Starting phenix.real_space_refine on Fri Jul 3 19:48:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byt_45044/07_2026/9byt_45044_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byt_45044/07_2026/9byt_45044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9byt_45044/07_2026/9byt_45044_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byt_45044/07_2026/9byt_45044_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9byt_45044/07_2026/9byt_45044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byt_45044/07_2026/9byt_45044.map" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.23, per 1000 atoms: 0.20 Number of scatterers: 16038 At special positions: 0 Unit cell: (94.581, 132.21, 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: 1.29 Conformation dependent library (CDL) restraints added in 718.2 milliseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.104A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.985A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.953A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.664A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.694A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.627A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.118A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.074A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.677A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.878A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.645A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.729A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.026A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.068A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.669A 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: 6.360A 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: 6.605A 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: 6.453A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.478A pdb=" N LEU A 656 " --> pdb=" O ARG A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.185A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.050A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.749A 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: 2.55 Time building geometry restraints manager: 1.74 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: 4852 1.34 - 1.46: 3027 1.46 - 1.58: 8326 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 4.82e+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 2.31e+01 bond pdb=" O3A TTP A 803 " pdb=" PB TTP A 803 " ideal model delta sigma weight residual 1.675 1.606 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.608 0.067 2.00e-02 2.50e+03 1.14e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21523 2.09 - 4.18: 529 4.18 - 6.26: 64 6.26 - 8.35: 9 8.35 - 10.44: 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 110.54 116.62 -6.08 1.36e+00 5.41e-01 2.00e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.11 -4.40 1.15e+00 7.56e-01 1.46e+01 angle pdb=" N SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.23 -3.95 1.09e+00 8.42e-01 1.31e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.88 -4.38 1.23e+00 6.61e-01 1.27e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.72 -4.01 1.15e+00 7.56e-01 1.22e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.04: 9091 25.04 - 50.09: 653 50.09 - 75.13: 126 75.13 - 100.17: 26 100.17 - 125.21: 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 -98.19 125.21 1 2.00e+01 2.50e-03 3.78e+01 dihedral pdb=" O4' GDP B 804 " pdb=" C1' GDP B 804 " pdb=" N9 GDP B 804 " pdb=" C8 GDP B 804 " ideal model delta sinusoidal sigma weight residual 27.02 -95.55 122.57 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 -134.24 12.24 0 2.50e+00 1.60e-01 2.40e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2132 0.093 - 0.185: 194 0.185 - 0.278: 29 0.278 - 0.371: 3 0.371 - 0.463: 2 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.36e+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 4.69e+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 2.97e+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 4.13e-02 2.73e+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 1.12e-02 2.19e+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 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 179 " -0.017 2.00e-02 2.50e+03 9.85e-03 1.94e+00 pdb=" CG TYR D 179 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR D 179 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 179 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR D 179 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 179 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR D 179 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 179 " -0.005 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 129 2.51 - 3.11: 11548 3.11 - 3.70: 27039 3.70 - 4.30: 41566 4.30 - 4.90: 65461 Nonbonded interactions: 145743 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.911 3.060 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 3.060 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 3.060 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 3.060 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.013 3.040 ... (remaining 145738 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.200 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 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 : 0.787 10.439 22134 Z= 0.472 Chirality : 0.058 0.463 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.658 125.214 6202 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.28 % Allowed : 15.27 % Favored : 83.45 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.18), residues: 1932 helix: 0.59 (0.14), residues: 1151 sheet: 0.47 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 196 TYR 0.021 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.33 (16386) covalent geometry : angle 0.78749 / 0.47 (22134) hydrogen bonds : bond 0.15418 / 9.51 ( 871) hydrogen bonds : angle 6.51825 / 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 865 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 843 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.8483 (mt0) cc_final: 0.7267 (mt0) REVERT: A 157 LEU cc_start: 0.9043 (tp) cc_final: 0.8827 (tt) REVERT: A 158 ASN cc_start: 0.8905 (m-40) cc_final: 0.8612 (m-40) REVERT: A 179 LEU cc_start: 0.9247 (tp) cc_final: 0.8708 (tp) REVERT: A 194 LYS cc_start: 0.8983 (tttt) cc_final: 0.8756 (tttm) REVERT: A 588 GLN cc_start: 0.7707 (mm-40) cc_final: 0.7340 (mm-40) REVERT: A 598 MET cc_start: 0.7934 (mtm) cc_final: 0.7339 (mtp) REVERT: A 606 TYR cc_start: 0.7291 (m-80) cc_final: 0.7054 (m-80) REVERT: B 355 TYR cc_start: 0.7743 (m-80) cc_final: 0.7489 (m-80) REVERT: B 358 ILE cc_start: 0.9170 (mm) cc_final: 0.8930 (mm) REVERT: B 421 GLU cc_start: 0.7475 (tt0) cc_final: 0.7267 (tt0) REVERT: B 602 GLU cc_start: 0.6377 (pt0) cc_final: 0.6086 (pt0) REVERT: B 615 MET cc_start: 0.8772 (mmp) cc_final: 0.8472 (mmp) REVERT: C 250 VAL cc_start: 0.4562 (m) cc_final: 0.4328 (p) REVERT: D 178 PHE cc_start: 0.6980 (m-80) cc_final: 0.5802 (m-10) outliers start: 22 outliers final: 7 residues processed: 848 average time/residue: 0.1221 time to fit residues: 150.7321 Evaluate side-chains 552 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 545 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain D residue 59 LEU 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: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 304 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS D 50 ASN D 127 GLN D 201 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.153331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.099643 restraints weight = 27082.