Starting phenix.real_space_refine on Fri Jul 3 19:48:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz2_45051/07_2026/9bz2_45051_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz2_45051/07_2026/9bz2_45051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bz2_45051/07_2026/9bz2_45051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz2_45051/07_2026/9bz2_45051.map" model { file = "/net/cci-nas-00/data/ceres_data/9bz2_45051/07_2026/9bz2_45051_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz2_45051/07_2026/9bz2_45051_neut.cif" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-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: 3.75, per 1000 atoms: 0.23 Number of scatterers: 16038 At special positions: 0 Unit cell: (94.581, 131.193, 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 760.9 milliseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.984A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.954A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.665A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.694A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.627A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.073A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.958A 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: 3.879A 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: 3.730A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.027A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.118A 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: 3.514A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A 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: 7.426A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.478A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.478A pdb=" N LEU A 656 " --> pdb=" O ARG A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.185A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.049A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.46 Time building geometry restraints manager: 1.78 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: 4872 1.34 - 1.46: 3042 1.46 - 1.58: 8291 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 1.610 0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" O3B TTP A 803 " pdb=" PG TTP A 803 " ideal model delta sigma weight residual 1.748 1.610 0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.060 1.25e-02 6.40e+03 2.33e+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 1.20e+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 1.12e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 21698 2.46 - 4.91: 384 4.91 - 7.37: 37 7.37 - 9.83: 11 9.83 - 12.28: 4 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N LEU D 42 " pdb=" CA LEU D 42 " pdb=" CB LEU D 42 " ideal model delta sigma weight residual 110.07 97.79 12.28 1.45e+00 4.76e-01 7.18e+01 angle pdb=" C LEU D 42 " pdb=" CA LEU D 42 " pdb=" CB LEU D 42 " ideal model delta sigma weight residual 110.90 118.75 -7.85 1.58e+00 4.01e-01 2.47e+01 angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.66 -6.12 1.36e+00 5.41e-01 2.02e+01 angle pdb=" N LEU D 42 " pdb=" CA LEU D 42 " pdb=" C LEU D 42 " ideal model delta sigma weight residual 111.14 106.48 4.66 1.08e+00 8.57e-01 1.86e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.12 -4.41 1.15e+00 7.56e-01 1.47e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.06: 9095 25.06 - 50.12: 650 50.12 - 75.18: 125 75.18 - 100.25: 26 100.25 - 125.31: 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 -98.29 125.31 1 2.00e+01 2.50e-03 3.79e+01 dihedral pdb=" O4' GDP B 804 " pdb=" C1' GDP B 804 " pdb=" N9 GDP B 804 " pdb=" C8 GDP B 804 " ideal model delta sinusoidal sigma weight residual 27.02 -95.64 122.66 1 2.00e+01 2.50e-03 3.70e+01 dihedral pdb=" N LEU D 42 " pdb=" C LEU D 42 " pdb=" CA LEU D 42 " pdb=" CB LEU D 42 " ideal model delta harmonic sigma weight residual 122.80 108.88 13.92 0 2.50e+00 1.60e-01 3.10e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2144 0.093 - 0.187: 184 0.187 - 0.280: 27 0.280 - 0.374: 3 0.374 - 0.467: 2 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.46e+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 4.60e+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 2.91e+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 1.10e-02 2.13e+00 pdb=" CG PHE D 92 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 42 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C LEU D 42 " 0.025 2.00e-02 2.50e+03 pdb=" O LEU D 42 " -0.009 2.00e-02 2.50e+03 pdb=" N THR D 43 " -0.009 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 133 2.51 - 3.11: 11586 3.11 - 3.70: 27085 3.70 - 4.30: 41605 4.30 - 4.90: 65537 Nonbonded interactions: 145946 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 3.060 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 3.060 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 3.060 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.991 3.060 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.013 3.040 ... (remaining 145941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 16.620 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 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 0.138 16386 Z= 0.336 Angle : 0.797 12.283 22134 Z= 0.480 Chirality : 0.058 0.467 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.615 125.307 6202 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.40 % Allowed : 15.15 % Favored : 83.45 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.18), residues: 1932 helix: 0.58 (0.14), residues: 1151 sheet: 0.46 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 196 TYR 0.020 0.002 TYR C 169 PHE 0.021 0.002 PHE C 168 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.34 (16386) covalent geometry : angle 0.79681 / 0.48 (22134) hydrogen bonds : bond 0.15423 / 9.51 ( 871) hydrogen bonds : angle 6.51784 / 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 833 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 809 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ILE cc_start: 0.9185 (mt) cc_final: 0.8940 (mt) REVERT: A 127 LEU cc_start: 0.9149 (mt) cc_final: 0.8850 (mt) REVERT: A 131 ASN cc_start: 0.8653 (t0) cc_final: 0.8375 (t0) REVERT: A 138 LYS cc_start: 0.8180 (mtpt) cc_final: 0.7826 (mtpp) REVERT: A 145 ILE cc_start: 0.9125 (tp) cc_final: 0.8904 (tp) REVERT: A 172 LEU cc_start: 0.9004 (mp) cc_final: 0.8771 (mp) REVERT: A 179 LEU cc_start: 0.8997 (tp) cc_final: 0.8450 (tp) REVERT: A 220 THR cc_start: 0.8806 (m) cc_final: 0.8516 (p) REVERT: A 227 MET cc_start: 0.7829 (mtp) cc_final: 0.7585 (mtp) REVERT: A 319 MET cc_start: 0.7850 (tpp) cc_final: 0.7399 (tpp) REVERT: A 367 VAL cc_start: 0.9098 (m) cc_final: 0.8773 (t) REVERT: A 380 ASN cc_start: 0.8968 (p0) cc_final: 0.8736 (p0) REVERT: A 446 ARG cc_start: 0.7519 (mmm-85) cc_final: 0.7225 (mtp85) REVERT: A 447 ASN cc_start: 0.7944 (m-40) cc_final: 0.7323 (m110) REVERT: A 546 LEU cc_start: 0.8855 (mt) cc_final: 0.8648 (mt) REVERT: A 550 MET cc_start: 0.8096 (mtm) cc_final: 0.7880 (mtt) REVERT: A 598 MET cc_start: 0.8373 (mtm) cc_final: 0.7775 (mtp) REVERT: B 51 LEU cc_start: 0.8213 (tp) cc_final: 0.7882 (tp) REVERT: B 67 GLU cc_start: 0.7745 (mp0) cc_final: 0.7137 (mp0) REVERT: B 106 LEU cc_start: 0.8835 (tp) cc_final: 0.7901 (tt) REVERT: B 127 LEU cc_start: 0.9042 (mt) cc_final: 0.8806 (mt) REVERT: B 129 PHE cc_start: 0.8421 (m-10) cc_final: 0.8054 (m-10) REVERT: B 180 ASN cc_start: 0.7535 (m-40) cc_final: 0.7323 (m110) REVERT: B 186 ILE cc_start: 0.9217 (mt) cc_final: 0.9013 (mt) REVERT: B 211 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7475 (mm-30) REVERT: B 286 ASP cc_start: 0.6894 (OUTLIER) cc_final: 0.6684 (m-30) REVERT: B 319 MET cc_start: 0.7903 (tpp) cc_final: 0.7651 (tpp) REVERT: B 348 MET cc_start: 0.7346 (tmm) cc_final: 0.7076 (ttm) REVERT: B 358 ILE cc_start: 0.9193 (mm) cc_final: 0.8933 (mm) REVERT: B 381 LEU cc_start: 0.9246 (tp) cc_final: 0.8968 (tp) REVERT: B 384 GLU cc_start: 0.8948 (pm20) cc_final: 0.8158 (pm20) REVERT: B 389 SER cc_start: 0.8046 (p) cc_final: 0.7833 (p) REVERT: B 458 MET cc_start: 0.8463 (mmm) cc_final: 0.8144 (mmm) REVERT: B 460 SER cc_start: 0.8912 (t) cc_final: 0.8699 (p) REVERT: B 471 TYR cc_start: 0.8260 (t80) cc_final: 0.7677 (t80) REVERT: B 491 PHE cc_start: 0.8629 (t80) cc_final: 0.8429 (t80) REVERT: B 500 ILE cc_start: 0.9095 (mt) cc_final: 0.8889 (mt) REVERT: B 585 SER cc_start: 0.9148 (p) cc_final: 0.8862 (p) REVERT: C 89 VAL cc_start: 0.5232 (t) cc_final: 0.3662 (t) REVERT: C 229 ILE cc_start: 0.5031 (mt) cc_final: 0.4258 (mm) REVERT: D 42 LEU cc_start: 0.1877 (mt) cc_final: 0.1452 (mt) REVERT: D 185 MET cc_start: 0.0973 (mmm) cc_final: 0.0569 (mmm) REVERT: D 282 ILE cc_start: 0.3799 (OUTLIER) cc_final: 0.3394 (pt) outliers start: 24 outliers final: 5 residues processed: 822 average time/residue: 0.1243 time to fit residues: 150.7444 Evaluate side-chains 566 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 559 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 286 ASP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 239 GLN A 365 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN B 11 GLN B 14 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN B 312 GLN B 329 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN B 410 ASN B 467 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 233 ASN D 71 ASN D 80 HIS D 91 ASN D 186 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.153756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.106294 restraints weight = 31402.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.109851 restraints weight = 15093.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.112110 restraints weight = 9184.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.113354 restraints weight = 6600.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.114182 restraints weight = 5395.037| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 13 (19 function evaluations) r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16386 Z= 0.238 Angle : 0.677 7.310 22134 Z= 0.359 Chirality : 0.045 0.315 2360 Planarity : 0.004 0.040 2818 Dihedral : 9.954 133.143 2302 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.20 % Allowed : 18.30 % Favored : 77.51 % 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: 1.45 (0.19), residues: 1932 helix: 1.36 (0.15), residues: 1137 sheet: -0.22 (0.46), residues: 114 loop : 0.72 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 164 TYR 0.032 0.002 TYR D 174 PHE 0.028 0.002 PHE B 261 TRP 0.017 0.002 TRP D 44 HIS 0.007 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.24 (16386) covalent geometry : angle 0.67717 / 0.36 (22134) hydrogen bonds : bond 0.04858 / 3.11 ( 871) hydrogen bonds : angle 5.11346 / 3.67 ( 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 648 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 576 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8871 (p0) cc_final: 0.8543 (p0) REVERT: A 65 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7251 (mp0) REVERT: A 138 LYS cc_start: 0.9078 (mtpt) cc_final: 0.8823 (mtpp) REVERT: A 172 LEU cc_start: 0.9307 (mp) cc_final: 0.8977 (mp) REVERT: A 191 GLN cc_start: 0.8362 (mm-40) cc_final: 0.7989 (mm-40) REVERT: A 276 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8522 (mmtm) REVERT: A 317 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7914 (ptp) REVERT: A 357 TYR cc_start: 0.8986 (m-10) cc_final: 0.8021 (m-10) REVERT: A 362 ASP cc_start: 0.8436 (m-30) cc_final: 0.8150 (m-30) REVERT: A 384 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.7560 (pm20) REVERT: A 402 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7280 (tm-30) REVERT: A 444 ASP cc_start: 0.8405 (t70) cc_final: 0.8200 (t70) REVERT: A 447 ASN cc_start: 0.8810 (m-40) cc_final: 0.8386 (m-40) REVERT: A 456 LYS cc_start: 0.8931 (mtmm) cc_final: 0.8543 (mtmm) REVERT: A 493 MET cc_start: 0.8932 (tmm) cc_final: 0.8517 (tmm) REVERT: A 548 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8254 (mm-30) REVERT: A 588 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8604 (mm-40) REVERT: A 602 GLU cc_start: 0.7690 (pt0) cc_final: 0.7132 (pt0) REVERT: A 663 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8119 (t) REVERT: B 41 ILE cc_start: 0.9280 (mm) cc_final: 0.9079 (mm) REVERT: B 52 LYS cc_start: 0.9401 (tppt) cc_final: 0.9077 (tppt) REVERT: B 118 TYR cc_start: 0.9381 (t80) cc_final: 0.9152 (t80) REVERT: B 214 LYS cc_start: 0.8359 (ttmm) cc_final: 0.7952 (mmtm) REVERT: B 362 ASP cc_start: 0.8036 (m-30) cc_final: 0.7739 (m-30) REVERT: B 420 MET cc_start: 0.9364 (mmm) cc_final: 0.9145 (mmm) REVERT: B 425 ILE cc_start: 0.9492 (mt) cc_final: 0.9213 (mt) REVERT: B 493 MET cc_start: 0.9506 (tmm) cc_final: 0.9295 (tmm) REVERT: B 602 GLU cc_start: 0.7995 (pt0) cc_final: 0.7545 (pt0) REVERT: B 604 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8393 (mmt-90) REVERT: B 610 LYS cc_start: 0.9070 (ptpt) cc_final: 0.8691 (ptmm) REVERT: B 612 TYR cc_start: 0.9004 (m-80) cc_final: 0.8062 (m-80) REVERT: B 648 ILE cc_start: 0.9110 (mm) cc_final: 0.8838 (mt) REVERT: B 650 GLN cc_start: 0.8433 (mt0) cc_final: 0.8118 (mt0) REVERT: B 656 LEU cc_start: 0.9564 (mt) cc_final: 0.9357 (mt) REVERT: B 667 LEU cc_start: 0.8959 (tp) cc_final: 0.8476 (tp) REVERT: C 56 MET cc_start: 0.4819 (ptt) cc_final: 0.4227 (ppp) REVERT: C 90 LEU cc_start: 0.7522 (mt) cc_final: 0.6943 (mt) REVERT: C 164 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7824 (tp30) REVERT: C 178 PHE cc_start: 0.7599 (m-80) cc_final: 0.7388 (m-80) REVERT: C 278 GLU cc_start: 0.8820 (tt0) cc_final: 0.8608 (tp30) outliers start: 72 outliers final: 27 residues processed: 614 average time/residue: 0.1169 time to fit residues: 108.0806 Evaluate side-chains 506 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 473 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 182 optimal weight: 7.9990 chunk 159 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 150 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 ASN A 438 HIS A 645 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 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 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.150533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.105217 restraints weight = 32165.