Starting phenix.real_space_refine on Thu Aug 6 15:13:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz2_45051/08_2026/9bz2_45051_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz2_45051/08_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_45051/08_2026/9bz2_45051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz2_45051/08_2026/9bz2_45051.map" model { file = "/net/cci-nas-00/data/ceres_data/9bz2_45051/08_2026/9bz2_45051_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz2_45051/08_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.30, per 1000 atoms: 0.21 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: 1.18 Conformation dependent library (CDL) restraints added in 553.1 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: 2.50 Time building geometry restraints manager: 1.62 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 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.991 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.013 3.040 ... (remaining 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.250 Find NCS groups from input model: 0.310 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.100 ------------------------------------------------------------------------------- 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 : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ILE cc_start: 0.9185 (mt) cc_final: 0.8940 (mt) REVERT: A 127 LEU cc_start: 0.9149 (mt) cc_final: 0.8851 (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: 0.8451 (tp) REVERT: A 220 THR cc_start: 0.8806 (m) cc_final: 0.8515 (p) REVERT: A 227 MET cc_start: 0.7829 (mtp) cc_final: 0.7584 (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: 0.7322 (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: 0.7776 (mtp) REVERT: B 51 LEU cc_start: 0.8213 (tp) cc_final: 0.7883 (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: 0.8932 (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: 0.8157 (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: 0.7678 (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: 0.8861 (p) REVERT: C 89 VAL cc_start: 0.5232 (t) cc_final: 0.3665 (t) REVERT: C 229 ILE cc_start: 0.5031 (mt) cc_final: 0.4262 (mm) REVERT: D 42 LEU cc_start: 0.1877 (mt) cc_final: 0.1451 (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: 0.3395 (pt) outliers start: 24 outliers final: 5 residues processed: 822 average time/residue: 0.1337 time to fit residues: 163.1292 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 : 0.587 ------------------------------------------------------------------------------- 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 438 HIS 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** ** B 668 ASN ** 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 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.155996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.107687 restraints weight = 31178.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.111266 restraints weight = 15091.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.113521 restraints weight = 9205.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.114958 restraints weight = 6653.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.115742 restraints weight = 5375.484| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.111 | | 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) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 12 (20 function evaluations) r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16386 Z= 0.239 Angle : 0.676 7.065 22134 Z= 0.358 Chirality : 0.045 0.332 2360 Planarity : 0.004 0.041 2818 Dihedral : 9.949 133.359 2302 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.31 % Allowed : 18.07 % Favored : 77.62 % 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: 1.42 (0.19), residues: 1932 helix: 1.33 (0.15), residues: 1137 sheet: -0.24 (0.46), residues: 114 loop : 0.71 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 225 TYR 0.033 0.002 TYR D 174 PHE 0.027 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 0.00523 / 0.24 (16386) covalent geometry : angle 0.67553 / 0.36 (22134) hydrogen bonds : bond 0.04747 / 3.05 ( 871) hydrogen bonds : angle 5.10145 / 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 651 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 577 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8874 (p0) cc_final: 0.8527 (p0) REVERT: A 65 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7258 (mp0) REVERT: A 117 ARG cc_start: 0.8365 (mtp85) cc_final: 0.8108 (mtp85) REVERT: A 119 GLU cc_start: 0.8499 (mp0) cc_final: 0.8201 (mp0) REVERT: A 138 LYS cc_start: 0.9074 (mtpt) cc_final: 0.8812 (mtpp) REVERT: A 172 LEU cc_start: 0.9315 (mp) cc_final: 0.8992 (mp) REVERT: A 191 GLN cc_start: 0.8353 (mm-40) cc_final: 0.7987 (mm-40) REVERT: A 276 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8520 (mmtm) REVERT: A 317 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7908 (ptp) REVERT: A 357 TYR cc_start: 0.8990 (m-10) cc_final: 0.8048 (m-10) REVERT: A 362 ASP cc_start: 0.8429 (m-30) cc_final: 0.8126 (m-30) REVERT: A 384 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.7570 (pm20) REVERT: A 402 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7280 (tm-30) REVERT: A 415 ASN cc_start: 0.9018 (t0) cc_final: 0.8751 (t0) REVERT: A 447 ASN cc_start: 0.8804 (m-40) cc_final: 0.8388 (m-40) REVERT: A 456 LYS cc_start: 0.8930 (mtmm) cc_final: 0.8537 (mtmm) REVERT: A 493 MET cc_start: 0.8933 (tmm) cc_final: 0.8527 (tmm) REVERT: A 548 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8252 (mm-30) REVERT: A 588 GLN cc_start: 0.9101 (mm-40) cc_final: 0.8718 (mm-40) REVERT: A 602 GLU cc_start: 0.7695 (pt0) cc_final: 0.7136 (pt0) REVERT: A 663 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8116 (t) REVERT: B 41 ILE cc_start: 0.9283 (mm) cc_final: 0.9072 (mm) REVERT: B 52 LYS cc_start: 0.9394 (tppt) cc_final: 0.9059 (tppt) REVERT: B 71 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9324 (mt) REVERT: B 118 TYR cc_start: 0.9375 (t80) cc_final: 0.9150 (t80) REVERT: B 214 LYS cc_start: 0.8347 (ttmm) cc_final: 0.7951 (mmtm) REVERT: B 362 ASP cc_start: 0.8069 (m-30) cc_final: 0.7779 (m-30) REVERT: B 425 ILE cc_start: 0.9491 (mt) cc_final: 0.9214 (mt) REVERT: B 493 MET cc_start: 0.9504 (tmm) cc_final: 0.9300 (tmm) REVERT: B 602 GLU cc_start: 0.8016 (pt0) cc_final: 0.7596 (pt0) REVERT: B 604 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8469 (mmt-90) REVERT: B 610 LYS cc_start: 0.9073 (ptpt) cc_final: 0.8687 (ptmm) REVERT: B 612 TYR cc_start: 0.9000 (m-80) cc_final: 0.8096 (m-80) REVERT: B 632 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8166 (mtm) REVERT: B 648 ILE cc_start: 0.9113 (mm) cc_final: 0.8845 (mt) REVERT: B 650 GLN cc_start: 0.8431 (mt0) cc_final: 0.8122 (mt0) REVERT: B 656 LEU cc_start: 0.9564 (mt) cc_final: 0.9353 (mt) REVERT: B 667 LEU cc_start: 0.8949 (tp) cc_final: 0.8458 (tp) REVERT: C 56 MET cc_start: 0.4818 (ptt) cc_final: 0.4239 (ppp) REVERT: C 90 LEU cc_start: 0.7572 (mt) cc_final: 0.7007 (mt) REVERT: C 178 PHE cc_start: 0.7599 (m-80) cc_final: 0.7373 (m-80) REVERT: C 263 ASN cc_start: 0.6607 (p0) cc_final: 0.6260 (p0) REVERT: C 278 GLU cc_start: 0.8829 (tt0) cc_final: 0.8620 (tp30) outliers start: 74 outliers final: 30 residues processed: 617 average time/residue: 0.1217 time to fit residues: 113.8702 Evaluate side-chains 516 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 478 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 71 LEU 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 232 ASN Chi-restraints excluded: chain B residue 314 MET 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 604 ARG Chi-restraints excluded: chain B residue 632 MET 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: 5.9990 chunk 28 optimal weight: 0.8980 chunk 182 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN A 410 ASN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.153137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.106349 restraints weight = 32169.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.109681 restraints weight = 15385.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.111924 restraints weight = 9276.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.113285 restraints weight = 6648.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.114216 restraints weight = 5398.807| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3314 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (11 function evaluations) r_final: 0.3315 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16386 Z= 0.179 Angle : 0.625 11.545 22134 Z= 0.327 Chirality : 0.044 0.300 2360 Planarity : 0.003 0.040 2818 Dihedral : 9.245 135.200 2296 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.79 % Allowed : 22.20 % Favored : 74.01 % 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: 1.41 (0.19), residues: 1932 helix: 1.41 (0.15), residues: 1125 sheet: -0.12 (0.48), residues: 106 loop : 0.53 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 164 TYR 0.040 0.002 TYR D 174 PHE 0.026 0.002 PHE A 492 TRP 0.014 0.002 TRP D 124 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (16386) covalent geometry : angle 0.62456 / 0.33 (22134) hydrogen bonds : bond 0.04228 / 2.67 ( 871) hydrogen bonds : angle 4.98692 / 3.60 ( 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 596 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 531 time to evaluate : 0.610 