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.103512 restraints weight = 11337.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.105942 restraints weight = 6599.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.107330 restraints weight = 4678.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.108252 restraints weight = 3782.600| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3216 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (5 function evaluations) r_final: 0.3216 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16386 Z= 0.216 Angle : 0.664 11.619 22134 Z= 0.348 Chirality : 0.045 0.249 2360 Planarity : 0.004 0.046 2818 Dihedral : 9.606 129.514 2301 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.31 % Allowed : 18.53 % Favored : 77.16 % 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: 1.35 (0.15), residues: 1130 sheet: -0.05 (0.41), residues: 142 loop : 0.57 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 235 TYR 0.020 0.002 TYR A 612 PHE 0.032 0.002 PHE C 168 TRP 0.012 0.002 TRP C 30 HIS 0.006 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 (16386) covalent geometry : angle 0.66408 / 0.35 (22134) hydrogen bonds : bond 0.04765 / 3.03 ( 871) hydrogen bonds : angle 5.00017 / 3.57 ( 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 653 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 579 time to evaluate : 0.550 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 103 ASP cc_start: 0.8593 (m-30) cc_final: 0.8282 (m-30) REVERT: A 144 MET cc_start: 0.9033 (mtm) cc_final: 0.8393 (mtm) REVERT: A 147 GLN cc_start: 0.9184 (mt0) cc_final: 0.8694 (mt0) REVERT: A 148 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8223 (mt-10) REVERT: A 158 ASN cc_start: 0.9124 (m-40) cc_final: 0.8770 (m-40) REVERT: A 250 TYR cc_start: 0.9095 (m-80) cc_final: 0.8720 (m-80) REVERT: A 259 ASN cc_start: 0.8977 (m-40) cc_final: 0.8360 (m-40) REVERT: A 263 ASP cc_start: 0.8689 (m-30) cc_final: 0.8359 (m-30) REVERT: A 379 SER cc_start: 0.9365 (t) cc_final: 0.8883 (t) REVERT: A 384 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.7153 (pm20) REVERT: A 415 ASN cc_start: 0.9338 (t0) cc_final: 0.9056 (t0) REVERT: A 436 LEU cc_start: 0.9411 (mt) cc_final: 0.9128 (mp) REVERT: A 459 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.9031 (mttp) REVERT: A 583 SER cc_start: 0.9180 (m) cc_final: 0.8731 (t) REVERT: A 628 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8404 (mm-30) REVERT: A 658 LEU cc_start: 0.9557 (mt) cc_final: 0.9323 (mp) REVERT: B 95 MET cc_start: 0.9010 (tpp) cc_final: 0.8798 (mmm) REVERT: B 101 TYR cc_start: 0.8955 (m-80) cc_final: 0.8685 (m-80) REVERT: B 109 ASN cc_start: 0.9267 (OUTLIER) cc_final: 0.8944 (m110) REVERT: B 172 LEU cc_start: 0.9498 (mp) cc_final: 0.9289 (mt) REVERT: B 213 ILE cc_start: 0.9033 (mp) cc_final: 0.8807 (mt) REVERT: B 263 ASP cc_start: 0.8804 (m-30) cc_final: 0.8540 (m-30) REVERT: B 274 ARG cc_start: 0.7945 (ttm110) cc_final: 0.7726 (ptp90) REVERT: B 317 MET cc_start: 0.8780 (ptt) cc_final: 0.8442 (ptp) REVERT: B 355 TYR cc_start: 0.8483 (m-80) cc_final: 0.7765 (m-80) REVERT: B 358 ILE cc_start: 0.9620 (mm) cc_final: 0.9371 (mm) REVERT: B 515 ASP cc_start: 0.8818 (m-30) cc_final: 0.8331 (m-30) REVERT: B 599 GLU cc_start: 0.8109 (pt0) cc_final: 0.7832 (pt0) REVERT: B 612 TYR cc_start: 0.8655 (m-80) cc_final: 0.8246 (m-80) REVERT: B 615 MET cc_start: 0.9525 (mmp) cc_final: 0.9208 (mmp) REVERT: C 21 PHE cc_start: 0.9030 (m-80) cc_final: 0.8759 (m-80) REVERT: C 66 ASP cc_start: 0.6977 (OUTLIER) cc_final: 0.6630 (m-30) REVERT: C 92 PHE cc_start: 0.8048 (t80) cc_final: 0.7827 (t80) REVERT: C 154 PHE cc_start: 0.9022 (t80) cc_final: 0.8577 (t80) REVERT: C 157 MET cc_start: 0.9331 (mtp) cc_final: 0.8878 (mtp) REVERT: C 196 ARG cc_start: 0.9214 (ptm-80) cc_final: 0.8895 (ptm-80) REVERT: C 243 THR cc_start: 0.8665 (p) cc_final: 0.8460 (t) REVERT: D 92 PHE cc_start: 0.6767 (t80) cc_final: 0.6412 (t80) REVERT: D 130 TYR cc_start: 0.7660 (m-80) cc_final: 0.7459 (m-80) REVERT: D 131 LEU cc_start: 0.8155 (tt) cc_final: 0.7572 (tp) REVERT: D 138 ILE cc_start: 0.9413 (mm) cc_final: 0.8785 (mm) REVERT: D 153 LEU cc_start: 0.6119 (tp) cc_final: 0.5705 (mm) REVERT: D 162 TYR cc_start: 0.7826 (t80) cc_final: 0.7363 (t80) REVERT: D 185 MET cc_start: 0.6004 (mmm) cc_final: 0.5669 (mmm) REVERT: D 197 ASP cc_start: 0.8801 (m-30) cc_final: 0.8566 (m-30) REVERT: D 224 LEU cc_start: 0.8367 (mt) cc_final: 0.8042 (mt) REVERT: D 233 ASN cc_start: 0.9173 (m-40) cc_final: 0.8879 (m110) REVERT: D 235 LEU cc_start: 0.9249 (mt) cc_final: 0.9035 (mt) REVERT: D 269 MET cc_start: 0.9106 (tmm) cc_final: 0.8631 (tmm) REVERT: D 287 LEU cc_start: 0.6430 (mt) cc_final: 0.6208 (mt) outliers start: 74 outliers final: 38 residues processed: 621 average time/residue: 0.1031 time to fit residues: 97.5476 Evaluate side-chains 551 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 509 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 256 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 164 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 159 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 chunk 150 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN A 668 ASN B 14 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN B 474 GLN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 ASN D 71 ASN D 107 ASN D 128 ASN D 263 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.151270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.098745 restraints weight = 27532.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.102589 restraints weight = 11604.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.104841 restraints weight = 6719.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.106375 restraints weight = 4753.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.107276 restraints weight = 3776.934| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16386 Z= 0.168 Angle : 0.621 11.148 22134 Z= 0.327 Chirality : 0.044 0.336 2360 Planarity : 0.003 0.048 2818 Dihedral : 9.106 130.187 2297 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.67 % Allowed : 20.92 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.19), residues: 1932 helix: 1.32 (0.15), residues: 1141 sheet: -0.29 (0.40), residues: 148 loop : 0.44 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 235 TYR 0.029 0.002 TYR D 142 PHE 0.038 0.002 PHE D 172 TRP 0.019 0.002 TRP D 30 HIS 0.005 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (16386) covalent geometry : angle 0.62094 / 0.33 (22134) hydrogen bonds : bond 0.04282 / 2.73 ( 871) hydrogen bonds : angle 4.88785 / 3.49 ( 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 617 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 554 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.8571 (m-30) cc_final: 0.8307 (m-30) REVERT: A 106 LEU cc_start: 0.9111 (tp) cc_final: 0.8880 (tp) REVERT: A 119 GLU cc_start: 0.8152 (mp0) cc_final: 0.7929 (mp0) REVERT: A 144 MET cc_start: 0.8902 (mtm) cc_final: 0.8314 (mtm) REVERT: A 147 GLN cc_start: 0.9157 (mt0) cc_final: 0.7571 (mt0) REVERT: A 148 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8302 (mt-10) REVERT: A 259 ASN cc_start: 0.9058 (m-40) cc_final: 0.8454 (m-40) REVERT: A 263 ASP cc_start: 0.8704 (m-30) cc_final: 0.8293 (m-30) REVERT: A 277 THR cc_start: 0.8436 (p) cc_final: 0.8146 (t) REVERT: A 384 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.7001 (pm20) REVERT: A 390 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8456 (mt0) REVERT: A 415 ASN cc_start: 0.9332 (t0) cc_final: 0.9100 (t0) REVERT: A 459 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8955 (mttp) REVERT: A 583 SER cc_start: 0.9245 (OUTLIER) cc_final: 0.8843 (t) REVERT: A 588 GLN cc_start: 0.8935 (mm-40) cc_final: 0.7900 (mm-40) REVERT: A 628 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8441 (mm-30) REVERT: A 663 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8892 (t) REVERT: A 683 TYR cc_start: 0.9208 (t80) cc_final: 0.8876 (t80) REVERT: B 101 TYR cc_start: 0.9008 (m-80) cc_final: 0.8725 (m-80) REVERT: B 111 LYS cc_start: 0.9345 (mmtp) cc_final: 0.8952 (mmtm) REVERT: B 257 ASP cc_start: 0.8938 (m-30) cc_final: 0.8721 (m-30) REVERT: B 263 ASP cc_start: 0.8773 (m-30) cc_final: 0.8469 (m-30) REVERT: B 270 ASP cc_start: 0.8684 (t0) cc_final: 0.8413 (t0) REVERT: B 274 ARG cc_start: 0.8007 (ttm110) cc_final: 0.7643 (ptp90) REVERT: B 317 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8302 (ptp) REVERT: B 355 TYR cc_start: 0.8410 (m-80) cc_final: 0.7756 (m-80) REVERT: B 358 ILE cc_start: 0.9632 (mm) cc_final: 0.9372 (mm) REVERT: B 384 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.7367 (pm20) REVERT: B 515 ASP cc_start: 0.8821 (m-30) cc_final: 0.8273 (m-30) REVERT: B 599 GLU cc_start: 0.8106 (pt0) cc_final: 0.7829 (pt0) REVERT: B 602 GLU cc_start: 0.7993 (pt0) cc_final: 0.7487 (pt0) REVERT: B 610 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8050 (ptmt) REVERT: B 615 MET cc_start: 0.9479 (mmp) cc_final: 0.9159 (mmp) REVERT: C 21 PHE cc_start: 0.9166 (m-80) cc_final: 0.8721 (m-80) REVERT: C 56 MET cc_start: 0.7062 (ptm) cc_final: 0.6489 (ttp) REVERT: C 69 GLN cc_start: 0.8703 (tp40) cc_final: 0.7919 (tp40) REVERT: C 92 PHE cc_start: 0.8242 (t80) cc_final: 0.7966 (t80) REVERT: C 154 PHE cc_start: 0.9089 (t80) cc_final: 0.8701 (t80) REVERT: C 168 PHE cc_start: 0.8851 (m-80) cc_final: 0.8624 (m-80) REVERT: C 189 GLU cc_start: 0.9127 (tp30) cc_final: 0.8921 (tp30) REVERT: C 192 ASN cc_start: 0.8663 (m-40) cc_final: 0.8435 (m110) REVERT: C 196 ARG cc_start: 0.9219 (ptm-80) cc_final: 0.8976 (ptm160) REVERT: C 244 GLU cc_start: 0.9564 (pt0) cc_final: 0.9256 (pp20) REVERT: C 259 PHE cc_start: 0.8353 (t80) cc_final: 0.8082 (t80) REVERT: C 321 TYR cc_start: 0.9057 (m-80) cc_final: 0.6865 (t80) REVERT: D 30 TRP cc_start: 0.6962 (p-90) cc_final: 0.6026 (p-90) REVERT: D 132 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8122 (mm110) REVERT: D 138 ILE cc_start: 0.9332 (mm) cc_final: 0.9125 (mm) REVERT: D 153 LEU cc_start: 0.6253 (tp) cc_final: 0.5519 (mm) REVERT: D 154 PHE cc_start: 0.7804 (t80) cc_final: 0.7533 (t80) REVERT: D 162 TYR cc_start: 0.7855 (t80) cc_final: 0.7346 (t80) REVERT: D 195 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8629 (tt) REVERT: D 224 LEU cc_start: 0.8068 (mt) cc_final: 0.7837 (mt) REVERT: D 233 ASN cc_start: 0.9238 (m-40) cc_final: 0.8932 (m110) REVERT: D 265 ASN cc_start: 0.8155 (m-40) cc_final: 0.7951 (m-40) outliers start: 63 outliers final: 36 residues processed: 586 average time/residue: 0.1233 time to fit residues: 110.7111 Evaluate side-chains 552 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 506 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 0.6980 chunk 157 optimal weight: 20.0000 chunk 168 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 191 optimal weight: 5.9990 chunk 159 optimal weight: 30.0000 chunk 182 optimal weight: 9.9990 chunk 93 optimal weight: 0.6980 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN A 320 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN D 69 GLN D 119 ASN D 128 ASN D 216 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.146435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.094195 restraints weight = 27838.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.097743 restraints weight = 11644.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.099955 restraints weight = 6830.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.101254 restraints weight = 4877.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.102162 restraints weight = 3973.554| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (22 function evaluations) r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 16386 Z= 0.336 Angle : 0.712 13.652 22134 Z= 0.369 Chirality : 0.047 0.374 2360 Planarity : 0.004 0.050 2818 Dihedral : 9.083 134.701 2297 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.90 % Allowed : 20.92 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.19), residues: 1932 helix: 1.10 (0.15), residues: 1149 sheet: -0.29 (0.42), residues: 144 loop : 0.46 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 235 TYR 0.030 0.002 TYR D 142 PHE 0.034 0.002 PHE D 172 TRP 0.013 0.002 TRP A 558 HIS 0.006 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00750 / 0.34 (16386) covalent geometry : angle 0.71179 / 0.37 (22134) hydrogen bonds : bond 0.04460 / 2.88 ( 871) hydrogen bonds : angle 5.04809 / 3.60 ( 2571) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 493 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8227 (pm20) cc_final: 0.7853 (pm20) REVERT: A 103 ASP cc_start: 0.8646 (m-30) cc_final: 0.8393 (m-30) REVERT: A 117 ARG cc_start: 0.8537 (mtp85) cc_final: 0.8165 (ttm-80) REVERT: A 119 GLU cc_start: 0.8259 (mp0) cc_final: 0.8003 (mp0) REVERT: A 144 MET cc_start: 0.9021 (mtm) cc_final: 0.8493 (mtm) REVERT: A 147 GLN cc_start: 0.9264 (mt0) cc_final: 0.8806 (mt0) REVERT: A 148 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8252 (mt-10) REVERT: A 209 LYS cc_start: 0.9112 (tttm) cc_final: 0.8471 (ttmm) REVERT: A 221 LYS cc_start: 0.9137 (mmmt) cc_final: 0.8735 (mmtp) REVERT: A 250 TYR cc_start: 0.9140 (m-80) cc_final: 0.8767 (m-80) REVERT: A 259 ASN cc_start: 0.9097 (m-40) cc_final: 0.8499 (m-40) REVERT: A 263 ASP cc_start: 0.8688 (m-30) cc_final: 0.8339 (m-30) REVERT: A 277 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8282 (t) REVERT: A 381 LEU cc_start: 0.9534 (tp) cc_final: 0.9256 (tp) REVERT: A 384 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.6900 (pm20) REVERT: A 415 ASN cc_start: 0.9392 (t0) cc_final: 0.9143 (t0) REVERT: A 583 SER cc_start: 0.9377 (OUTLIER) cc_final: 0.8992 (t) REVERT: A 589 SER cc_start: 0.9386 (m) cc_final: 0.9071 (p) REVERT: A 628 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8485 (mm-30) REVERT: A 683 TYR cc_start: 0.9156 (t80) cc_final: 0.8933 (t80) REVERT: B 111 LYS cc_start: 0.9432 (mmtp) cc_final: 0.9149 (mmtt) REVERT: B 253 ILE cc_start: 0.9575 (tt) cc_final: 0.9252 (tt) REVERT: B 263 ASP cc_start: 0.8797 (m-30) cc_final: 0.8511 (m-30) REVERT: B 272 ASP cc_start: 0.8633 (p0) cc_final: 0.8378 (p0) REVERT: B 317 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8831 (ptp) REVERT: B 318 ASP cc_start: 0.8549 (t0) cc_final: 0.8273 (t0) REVERT: B 336 LYS cc_start: 0.9416 (OUTLIER) cc_final: 0.9039 (ttmm) REVERT: B 355 TYR cc_start: 0.8570 (m-80) cc_final: 0.7916 (m-80) REVERT: B 362 ASP cc_start: 0.8356 (m-30) cc_final: 0.8094 (m-30) REVERT: B 384 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.7481 (pm20) REVERT: B 515 ASP cc_start: 0.8883 (m-30) cc_final: 0.8345 (m-30) REVERT: B 586 TYR cc_start: 0.9028 (m-80) cc_final: 0.8664 (m-80) REVERT: B 599 GLU cc_start: 0.8227 (pt0) cc_final: 0.7964 (pt0) REVERT: B 602 GLU cc_start: 0.7973 (pt0) cc_final: 0.7190 (pt0) REVERT: B 610 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7858 (ptmm) REVERT: B 612 TYR cc_start: 0.8656 (m-80) cc_final: 0.8123 (m-80) REVERT: B 615 MET cc_start: 0.9555 (mmp) cc_final: 0.9230 (mmp) REVERT: B 628 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8454 (mt-10) REVERT: C 21 PHE cc_start: 0.9196 (m-80) cc_final: 0.8803 (m-80) REVERT: C 56 MET cc_start: 0.6877 (ptm) cc_final: 0.6272 (ttp) REVERT: C 122 PHE cc_start: 0.8734 (m-80) cc_final: 0.8519 (m-80) REVERT: C 162 TYR cc_start: 0.9034 (m-80) cc_final: 0.8323 (m-80) REVERT: C 189 GLU cc_start: 0.9099 (tp30) cc_final: 0.8894 (tp30) REVERT: C 192 ASN cc_start: 0.8823 (m-40) cc_final: 0.8530 (m-40) REVERT: C 196 ARG cc_start: 0.9217 (ptm-80) cc_final: 0.8951 (ptm-80) REVERT: C 244 GLU cc_start: 0.9555 (pt0) cc_final: 0.9238 (pp20) REVERT: C 259 PHE cc_start: 0.8235 (t80) cc_final: 0.7911 (t80) REVERT: C 270 ASN cc_start: 0.8408 (m-40) cc_final: 0.8061 (m110) REVERT: D 30 TRP cc_start: 0.7143 (p-90) cc_final: 0.6156 (p-90) REVERT: D 132 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8000 (mm110) REVERT: D 142 TYR cc_start: 0.7838 (m-10) cc_final: 0.7415 (m-10) REVERT: D 157 MET cc_start: 0.2156 (ptt) cc_final: 0.1844 (ptt) REVERT: D 195 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8787 (tt) REVERT: D 261 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7306 (mpt-90) REVERT: D 265 ASN cc_start: 0.8058 (m-40) cc_final: 0.7773 (m-40) outliers start: 84 outliers final: 49 residues processed: 540 average time/residue: 0.1299 time to fit residues: 106.2147 Evaluate side-chains 509 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 450 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 312 GLN 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 442 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 261 ARG Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 126 optimal weight: 0.0980 chunk 129 optimal weight: 0.9980 chunk 32 optimal weight: 0.3980 chunk 122 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN B 447 ASN B 645 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 127 GLN D 132 GLN D 233 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.151097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.099905 restraints weight = 27581.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.103589 restraints weight = 11294.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.105824 restraints weight = 6503.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.107246 restraints weight = 4574.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.108077 restraints weight = 3661.052| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (22 function evaluations) r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16386 Z= 0.138 Angle : 0.621 13.864 22134 Z= 0.322 Chirality : 0.043 0.401 2360 Planarity : 0.003 0.036 2818 Dihedral : 8.684 134.110 2296 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.44 % Allowed : 23.02 % Favored : 73.54 % 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: 1.18 (0.15), residues: 1143 sheet: -0.37 (0.41), residues: 148 loop : 0.46 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 235 TYR 0.021 0.001 TYR C 236 PHE 0.041 0.002 PHE C 154 TRP 0.013 0.001 TRP D 44 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (16386) covalent geometry : angle 0.62105 / 0.32 (22134) hydrogen bonds : bond 0.04047 / 2.59 ( 871) hydrogen bonds : angle 4.88495 / 3.49 ( 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 572 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 513 time to evaluate : 0.672 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 103 ASP cc_start: 0.8663 (m-30) cc_final: 0.8375 (m-30) REVERT: A 144 MET cc_start: 0.8849 (mtm) cc_final: 0.8305 (mtm) REVERT: A 147 GLN cc_start: 0.9145 (mt0) cc_final: 0.7599 (mt0) REVERT: A 148 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8285 (mt-10) REVERT: A 209 LYS cc_start: 0.8997 (tttm) cc_final: 0.8384 (ttmm) REVERT: A 259 ASN cc_start: 0.9086 (m-40) cc_final: 0.8437 (m-40) REVERT: A 263 ASP cc_start: 0.8691 (m-30) cc_final: 0.8302 (m-30) REVERT: A 277 THR cc_start: 0.8370 (p) cc_final: 0.8112 (t) REVERT: A 357 TYR cc_start: 0.9091 (m-10) cc_final: 0.8708 (m-10) REVERT: A 384 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.6688 (pm20) REVERT: A 415 ASN cc_start: 0.9342 (t0) cc_final: 0.9095 (t0) REVERT: A 583 SER cc_start: 0.9337 (OUTLIER) cc_final: 0.8988 (t) REVERT: A 586 TYR cc_start: 0.8935 (m-80) cc_final: 0.8694 (m-10) REVERT: A 588 GLN cc_start: 0.8990 (mm-40) cc_final: 0.7993 (mm-40) REVERT: A 589 SER cc_start: 0.9361 (m) cc_final: 0.9020 (p) REVERT: A 628 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8474 (mm-30) REVERT: A 683 TYR cc_start: 0.9170 (t80) cc_final: 0.8827 (t80) REVERT: B 65 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7835 (mm-30) REVERT: B 235 ARG cc_start: 0.8953 (ttm-80) cc_final: 0.8753 (ttm-80) REVERT: B 263 ASP cc_start: 0.8785 (m-30) cc_final: 0.8415 (m-30) REVERT: B 317 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8314 (ptp) REVERT: B 359 MET cc_start: 0.9044 (ttp) cc_final: 0.8811 (tmm) REVERT: B 362 ASP cc_start: 0.8282 (m-30) cc_final: 0.8005 (m-30) REVERT: B 384 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.7286 (pm20) REVERT: B 394 TYR cc_start: 0.9177 (m-80) cc_final: 0.8515 (m-80) REVERT: B 515 ASP cc_start: 0.8788 (m-30) cc_final: 0.8229 (m-30) REVERT: B 571 TYR cc_start: 0.8823 (t80) cc_final: 0.7872 (t80) REVERT: B 595 MET cc_start: 0.9034 (mmm) cc_final: 0.8379 (mmm) REVERT: B 599 GLU cc_start: 0.8191 (pt0) cc_final: 0.7927 (pt0) REVERT: B 602 GLU cc_start: 0.8078 (pt0) cc_final: 0.7340 (pt0) REVERT: B 610 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8139 (ptmt) REVERT: B 615 MET cc_start: 0.9519 (mmp) cc_final: 0.9286 (mmp) REVERT: C 21 PHE cc_start: 0.9219 (m-80) cc_final: 0.8817 (m-80) REVERT: C 56 MET cc_start: 0.6811 (ptm) cc_final: 0.6197 (ttp) REVERT: C 92 PHE cc_start: 0.8084 (t80) cc_final: 0.7862 (t80) REVERT: C 95 MET cc_start: 0.9044 (tmm) cc_final: 0.8741 (tmm) REVERT: C 122 PHE cc_start: 0.8684 (m-80) cc_final: 0.8464 (m-80) REVERT: C 189 GLU cc_start: 0.9147 (tp30) cc_final: 0.8946 (tp30) REVERT: C 196 ARG cc_start: 0.9202 (ptm-80) cc_final: 0.8921 (ptm-80) REVERT: C 244 GLU cc_start: 0.9547 (pt0) cc_final: 0.9248 (pp20) REVERT: C 270 ASN cc_start: 0.8425 (m-40) cc_final: 0.8071 (m110) REVERT: D 30 TRP cc_start: 0.7012 (p-90) cc_final: 0.6514 (p-90) REVERT: D 56 MET cc_start: 0.8117 (ptp) cc_final: 0.7710 (mmp) REVERT: D 109 PHE cc_start: 0.8225 (m-80) cc_final: 0.7970 (m-80) REVERT: D 119 ASN cc_start: 0.8878 (m110) cc_final: 0.8668 (m-40) REVERT: D 132 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8063 (mm-40) REVERT: D 154 PHE cc_start: 0.7708 (t80) cc_final: 0.7346 (t80) REVERT: D 162 TYR cc_start: 0.7648 (t80) cc_final: 0.6872 (t80) REVERT: D 227 PHE cc_start: 0.9226 (t80) cc_final: 0.9012 (t80) REVERT: D 265 ASN cc_start: 0.8122 (m-40) cc_final: 0.7823 (m-40) REVERT: D 287 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6468 (mt) outliers start: 59 outliers final: 33 residues processed: 544 average time/residue: 0.1255 time to fit residues: 104.5574 Evaluate side-chains 520 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 480 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 306 ILE 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 565 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 145 ILE 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 317 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 261 ARG Chi-restraints excluded: chain D residue 287 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 249 GLN D 270 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.150303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.100038 restraints weight = 27640.