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.108526 restraints weight = 15120.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.110810 restraints weight = 9093.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.112181 restraints weight = 6435.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.112973 restraints weight = 5171.458| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16386 Z= 0.195 Angle : 0.635 11.781 22134 Z= 0.332 Chirality : 0.044 0.272 2360 Planarity : 0.003 0.040 2818 Dihedral : 9.265 135.330 2294 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.96 % Allowed : 21.74 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.19), residues: 1932 helix: 1.40 (0.15), residues: 1126 sheet: -0.29 (0.47), residues: 114 loop : 0.63 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 164 TYR 0.042 0.002 TYR D 174 PHE 0.026 0.002 PHE A 492 TRP 0.015 0.002 TRP D 124 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (16386) covalent geometry : angle 0.63464 / 0.33 (22134) hydrogen bonds : bond 0.04331 / 2.74 ( 871) hydrogen bonds : angle 5.00569 / 3.62 ( 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 587 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 519 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8957 (p0) cc_final: 0.8667 (p0) REVERT: A 65 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7292 (mp0) REVERT: A 119 GLU cc_start: 0.8474 (mp0) cc_final: 0.8078 (mp0) REVERT: A 138 LYS cc_start: 0.9060 (mtpt) cc_final: 0.8854 (mtpp) REVERT: A 145 ILE cc_start: 0.9549 (tp) cc_final: 0.9271 (tp) REVERT: A 150 GLN cc_start: 0.8992 (tm-30) cc_final: 0.8744 (tm-30) REVERT: A 172 LEU cc_start: 0.9287 (mp) cc_final: 0.8980 (mp) REVERT: A 317 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7936 (ptp) REVERT: A 346 LEU cc_start: 0.9369 (mp) cc_final: 0.9168 (mp) REVERT: A 348 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.7270 (ptm) REVERT: A 357 TYR cc_start: 0.8994 (m-10) cc_final: 0.8028 (m-10) REVERT: A 362 ASP cc_start: 0.8423 (m-30) cc_final: 0.7977 (m-30) REVERT: A 384 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7394 (pm20) REVERT: A 402 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7205 (tm-30) REVERT: A 447 ASN cc_start: 0.8716 (m-40) cc_final: 0.8147 (m-40) REVERT: A 453 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8277 (ttt-90) REVERT: A 456 LYS cc_start: 0.8931 (mtmm) cc_final: 0.8665 (mtmm) REVERT: A 493 MET cc_start: 0.8881 (tmm) cc_final: 0.8268 (tmm) REVERT: A 505 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8075 (mt-10) REVERT: A 515 ASP cc_start: 0.8793 (m-30) cc_final: 0.8553 (m-30) REVERT: A 548 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8261 (mm-30) REVERT: A 570 MET cc_start: 0.8896 (mtp) cc_final: 0.8661 (mtp) REVERT: A 588 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8675 (mm-40) REVERT: A 640 MET cc_start: 0.9317 (tpp) cc_final: 0.8855 (tpp) REVERT: A 663 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8336 (t) REVERT: B 52 LYS cc_start: 0.9407 (tppt) cc_final: 0.9091 (tppt) REVERT: B 118 TYR cc_start: 0.9327 (t80) cc_final: 0.9093 (t80) REVERT: B 214 LYS cc_start: 0.8249 (ttmm) cc_final: 0.7889 (mmtm) REVERT: B 257 ASP cc_start: 0.8958 (m-30) cc_final: 0.8757 (m-30) REVERT: B 352 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8273 (mt-10) REVERT: B 420 MET cc_start: 0.9388 (mmm) cc_final: 0.9128 (mmm) REVERT: B 458 MET cc_start: 0.9053 (mmm) cc_final: 0.8811 (mmm) REVERT: B 467 ASN cc_start: 0.9212 (t0) cc_final: 0.8324 (t0) REVERT: B 493 MET cc_start: 0.9460 (tmm) cc_final: 0.9239 (tmm) REVERT: B 526 GLU cc_start: 0.8654 (mp0) cc_final: 0.8384 (mm-30) REVERT: B 599 GLU cc_start: 0.8772 (pm20) cc_final: 0.8496 (pm20) REVERT: B 602 GLU cc_start: 0.7799 (pt0) cc_final: 0.7366 (pt0) REVERT: B 604 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8650 (mmt-90) REVERT: B 610 LYS cc_start: 0.9170 (ptpt) cc_final: 0.8794 (ptmm) REVERT: C 56 MET cc_start: 0.4854 (ptt) cc_final: 0.4202 (ppp) REVERT: C 133 LYS cc_start: 0.6957 (OUTLIER) cc_final: 0.6502 (tptm) REVERT: C 157 MET cc_start: 0.8582 (mtp) cc_final: 0.8083 (ttt) REVERT: C 164 GLU cc_start: 0.8465 (mm-30) cc_final: 0.7300 (tp30) REVERT: C 168 PHE cc_start: 0.8613 (m-80) cc_final: 0.8267 (m-80) REVERT: C 169 TYR cc_start: 0.8550 (m-80) cc_final: 0.8302 (m-80) REVERT: C 178 PHE cc_start: 0.7582 (m-80) cc_final: 0.7358 (m-80) REVERT: C 201 HIS cc_start: 0.8737 (m170) cc_final: 0.8535 (m90) REVERT: C 278 GLU cc_start: 0.8858 (tt0) cc_final: 0.8622 (tp30) outliers start: 68 outliers final: 32 residues processed: 553 average time/residue: 0.1140 time to fit residues: 95.8715 Evaluate side-chains 503 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 463 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 0.9980 chunk 157 optimal weight: 20.0000 chunk 168 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 185 optimal weight: 20.0000 chunk 191 optimal weight: 0.6980 chunk 159 optimal weight: 20.0000 chunk 182 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 146 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 HIS D 128 ASN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.151826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.105697 restraints weight = 32201.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.109101 restraints weight = 15675.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.111388 restraints weight = 9453.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.112800 restraints weight = 6623.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.113627 restraints weight = 5378.470| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (14 function evaluations) r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16386 Z= 0.204 Angle : 0.633 10.712 22134 Z= 0.332 Chirality : 0.044 0.253 2360 Planarity : 0.003 0.043 2818 Dihedral : 9.033 136.691 2293 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.85 % Allowed : 22.67 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.19), residues: 1932 helix: 1.35 (0.15), residues: 1125 sheet: -0.53 (0.47), residues: 118 loop : 0.54 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 121 TYR 0.027 0.002 TYR D 174 PHE 0.025 0.002 PHE A 492 TRP 0.031 0.002 TRP D 124 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (16386) covalent geometry : angle 0.63252 / 0.33 (22134) hydrogen bonds : bond 0.04185 / 2.66 ( 871) hydrogen bonds : angle 5.04094 / 3.64 ( 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 576 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 510 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8954 (p0) cc_final: 0.8720 (p0) REVERT: A 65 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7373 (mp0) REVERT: A 119 GLU cc_start: 0.8432 (mp0) cc_final: 0.8067 (mp0) REVERT: A 150 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8798 (tm-30) REVERT: A 161 ARG cc_start: 0.7930 (ttm-80) cc_final: 0.7370 (ttm-80) REVERT: A 172 LEU cc_start: 0.9315 (mp) cc_final: 0.8989 (mp) REVERT: A 191 GLN cc_start: 0.8234 (mm-40) cc_final: 0.8007 (mm-40) REVERT: A 317 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7715 (ptp) REVERT: A 346 LEU cc_start: 0.9437 (mp) cc_final: 0.9191 (mp) REVERT: A 348 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.7305 (ptm) REVERT: A 357 TYR cc_start: 0.9019 (m-10) cc_final: 0.8096 (m-10) REVERT: A 362 ASP cc_start: 0.8412 (m-30) cc_final: 0.8037 (m-30) REVERT: A 384 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7476 (pm20) REVERT: A 402 GLU cc_start: 0.7436 (tm-30) cc_final: 0.7187 (tm-30) REVERT: A 444 ASP cc_start: 0.8472 (t70) cc_final: 0.7817 (t70) REVERT: A 446 ARG cc_start: 0.7933 (mtp85) cc_final: 0.7703 (mmm-85) REVERT: A 447 ASN cc_start: 0.8611 (m-40) cc_final: 0.7816 (m-40) REVERT: A 456 LYS cc_start: 0.8936 (mtmm) cc_final: 0.8683 (mtmm) REVERT: A 505 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8104 (mt-10) REVERT: A 515 ASP cc_start: 0.8800 (m-30) cc_final: 0.8520 (m-30) REVERT: A 571 TYR cc_start: 0.9208 (t80) cc_final: 0.8643 (t80) REVERT: A 588 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8732 (mm-40) REVERT: A 606 TYR cc_start: 0.8292 (m-80) cc_final: 0.8090 (m-10) REVERT: A 645 GLN cc_start: 0.9031 (tp-100) cc_final: 0.8808 (tp40) REVERT: A 663 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8464 (t) REVERT: B 52 LYS cc_start: 0.9381 (tppt) cc_final: 0.9049 (tppt) REVERT: B 104 TYR cc_start: 0.8670 (m-80) cc_final: 0.8340 (m-80) REVERT: B 116 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8492 (mt-10) REVERT: B 118 TYR cc_start: 0.9309 (t80) cc_final: 0.9097 (t80) REVERT: B 214 LYS cc_start: 0.8206 (ttmm) cc_final: 0.7875 (mmtm) REVERT: B 352 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8121 (mt-10) REVERT: B 384 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.7299 (pm20) REVERT: B 458 MET cc_start: 0.9051 (mmm) cc_final: 0.8815 (mmm) REVERT: B 467 ASN cc_start: 0.9214 (t0) cc_final: 0.8487 (t0) REVERT: B 493 MET cc_start: 0.9437 (tmm) cc_final: 0.9214 (tmm) REVERT: B 494 MET cc_start: 0.9165 (mtp) cc_final: 0.8924 (mtp) REVERT: B 586 TYR cc_start: 0.8550 (m-80) cc_final: 0.8343 (m-80) REVERT: B 599 GLU cc_start: 0.8743 (pm20) cc_final: 0.8268 (pm20) REVERT: B 602 GLU cc_start: 0.7601 (pt0) cc_final: 0.6909 (pt0) REVERT: B 604 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8688 (mmt-90) REVERT: B 610 LYS cc_start: 0.9194 (ptpt) cc_final: 0.8824 (ptmm) REVERT: C 157 MET cc_start: 0.8674 (mtp) cc_final: 0.8357 (ttt) REVERT: C 164 GLU cc_start: 0.8522 (mm-30) cc_final: 0.7782 (tp30) REVERT: C 169 TYR cc_start: 0.8688 (m-80) cc_final: 0.8420 (m-80) REVERT: C 178 PHE cc_start: 0.7639 (m-80) cc_final: 0.7410 (m-80) REVERT: C 227 PHE cc_start: 0.6445 (m-80) cc_final: 0.5911 (m-80) REVERT: C 238 ASN cc_start: 0.7219 (m-40) cc_final: 0.6418 (m110) outliers start: 66 outliers final: 40 residues processed: 546 average time/residue: 0.1131 time to fit residues: 93.7231 Evaluate side-chains 505 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 459 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 223 VAL 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 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 37 optimal weight: 0.3980 chunk 126 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 168 optimal weight: 6.9990 chunk 157 optimal weight: 20.0000 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 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 107 ASN C 132 GLN C 233 ASN D 128 ASN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.153435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108946 restraints weight = 32010.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.112368 restraints weight = 15209.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.114633 restraints weight = 9128.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.116021 restraints weight = 6454.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.116755 restraints weight = 5164.003| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16386 Z= 0.138 Angle : 0.608 10.028 22134 Z= 0.318 Chirality : 0.043 0.247 2360 Planarity : 0.003 0.042 2818 Dihedral : 8.766 136.403 2293 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.86 % Allowed : 24.13 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.19), residues: 1932 helix: 1.39 (0.15), residues: 1122 sheet: -0.14 (0.49), residues: 106 loop : 0.33 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 350 TYR 0.022 0.001 TYR A 571 PHE 0.026 0.001 PHE C 168 TRP 0.027 0.002 TRP D 124 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (16386) covalent geometry : angle 0.60790 / 0.32 (22134) hydrogen bonds : bond 0.03965 / 2.52 ( 871) hydrogen bonds : angle 5.00641 / 3.62 ( 2571) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 517 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8928 (p0) cc_final: 0.8682 (p0) REVERT: A 65 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7323 (mp0) REVERT: A 119 GLU cc_start: 0.8294 (mp0) cc_final: 0.7979 (mp0) REVERT: A 158 ASN cc_start: 0.8953 (m-40) cc_final: 0.8644 (m-40) REVERT: A 172 LEU cc_start: 0.9234 (mp) cc_final: 0.8905 (mp) REVERT: A 346 LEU cc_start: 0.9421 (mt) cc_final: 0.9188 (mp) REVERT: A 348 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7279 (ptm) REVERT: A 357 TYR cc_start: 0.8943 (m-10) cc_final: 0.7879 (m-10) REVERT: A 361 GLN cc_start: 0.8739 (tp40) cc_final: 0.8513 (tp40) REVERT: A 362 ASP cc_start: 0.8268 (m-30) cc_final: 0.7920 (m-30) REVERT: A 384 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7409 (pm20) REVERT: A 402 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7204 (tm-30) REVERT: A 415 ASN cc_start: 0.8888 (t0) cc_final: 0.8675 (t0) REVERT: A 444 ASP cc_start: 0.8476 (t70) cc_final: 0.8252 (t70) REVERT: A 446 ARG cc_start: 0.7919 (mtp85) cc_final: 0.7605 (mmm-85) REVERT: A 447 ASN cc_start: 0.8426 (m-40) cc_final: 0.7772 (m-40) REVERT: A 456 LYS cc_start: 0.8988 (mtmm) cc_final: 0.8775 (mtmm) REVERT: A 505 GLU cc_start: 0.8485 (mt-10) cc_final: 0.7965 (mt-10) REVERT: A 515 ASP cc_start: 0.8748 (m-30) cc_final: 0.8482 (m-30) REVERT: A 571 TYR cc_start: 0.9208 (t80) cc_final: 0.8815 (t80) REVERT: A 640 MET cc_start: 0.9239 (tpp) cc_final: 0.8785 (tpt) REVERT: A 645 GLN cc_start: 0.8844 (tp-100) cc_final: 0.8558 (tp-100) REVERT: A 663 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8508 (t) REVERT: B 18 ILE cc_start: 0.9445 (mm) cc_final: 0.9190 (mp) REVERT: B 27 ASP cc_start: 0.8861 (p0) cc_final: 0.8462 (p0) REVERT: B 31 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8011 (mt-10) REVERT: B 52 LYS cc_start: 0.9400 (tppt) cc_final: 0.9089 (tppt) REVERT: B 79 GLU cc_start: 0.8832 (tp30) cc_final: 0.8207 (tp30) REVERT: B 147 GLN cc_start: 0.9222 (mt0) cc_final: 0.8543 (mm-40) REVERT: B 180 ASN cc_start: 0.7974 (m-40) cc_final: 0.7748 (m110) REVERT: B 257 ASP cc_start: 0.8948 (m-30) cc_final: 0.8725 (m-30) REVERT: B 314 MET cc_start: 0.9126 (ttp) cc_final: 0.8917 (tmm) REVERT: B 319 MET cc_start: 0.8745 (tpp) cc_final: 0.8515 (tpp) REVERT: B 352 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8153 (mt-10) REVERT: B 416 ILE cc_start: 0.9164 (mm) cc_final: 0.8913 (mm) REVERT: B 467 ASN cc_start: 0.9097 (t0) cc_final: 0.8495 (t0) REVERT: B 493 MET cc_start: 