ILE cc_start: 0.6648 (tp) cc_final: 0.6054 (mm) REVERT: C 285 ILE cc_start: 0.8863 (mp) cc_final: 0.8600 (tp) REVERT: D 59 LEU cc_start: 0.6734 (pp) cc_final: 0.5818 (tt) REVERT: D 80 HIS cc_start: 0.7403 (m-70) cc_final: 0.7006 (m-70) REVERT: D 112 LEU cc_start: 0.3916 (tt) cc_final: 0.3610 (tt) REVERT: D 116 GLU cc_start: 0.9136 (tp30) cc_final: 0.8792 (tp30) REVERT: D 149 ASP cc_start: 0.7658 (t0) cc_final: 0.6969 (p0) REVERT: D 157 MET cc_start: 0.8921 (ttm) cc_final: 0.8689 (ptm) REVERT: D 174 TYR cc_start: 0.7852 (t80) cc_final: 0.7038 (t80) REVERT: D 210 GLN cc_start: 0.8345 (tp40) cc_final: 0.7964 (tp40) REVERT: D 219 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.6959 (pm20) outliers start: 75 outliers final: 43 residues processed: 562 average time/residue: 0.1217 time to fit residues: 105.5670 Evaluate side-chains 538 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 484 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 230 ASP 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: 7.9990 chunk 74 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 140 optimal weight: 20.0000 chunk 115 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 156 optimal weight: 10.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 370 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN B 147 GLN B 312 GLN B 320 ASN B 387 GLN B 410 ASN B 588 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 GLN C 181 GLN ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.140112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.097749 restraints weight = 32903.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.101089 restraints weight = 15874.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.103185 restraints weight = 9511.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.104496 restraints weight = 6688.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.105396 restraints weight = 5308.904| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.5914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16386 Z= 0.251 Angle : 0.708 13.862 22134 Z= 0.365 Chirality : 0.047 0.532 2360 Planarity : 0.004 0.052 2818 Dihedral : 8.427 142.544 2299 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.55 % Allowed : 25.64 % 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: 1.05 (0.19), residues: 1932 helix: 1.27 (0.15), residues: 1146 sheet: -0.86 (0.39), residues: 150 loop : 0.24 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 261 TYR 0.036 0.002 TYR C 105 PHE 0.041 0.002 PHE D 168 TRP 0.038 0.002 TRP C 44 HIS 0.014 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.25 (16386) covalent geometry : angle 0.70753 / 0.36 (22134) hydrogen bonds : bond 0.04054 / 2.53 ( 871) hydrogen bonds : angle 5.03180 / 3.59 ( 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 567 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 489 time to evaluate : 0.679 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: A 8 LYS cc_start: 0.8857 (tptp) cc_final: 0.8583 (tppt) REVERT: A 40 TYR cc_start: 0.8957 (t80) cc_final: 0.8469 (t80) REVERT: A 65 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7799 (mp0) REVERT: A 119 GLU cc_start: 0.8574 (mp0) cc_final: 0.8312 (mp0) REVERT: A 144 MET cc_start: 0.8663 (mtm) cc_final: 0.8391 (mtm) REVERT: A 214 LYS cc_start: 0.8273 (mmtt) cc_final: 0.7861 (mmtp) REVERT: A 232 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8363 (m-40) REVERT: A 250 TYR cc_start: 0.8725 (m-80) cc_final: 0.8251 (m-80) REVERT: A 263 ASP cc_start: 0.8109 (m-30) cc_final: 0.7870 (m-30) REVERT: A 290 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8218 (mt-10) REVERT: A 348 MET cc_start: 0.8258 (tmm) cc_final: 0.7909 (tmm) REVERT: A 384 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.6910 (pm20) REVERT: A 389 SER cc_start: 0.9308 (OUTLIER) cc_final: 0.8872 (p) REVERT: A 406 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8081 (t70) REVERT: A 427 LYS cc_start: 0.9068 (tppp) cc_final: 0.8634 (tppp) REVERT: A 446 ARG cc_start: 0.7702 (mmm160) cc_final: 0.7286 (mmm160) REVERT: A 640 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8927 (tpp) REVERT: A 667 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8708 (tt) REVERT: B 27 ASP cc_start: 0.9103 (p0) cc_final: 0.8729 (p0) REVERT: B 40 TYR cc_start: 0.9162 (t80) cc_final: 0.8633 (t80) REVERT: B 65 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7548 (mp0) REVERT: B 82 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8918 (mttp) REVERT: B 95 MET cc_start: 0.8971 (tpp) cc_final: 0.8749 (mmm) REVERT: B 174 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7455 (tt0) REVERT: B 184 ARG cc_start: 0.8938 (tpp-160) cc_final: 0.8633 (mmm-85) REVERT: B 218 ASN cc_start: 0.9008 (m110) cc_final: 0.8501 (t0) REVERT: B 274 ARG cc_start: 0.8358 (tpp80) cc_final: 0.7897 (ttm-80) REVERT: B 434 ASP cc_start: 0.8623 (m-30) cc_final: 0.8233 (m-30) REVERT: B 467 ASN cc_start: 0.9176 (t0) cc_final: 0.8757 (t0) REVERT: B 483 GLU cc_start: 0.9340 (mp0) cc_final: 0.8916 (pm20) REVERT: B 493 MET cc_start: 0.9615 (tmm) cc_final: 0.9230 (tmm) REVERT: B 571 TYR cc_start: 0.8835 (t80) cc_final: 0.8461 (t80) REVERT: B 586 TYR cc_start: 0.9106 (m-80) cc_final: 0.8490 (m-80) REVERT: B 595 MET cc_start: 0.8631 (mmm) cc_final: 0.8185 (mmm) REVERT: B 602 GLU cc_start: 0.8004 (pp20) cc_final: 0.7354 (pp20) REVERT: B 627 LYS cc_start: 0.8940 (tttt) cc_final: 0.8382 (tttm) REVERT: B 628 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8170 (mp0) REVERT: C 55 TYR cc_start: 0.5692 (t80) cc_final: 0.5159 (t80) REVERT: C 56 MET cc_start: 0.3220 (tpt) cc_final: 0.2836 (tpt) REVERT: C 82 ASP cc_start: 0.8052 (m-30) cc_final: 0.7362 (t70) REVERT: C 103 LYS cc_start: 0.8348 (tppt) cc_final: 0.7977 (tppt) REVERT: C 107 ASN cc_start: 0.9085 (m-40) cc_final: 0.8578 (m-40) REVERT: C 124 TRP cc_start: 0.8312 (t60) cc_final: 0.7986 (t60) REVERT: C 127 GLN cc_start: 0.9075 (tp40) cc_final: 0.8765 (mm-40) REVERT: C 137 MET cc_start: 0.6928 (mpp) cc_final: 0.6679 (mpp) REVERT: C 154 PHE cc_start: 0.9190 (t80) cc_final: 0.8754 (t80) REVERT: C 174 TYR cc_start: 0.7280 (OUTLIER) cc_final: 0.6640 (t80) REVERT: C 185 MET cc_start: 0.7168 (mmt) cc_final: 0.6734 (pmm) REVERT: C 269 MET cc_start: 0.8791 (tpt) cc_final: 0.8404 (tmm) REVERT: D 59 LEU cc_start: 0.6789 (pp) cc_final: 0.5882 (tt) REVERT: D 80 HIS cc_start: 0.7583 (m-70) cc_final: 0.7181 (m-70) REVERT: D 87 LYS cc_start: 0.7636 (mttm) cc_final: 0.7173 (mttm) REVERT: D 112 LEU cc_start: 0.4182 (tt) cc_final: 0.3960 (tt) REVERT: D 116 GLU cc_start: 0.9070 (tp30) cc_final: 0.8697 (tp30) REVERT: D 149 ASP cc_start: 0.7804 (t0) cc_final: 0.7165 (p0) REVERT: D 178 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8400 (m-80) REVERT: D 210 GLN cc_start: 0.8342 (tp40) cc_final: 0.7986 (tp40) REVERT: D 219 