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.103634 restraints weight = 11325.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.105765 restraints weight = 6500.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.107259 restraints weight = 4595.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.108137 restraints weight = 3661.927| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16386 Z= 0.161 Angle : 0.631 13.979 22134 Z= 0.329 Chirality : 0.044 0.397 2360 Planarity : 0.003 0.040 2818 Dihedral : 8.503 134.491 2296 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.67 % Allowed : 24.01 % Favored : 72.32 % 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: 1.17 (0.15), residues: 1149 sheet: -0.46 (0.41), residues: 148 loop : 0.48 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 235 TYR 0.017 0.001 TYR D 142 PHE 0.031 0.002 PHE C 259 TRP 0.024 0.002 TRP D 44 HIS 0.003 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (16386) covalent geometry : angle 0.63145 / 0.33 (22134) hydrogen bonds : bond 0.04029 / 2.57 ( 871) hydrogen bonds : angle 4.91315 / 3.53 ( 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 551 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 488 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.8678 (m-30) cc_final: 0.8399 (m-30) REVERT: A 144 MET cc_start: 0.8855 (mtm) cc_final: 0.8288 (mtm) REVERT: A 148 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8271 (mt-10) REVERT: A 209 LYS cc_start: 0.8984 (tttm) cc_final: 0.8386 (ttmm) REVERT: A 259 ASN cc_start: 0.9073 (m-40) cc_final: 0.8429 (m-40) REVERT: A 263 ASP cc_start: 0.8714 (m-30) cc_final: 0.8311 (m-30) REVERT: A 277 THR cc_start: 0.8353 (p) cc_final: 0.8097 (t) REVERT: A 286 ASP cc_start: 0.8735 (t0) cc_final: 0.8534 (t0) REVERT: A 381 LEU cc_start: 0.9524 (tp) cc_final: 0.9230 (tp) REVERT: A 384 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.6641 (pm20) REVERT: A 493 MET cc_start: 0.9130 (tmm) cc_final: 0.8866 (tmm) REVERT: A 583 SER cc_start: 0.9272 (OUTLIER) cc_final: 0.8927 (t) REVERT: A 589 SER cc_start: 0.9342 (m) cc_final: 0.9030 (p) REVERT: A 604 ARG cc_start: 0.8469 (mmp80) cc_final: 0.8268 (mmt-90) REVERT: A 628 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8474 (mm-30) REVERT: A 683 TYR cc_start: 0.9137 (t80) cc_final: 0.8851 (t80) REVERT: B 51 LEU cc_start: 0.9482 (tt) cc_final: 0.9273 (mt) REVERT: B 111 LYS cc_start: 0.9170 (mmtm) cc_final: 0.8892 (mmtt) REVERT: B 263 ASP cc_start: 0.8780 (m-30) cc_final: 0.8396 (m-30) REVERT: B 274 ARG cc_start: 0.8251 (ttm110) cc_final: 0.7438 (ptp-110) REVERT: B 317 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8366 (ptp) REVERT: B 355 TYR cc_start: 0.8399 (m-80) cc_final: 0.7803 (m-80) REVERT: B 359 MET cc_start: 0.9015 (ttp) cc_final: 0.8724 (tmm) REVERT: B 362 ASP cc_start: 0.8295 (m-30) cc_final: 0.8016 (m-30) REVERT: B 384 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.7239 (pm20) REVERT: B 394 TYR cc_start: 0.9195 (m-80) cc_final: 0.8518 (m-80) REVERT: B 447 ASN cc_start: 0.8568 (m110) cc_final: 0.8046 (m-40) REVERT: B 515 ASP cc_start: 0.8779 (m-30) cc_final: 0.8216 (m-30) REVERT: B 571 TYR cc_start: 0.8738 (t80) cc_final: 0.7734 (t80) REVERT: B 586 TYR cc_start: 0.8868 (m-80) cc_final: 0.8567 (m-80) REVERT: B 595 MET cc_start: 0.9035 (mmm) cc_final: 0.8360 (mmm) REVERT: B 599 GLU cc_start: 0.8215 (pt0) cc_final: 0.7979 (pt0) REVERT: B 602 GLU cc_start: 0.7907 (pt0) cc_final: 0.7557 (pt0) REVERT: B 610 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8168 (ptmt) REVERT: B 615 MET cc_start: 0.9516 (mmp) cc_final: 0.9279 (mmp) REVERT: C 21 PHE cc_start: 0.9240 (m-80) cc_final: 0.8871 (m-80) REVERT: C 56 MET cc_start: 0.6850 (ptm) cc_final: 0.6257 (ttp) REVERT: C 93 MET cc_start: 0.8684 (mtt) cc_final: 0.8393 (ttt) REVERT: C 95 MET cc_start: 0.9031 (tmm) cc_final: 0.8768 (tmm) REVERT: C 107 ASN cc_start: 0.8075 (OUTLIER) cc_final: 0.7562 (p0) REVERT: C 122 PHE cc_start: 0.8704 (m-80) cc_final: 0.8489 (m-80) REVERT: C 129 LYS cc_start: 0.9134 (tptt) cc_final: 0.8875 (tmtt) REVERT: C 154 PHE cc_start: 0.9188 (t80) cc_final: 0.8908 (t80) REVERT: C 162 TYR cc_start: 0.8921 (m-80) cc_final: 0.7675 (m-80) REVERT: C 196 ARG cc_start: 0.9253 (ptm-80) cc_final: 0.9021 (ptm-80) REVERT: C 244 GLU cc_start: 0.9535 (pt0) cc_final: 0.9259 (pp20) REVERT: C 259 PHE cc_start: 0.8292 (t80) cc_final: 0.8050 (t80) REVERT: D 56 MET cc_start: 0.8022 (ptp) cc_final: 0.7639 (mmp) REVERT: D 132 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8058 (mm-40) REVERT: D 137 MET cc_start: 0.8474 (mtt) cc_final: 0.8254 (mtm) REVERT: D 154 PHE cc_start: 0.7748 (t80) cc_final: 0.7264 (t80) REVERT: D 198 GLU cc_start: 0.8577 (tt0) cc_final: 0.8291 (tt0) REVERT: D 233 ASN cc_start: 0.9372 (p0) cc_final: 0.9154 (m110) REVERT: D 269 MET cc_start: 0.8999 (tmm) cc_final: 0.8717 (tmm) REVERT: D 287 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6498 (mt) outliers start: 63 outliers final: 38 residues processed: 521 average time/residue: 0.1283 time to fit residues: 101.2152 Evaluate side-chains 512 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 466 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 359 MET 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 565 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 261 ARG Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 287 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 chunk 74 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 645 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN D 80 HIS D 119 ASN D 132 GLN D 265 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.151356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.101170 restraints weight = 27587.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.104847 restraints weight = 11505.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.106989 restraints weight = 6560.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.108488 restraints weight = 4623.