0.9417 (tmm) cc_final: 0.9200 (tmm) REVERT: B 526 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8343 (mm-30) REVERT: B 570 MET cc_start: 0.8588 (mmm) cc_final: 0.7937 (mtt) REVERT: B 586 TYR cc_start: 0.8530 (m-80) cc_final: 0.8079 (m-80) REVERT: B 599 GLU cc_start: 0.8743 (pm20) cc_final: 0.8278 (pm20) REVERT: B 602 GLU cc_start: 0.7719 (pt0) cc_final: 0.6427 (pt0) REVERT: B 604 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8767 (mmt-90) REVERT: B 610 LYS cc_start: 0.9249 (ptpt) cc_final: 0.8945 (ptmm) REVERT: B 612 TYR cc_start: 0.8796 (m-80) cc_final: 0.7692 (m-80) REVERT: C 56 MET cc_start: 0.5150 (ptt) cc_final: 0.4631 (ppp) REVERT: C 64 LEU cc_start: 0.8246 (tp) cc_final: 0.8045 (pp) REVERT: C 157 MET cc_start: 0.8749 (mtp) cc_final: 0.8190 (ttt) REVERT: C 164 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7814 (tp30) REVERT: C 169 TYR cc_start: 0.8793 (m-80) cc_final: 0.8567 (m-80) REVERT: C 201 HIS cc_start: 0.8871 (m90) cc_final: 0.8659 (m90) REVERT: C 227 PHE cc_start: 0.6565 (m-80) cc_final: 0.5928 (m-80) REVERT: C 233 ASN cc_start: 0.8364 (m-40) cc_final: 0.8084 (m-40) REVERT: C 238 ASN cc_start: 0.6942 (m-40) cc_final: 0.6319 (m110) REVERT: D 259 PHE cc_start: 0.3897 (m-80) cc_final: 0.3371 (m-80) outliers start: 49 outliers final: 29 residues processed: 543 average time/residue: 0.1180 time to fit residues: 97.1320 Evaluate side-chains 512 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 478 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 0.8980 chunk 183 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 172 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 ASN A 239 GLN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 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 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.153673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.109748 restraints weight = 32093.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.113319 restraints weight = 15007.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.115521 restraints weight = 8854.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.116872 restraints weight = 6283.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.117650 restraints weight = 5047.679| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.5491 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= 0.135 Angle : 0.609 8.792 22134 Z= 0.320 Chirality : 0.043 0.204 2360 Planarity : 0.003 0.043 2818 Dihedral : 8.619 137.148 2293 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.86 % Allowed : 23.37 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.19), residues: 1932 helix: 1.22 (0.15), residues: 1135 sheet: -0.06 (0.43), residues: 136 loop : 0.33 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 686 TYR 0.021 0.001 TYR B 36 PHE 0.025 0.001 PHE C 168 TRP 0.015 0.002 TRP D 44 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (16386) covalent geometry : angle 0.60890 / 0.32 (22134) hydrogen bonds : bond 0.03873 / 2.46 ( 871) hydrogen bonds : angle 5.02291 / 3.63 ( 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 547 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 498 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7670 (mp0) REVERT: A 108 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8811 (p) REVERT: A 119 GLU cc_start: 0.8251 (mp0) cc_final: 0.7988 (mp0) REVERT: A 150 GLN cc_start: 0.9158 (tm-30) cc_final: 0.8808 (tm-30) REVERT: A 158 ASN cc_start: 0.8838 (m-40) cc_final: 0.8556 (m-40) REVERT: A 161 ARG cc_start: 0.7684 (ttm-80) cc_final: 0.7124 (ttm-80) REVERT: A 172 LEU cc_start: 0.9241 (mp) cc_final: 0.8911 (mp) REVERT: A 191 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7661 (mm-40) REVERT: A 232 ASN cc_start: 0.8666 (m110) cc_final: 0.8194 (m-40) REVERT: A 346 LEU cc_start: 0.9416 (mt) cc_final: 0.9184 (mp) REVERT: A 348 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7286 (ptm) REVERT: A 357 TYR cc_start: 0.8904 (m-10) cc_final: 0.7754 (m-10) REVERT: A 361 GLN cc_start: 0.8633 (tp40) cc_final: 0.8396 (tp40) REVERT: A 384 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7440 (pm20) REVERT: A 402 GLU cc_start: 0.7452 (tm-30) cc_final: 0.7170 (tm-30) REVERT: A 447 ASN cc_start: 0.8191 (m-40) cc_final: 0.7550 (m-40) REVERT: A 466 MET cc_start: 0.8663 (ptt) cc_final: 0.8367 (ptt) REVERT: A 505 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8056 (mt-10) REVERT: A 515 ASP cc_start: 0.8749 (m-30) cc_final: 0.8477 (m-30) REVERT: A 571 TYR cc_start: 0.9157 (t80) cc_final: 0.8732 (t80) REVERT: A 645 GLN cc_start: 0.8757 (tp-100) cc_final: 0.8501 (tp-100) REVERT: B 27 ASP cc_start: 0.8690 (p0) cc_final: 0.7928 (p0) REVERT: B 52 LYS cc_start: 0.9415 (tppt) cc_final: 0.9096 (tppt) REVERT: B 79 GLU cc_start: 0.8844 (tp30) cc_final: 0.8227 (tp30) REVERT: B 111 LYS cc_start: 0.9305 (mmtp) cc_final: 0.9066 (mmtt) REVERT: B 257 ASP cc_start: 0.8939 (m-30) cc_final: 0.8721 (m-30) REVERT: B 319 MET cc_start: 0.8814 (tpp) cc_final: 0.8555 (tpp) REVERT: B 338 ASN cc_start: 0.9311 (OUTLIER) cc_final: 0.8992 (t0) REVERT: B 384 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.7212 (pm20) REVERT: B 467 ASN cc_start: 0.9113 (t0) cc_final: 0.8555 (t0) REVERT: B 493 MET cc_start: 0.9406 (tmm) cc_final: 0.9188 (tmm) REVERT: B 522 TYR cc_start: 0.9125 (m-80) cc_final: 0.8769 (m-80) REVERT: B 526 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8308 (mm-30) REVERT: B 570 MET cc_start: 0.8577 (mmm) cc_final: 0.7977 (mtt) REVERT: B 586 TYR cc_start: 0.8520 (m-80) cc_final: 0.8133 (m-80) REVERT: B 599 GLU cc_start: 0.8739 (pm20) cc_final: 0.8304 (pm20) REVERT: B 602 GLU cc_start: 0.7719 (pt0) cc_final: 0.6146 (pt0) REVERT: B 610 LYS cc_start: 0.9365 (ptpt) cc_final: 0.8983 (ptmm) REVERT: C 56 MET cc_start: 0.5425 (ptt) cc_final: 0.4873 (ppp) REVERT: C 64 LEU cc_start: 0.8170 (tp) cc_final: 0.7907 (pp) REVERT: C 157 MET cc_start: 0.8667 (mtp) cc_final: 0.8203 (ttt) REVERT: C 164 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7896 (tp30) REVERT: C 169 TYR cc_start: 0.8798 (m-80) cc_final: 0.8540 (m-80) REVERT: C 178 PHE cc_start: 0.7851 (m-80) cc_final: 0.7440 (m-80) REVERT: C 201 HIS cc_start: 0.8681 (m90) cc_final: 0.8447 (m90) REVERT: C 238 ASN cc_start: 0.6978 (m-40) cc_final: 0.6680 (m110) REVERT: D 21 PHE cc_start: 0.7946 (m-80) cc_final: 0.7713 (m-80) outliers start: 49 outliers final: 29 residues processed: 524 average time/residue: 0.1126 time to fit residues: 90.7658 Evaluate side-chains 501 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 466 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 289 VAL 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 411 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 338 ASN 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 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 186 optimal weight: 30.0000 chunk 140 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 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 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN C 107 ASN D 201 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.155052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.110867 restraints weight = 31863.