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: 0.8940 (p0) cc_final: 0.8690 (p0) REVERT: A 64 TYR cc_start: 0.8461 (m-10) cc_final: 0.7409 (m-10) REVERT: A 65 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7279 (mp0) REVERT: A 117 ARG cc_start: 0.8450 (mtp85) cc_final: 0.8195 (mtp85) REVERT: A 119 GLU cc_start: 0.8465 (mp0) cc_final: 0.8114 (mp0) REVERT: A 138 LYS cc_start: 0.9037 (mtpt) cc_final: 0.8832 (mtpp) REVERT: A 150 GLN cc_start: 0.9003 (tm-30) cc_final: 0.8793 (tm-30) REVERT: A 161 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7354 (ttm-80) REVERT: A 172 LEU cc_start: 0.9285 (mp) cc_final: 0.8971 (mp) REVERT: A 276 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8485 (mmtt) REVERT: A 317 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7938 (ptp) REVERT: A 348 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.7181 (ptm) REVERT: A 357 TYR cc_start: 0.8998 (m-10) cc_final: 0.7984 (m-10) REVERT: A 361 GLN cc_start: 0.8724 (tp40) cc_final: 0.8504 (tp40) REVERT: A 362 ASP cc_start: 0.8377 (m-30) cc_final: 0.7952 (m-30) REVERT: A 384 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7430 (pm20) REVERT: A 402 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7270 (tm-30) REVERT: A 447 ASN cc_start: 0.8751 (m-40) cc_final: 0.8181 (m-40) REVERT: A 456 LYS cc_start: 0.8940 (mtmm) cc_final: 0.8691 (mtmm) REVERT: A 493 MET cc_start: 0.8911 (tmm) cc_final: 0.8319 (tmm) REVERT: A 505 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8096 (mt-10) REVERT: A 515 ASP cc_start: 0.8786 (m-30) cc_final: 0.8571 (m-30) REVERT: A 548 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8262 (mm-30) REVERT: A 588 GLN cc_start: 0.9020 (mm-40) cc_final: 0.8677 (mm-40) REVERT: A 615 MET cc_start: 0.9271 (mmt) cc_final: 0.8991 (mmm) REVERT: A 639 ASP cc_start: 0.8848 (m-30) cc_final: 0.8620 (m-30) REVERT: A 663 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8318 (t) REVERT: B 52 LYS cc_start: 0.9399 (tppt) cc_final: 0.9075 (tppt) REVERT: B 118 TYR cc_start: 0.9301 (t80) cc_final: 0.9090 (t80) REVERT: B 209 LYS cc_start: 0.8249 (ttmm) cc_final: 0.7832 (ttmm) REVERT: B 214 LYS cc_start: 0.8240 (ttmm) cc_final: 0.7888 (mmtm) REVERT: B 335 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7167 (mt-10) REVERT: B 352 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8256 (mt-10) REVERT: B 362 ASP cc_start: 0.7780 (m-30) cc_final: 0.7528 (m-30) REVERT: B 425 ILE cc_start: 0.9480 (mt) cc_final: 0.9267 (mt) REVERT: B 458 MET cc_start: 0.9043 (mmm) cc_final: 0.8809 (mmm) REVERT: B 467 ASN cc_start: 0.9198 (t0) cc_final: 0.8287 (t0) REVERT: B 493 MET cc_start: 0.9435 (tmm) cc_final: 0.9223 (tmm) REVERT: B 494 MET cc_start: 0.9156 (mtp) cc_final: 0.8910 (mtp) REVERT: B 599 GLU cc_start: 0.8776 (pm20) cc_final: 0.8244 (pm20) REVERT: B 602 GLU cc_start: 0.7678 (pt0) cc_final: 0.7101 (pt0) REVERT: B 604 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8699 (mmt-90) REVERT: B 610 LYS cc_start: 0.9173 (ptpt) cc_final: 0.8856 (ptmm) REVERT: B 612 TYR cc_start: 0.8847 (m-80) cc_final: 0.7951 (m-80) REVERT: C 56 MET cc_start: 0.4919 (ptt) cc_final: 0.4286 (ppp) REVERT: C 133 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6678 (tptm) REVERT: C 157 MET cc_start: 0.8546 (mtp) cc_final: 0.8084 (ttt) REVERT: C 169 TYR cc_start: 0.8625 (m-80) cc_final: 0.8352 (m-80) REVERT: C 178 PHE cc_start: 0.7602 (m-80) cc_final: 0.7392 (m-80) REVERT: C 278 GLU cc_start: 0.8884 (tt0) cc_final: 0.8638 (tp30) outliers start: 65 outliers final: 28 residues processed: 564 average time/residue: 0.1156 time to fit residues: 99.2695 Evaluate side-chains 511 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 475 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 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 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 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 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 598 MET Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 661 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 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 207 LEU 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: 1.9990 chunk 157 optimal weight: 20.0000 chunk 168 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 185 optimal weight: 20.0000 chunk 191 optimal weight: 20.0000 chunk 159 optimal weight: 20.0000 chunk 182 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 232 ASN B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 146 GLN C 233 ASN D 25 ASN D 91 ASN D 128 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.144701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.100239 restraints weight = 32677.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.103464 restraints weight = 15828.