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.109326 restraints weight = 3681.401| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16386 Z= 0.147 Angle : 0.646 13.869 22134 Z= 0.335 Chirality : 0.044 0.391 2360 Planarity : 0.003 0.044 2818 Dihedral : 8.155 134.702 2294 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.55 % Allowed : 24.65 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.19), residues: 1932 helix: 1.19 (0.15), residues: 1140 sheet: -0.31 (0.42), residues: 136 loop : 0.28 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 235 TYR 0.017 0.001 TYR D 142 PHE 0.031 0.002 PHE C 172 TRP 0.022 0.002 TRP D 44 HIS 0.004 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (16386) covalent geometry : angle 0.64593 / 0.33 (22134) hydrogen bonds : bond 0.04032 / 2.57 ( 871) hydrogen bonds : angle 4.93290 / 3.55 ( 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 569 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 508 time to evaluate : 0.641 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 103 ASP cc_start: 0.8636 (m-30) cc_final: 0.8377 (m-30) REVERT: A 144 MET cc_start: 0.8821 (mtm) cc_final: 0.8246 (mtm) REVERT: A 148 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8274 (mt-10) REVERT: A 209 LYS cc_start: 0.9014 (tttm) cc_final: 0.8601 (ttmm) REVERT: A 228 LYS cc_start: 0.9011 (ttmm) cc_final: 0.8524 (mttp) REVERT: A 259 ASN cc_start: 0.9055 (m-40) cc_final: 0.8441 (m110) REVERT: A 263 ASP cc_start: 0.8692 (m-30) cc_final: 0.8362 (m-30) REVERT: A 277 THR cc_start: 0.8296 (p) cc_final: 0.8061 (t) REVERT: A 286 ASP cc_start: 0.8734 (t0) cc_final: 0.8501 (t0) REVERT: A 381 LEU cc_start: 0.9530 (tp) cc_final: 0.9221 (tp) REVERT: A 384 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.6749 (pm20) REVERT: A 486 ASP cc_start: 0.8425 (t0) cc_final: 0.8170 (t0) REVERT: A 583 SER cc_start: 0.9290 (OUTLIER) cc_final: 0.8979 (t) REVERT: A 589 SER cc_start: 0.9349 (m) cc_final: 0.9036 (p) REVERT: A 628 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8529 (mm-30) REVERT: A 662 MET cc_start: 0.8246 (pmm) cc_final: 0.7952 (pmm) REVERT: A 683 TYR cc_start: 0.9187 (t80) cc_final: 0.8889 (t80) REVERT: A 686 ARG cc_start: 0.8231 (ttm-80) cc_final: 0.7749 (mmt-90) REVERT: B 65 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7867 (mm-30) REVERT: B 263 ASP cc_start: 0.8767 (m-30) cc_final: 0.8388 (m-30) REVERT: B 274 ARG cc_start: 0.8259 (ttm110) cc_final: 0.7425 (ptp-110) REVERT: B 317 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8273 (ptp) REVERT: B 355 TYR cc_start: 0.8368 (m-80) cc_final: 0.7856 (m-80) REVERT: B 359 MET cc_start: 0.9007 (ttp) cc_final: 0.8760 (tmm) REVERT: B 362 ASP cc_start: 0.8285 (m-30) cc_final: 0.7999 (m-30) REVERT: B 384 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.7192 (pm20) REVERT: B 394 TYR cc_start: 0.9191 (m-80) cc_final: 0.8439 (m-80) REVERT: B 447 ASN cc_start: 0.8294 (m110) cc_final: 0.7569 (m110) REVERT: B 515 ASP cc_start: 0.8757 (m-30) cc_final: 0.8212 (m-30) REVERT: B 571 TYR cc_start: 0.8741 (t80) cc_final: 0.7651 (t80) REVERT: B 595 MET cc_start: 0.9000 (mmm) cc_final: 0.8311 (mmm) REVERT: B 599 GLU cc_start: 0.8221 (pt0) cc_final: 0.7984 (pt0) REVERT: B 602 GLU cc_start: 0.7926 (pt0) cc_final: 0.7426 (pt0) REVERT: B 610 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8129 (ptmt) REVERT: B 615 MET cc_start: 0.9503 (mmp) cc_final: 0.9263 (mmp) REVERT: C 21 PHE cc_start: 0.9256 (m-80) cc_final: 0.8868 (m-80) REVERT: C 33 GLU cc_start: 0.9140 (tp30) cc_final: 0.8938 (tp30) REVERT: C 56 MET cc_start: 0.6866 (ptm) cc_final: 0.5803 (ttm) REVERT: C 92 PHE cc_start: 0.7849 (t80) cc_final: 0.7492 (t80) REVERT: C 95 MET cc_start: 0.8991 (tmm) cc_final: 0.8761 (tmm) REVERT: C 122 PHE cc_start: 0.8711 (m-80) cc_final: 0.8492 (m-80) REVERT: C 129 LYS cc_start: 0.9183 (tptt) cc_final: 0.8961 (tmtt) REVERT: C 162 TYR cc_start: 0.8903 (m-80) cc_final: 0.7567 (m-80) REVERT: C 196 ARG cc_start: 0.9196 (ptm-80) cc_final: 0.8898 (ptt90) REVERT: C 244 GLU cc_start: 0.9523 (pt0) cc_final: 0.9220 (pp20) REVERT: C 259 PHE cc_start: 0.8346 (t80) cc_final: 0.8135 (t80) REVERT: D 31 LEU cc_start: 0.9042 (mt) cc_final: 0.8603 (mt) REVERT: D 109 PHE cc_start: 0.8281 (m-80) cc_final: 0.7970 (m-80) REVERT: D 132 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8061 (mm-40) REVERT: D 154 PHE cc_start: 0.7585 (t80) cc_final: 0.7192 (t80) REVERT: D 198 GLU cc_start: 0.8594 (tt0) cc_final: 0.8294 (tt0) REVERT: D 212 ILE cc_start: 0.7002 (OUTLIER) cc_final: 0.6794 (pt) REVERT: D 213 TYR cc_start: 0.4372 (t80) cc_final: 0.4073 (t80) REVERT: D 233 ASN cc_start: 0.9400 (p0) cc_final: 0.9158 (m110) outliers start: 61 outliers final: 39 residues processed: 541 average time/residue: 0.1261 time to fit residues: 103.8184 Evaluate side-chains 508 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 462 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 624 PHE Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 158 optimal weight: 20.0000 chunk 97 optimal weight: 0.3980 chunk 151 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 107 ASN D 132 GLN ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.151303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.101555 restraints weight = 27704.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.105012 restraints weight = 11677.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107180 restraints weight = 6807.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.108496 restraints weight = 4830.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109392 restraints weight = 3895.929| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16386 Z= 0.166 Angle : 0.670 13.921 22134 Z= 0.350 Chirality : 0.045 0.391 2360 Planarity : 0.004 0.066 2818 Dihedral : 7.968 135.113 2292 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.21 % Allowed : 25.87 % Favored : 70.92 % 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: 1.14 (0.15), residues: 1135 sheet: -0.66 (0.41), residues: 152 loop : 0.36 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 261 TYR 0.028 0.001 TYR D 162 PHE 0.032 0.001 PHE C 172 TRP 0.020 0.002 TRP D 44 HIS 0.004 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (16386) covalent geometry : angle 0.66991 / 0.35 (22134) hydrogen bonds : bond 0.03977 / 2.53 ( 871) hydrogen bonds : angle 4.96005 / 3.56 ( 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 534 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 479 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.8580 (m-30) cc_final: 0.8348 (m-30) REVERT: A 144 MET cc_start: 0.8763 (mtm) cc_final: 0.8220 (mtm) REVERT: A 148 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8128 (mt-10) REVERT: A 209 LYS cc_start: 0.9040 (tttm) cc_final: 0.8577 (ttmm) REVERT: A 259 ASN cc_start: 0.9015 (m-40) cc_final: 0.8388 (m110) REVERT: A 263 ASP cc_start: 0.8632 (m-30) cc_final: 0.8342 (m-30) REVERT: A 277 THR cc_start: 0.8248 (p) cc_final: 0.8000 (t) REVERT: A 286 ASP cc_start: 0.8657 (t0) cc_final: 0.8436 (t0) REVERT: A 381 LEU cc_start: 0.9523 (tp) cc_final: 0.9225 (tp) REVERT: A 384 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.6870 (pm20) REVERT: A 486 ASP cc_start: 0.8369 (t0) cc_final: 0.8165 (t0) REVERT: A 493 MET cc_start: 0.9114 (tmm) cc_final: 0.8886 (tmm) REVERT: A 583 SER cc_start: 0.9258 (OUTLIER) cc_final: 0.8970 (t) REVERT: A 589 SER cc_start: 0.9250 (m) cc_final: 0.8904 (p) REVERT: A 598 MET cc_start: 0.8311 (mtp) cc_final: 0.8018 (mtp) REVERT: A 686 ARG cc_start: 0.8182 (ttm-80) cc_final: 0.7805 (mmt-90) REVERT: B 108 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8160 (p) REVERT: B 263 ASP cc_start: 