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114214 restraints weight = 15168.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.116413 restraints weight = 9194.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.117181 restraints weight = 6538.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.118299 restraints weight = 5430.530| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16386 Z= 0.132 Angle : 0.626 11.808 22134 Z= 0.325 Chirality : 0.044 0.403 2360 Planarity : 0.003 0.042 2818 Dihedral : 8.493 138.957 2292 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.97 % Allowed : 24.01 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.19), residues: 1932 helix: 1.17 (0.15), residues: 1125 sheet: -0.17 (0.50), residues: 106 loop : 0.35 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 225 TYR 0.033 0.001 TYR B 36 PHE 0.045 0.001 PHE C 92 TRP 0.026 0.002 TRP D 44 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (16386) covalent geometry : angle 0.62595 / 0.32 (22134) hydrogen bonds : bond 0.03933 / 2.49 ( 871) hydrogen bonds : angle 5.00493 / 3.61 ( 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 546 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 495 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8830 (p0) cc_final: 0.8577 (p0) REVERT: A 51 LEU cc_start: 0.9053 (mt) cc_final: 0.8811 (mt) REVERT: A 65 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7685 (mp0) REVERT: A 119 GLU cc_start: 0.8262 (mp0) cc_final: 0.7988 (mp0) REVERT: A 158 ASN cc_start: 0.8809 (m-40) cc_final: 0.8440 (m-40) REVERT: A 162 LYS cc_start: 0.8751 (ttpt) cc_final: 0.8539 (ttpt) REVERT: A 172 LEU cc_start: 0.9224 (mp) cc_final: 0.8897 (mp) REVERT: A 191 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7678 (mm-40) REVERT: A 232 ASN cc_start: 0.8581 (OUTLIER) cc_final: 0.8130 (m-40) REVERT: A 346 LEU cc_start: 0.9382 (mt) cc_final: 0.9147 (mp) REVERT: A 357 TYR cc_start: 0.8852 (m-10) cc_final: 0.7717 (m-10) REVERT: A 361 GLN cc_start: 0.8596 (tp40) cc_final: 0.8369 (tp40) REVERT: A 384 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7379 (pm20) REVERT: A 402 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7211 (tm-30) REVERT: A 447 ASN cc_start: 0.8163 (m-40) cc_final: 0.7474 (m-40) REVERT: A 466 MET cc_start: 0.8624 (ptt) cc_final: 0.8358 (ptt) REVERT: A 505 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8245 (mt-10) REVERT: A 515 ASP cc_start: 0.8746 (m-30) cc_final: 0.8505 (m-30) REVERT: A 571 TYR cc_start: 0.9141 (t80) cc_final: 0.8790 (t80) REVERT: A 576 LEU cc_start: 0.9019 (mt) cc_final: 0.8802 (mp) REVERT: A 628 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8575 (mt-10) REVERT: A 645 GLN cc_start: 0.8838 (tp-100) cc_final: 0.8538 (tp-100) REVERT: B 27 ASP cc_start: 0.8695 (p0) cc_final: 0.8242 (p0) REVERT: B 52 LYS cc_start: 0.9403 (tppt) cc_final: 0.9044 (tppt) REVERT: B 79 GLU cc_start: 0.8862 (tp30) cc_final: 0.8238 (tp30) REVERT: B 87 LYS cc_start: 0.8815 (tptm) cc_final: 0.8572 (tttt) REVERT: B 111 LYS cc_start: 0.9295 (mmtp) cc_final: 0.9057 (mmtt) REVERT: B 116 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8656 (mt-10) REVERT: B 147 GLN cc_start: 0.9273 (mt0) cc_final: 0.8837 (mm-40) REVERT: B 338 ASN cc_start: 0.9292 (OUTLIER) cc_final: 0.8948 (t0) REVERT: B 344 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8193 (mt-10) REVERT: B 384 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.7183 (pm20) REVERT: B 467 ASN cc_start: 0.9125 (t0) cc_final: 0.8576 (t0) REVERT: B 493 MET cc_start: 0.9372 (tmm) cc_final: 0.9158 (tmm) REVERT: B 522 TYR cc_start: 0.9104 (m-80) cc_final: 0.8756 (m-80) REVERT: B 526 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8303 (mm-30) REVERT: B 570 MET cc_start: 0.8575 (mmm) cc_final: 0.7864 (mtt) REVERT: B 586 TYR cc_start: 0.8517 (m-80) cc_final: 0.8095 (m-80) REVERT: B 599 GLU cc_start: 0.8758 (pm20) cc_final: 0.8240 (pm20) REVERT: B 602 GLU cc_start: 0.7715 (pt0) cc_final: 0.6126 (pt0) REVERT: B 604 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8769 (mmt-90) REVERT: B 610 LYS cc_start: 0.9386 (ptpt) cc_final: 0.9074 (ptmm) REVERT: B 612 TYR cc_start: 0.8783 (m-80) cc_final: 0.7585 (m-80) REVERT: C 56 MET cc_start: 0.5243 (ptt) cc_final: 0.4684 (ppp) REVERT: C 64 LEU cc_start: 0.8040 (tp) cc_final: 0.7753 (pp) REVERT: C 157 MET cc_start: 0.8639 (mtp) cc_final: 0.8176 (ttt) REVERT: C 164 GLU cc_start: 0.8505 (mm-30) cc_final: 0.7992 (tp30) REVERT: C 169 TYR cc_start: 0.8844 (m-80) cc_final: 0.8599 (m-80) REVERT: C 178 PHE cc_start: 0.7832 (m-80) cc_final: 0.7427 (m-80) REVERT: C 201 HIS cc_start: 0.8561 (m90) cc_final: 0.8326 (m90) REVERT: C 227 PHE cc_start: 0.6175 (m-10) cc_final: 0.5929 (m-80) REVERT: C 238 ASN cc_start: 0.7307 (m-40) cc_final: 0.6705 (m110) REVERT: D 93 MET cc_start: 0.7379 (mtp) cc_final: 0.7152 (mtp) REVERT: D 174 TYR cc_start: 0.5700 (OUTLIER) cc_final: 0.5101 (t80) REVERT: D 204 TYR cc_start: 0.7382 (OUTLIER) cc_final: 0.7101 (t80) outliers start: 51 outliers final: 33 residues processed: 514 average time/residue: 0.1140 time to fit residues: 89.3149 Evaluate side-chains 503 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 462 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 338 ASN 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 443 THR Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 61 optimal weight: 0.4980 chunk 19 optimal weight: 8.9990 chunk 134 optimal weight: 0.6980 chunk 153 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 158 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 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** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.152761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.107702 restraints weight = 32696.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.111218 restraints weight = 15849.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113495 restraints weight = 9597.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.114832 restraints weight = 6749.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.115613 restraints weight = 5497.866| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.5846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16386 Z= 0.190 Angle : 0.660 10.966 22134 Z= 0.345 Chirality : 0.045 0.381 2360 Planarity : 0.003 0.042 2818 Dihedral : 8.521 140.082 2292 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.91 % Allowed : 24.77 % 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: 1.09 (0.19), residues: 1932 helix: 1.15 (0.15), residues: 1135 sheet: -0.10 (0.44), residues: 132 loop : 0.36 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 235 TYR 0.024 0.002 TYR B 36 PHE 0.023 0.002 PHE C 320 TRP 0.031 0.002 TRP D 44 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (16386) covalent geometry : angle 0.65982 / 0.35 (22134) hydrogen bonds : bond 0.04049 / 2.58 ( 871) hydrogen bonds : angle 5.10405 / 3.67 ( 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 510 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 460 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8265 (mp0) cc_final: 0.7994 (mp0) REVERT: A 158 ASN cc_start: 0.8686 (m-40) cc_final: 0.8356 (m-40) REVERT: A 162 LYS cc_start: 0.8709 (ttpt) cc_final: 0.8141 (ttpt) REVERT: A 172 LEU cc_start: 0.9276 (mp) cc_final: 0.8936 (mp) REVERT: A 232 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8429 (m-40) REVERT: A 277 THR cc_start: 0.9177 (p) cc_final: 0.8846 (t) REVERT: A 346 LEU cc_start: 0.9420 (mt) cc_final: 0.9167 (mp) REVERT: A 357 TYR cc_start: 0.8967 (m-10) cc_final: 0.7907 (m-10) REVERT: A 361 GLN cc_start: 0.8639 (tp40) cc_final: 0.8413 (tp40) REVERT: A 384 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7245 (pm20) REVERT: A 402 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7261 (tm-30) REVERT: A 505 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8151 (mt-10) REVERT: A 515 ASP cc_start: 0.8793 (m-30) cc_final: 0.8562 (m-30) REVERT: A 571 TYR cc_start: 0.9166 (t80) cc_final: 0.8632 (t80) REVERT: A 645 GLN cc_start: 0.8978 (tp-100) cc_final: 0.8613 (tp-100) REVERT: B 52 LYS cc_start: 0.9391 (tppt) cc_final: 0.9024 (tppt) REVERT: B 79 GLU cc_start: 0.8868 (tp30) cc_final: 0.8237 (tp30) REVERT: B 116 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8683 (mt-10) REVERT: B 338 ASN cc_start: 0.9373 (OUTLIER) cc_final: 0.9047 (t0) REVERT: B 344 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8219 (mt-10) REVERT: B 384 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.7252 (pm20) REVERT: B 447 ASN cc_start: 0.8267 (m-40) cc_final: 0.8035 (m-40) REVERT: B 467 ASN cc_start: 0.9240 (t0) cc_final: 0.8639 (t0) REVERT: B 493 MET cc_start: 0.9407 (tmm) cc_final: 0.9118 (tmm) REVERT: B 522 TYR cc_start: 0.9116 (m-80) cc_final: 0.8721 (m-80) REVERT: B 570 MET cc_start: 0.8621 (mmm) cc_final: 0.7635 (mtt) REVERT: B 586 TYR cc_start: 0.8550 (m-80) cc_final: 0.8183 (m-80) REVERT: B 599 GLU cc_start: 0.8768 (pm20) cc_final: 0.8282 (pm20) REVERT: B 602 GLU cc_start: 0.7676 (pt0) cc_final: 0.6239 (pt0) REVERT: B 604 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8734 (mmt-90) REVERT: B 610 LYS cc_start: 0.9398 (ptpt) cc_final: 0.9022 (ptmm) REVERT: C 56 MET cc_start: 0.5429 (ptt) cc_final: 0.4825 (ppp) REVERT: C 157 MET cc_start: 0.8658 (mtp) cc_final: 0.8239 (ttt) REVERT: C 164 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8033 (tp30) REVERT: C 169 TYR cc_start: 0.8771 (m-80) cc_final: 0.8546 (m-80) REVERT: C 178 PHE cc_start: 0.7873 (m-80) cc_final: 0.7471 (m-80) REVERT: C 201 HIS cc_start: 0.8531 (m170) cc_final: 0.8310 (m90) REVERT: C 227 PHE cc_start: 0.6024 (m-10) cc_final: 0.5812 (m-80) REVERT: D 157 MET cc_start: -0.0454 (ppp) cc_final: -0.0893 (ppp) REVERT: D 185 MET cc_start: -0.0968 (mmm) cc_final: -0.1226 (mmm) outliers start: 50 outliers final: 35 residues processed: 484 average time/residue: 0.1077 time to fit residues: 80.3429 Evaluate side-chains 487 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 447 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 338 ASN 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 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 8.9990 chunk 133 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 0.4980 chunk 88 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN C 107 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.155120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.111266 restraints weight = 32275.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.114656 restraints weight = 15585.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.116811 restraints weight = 9371.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.118165 restraints weight = 6720.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.118967 restraints weight = 5447.670| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.6058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16386 Z= 0.139 Angle : 0.659 11.444 22134 Z= 0.341 Chirality : 0.044 0.337 2360 Planarity : 0.003 0.041 2818 Dihedral : 8.414 139.088 2292 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.68 % Allowed : 25.23 % Favored : 72.09 % 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: 0.95 (0.19), residues: 1932 helix: 1.10 (0.15), residues: 1143 sheet: -0.42 (0.50), residues: 106 loop : 0.20 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 235 TYR 0.019 0.001 TYR B 683 PHE 0.042 0.002 PHE C 92 TRP 0.030 0.002 TRP D 44 HIS 0.009 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (16386) covalent geometry : angle 0.65920 / 0.34 (22134) hydrogen bonds : bond 0.03947 / 2.49 ( 871) hydrogen bonds : angle 5.08145 / 3.65 ( 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 515 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 469 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8734 (p0) cc_final: 0.8493 (p0) REVERT: A 119 GLU cc_start: 0.8229 (mp0) cc_final: 0.7904 (mp0) REVERT: A 150 GLN cc_start: 0.9174 (tm-30) cc_final: 0.8855 (tm-30) REVERT: A 158 ASN cc_start: 0.8584 (m-40) cc_final: 0.8337 (m-40) REVERT: A 172 LEU cc_start: 0.9220 (mp) cc_final: 0.8880 (mp) REVERT: A 232 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8215 (m-40) REVERT: A 277 THR cc_start: 0.9192 (p) cc_final: 0.8813 (t) REVERT: A 357 TYR cc_start: 0.8883 (m-10) cc_final: 0.7667 (m-10) REVERT: A 361 GLN cc_start: 0.8527 (tp40) cc_final: 0.8284 (tp40) REVERT: A 384 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7266 (pm20) REVERT: A 456 LYS cc_start: 0.8962 (mtmm) cc_final: 0.8681 (mtmm) REVERT: A 505 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8213 (mt-10) REVERT: A 515 ASP cc_start: 0.8755 (m-30) cc_final: 0.8506 (m-30) REVERT: A 570 MET cc_start: 0.8827 (mtp) cc_final: 0.8566 (mtp) REVERT: A 571 TYR cc_start: 0.9114 (t80) cc_final: 0.8727 (t80) REVERT: A 640 MET cc_start: 0.9094 (tpp) cc_final: 0.8664 (tpp) REVERT: A 645 GLN cc_start: 0.8911 (tp-100) cc_final: 0.8566 (tp-100) REVERT: B 27 ASP cc_start: 0.8675 (p0) cc_final: 0.8285 (p0) REVERT: B 52 LYS cc_start: 0.9412 (tppt) cc_final: 0.9052 (tppt) REVERT: B 79 GLU cc_start: 0.8820 (tp30) cc_final: 0.8294 (tp30) REVERT: B 116 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8644 (mt-10) REVERT: B 338 ASN cc_start: 0.9349 (OUTLIER) cc_final: 0.9007 (t0) REVERT: B 344 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8145 (mt-10) REVERT: B 384 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.7210 (pm20) REVERT: B 467 ASN cc_start: 0.9148 (t0) cc_final: 0.8592 (t0) REVERT: B 522 TYR cc_start: 0.9078 (m-80) cc_final: 0.8717 (m-80) REVERT: B 570 MET cc_start: 0.8720 (mmm) cc_final: 0.7680 (mtt) REVERT: B 586 TYR cc_start: 0.8499 (m-80) cc_final: 0.8099 (m-80) REVERT: B 599 GLU cc_start: 0.8737 (pm20) cc_final: 0.8244 (pm20) REVERT: B 602 GLU cc_start: 0.7679 (pt0) cc_final: 0.6010 (pt0) REVERT: B 604 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8729 (mmt-90) REVERT: B 610 LYS cc_start: 0.9403 (ptpt) cc_final: 0.9078 (ptmm) REVERT: B 612 TYR cc_start: 0.8708 (m-80) cc_final: 0.7363 (m-80) REVERT: C 56 MET cc_start: 0.5392 (ptt) cc_final: 0.4870 (ppp) REVERT: C 157 MET cc_start: 0.8663 (mtp) cc_final: 0.8133 (ttt) REVERT: C 164 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8012 (tp30) REVERT: C 169 TYR cc_start: 0.8881 (m-80) cc_final: 0.8659 (m-80) REVERT: C 227 PHE cc_start: 0.6026 (m-10) cc_final: 0.5805 (m-80) REVERT: D 74 MET cc_start: 0.1305 (ppp) cc_final: 0.1074 (ppp) REVERT: D 93 MET cc_start: 0.7402 (mtp) cc_final: 0.7031 (mtp) REVERT: D 157 MET cc_start: -0.0947 (ppp) cc_final: -0.1354 (ppp) REVERT: D 174 TYR cc_start: 0.5588 (OUTLIER) cc_final: 0.4910 (t80) REVERT: D 185 MET cc_start: -0.1347 (mmm) cc_final: -0.1624 (mmm) outliers start: 46 outliers final: 33 residues processed: 488 average time/residue: 0.1160 time to fit residues: 86.4030 Evaluate side-chains 485 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 446 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 338 ASN 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 443 THR Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 189 optimal weight: 0.0270 chunk 181 optimal weight: 20.0000 chunk 165 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN D 25 ASN D 28 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.156262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.112454 restraints weight = 32157.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.115863 restraints weight = 15607.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.118113 restraints weight = 9288.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.119352 restraints weight = 6654.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.120158 restraints weight = 5411.176| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.6206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16386 Z= 0.137 Angle : 0.680 11.528 22134 Z= 0.350 Chirality : 0.044 0.312 2360 Planarity : 0.003 0.041 2818 Dihedral : 8.400 139.452 2292 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.45 % Allowed : 25.41 % Favored : 72.14 % 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: 0.94 (0.19), residues: 1932 helix: 1.08 (0.15), residues: 1143 sheet: -0.39 (0.44), residues: 132 loop : 0.23 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 686 TYR 0.035 0.001 TYR C 55 PHE 0.023 0.001 PHE C 320 TRP 0.030 0.002 TRP D 44 HIS 0.015 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (16386) covalent geometry : angle 0.67996 / 0.35 (22134) hydrogen bonds : bond 0.03955 / 2.51 ( 871) hydrogen bonds : angle 5.11367 / 3.69 ( 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 506 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 464 time to evaluate : 0.595 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 27 ASP cc_start: 0.8740 (p0) cc_final: 0.8501 (p0) REVERT: A 119 GLU cc_start: 0.8258 (mp0) cc_final: 0.7939 (mp0) REVERT: A 150 GLN cc_start: 0.9146 (tm-30) cc_final: 0.8822 (tm-30) REVERT: A 158 ASN cc_start: 0.8561 (m-40) cc_final: 0.8356 (m-40) REVERT: A 172 LEU cc_start: 0.9178 (mp) cc_final: 0.8842 (mp) REVERT: A 232 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.8200 (m-40) REVERT: A 357 TYR cc_start: 0.8737 (m-10) cc_final: 0.7761 (m-10) REVERT: A 384 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7391 (pm20) REVERT: A 456 LYS cc_start: 0.8986 (mtmm) cc_final: 0.8677 (mtmm) REVERT: A 493 MET cc_start: 0.8615 (tmm) cc_final: 0.8324 (tmm) REVERT: A 505 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8290 (mt-10) REVERT: A 515 ASP cc_start: 0.8736 (m-30) cc_final: 0.8504 (m-30) REVERT: A 571 TYR cc_start: 0.9113 (t80) cc_final: 0.8833 (t80) REVERT: A 640 MET cc_start: 0.9051 (tpp) cc_final: 0.8505 (tpp) REVERT: B 27 ASP cc_start: 0.8736 (p0) cc_final: 0.8297 (p0) REVERT: B 52 LYS cc_start: 0.9418 (tppt) cc_final: 0.9128 (tppt) REVERT: B 79 GLU cc_start: 0.8852 (tp30) cc_final: 0.8320 (tp30) REVERT: B 111 LYS cc_start: 0.9209 (mmtp) cc_final: 0.8983 (mmtt) REVERT: B 116 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8652 (mt-10) REVERT: B 338 ASN cc_start: 0.9342 (OUTLIER) cc_final: 0.9013 (t0) REVERT: B 344 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8167 (mt-10) REVERT: B 384 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.7112 (pm20) REVERT: B 467 ASN cc_start: 0.9104 (t0) cc_final: 0.8604 (t0) REVERT: B 522 TYR cc_start: 0.9051 (m-80) cc_final: 0.8690 (m-80) REVERT: B 570 MET cc_start: 0.8732 (mmm) cc_final: 0.7664 (mtt) REVERT: B 586 TYR cc_start: 0.8477 (m-80) cc_final: 0.8025 (m-10) REVERT: B 599 GLU cc_start: 0.8729 (pm20) cc_final: 0.8283 (pm20) REVERT: B 610 LYS cc_start: 0.9418 (ptpt) cc_final: 0.9099 (ptmm) REVERT: B 612 TYR cc_start: 0.8720 (m-80) cc_final: 0.7435 (m-80) REVERT: B 632 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7747 (mtm) REVERT: C 56 MET cc_start: 0.5402 (ptt) cc_final: 0.4877 (ppp) REVERT: C 157 MET cc_start: 0.8698 (mtp) cc_final: 0.8132 (ttt) REVERT: C 164 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8399 (tp30) REVERT: C 178 PHE cc_start: 0.7922 (m-80) cc_final: 0.7522 (m-80) REVERT: C 227 PHE cc_start: 0.6021 (m-10) cc_final: 0.5794 (m-80) REVERT: C 248 ASP cc_start: 0.8749 (m-30) cc_final: 0.8505 (m-30) REVERT: D 74 MET cc_start: 0.1247 (ppp) cc_final: 0.0967 (ppp) REVERT: D 93 MET cc_start: 0.7352 (mtp) cc_final: 0.6870 (mtp) REVERT: D 157 MET cc_start: -0.1142 (ppp) cc_final: -0.1528 (ppp) REVERT: D 174 TYR cc_start: 0.5630 (OUTLIER) cc_final: 0.4960 (t80) REVERT: D 185 MET cc_start: -0.1630 (mmm) cc_final: -0.1895 (mmm) outliers start: 42 outliers final: 31 residues processed: 481 average time/residue: 0.1131 time to fit residues: 83.4862 Evaluate side-chains 487 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 450 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 148 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 191 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN D 91 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.153990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.111032 restraints weight = 32063.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.114459 restraints weight = 15424.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.116628 restraints weight = 9299.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.117998 restraints weight = 6596.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.118845 restraints weight = 5298.182| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.6327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 16386 Z= 0.166 Angle : 0.702 15.589 22134 Z= 0.362 Chirality : 0.045 0.327 2360 Planarity : 0.003 0.038 2818 Dihedral : 8.414 140.255 2290 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.56 % Allowed : 25.82 % Favored : 71.62 % 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: 0.92 (0.19), residues: 1932 helix: 1.06 (0.15), residues: 1138 sheet: -0.43 (0.43), residues: 132 loop : 0.27 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 686 TYR 0.026 0.001 TYR C 55 PHE 0.025 0.002 PHE C 320 TRP 0.039 0.003 TRP D 44 HIS 0.016 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (16386) covalent geometry : angle 0.70247 / 0.36 (22134) hydrogen bonds : bond 0.04001 / 2.54 ( 871) hydrogen bonds : angle 5.15706 / 3.72 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3098.97 seconds wall clock time: 54 minutes 38.47 seconds (3278.47 seconds total)