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.6987 (pm20) REVERT: D 232 LEU cc_start: 0.6842 (mt) cc_final: 0.6546 (mt) outliers start: 78 outliers final: 50 residues processed: 526 average time/residue: 0.1226 time to fit residues: 98.6781 Evaluate side-chains 527 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 467 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 230 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 0.9980 chunk 99 optimal weight: 0.4980 chunk 61 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 158 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN A 387 GLN A 410 ASN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 312 GLN B 320 ASN B 387 GLN C 98 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.144385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.101920 restraints weight = 32829.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.105428 restraints weight = 15744.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.107668 restraints weight = 9258.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109068 restraints weight = 6477.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.109962 restraints weight = 5071.105| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.6107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16386 Z= 0.143 Angle : 0.684 15.020 22134 Z= 0.349 Chirality : 0.046 0.542 2360 Planarity : 0.003 0.054 2818 Dihedral : 8.098 140.229 2299 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.73 % Allowed : 26.75 % Favored : 69.52 % 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: 1.10 (0.19), residues: 1932 helix: 1.31 (0.15), residues: 1144 sheet: -0.75 (0.40), residues: 150 loop : 0.24 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 243 TYR 0.034 0.001 TYR C 173 PHE 0.040 0.002 PHE D 168 TRP 0.034 0.001 TRP C 44 HIS 0.011 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (16386) covalent geometry : angle 0.68359 / 0.35 (22134) hydrogen bonds : bond 0.03881 / 2.43 ( 871) hydrogen bonds : angle 4.95016 / 3.54 ( 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 575 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 511 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8835 (tptp) cc_final: 0.8561 (tppt) REVERT: A 40 TYR cc_start: 0.8913 (t80) cc_final: 0.8413 (t80) REVERT: A 65 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7924 (mp0) REVERT: A 119 GLU cc_start: 0.8512 (mp0) cc_final: 0.8221 (mp0) REVERT: A 144 MET cc_start: 0.8653 (mtm) cc_final: 0.8326 (mtm) REVERT: A 173 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9101 (mt) REVERT: A 179 LEU cc_start: 0.9257 (tp) cc_final: 0.8918 (tp) REVERT: A 188 ILE cc_start: 0.9390 (mm) cc_final: 0.9119 (mm) REVERT: A 214 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7753 (mmtp) REVERT: A 232 ASN cc_start: 0.8563 (OUTLIER) cc_final: 0.8057 (m-40) REVERT: A 250 TYR cc_start: 0.8650 (m-80) cc_final: 0.8284 (m-80) REVERT: A 263 ASP cc_start: 0.8141 (m-30) cc_final: 0.7912 (m-30) REVERT: A 290 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8211 (mt-10) REVERT: A 348 MET cc_start: 0.8270 (tmm) cc_final: 0.7965 (tmm) REVERT: A 384 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7522 (pm20) REVERT: A 389 SER cc_start: 0.9289 (OUTLIER) cc_final: 0.8908 (p) REVERT: A 406 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.7634 (t70) REVERT: A 410 ASN cc_start: 0.8062 (OUTLIER) cc_final: 0.7830 (t160) REVERT: A 446 ARG cc_start: 0.7647 (mmm160) cc_final: 0.7254 (mmm160) REVERT: A 505 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8391 (mt-10) REVERT: A 640 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8813 (tpp) REVERT: A 667 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8601 (tt) REVERT: B 27 ASP cc_start: 0.9082 (p0) cc_final: 0.8726 (p0) REVERT: B 65 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7483 (mp0) REVERT: B 82 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8853 (mttp) REVERT: B 174 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7381 (tt0) REVERT: B 184 ARG cc_start: 0.8903 (tpp-160) cc_final: 0.8620 (mmm-85) REVERT: B 218 ASN cc_start: 0.9000 (m110) cc_final: 0.8488 (t0) REVERT: B 274 ARG cc_start: 0.8361 (tpp80) cc_final: 0.7990 (ttm-80) REVERT: B 374 SER cc_start: 0.9494 (t) cc_final: 0.9189 (t) REVERT: B 398 ASP cc_start: 0.8112 (t0) cc_final: 0.7853 (t0) REVERT: B 434 ASP cc_start: 0.8649 (m-30) cc_final: 0.8239 (m-30) REVERT: B 467 ASN cc_start: 0.9059 (t0) cc_final: 0.8643 (t0) REVERT: B 483 GLU cc_start: 0.9347 (mp0) cc_final: 0.8880 (pm20) REVERT: B 493 MET cc_start: 0.9550 (tmm) cc_final: 0.9208 (tmm) REVERT: B 586 TYR cc_start: 0.8996 (m-80) cc_final: 0.8696 (m-80) REVERT: B 595 MET cc_start: 0.8517 (mmm) cc_final: 0.8174 (mmm) REVERT: B 602 GLU cc_start: 0.8066 (pp20) cc_final: 0.7307 (pp20) REVERT: B 627 LYS cc_start: 0.8966 (tttt) cc_final: 0.8435 (tttt) REVERT: B 628 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8215 (mp0) REVERT: C 55 TYR cc_start: 0.5614 (t80) cc_final: 0.5032 (t80) REVERT: C 82 ASP cc_start: 0.8209 (m-30) cc_final: 0.7399 (t70) REVERT: C 103 LYS cc_start: 0.8450 (tppt) cc_final: 0.8041 (tppt) REVERT: C 107 ASN cc_start: 0.9109 (m-40) cc_final: 0.8576 (m-40) REVERT: C 124 TRP cc_start: 0.8248 (t60) cc_final: 0.7927 (t60) REVERT: C 127 GLN cc_start: 0.9057 (tp40) cc_final: 0.8771 (mm-40) REVERT: C 154 PHE cc_start: 0.9144 (t80) cc_final: 0.8708 (t80) REVERT: C 174 TYR cc_start: 0.7058 (OUTLIER) cc_final: 0.6568 (t80) REVERT: C 210 GLN cc_start: 0.4774 (mm110) cc_final: 0.4465 (mm110) REVERT: D 59 LEU cc_start: 0.6695 (pp) cc_final: 0.5794 (tt) REVERT: D 80 HIS cc_start: 0.7508 (m-70) cc_final: 0.7089 (m-70) REVERT: D 116 GLU cc_start: 0.9077 (tp30) cc_final: 0.8707 (tp30) REVERT: D 149 ASP cc_start: 0.7705 (t0) cc_final: 0.7117 (p0) REVERT: D 174 TYR cc_start: 0.8036 (t80) cc_final: 0.7213 (t80) REVERT: D 210 GLN cc_start: 0.8294 (tp40) cc_final: 0.7702 (mm110) REVERT: D 219 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.6826 (pm20) REVERT: D 242 TYR cc_start: 0.6499 (t80) cc_final: 0.5188 (m-80) outliers start: 64 outliers final: 40 residues processed: 538 average time/residue: 0.1230 time to fit residues: 100.3445 Evaluate side-chains 534 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 483 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 230 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 9.9990 chunk 133 optimal weight: 0.3980 chunk 149 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 100 optimal weight: 0.0470 chunk 88 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 147 GLN B 312 GLN B 320 ASN B 475 ASN C 98 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.145323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.103593 restraints weight = 32493.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.107127 restraints weight = 15324.