0.8638 (m-30) cc_final: 0.8295 (m-30) REVERT: B 274 ARG cc_start: 0.8247 (ttm110) cc_final: 0.7539 (ptp-110) REVERT: B 317 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8284 (ptp) REVERT: B 362 ASP cc_start: 0.8238 (m-30) cc_final: 0.7978 (m-30) REVERT: B 384 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.7170 (pm20) REVERT: B 394 TYR cc_start: 0.9218 (m-80) cc_final: 0.8487 (m-80) REVERT: B 515 ASP cc_start: 0.8660 (m-30) cc_final: 0.8153 (m-30) REVERT: B 571 TYR cc_start: 0.8763 (t80) cc_final: 0.7717 (t80) REVERT: B 586 TYR cc_start: 0.8735 (m-80) cc_final: 0.8443 (m-80) REVERT: B 595 MET cc_start: 0.8950 (mmm) cc_final: 0.8272 (mmm) REVERT: B 610 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8124 (ptmt) REVERT: B 615 MET cc_start: 0.9445 (mmp) cc_final: 0.9197 (mmp) REVERT: C 20 MET cc_start: 0.8987 (ptp) cc_final: 0.8727 (pmm) REVERT: C 21 PHE cc_start: 0.9273 (m-80) cc_final: 0.8753 (m-80) REVERT: C 56 MET cc_start: 0.6832 (ptm) cc_final: 0.6453 (ttp) REVERT: C 92 PHE cc_start: 0.8087 (t80) cc_final: 0.7620 (t80) REVERT: C 95 MET cc_start: 0.8967 (tmm) cc_final: 0.8604 (tmm) REVERT: C 122 PHE cc_start: 0.8718 (m-80) cc_final: 0.8489 (m-80) REVERT: C 129 LYS cc_start: 0.9105 (tptt) cc_final: 0.8888 (tmtt) REVERT: C 162 TYR cc_start: 0.8905 (m-80) cc_final: 0.7576 (m-80) REVERT: C 196 ARG cc_start: 0.9193 (ptm-80) cc_final: 0.8903 (ptt90) REVERT: C 259 PHE cc_start: 0.8488 (t80) cc_final: 0.8226 (t80) REVERT: D 34 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: D 56 MET cc_start: 0.8635 (mmp) cc_final: 0.7736 (ptp) REVERT: D 93 MET cc_start: 0.8403 (mtp) cc_final: 0.8149 (mtp) REVERT: D 109 PHE cc_start: 0.8289 (m-80) cc_final: 0.8016 (m-80) REVERT: D 132 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7900 (mm110) REVERT: D 198 GLU cc_start: 0.8553 (tt0) cc_final: 0.8269 (tt0) REVERT: D 233 ASN cc_start: 0.9371 (p0) cc_final: 0.9152 (m110) outliers start: 55 outliers final: 38 residues processed: 510 average time/residue: 0.1270 time to fit residues: 98.9061 Evaluate side-chains 504 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 458 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 145 ILE 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 317 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 624 PHE Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 0.0970 chunk 133 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 16 optimal weight: 0.3980 chunk 114 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 418 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 270 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.153236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.103615 restraints weight = 27543.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.107248 restraints weight = 11453.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109526 restraints weight = 6524.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.110913 restraints weight = 4540.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.111733 restraints weight = 3632.675| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.5964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16386 Z= 0.145 Angle : 0.678 14.087 22134 Z= 0.353 Chirality : 0.045 0.402 2360 Planarity : 0.003 0.040 2818 Dihedral : 7.795 135.198 2292 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.97 % Allowed : 26.63 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.19), residues: 1932 helix: 1.16 (0.15), residues: 1126 sheet: -0.52 (0.42), residues: 140 loop : 0.27 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 235 TYR 0.017 0.001 TYR A 571 PHE 0.036 0.001 PHE C 172 TRP 0.021 0.001 TRP D 44 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (16386) covalent geometry : angle 0.67815 / 0.35 (22134) hydrogen bonds : bond 0.03951 / 2.51 ( 871) hydrogen bonds : angle 4.92500 / 3.53 ( 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 552 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 501 time to evaluate : 0.648 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 67 GLU cc_start: 0.8414 (pm20) cc_final: 0.7776 (pm20) REVERT: A 103 ASP cc_start: 0.8645 (m-30) cc_final: 0.8440 (m-30) REVERT: A 144 MET cc_start: 0.8745 (mtm) cc_final: 0.8152 (mtm) REVERT: A 148 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8229 (mt-10) REVERT: A 209 LYS cc_start: 0.9016 (tttm) cc_final: 0.8616 (ttmm) REVERT: A 228 LYS cc_start: 0.8998 (ttmm) cc_final: 0.8499 (mttp) REVERT: A 259 ASN cc_start: 0.9042 (m-40) cc_final: 0.8439 (m-40) REVERT: A 263 ASP cc_start: 0.8720 (m-30) cc_final: 0.8400 (m-30) REVERT: A 277 THR cc_start: 0.8238 (p) cc_final: 0.8019 (t) REVERT: A 357 TYR cc_start: 0.8981 (m-10) cc_final: 0.8562 (m-10) REVERT: A 384 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.6713 (pm20) REVERT: A 453 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.8857 (ttt90) REVERT: A 486 ASP cc_start: 0.8411 (t0) cc_final: 0.8198 (t0) REVERT: A 493 MET cc_start: 0.9109 (tmm) cc_final: 0.8856 (tmm) REVERT: A 583 SER cc_start: 0.9254 (OUTLIER) cc_final: 0.8912 (t) REVERT: A 586 TYR cc_start: 0.8738 (m-10) cc_final: 0.8334 (m-80) REVERT: A 589 SER cc_start: 0.9171 (m) cc_final: 0.8898 (p) REVERT: A 598 MET cc_start: 0.8399 (mtp) cc_final: 0.7972 (mtp) REVERT: A 686 ARG cc_start: 0.8198 (ttm-80) cc_final: 0.7915 (mmm-85) REVERT: B 108 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8302 (p) REVERT: B 263 ASP cc_start: 0.8706 (m-30) cc_final: 0.8303 (m-30) REVERT: B 274 ARG cc_start: 0.8284 (ttm110) cc_final: 0.7492 (ptp-110) REVERT: B 317 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8275 (ptp) REVERT: B 362 ASP cc_start: 0.8272 (m-30) cc_final: 0.8010 (m-30) REVERT: B 384 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.7066 (pm20) REVERT: B 394 TYR cc_start: 0.9222 (m-80) cc_final: 0.8470 (m-80) REVERT: B 515 ASP cc_start: 0.8727 (m-30) cc_final: 0.8180 (m-30) REVERT: B 595 MET cc_start: 0.8973 (mmm) cc_final: 0.8305 (mmm) REVERT: B 599 GLU cc_start: 0.7872 (pt0) cc_final: 0.7655 (pt0) REVERT: B 602 GLU cc_start: 0.7783 (pt0) cc_final: 0.7434 (pt0) REVERT: B 610 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8171 (ptmt) REVERT: C 20 MET cc_start: 0.8887 (ptp) cc_final: 0.8635 (pmm) REVERT: C 21 PHE cc_start: 0.9299 (m-80) cc_final: 0.8746 (m-80) REVERT: C 56 MET cc_start: 0.6859 (ptm) cc_final: 0.6492 (ttp) REVERT: C 95 MET cc_start: 0.8830 (tmm) cc_final: 0.8471 (tmm) REVERT: C 96 MET cc_start: 0.7615 (mmt) cc_final: 0.7200 (mmm) REVERT: C 107 ASN cc_start: 0.8131 (OUTLIER) cc_final: 0.7822 (p0) REVERT: C 122 PHE cc_start: 0.8796 (m-80) cc_final: 0.8555 (m-80) REVERT: C 162 TYR cc_start: 0.8910 (m-80) cc_final: 0.7557 (m-80) REVERT: C 196 ARG cc_start: 0.9180 (ptm-80) cc_final: 0.8940 (ptt90) REVERT: C 259 PHE cc_start: 0.8453 (t80) cc_final: 0.8186 (t80) REVERT: D 56 MET cc_start: 0.8716 (mmp) cc_final: 0.7806 (mtt) REVERT: D 74 MET cc_start: 0.5272 (tpt) cc_final: 0.3895 (ttp) REVERT: D 198 GLU cc_start: 0.8631 (tt0) cc_final: 0.8328 (tt0) REVERT: D 232 LEU cc_start: 0.8883 (mt) cc_final: 0.8377 (tt) REVERT: D 233 ASN cc_start: 0.9383 (p0) cc_final: 0.9124 (m110) outliers start: 51 outliers final: 32 residues processed: 528 average time/residue: 0.1252 time to fit residues: 100.9583 Evaluate side-chains 512 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 472 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 359 MET 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 453 ARG Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 33 optimal weight: 0.0870 chunk 35 optimal weight: 0.2980 chunk 189 optimal weight: 7.9990 chunk 181 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.154271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.104615 restraints weight = 27640.