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.105572 restraints weight = 9573.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.106798 restraints weight = 6941.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107590 restraints weight = 5643.901| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 16386 Z= 0.370 Angle : 0.750 10.681 22134 Z= 0.396 Chirality : 0.048 0.307 2360 Planarity : 0.004 0.042 2818 Dihedral : 9.364 138.969 2293 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.95 % Allowed : 21.79 % Favored : 73.25 % 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: 1.04 (0.15), residues: 1135 sheet: -0.62 (0.47), residues: 118 loop : 0.39 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 163 TYR 0.030 0.002 TYR D 174 PHE 0.034 0.002 PHE A 492 TRP 0.028 0.003 TRP D 124 HIS 0.010 0.002 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00805 / 0.37 (16386) covalent geometry : angle 0.74989 / 0.40 (22134) hydrogen bonds : bond 0.04652 / 2.95 ( 871) hydrogen bonds : angle 5.28837 / 3.83 ( 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 582 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 497 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.8322 (m-10) cc_final: 0.8088 (m-10) REVERT: A 65 GLU cc_start: 0.8500 (mm-30) cc_final: 0.7631 (mp0) REVERT: A 119 GLU cc_start: 0.8421 (mp0) cc_final: 0.8120 (mp0) REVERT: A 150 GLN cc_start: 0.9113 (tm-30) cc_final: 0.8679 (tm-30) REVERT: A 172 LEU cc_start: 0.9370 (mp) cc_final: 0.9126 (mp) REVERT: A 188 ILE cc_start: 0.9517 (mt) cc_final: 0.9243 (mm) REVERT: A 317 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7818 (ptp) REVERT: A 348 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7533 (ptt) REVERT: A 357 TYR cc_start: 0.9064 (m-10) cc_final: 0.8269 (m-10) REVERT: A 362 ASP cc_start: 0.8546 (m-30) cc_final: 0.8078 (m-30) REVERT: A 384 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7467 (pm20) REVERT: A 453 ARG cc_start: 0.9285 (OUTLIER) cc_final: 0.8503 (ttt-90) REVERT: A 456 LYS cc_start: 0.8925 (mtmm) cc_final: 0.8698 (mtmm) REVERT: A 493 MET cc_start: 0.8954 (tmm) cc_final: 0.8554 (tmm) REVERT: A 515 ASP cc_start: 0.8854 (m-30) cc_final: 0.8620 (m-30) REVERT: A 588 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8705 (mm-40) REVERT: A 639 ASP cc_start: 0.8964 (m-30) cc_final: 0.8635 (m-30) REVERT: A 663 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8560 (t) REVERT: B 52 LYS cc_start: 0.9351 (tppt) cc_final: 0.9056 (tppt) REVERT: B 79 GLU cc_start: 0.8954 (tp30) cc_final: 0.8302 (tp30) REVERT: B 232 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8779 (m110) REVERT: B 384 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.7454 (pm20) REVERT: B 420 MET cc_start: 0.9402 (mmm) cc_final: 0.9199 (mmm) REVERT: B 493 MET cc_start: 0.9472 (tmm) cc_final: 0.9217 (tmm) REVERT: B 599 GLU cc_start: 0.8797 (pm20) cc_final: 0.8426 (pm20) REVERT: B 602 GLU cc_start: 0.8014 (pt0) cc_final: 0.7560 (pt0) REVERT: B 604 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8639 (mmt-90) REVERT: B 610 LYS cc_start: 0.9224 (ptpt) cc_final: 0.8812 (ptmm) REVERT: C 56 MET cc_start: 0.5493 (ptt) cc_final: 0.5088 (ppp) REVERT: C 95 MET cc_start: 0.8465 (ppp) cc_final: 0.8227 (ppp) REVERT: C 122 PHE cc_start: 0.7160 (m-80) cc_final: 0.6458 (m-80) REVERT: C 157 MET cc_start: 0.8663 (mtp) cc_final: 0.8169 (ttt) REVERT: C 169 TYR cc_start: 0.8622 (m-80) cc_final: 0.8394 (m-80) REVERT: C 178 PHE cc_start: 0.7664 (m-80) cc_final: 0.7424 (m-80) REVERT: C 238 ASN cc_start: 0.7146 (m-40) cc_final: 0.6353 (m110) REVERT: D 207 LEU cc_start: 0.2571 (OUTLIER) cc_final: 0.2330 (mp) outliers start: 85 outliers final: 49 residues processed: 539 average time/residue: 0.1179 time to fit residues: 95.9691 Evaluate side-chains 492 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 434 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE 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 267 ILE 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 443 THR Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR 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 155 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 260 ASP 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 31 LEU Chi-restraints excluded: chain C residue 41 LEU 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 125 VAL 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 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 207 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** 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 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 270 ASN D 128 ASN D 233 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.150579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.105051 restraints weight = 32233.