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.109306 restraints weight = 9017.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.110665 restraints weight = 6326.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.111436 restraints weight = 4998.906| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.6359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 16386 Z= 0.142 Angle : 0.710 17.637 22134 Z= 0.362 Chirality : 0.047 0.517 2360 Planarity : 0.004 0.055 2818 Dihedral : 7.999 140.712 2298 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.21 % Allowed : 27.80 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.19), residues: 1932 helix: 1.23 (0.15), residues: 1144 sheet: -0.38 (0.42), residues: 138 loop : 0.15 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 235 TYR 0.029 0.001 TYR B 471 PHE 0.040 0.002 PHE D 168 TRP 0.055 0.002 TRP C 44 HIS 0.006 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (16386) covalent geometry : angle 0.71023 / 0.36 (22134) hydrogen bonds : bond 0.03949 / 2.48 ( 871) hydrogen bonds : angle 5.02464 / 3.60 ( 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 571 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 516 time to evaluate : 0.669 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: A 8 LYS cc_start: 0.8815 (tptp) cc_final: 0.8555 (tppt) REVERT: A 31 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8093 (mp0) REVERT: A 40 TYR cc_start: 0.8897 (t80) cc_final: 0.8375 (t80) REVERT: A 65 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7900 (mp0) REVERT: A 119 GLU cc_start: 0.8454 (mp0) cc_final: 0.8180 (mp0) REVERT: A 144 MET cc_start: 0.8607 (mtm) cc_final: 0.8228 (mtm) REVERT: A 173 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.8966 (mt) REVERT: A 179 LEU cc_start: 0.9228 (tp) cc_final: 0.8821 (tp) REVERT: A 188 ILE cc_start: 0.9399 (mm) cc_final: 0.9147 (mm) REVERT: A 214 LYS cc_start: 0.8434 (mmtt) cc_final: 0.8080 (mmtp) REVERT: A 221 LYS cc_start: 0.8004 (mttt) cc_final: 0.7796 (mttt) REVERT: A 232 ASN cc_start: 0.8487 (OUTLIER) cc_final: 0.8099 (m-40) REVERT: A 250 TYR cc_start: 0.8635 (m-80) cc_final: 0.8282 (m-80) REVERT: A 290 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8219 (mt-10) REVERT: A 348 MET cc_start: 0.8222 (tmm) cc_final: 0.7894 (tmm) REVERT: A 384 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7479 (pm20) REVERT: A 389 SER cc_start: 0.9305 (OUTLIER) cc_final: 0.8880 (p) REVERT: A 406 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.7446 (t70) REVERT: A 446 ARG cc_start: 0.7626 (mmm160) cc_final: 0.7227 (mmm160) REVERT: A 505 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8485 (mt-10) REVERT: A 615 MET cc_start: 0.9106 (mmp) cc_final: 0.8163 (mmp) REVERT: A 640 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8593 (tpp) REVERT: B 27 ASP cc_start: 0.9064 (p0) cc_final: 0.8713 (p0) REVERT: B 65 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7550 (mp0) REVERT: B 82 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8835 (mptp) REVERT: B 174 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7402 (tt0) REVERT: B 184 ARG cc_start: 0.8883 (tpp-160) cc_final: 0.8591 (mmm160) REVERT: B 191 GLN cc_start: 0.8276 (mm-40) cc_final: 0.8002 (mm-40) REVERT: B 218 ASN cc_start: 0.9018 (m110) cc_final: 0.8470 (t0) REVERT: B 274 ARG cc_start: 0.8323 (tpp80) cc_final: 0.7986 (ttm-80) REVERT: B 374 SER cc_start: 0.9515 (t) cc_final: 