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.108241 restraints weight = 11374.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.110538 restraints weight = 6524.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.111906 restraints weight = 4566.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.112760 restraints weight = 3654.132| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.6171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16386 Z= 0.146 Angle : 0.692 13.484 22134 Z= 0.363 Chirality : 0.045 0.385 2360 Planarity : 0.003 0.042 2818 Dihedral : 7.671 135.588 2291 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.39 % Allowed : 26.86 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.19), residues: 1932 helix: 1.08 (0.15), residues: 1129 sheet: -0.63 (0.43), residues: 140 loop : 0.22 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 235 TYR 0.027 0.001 TYR A 571 PHE 0.039 0.002 PHE C 172 TRP 0.017 0.001 TRP D 44 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (16386) covalent geometry : angle 0.69194 / 0.36 (22134) hydrogen bonds : bond 0.03996 / 2.52 ( 871) hydrogen bonds : angle 4.95706 / 3.56 ( 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 534 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 493 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.8739 (mtm) cc_final: 0.8155 (mtm) REVERT: A 148 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8237 (mt-10) REVERT: A 209 LYS cc_start: 0.9075 (tttm) cc_final: 0.8707 (ttmm) REVERT: A 228 LYS cc_start: 0.8988 (ttmm) cc_final: 0.8498 (mttp) REVERT: A 259 ASN cc_start: 0.9032 (m-40) cc_final: 0.8431 (m-40) REVERT: A 263 ASP cc_start: 0.8674 (m-30) cc_final: 0.8343 (m-30) REVERT: A 277 THR cc_start: 0.8193 (p) cc_final: 0.7980 (t) REVERT: A 357 TYR cc_start: 0.8998 (m-10) cc_final: 0.8629 (m-10) REVERT: A 381 LEU cc_start: 0.9373 (tp) cc_final: 0.9087 (tp) REVERT: A 384 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.6659 (pm20) REVERT: A 453 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.8897 (ttt90) REVERT: A 486 ASP cc_start: 0.8428 (t0) cc_final: 0.8197 (t0) REVERT: A 493 MET cc_start: 0.9096 (tmm) cc_final: 0.8843 (tmm) REVERT: A 583 SER cc_start: 0.9222 (OUTLIER) cc_final: 0.8854 (t) REVERT: A 586 TYR cc_start: 0.8698 (m-10) cc_final: 0.8201 (m-10) REVERT: A 589 SER cc_start: 0.9188 (m) cc_final: 0.8901 (p) REVERT: A 686 ARG cc_start: 0.8194 (ttm-80) cc_final: 0.7812 (mmt-90) REVERT: B 108 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8425 (p) REVERT: B 263 ASP cc_start: 0.8687 (m-30) cc_final: 0.8287 (m-30) REVERT: B 274 ARG cc_start: 0.8313 (ttm110) cc_final: 0.7512 (ptp-110) REVERT: B 317 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8205 (ptp) REVERT: B 362 ASP cc_start: 0.8271 (m-30) cc_final: 0.7996 (m-30) REVERT: B 384 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.7159 (pm20) REVERT: B 394 TYR cc_start: 0.9228 (m-80) cc_final: 0.8386 (m-80) REVERT: B 515 ASP cc_start: 0.8675 (m-30) cc_final: 0.8122 (m-30) REVERT: B 595 MET cc_start: 0.8945 (mmm) cc_final: 0.8253 (mmm) REVERT: B 599 GLU cc_start: 0.8007 (pt0) cc_final: 0.7666 (pt0) REVERT: B 610 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8174 (ptmt) REVERT: B 686 ARG cc_start: 0.7700 (mmt180) cc_final: 0.7391 (mmt-90) REVERT: C 17 PHE cc_start: 0.8389 (p90) cc_final: 0.8111 (p90) REVERT: C 20 MET cc_start: 0.8895 (ptp) cc_final: 0.8606 (pmm) REVERT: C 21 PHE cc_start: 0.9301 (m-80) cc_final: 0.8640 (m-80) REVERT: C 56 MET cc_start: 0.6740 (ptm) cc_final: 0.6423 (ttp) REVERT: C 92 PHE cc_start: 0.7908 (t80) cc_final: 0.7610 (t80) REVERT: C 95 MET cc_start: 0.8841 (tmm) cc_final: 0.8435 (tmm) REVERT: C 96 MET cc_start: 0.7520 (mmt) cc_final: 0.7147 (mmm) REVERT: C 107 ASN cc_start: 0.8068 (OUTLIER) cc_final: 0.7780 (p0) REVERT: C 122 PHE cc_start: 0.8802 (m-80) cc_final: 0.8569 (m-80) REVERT: C 124 TRP cc_start: 0.8709 (t60) cc_final: 0.8274 (t60) REVERT: C 162 TYR cc_start: 0.8921 (m-80) cc_final: 0.8479 (m-80) REVERT: C 196 ARG cc_start: 0.9212 (ptm-80) cc_final: 0.8990 (ptt90) REVERT: C 259 PHE cc_start: 0.8477 (t80) cc_final: 0.8210 (t80) REVERT: D 23 ASN cc_start: 0.9265 (p0) cc_final: 0.9062 (p0) REVERT: D 28 GLN cc_start: 0.7822 (mt0) cc_final: 0.7552 (tt0) REVERT: D 56 MET cc_start: 0.8732 (mmp) cc_final: 0.7827 (mtt) REVERT: D 74 MET cc_start: 0.6362 (tpt) cc_final: 0.4965 (ttp) REVERT: D 119 ASN cc_start: 0.8758 (m110) cc_final: 0.8137 (p0) REVERT: D 154 PHE cc_start: 0.7443 (t80) cc_final: 0.7181 (t80) REVERT: D 157 MET cc_start: 0.3019 (ppp) cc_final: 0.2698 (ppp) REVERT: D 164 GLU cc_start: 0.7634 (mm-30) cc_final: 0.6866 (pt0) REVERT: D 198 GLU cc_start: 0.8558 (tt0) cc_final: 0.7918 (tp30) REVERT: D 232 LEU cc_start: 0.8818 (mt) cc_final: 0.8394 (tt) REVERT: D 233 ASN cc_start: 0.9377 (p0) cc_final: 0.9143 (m110) REVERT: D 245 ASP cc_start: 0.7479 (t0) cc_final: 0.7127 (m-30) outliers start: 41 outliers final: 29 residues processed: 513 average time/residue: 0.1244 time to fit residues: 96.8591 Evaluate side-chains 512 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 475 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 359 MET 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 453 ARG Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 0.2980 chunk 1 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 148 optimal weight: 20.0000 chunk 125 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN D 132 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.153410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.104552 restraints weight = 27326.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.108032 restraints weight = 11696.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.110082 restraints weight = 6829.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.111472 restraints weight = 4859.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.112369 restraints weight = 3906.099| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.6287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16386 Z= 0.153 Angle : 0.711 14.103 22134 Z= 0.369 Chirality : 0.046 0.391 2360 Planarity : 0.003 0.043 2818 Dihedral : 7.602 135.735 2291 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.51 % Allowed : 26.86 % Favored : 70.63 % 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: 0.88 (0.19), residues: 1932 helix: 1.07 (0.15), residues: 1130 sheet: -0.72 (0.43), residues: 140 loop : 0.26 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 235 TYR 0.026 0.001 TYR D 236 PHE 0.038 0.002 PHE C 172 TRP 0.015 0.001 TRP D 44 HIS 0.005 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (16386) covalent geometry : angle 0.71083 / 0.37 (22134) hydrogen bonds : bond 0.03997 / 2.51 ( 871) hydrogen bonds : angle 4.95327 / 3.56 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3493.55 seconds wall clock time: 61 minutes 14.56 seconds (3674.56 seconds total)