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108579 restraints weight = 15409.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.110834 restraints weight = 9335.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.112072 restraints weight = 6694.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.112946 restraints weight = 5457.761| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3298 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16386 Z= 0.172 Angle : 0.627 10.171 22134 Z= 0.333 Chirality : 0.044 0.304 2360 Planarity : 0.003 0.044 2818 Dihedral : 8.982 136.332 2293 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.90 % Allowed : 23.25 % Favored : 72.84 % 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: 1.11 (0.19), residues: 1932 helix: 1.20 (0.15), residues: 1125 sheet: -0.61 (0.48), residues: 118 loop : 0.41 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 261 TYR 0.027 0.002 TYR A 118 PHE 0.026 0.002 PHE C 168 TRP 0.029 0.002 TRP D 124 HIS 0.013 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (16386) covalent geometry : angle 0.62696 / 0.33 (22134) hydrogen bonds : bond 0.04115 / 2.63 ( 871) hydrogen bonds : angle 5.09224 / 3.70 ( 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 568 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 501 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.8096 (m-10) cc_final: 0.7788 (m-10) REVERT: A 65 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7483 (mp0) REVERT: A 109 ASN cc_start: 0.9368 (m-40) cc_final: 0.9157 (m-40) REVERT: A 119 GLU cc_start: 0.8300 (mp0) cc_final: 0.8002 (mp0) REVERT: A 150 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8819 (tm-30) REVERT: A 158 ASN cc_start: 0.8882 (m-40) cc_final: 0.8601 (m-40) REVERT: A 172 LEU cc_start: 0.9338 (mp) cc_final: 0.9028 (mp) REVERT: A 317 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7661 (ptp) REVERT: A 344 GLU cc_start: 0.8239 (mp0) cc_final: 0.8020 (mp0) REVERT: A 348 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.7434 (ptt) REVERT: A 357 TYR cc_start: 0.9028 (m-10) cc_final: 0.8083 (m-10) REVERT: A 362 ASP cc_start: 0.8405 (m-30) cc_final: 0.8017 (m-30) REVERT: A 384 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7361 (pm20) REVERT: A 415 ASN cc_start: 0.8843 (t0) cc_final: 0.8634 (t0) REVERT: A 453 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.8392 (ttt-90) REVERT: A 456 LYS cc_start: 0.8966 (mtmm) cc_final: 0.8710 (mtmm) REVERT: A 505 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8141 (mt-10) REVERT: A 515 ASP cc_start: 0.8804 (m-30) cc_final: 0.8545 (m-30) REVERT: A 571 TYR cc_start: 0.9153 (t80) cc_final: 0.8619 (t80) REVERT: A 588 GLN cc_start: 0.9082 (mm-40) cc_final: 0.8836 (mm-40) REVERT: A 639 ASP cc_start: 0.8873 (m-30) cc_final: 0.8659 (m-30) REVERT: B 27 ASP cc_start: 0.8882 (p0) cc_final: 0.8462 (p0) REVERT: B 31 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7845 (mt-10) REVERT: B 52 LYS cc_start: 0.9393 (tppt) cc_final: 0.9060 (tppt) REVERT: B 79 GLU cc_start: 0.8867 (tp30) cc_final: 0.8234 (tp30) REVERT: B 87 LYS cc_start: 0.8830 (mmmm) cc_final: 0.8600 (tttt) REVERT: B 104 TYR cc_start: 0.8779 (m-80) cc_final: 0.8092 (m-80) REVERT: B 116 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8785 (mt-10) REVERT: B 232 ASN cc_start: 0.8951 (OUTLIER) cc_final: 0.8706 (m110) REVERT: B 384 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.7328 (pm20) REVERT: B 420 MET cc_start: 0.9432 (mmm) cc_final: 0.9224 (mmm) REVERT: B 493 MET cc_start: 0.9406 (tmm) cc_final: 0.9182 (tmm) REVERT: B 526 GLU cc_start: 0.8585 (mp0) cc_final: 0.8381 (mm-30) REVERT: B 586 TYR cc_start: 0.8542 (m-80) cc_final: 0.8282 (m-80) REVERT: B 589 SER cc_start: 0.9647 (OUTLIER) cc_final: 0.9389 (t) REVERT: B 599 GLU cc_start: 0.8744 (pm20) cc_final: 0.8335 (pm20) REVERT: B 602 GLU cc_start: 0.7742 (pt0) cc_final: 0.6777 (pt0) REVERT: B 604 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8657 (mmt-90) REVERT: B 610 LYS cc_start: 0.9283 (ptpt) cc_final: 0.8999 (ptmm) REVERT: C 56 MET cc_start: 0.5350 (ptt) cc_final: 0.4909 (ppp) REVERT: C 122 PHE cc_start: 0.7097 (m-80) cc_final: 0.6405 (m-80) REVERT: C 157 MET cc_start: 0.8755 (mtp) cc_final: 0.8208 (ttt) REVERT: C 169 TYR cc_start: 0.8843 (m-80) cc_final: 0.8555 (m-80) REVERT: C 178 PHE cc_start: 0.7647 (m-80) cc_final: 0.7440 (m-80) REVERT: C 238 ASN cc_start: 0.6891 (m-40) cc_final: 0.6223 (m-40) REVERT: C 285 ILE cc_start: 0.3126 (tt) cc_final: 0.2924 (tt) REVERT: D 185 MET cc_start: -0.0103 (mmm) cc_final: -0.0422 (mmm) outliers start: 67 outliers final: 40 residues processed: 534 average time/residue: 0.1126 time to fit residues: 91.5821 Evaluate side-chains 