0.9216 (t) REVERT: B 396 ASP cc_start: 0.8114 (m-30) cc_final: 0.7902 (m-30) REVERT: B 398 ASP cc_start: 0.8003 (t0) cc_final: 0.7739 (t0) REVERT: B 417 LEU cc_start: 0.9531 (tt) cc_final: 0.9281 (tp) REVERT: B 443 THR cc_start: 0.8996 (m) cc_final: 0.8761 (m) REVERT: B 447 ASN cc_start: 0.8510 (m-40) cc_final: 0.8244 (m-40) REVERT: B 467 ASN cc_start: 0.9017 (t0) cc_final: 0.8588 (t0) REVERT: B 483 GLU cc_start: 0.9325 (mp0) cc_final: 0.8885 (pm20) REVERT: B 493 MET cc_start: 0.9518 (tmm) cc_final: 0.9220 (tmm) REVERT: B 586 TYR cc_start: 0.8986 (m-80) cc_final: 0.8597 (m-10) REVERT: B 595 MET cc_start: 0.8508 (mmm) cc_final: 0.8181 (mmm) REVERT: B 602 GLU cc_start: 0.8051 (pp20) cc_final: 0.7265 (pp20) REVERT: B 627 LYS cc_start: 0.9010 (tttt) cc_final: 0.8505 (tttt) REVERT: B 628 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8228 (mp0) REVERT: C 27 LYS cc_start: 0.7779 (pttp) cc_final: 0.7369 (pttp) REVERT: C 45 LYS cc_start: 0.9241 (tptp) cc_final: 0.8998 (pttp) REVERT: C 56 MET cc_start: 0.2672 (tpt) cc_final: 0.2303 (tpt) REVERT: C 82 ASP cc_start: 0.8284 (m-30) cc_final: 0.7517 (t70) REVERT: C 103 LYS cc_start: 0.8412 (tppt) cc_final: 0.8010 (tppt) REVERT: C 107 ASN cc_start: 0.9120 (m-40) cc_final: 0.8538 (m-40) REVERT: C 124 TRP cc_start: 0.8340 (t60) cc_final: 0.8062 (t60) REVERT: C 127 GLN cc_start: 0.9012 (tp40) cc_final: 0.8737 (mm-40) REVERT: C 154 PHE cc_start: 0.9157 (t80) cc_final: 0.8757 (t80) REVERT: C 174 TYR cc_start: 0.7039 (OUTLIER) cc_final: 0.6769 (t80) REVERT: C 210 GLN cc_start: 0.4903 (mm110) cc_final: 0.4702 (mm110) REVERT: D 59 LEU cc_start: 0.6738 (pp) cc_final: 0.5838 (tt) REVERT: D 80 HIS cc_start: 0.7461 (m-70) cc_final: 0.7064 (m-70) REVERT: D 116 GLU cc_start: 0.9088 (tp30) cc_final: 0.8733 (tp30) REVERT: D 149 ASP cc_start: 0.7733 (t0) cc_final: 0.7196 (p0) REVERT: D 157 MET cc_start: 0.8411 (ptm) cc_final: 0.7584 (ppp) REVERT: D 178 PHE cc_start: 0.8756 (m-10) cc_final: 0.8408 (m-80) REVERT: D 210 GLN cc_start: 0.8347 (tp40) cc_final: 0.7779 (mm110) REVERT: D 219 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6858 (pm20) REVERT: D 242 TYR cc_start: 0.6642 (t80) cc_final: 0.5344 (m-80) outliers start: 55 outliers final: 34 residues processed: 534 average time/residue: 0.1232 time to fit residues: 100.6714 Evaluate side-chains 535 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 492 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 219 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 0.0040 chunk 62 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 189 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 chunk 165 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 overall best weight: 1.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 147 GLN B 312 GLN B 320 ASN C 98 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.143830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.101933 restraints weight = 32540.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.105360 restraints weight = 15462.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.107517 restraints weight = 9202.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.108755 restraints weight = 6466.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.109754 restraints weight = 5176.896| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.6447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16386 Z= 0.182 Angle : 0.744 15.129 22134 Z= 0.380 Chirality : 0.047 0.390 2360 Planarity : 0.004 0.054 2818 Dihedral : 7.992 142.586 2296 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.91 % Allowed : 28.55 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.19), residues: 1932 helix: 1.20 (0.15), residues: 1144 sheet: -0.38 (0.42), residues: 138 loop : 0.13 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 261 TYR 0.040 0.002 TYR C 204 PHE 0.064 0.002 PHE C 21 TRP 0.057 0.002 TRP C 44 HIS 0.010 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (16386) covalent geometry : angle 0.74397 / 0.38 (22134) hydrogen bonds : bond 0.03968 / 2.48 ( 871) hydrogen bonds : angle 5.10687 / 3.67 ( 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 538 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 488 time to evaluate : 0.603 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: A 8 LYS cc_start: 0.8804 (tptp) cc_final: 0.8537 (tppt) REVERT: A 40 TYR cc_start: 0.8905 (t80) cc_final: 0.8412 (t80) REVERT: A 65 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7920 (mp0) REVERT: A 119 GLU cc_start: 0.8501 (mp0) cc_final: 0.8223 (mp0) REVERT: A 144 MET cc_start: 0.8629 (mtm) cc_final: 0.8337 (mtm) REVERT: A 172 LEU cc_start: 0.9203 (mp) cc_final: 0.8543 (mt) REVERT: A 173 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9026 (mt) REVERT: A 179 LEU cc_start: 0.9278 (tp) cc_final: 0.8880 (tp) REVERT: A 188 ILE cc_start: 0.9375 (mm) cc_final: 0.9136 (mm) REVERT: A 193 SER cc_start: 0.9029 (m) cc_final: 0.8764 (p) REVERT: A 214 LYS cc_start: 0.8455 (mmtt) cc_final: 0.8137 (mmtp) REVERT: A 232 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.7988 (m110) REVERT: A 250 TYR cc_start: 0.8676 (m-80) cc_final: 0.8401 (m-80) REVERT: A 290 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8239 (mt-10) REVERT: A 348 MET cc_start: 0.8242 (tmm) cc_final: 0.7914 (tmm) REVERT: A 384 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.6666 (pm20) REVERT: A 389 SER cc_start: 0.9328 (OUTLIER) cc_final: 0.8887 (p) REVERT: A 406 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.7552 (t70) REVERT: A 427 LYS cc_start: 0.9033 (tppp) cc_final: 0.8605 (tppp) REVERT: A 446 ARG cc_start: 0.7713 (mmm160) cc_final: 0.7324 (mmm160) REVERT: A 505 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8427 (mt-10) REVERT: A 590 SER cc_start: 0.9204 (t) cc_final: 0.8756 (p) REVERT: A 640 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8611 (tpp) REVERT: B 27 ASP cc_start: 0.9031 (p0) cc_final: 0.8666 (p0) REVERT: B 82 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8822 (mttp) REVERT: B 174 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7486 (tt0) REVERT: B 184 ARG cc_start: 0.8920 (tpp-160) cc_final: 0.8621 (mmm160) REVERT: B 218 ASN cc_start: 0.9023 (m110) cc_final: 0.8449 (t0) REVERT: B 274 ARG cc_start: 0.8420 (tpp80) cc_final: 0.8077 (ttm-80) REVERT: B 362 ASP cc_start: 0.8184 (m-30) cc_final: 0.7939 (m-30) REVERT: B 374 SER cc_start: 0.9529 (t) cc_final: 0.9219 (t) REVERT: B 394 TYR cc_start: 0.9107 (m-80) cc_final: 0.8877 (m-80) REVERT: B 398 ASP cc_start: 0.8003 (t0) cc_final: 0.7752 (t0) REVERT: B 417 LEU cc_start: 0.9532 (tt) cc_final: 0.9292 (tp) REVERT: B 467 ASN cc_start: 0.9101 (t0) cc_final: 0.8667 (t0) REVERT: B 493 MET cc_start: 0.9554 (tmm) cc_final: 0.9207 (tmm) REVERT: B 570 MET cc_start: 0.7860 (mtp) cc_final: 0.7575 (mtt) REVERT: B 571 TYR cc_start: 0.8544 (t80) cc_final: 0.8281 (t80) REVERT: B 586 TYR cc_start: 0.9053 (m-80) cc_final: 0.8566 (m-80) REVERT: B 595 MET cc_start: 0.8539 (mmm) cc_final: 0.8212 (mmm) REVERT: B 602 GLU cc_start: 0.7956 (pp20) cc_final: 0.7037 (tm-30) REVERT: B 627 LYS cc_start: 0.9023 (tttt) cc_final: 0.8400 (ttpp) REVERT: B 628 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8212 (mp0) REVERT: C 46 TYR cc_start: 0.7376 (m-10) cc_final: 0.7097 (m-10) REVERT: C 56 MET cc_start: 0.2614 (tpt) cc_final: 0.2282 (tpt) REVERT: C 82 ASP cc_start: 0.8314 (m-30) cc_final: 0.7668 (t70) REVERT: C 103 LYS cc_start: 0.8505 (tppt) cc_final: 0.8134 (tppt) REVERT: C 107 ASN cc_start: 0.9037 (m-40) cc_final: 0.8464 (m-40) REVERT: C 130 TYR cc_start: 0.9117 (m-80) cc_final: 0.8856 (m-10) REVERT: C 154 PHE cc_start: 0.9116 (t80) cc_final: 0.8651 (t80) REVERT: C 174 TYR cc_start: 0.7244 (OUTLIER) cc_final: 0.6743 (t80) REVERT: C 177 TYR cc_start: 0.8642 (t80) cc_final: 0.8105 (t80) REVERT: D 59 LEU cc_start: 0.6463 (pp) cc_final: 0.5468 (tt) REVERT: D 80 HIS cc_start: 0.7476 (m-70) cc_final: 0.7143 (m-70) REVERT: D 116 GLU cc_start: 0.9051 (tp30) cc_final: 0.8651 (tp30) REVERT: D 130 TYR cc_start: 0.5016 (m-80) cc_final: 0.4060 (m-10) REVERT: D 149 ASP cc_start: 0.7681 (t0) cc_final: 0.7214 (p0) REVERT: D 157 MET cc_start: 0.8442 (ptm) cc_final: 0.7652 (ppp) REVERT: D 178 PHE cc_start: 0.8757 (m-10) cc_final: 0.8430 (m-80) REVERT: D 210 GLN cc_start: 0.8407 (tp40) cc_final: 0.7909 (mm110) REVERT: D 219 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6777 (pm20) REVERT: D 242 TYR cc_start: 0.6651 (t80) cc_final: 0.5357 (m-80) outliers start: 50 outliers final: 34 residues processed: 507 average time/residue: 0.1116 time to fit residues: 87.3589 Evaluate side-chains 530 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 487 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 230 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 147 GLN B 312 GLN B 320 ASN B 410 ASN C 98 ASN C 127 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.144511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.102707 restraints weight = 32389.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.106077 restraints weight = 15623.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.108301 restraints weight = 9246.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.109555 restraints weight = 6461.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.110448 restraints weight = 5156.226| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.6539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16386 Z= 0.164 Angle : 0.740 14.896 22134 Z= 0.377 Chirality : 0.047 0.381 2360 Planarity : 0.004 0.055 2818 Dihedral : 7.946 142.509 2295 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.09 % Allowed : 28.61 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.19), residues: 1932 helix: 1.19 (0.15), residues: 1144 sheet: -0.36 (0.42), residues: 138 loop : 0.11 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 235 TYR 0.032 0.002 TYR C 204 PHE 0.049 0.002 PHE C 21 TRP 0.055 0.002 TRP C 44 HIS 0.012 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (16386) covalent geometry : angle 0.74021 / 0.38 (22134) hydrogen bonds : bond 0.03950 / 2.47 ( 871) hydrogen bonds : angle 5.07190 / 3.65 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3212.00 seconds wall clock time: 56 minutes 28.36 seconds (3388.36 seconds total)