510 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 462 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 216 VAL 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 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 453 ARG Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 662 MET 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 96 SER Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 604 ARG 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 177 TYR 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 207 LEU Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 256 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: 4.9990 chunk 183 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 172 optimal weight: 8.9990 chunk 52 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 75 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.152470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108566 restraints weight = 32090.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.111750 restraints weight = 15236.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.113996 restraints weight = 9285.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.114714 restraints weight = 6422.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.115953 restraints weight = 5409.977| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16386 Z= 0.139 Angle : 0.620 13.350 22134 Z= 0.325 Chirality : 0.044 0.272 2360 Planarity : 0.003 0.042 2818 Dihedral : 8.769 137.089 2293 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.73 % Allowed : 23.78 % Favored : 72.49 % 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: 1.16 (0.19), residues: 1932 helix: 1.21 (0.15), residues: 1129 sheet: -0.10 (0.44), residues: 134 loop : 0.40 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 117 TYR 0.025 0.001 TYR A 571 PHE 0.027 0.002 PHE C 168 TRP 0.015 0.002 TRP D 124 HIS 0.014 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (16386) covalent geometry : angle 0.61968 / 0.32 (22134) hydrogen bonds : bond 0.03972 / 2.52 ( 871) hydrogen bonds : angle 5.00892 / 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 567 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 503 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7671 (mp0) REVERT: A 117 ARG cc_start: 0.8550 (mtp85) cc_final: 0.8089 (mtp85) REVERT: A 119 GLU cc_start: 0.8346 (mp0) cc_final: 0.8090 (mp0) REVERT: A 158 ASN cc_start: 0.8793 (m-40) cc_final: 0.8454 (m-40) REVERT: A 161 ARG cc_start: 0.8024 (ttm-80) cc_final: 0.7818 (ttm110) REVERT: A 172 LEU cc_start: 0.9298 (mp) cc_final: 0.8987 (mp) REVERT: A 232 ASN cc_start: 0.8920 (OUTLIER) cc_final: 0.8239 (m-40) REVERT: A 344 GLU cc_start: 0.8161 (mp0) cc_final: 0.7961 (mp0) REVERT: A 357 TYR cc_start: 0.8930 (m-10) cc_final: 0.7825 (m-10) REVERT: A 361 GLN cc_start: 0.8657 (tp40) cc_final: 0.8424 (tp40) REVERT: A 384 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7418 (pm20) REVERT: A 444 ASP cc_start: 0.8494 (t70) cc_final: 0.8252 (t70) REVERT: A 447 ASN cc_start: 0.8679 (m-40) cc_final: 0.7597 (m-40) REVERT: A 453 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.8372 (ttt-90) REVERT: A 456 LYS cc_start: 0.8955 (mtmm) cc_final: 0.8705 (mtmm) REVERT: A 505 GLU cc_start: 0.8460 (mt-10) cc_final: 0.7980 (mt-10) REVERT: A 515 ASP cc_start: 0.8771 (m-30) cc_final: 0.8515 (m-30) REVERT: A 571 TYR cc_start: 0.9194 (t80) cc_final: 0.8790 (t80) REVERT: A 640 MET cc_start: 0.9227 (tpp) cc_final: 0.8869 (tpt) REVERT: B 18 ILE cc_start: 0.9448 (mm) cc_final: 0.9229 (mm) REVERT: B 27 ASP cc_start: 0.8692 (p0) cc_final: 0.8008 (p0) REVERT: B 52 LYS cc_start: 0.9441 (tppt) cc_final: 0.9138 (tppt) REVERT: B 79 GLU cc_start: 0.8841 (tp30) cc_final: 0.8226 (tp30) REVERT: B 111 LYS cc_start: 0.9310 (mmtp) cc_final: 0.9044 (mmtt) REVERT: B 232 ASN cc_start: 0.8868 (OUTLIER) cc_final: 0.8544 (m110) REVERT: B 338 ASN cc_start: 0.9330 (OUTLIER) cc_final: 0.9076 (t0) REVERT: B 344 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8154 (mt-10) REVERT: B 384 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.7315 (pm20) REVERT: B 493 MET cc_start: 0.9386 (tmm) cc_final: 0.9144 (tmm) REVERT: B 526 GLU cc_start: 0.8529 (mp0) cc_final: 0.8312 (mm-30) REVERT: B 550 MET cc_start: 0.8037 (mtp) cc_final: 0.7804 (mtp) REVERT: B 570 MET cc_start: 0.8679 (mmm) cc_final: 0.7843 (mtt) REVERT: B 586 TYR cc_start: 0.8493 (m-80) cc_final: 0.8069 (m-10) REVERT: B 599 GLU cc_start: 0.8666 (pm20) cc_final: 0.8290 (pm20) REVERT: B 602 GLU cc_start: 0.7582 (pt0) cc_final: 0.6187 (pt0) REVERT: B 604 ARG cc_start: 0.8995 (mmp80) cc_final: 0.8722 (mmt-90) REVERT: B 610 LYS cc_start: 0.9377 (ptpt) cc_final: 0.9025 (ptmm) REVERT: C 95 MET cc_start: 0.8504 (ppp) cc_final: 0.8222 (ppp) REVERT: C 122 PHE cc_start: 0.7084 (m-80) cc_final: 0.6394 (m-80) REVERT: C 146 GLN cc_start: 0.6682 (tp-100) cc_final: 0.6411 (tp-100) REVERT: C 149 ASP cc_start: 0.7714 (m-30) cc_final: 0.7499 (m-30) REVERT: C 157 MET cc_start: 0.8741 (mtp) cc_final: 0.8254 (ttt) REVERT: C 169 TYR cc_start: 0.8782 (m-80) cc_final: 0.8527 (m-80) REVERT: C 178 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7405 (m-80) REVERT: C 285 ILE cc_start: 0.3390 (tt) cc_final: 0.3186 (tt) REVERT: D 21 PHE cc_start: 0.7994 (m-80) cc_final: 0.7642 (m-80) REVERT: D 185 MET cc_start: -0.0259 (mmm) cc_final: -0.0521 (mmm) outliers start: 64 outliers final: 39 residues processed: 529 average time/residue: 0.1190 time to fit residues: 96.4698 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 : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL 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 320 ASN 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 453 ARG 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 A residue 684 TYR 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 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 256 VAL 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: 0.0770 chunk 51 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 186 optimal weight: 20.0000 chunk 140 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 7.9990 overall best weight: 2.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.150721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.106838 restraints weight = 32240.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.110054 restraints weight = 15280.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.112249 restraints weight = 9499.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.113571 restraints weight = 6706.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.114506 restraints weight = 5369.119| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3298 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.5891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16386 Z= 0.209 Angle : 0.665 13.203 22134 Z= 0.349 Chirality : 0.046 0.300 2360 Planarity : 0.004 0.045 2818 Dihedral : 8.788 138.153 2293 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.08 % Allowed : 24.59 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.19), residues: 1932 helix: 1.11 (0.15), residues: 1136 sheet: -0.30 (0.49), residues: 110 loop : 0.26 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 117 TYR 0.022 0.002 TYR A 571 PHE 0.024 0.002 PHE C 168 TRP 0.014 0.002 TRP B 9 HIS 0.015 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 (16386) covalent geometry : angle 0.66475 / 0.35 (22134) hydrogen bonds : bond 0.04091 / 2.60 ( 871) hydrogen bonds : angle 5.13030 / 3.71 ( 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 556 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 486 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7435 (mp0) REVERT: A 116 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7968 (mm-30) REVERT: A 117 ARG cc_start: 0.8610 (mtp85) cc_final: 0.8091 (mtp85) REVERT: A 119 GLU cc_start: 0.8303 (mp0) cc_final: 0.7953 (mp0) REVERT: A 158 ASN cc_start: 0.8789 (m-40) cc_final: 0.8543 (m-40) REVERT: A 172 LEU cc_start: 0.9344 (mp) cc_final: 0.9043 (mp) REVERT: A 232 ASN cc_start: 0.8925 (OUTLIER) cc_final: 0.8695 (m110) REVERT: A 357 TYR cc_start: 0.9022 (m-10) cc_final: 0.7994 (m-10) REVERT: A 361 GLN cc_start: 0.8653 (tp40) cc_final: 0.8406 (tp40) REVERT: A 384 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7376 (pm20) REVERT: A 420 MET cc_start: 0.8840 (mmm) cc_final: 0.8631 (tpt) REVERT: A 453 ARG cc_start: 0.9214 (OUTLIER) cc_final: 0.8965 (ttt90) REVERT: A 456 LYS cc_start: 0.8980 (mtmm) cc_final: 0.8745 (mtmm) REVERT: A 505 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8092 (mt-10) REVERT: A 515 ASP cc_start: 0.8806 (m-30) cc_final: 0.8566 (m-30) REVERT: A 571 TYR cc_start: 0.9181 (t80) cc_final: 0.8788 (t80) REVERT: A 686 ARG cc_start: 0.7985 (mmt180) cc_final: 0.7702 (mmt-90) REVERT: B 27 ASP cc_start: 0.8705 (p0) cc_final: 0.8225 (p0) REVERT: B 52 LYS cc_start: 0.9436 (tppt) cc_final: 0.9182 (tppt) REVERT: B 79 GLU cc_start: 0.8854 (tp30) cc_final: 0.8252 (tp30) REVERT: B 232 ASN cc_start: 0.8943 (OUTLIER) cc_final: 0.8737 (m110) REVERT: B 338 ASN cc_start: 0.9358 (OUTLIER) cc_final: 0.9096 (t0) REVERT: B 384 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.7386 (pm20) REVERT: B 467 ASN cc_start: 0.9273 (t0) cc_final: 0.8982 (m-40) REVERT: B 493 MET cc_start: 0.9429 (tmm) cc_final: 0.9137 (tmm) REVERT: B 522 TYR cc_start: 0.8979 (m-80) cc_final: 0.8605 (m-10) REVERT: B 570 MET cc_start: 0.8667 (mmm) cc_final: 0.7423 (mtt) REVERT: B 586 TYR cc_start: 0.8481 (m-80) cc_final: 0.8123 (m-80) REVERT: B 599 GLU cc_start: 0.8683 (pm20) cc_final: 0.8322 (pm20) REVERT: B 602 GLU cc_start: 0.7568 (pt0) cc_final: 0.6352 (pt0) REVERT: B 604 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8661 (mmt-90) REVERT: B 610 LYS cc_start: 0.9392 (ptpt) cc_final: 0.9036 (ptmm) REVERT: C 95 MET cc_start: 0.8639 (ppp) cc_final: 0.8408 (ppp) REVERT: C 157 MET cc_start: 0.8788 (mtp) cc_final: 0.8311 (ttt) REVERT: C 169 TYR cc_start: 0.8757 (m-80) cc_final: 0.8474 (m-80) REVERT: C 178 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.7402 (m-80) REVERT: D 93 MET cc_start: 0.7857 (mtp) cc_final: 0.7602 (mtp) REVERT: D 150 GLU cc_start: 0.2041 (mm-30) cc_final: 0.1697 (tp30) REVERT: D 174 TYR cc_start: 0.5945 (OUTLIER) cc_final: 0.5389 (t80) REVERT: D 185 MET cc_start: 0.0030 (mmm) cc_final: -0.0306 (mmm) outliers start: 70 outliers final: 52 residues processed: 516 average time/residue: 0.1115 time to fit residues: 88.2290 Evaluate side-chains 526 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 465 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL 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 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 453 ARG 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 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 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 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 661 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 195 LEU 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 42 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 256 VAL 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: 2.9990 chunk 99 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 158 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** 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 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN D 28 GLN ** D 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.151997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.107806 restraints weight = 32419.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.111346 restraints weight = 15514.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.113555 restraints weight = 9384.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.115011 restraints weight = 6713.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.115386 restraints weight = 5366.273| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.6080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16386 Z= 0.184 Angle : 0.678 13.024 22134 Z= 0.353 Chirality : 0.046 0.281 2360 Planarity : 0.004 0.045 2818 Dihedral : 8.726 137.679 2293 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.02 % Allowed : 25.41 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.19), residues: 1932 helix: 1.05 (0.15), residues: 1142 sheet: -0.18 (0.44), residues: 134 loop : 0.31 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 117 TYR 0.034 0.002 TYR B 36 PHE 0.055 0.002 PHE C 92 TRP 0.017 0.002 TRP B 9 HIS 0.016 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (16386) covalent geometry : angle 0.67830 / 0.35 (22134) hydrogen bonds : bond 0.04038 / 2.56 ( 871) hydrogen bonds : angle 5.11951 / 3.70 ( 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 550 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 481 time to evaluate : 0.580 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: 0.8225 (mm-30) cc_final: 0.7427 (mp0) REVERT: A 117 ARG cc_start: 0.8587 (mtp85) cc_final: 0.8097 (mtp85) REVERT: A 119 GLU cc_start: 0.8355 (mp0) cc_final: 0.8047 (mp0) REVERT: A 158 ASN cc_start: 0.8761 (m-40) cc_final: 0.8516 (m-40) REVERT: A 172 LEU cc_start: 0.9351 (mp) cc_final: 0.9023 (mp) REVERT: A 214 LYS cc_start: 0.7914 (mmtt) cc_final: 0.7693 (mptt) REVERT: A 232 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8378 (m-40) REVERT: A 357 TYR cc_start: 0.9019 (m-10) cc_final: 0.7905 (m-10) REVERT: A 361 GLN cc_start: 0.8630 (tp40) cc_final: 0.8401 (tp40) REVERT: A 384 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7301 (pm20) REVERT: A 386 LEU cc_start: 0.9496 (mt) cc_final: 0.9294 (mt) REVERT: A 420 MET cc_start: 0.8616 (mmm) cc_final: 0.8227 (mmm) REVERT: A 453 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.8380 (ttt-90) REVERT: A 456 LYS cc_start: 0.8994 (mtmm) cc_final: 0.8743 (mtmm) REVERT: A 496 ASN cc_start: 0.9316 (t0) cc_final: 0.9045 (t0) REVERT: A 505 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8112 (mt-10) REVERT: A 515 ASP cc_start: 0.8792 (m-30) cc_final: 0.8553 (m-30) REVERT: A 571 TYR cc_start: 0.9146 (t80) cc_final: 0.8767 (t80) REVERT: A 686 ARG cc_start: 0.8022 (mmt180) cc_final: 0.7628 (mmt-90) REVERT: B 52 LYS cc_start: 0.9436 (tppt) cc_final: 0.9188 (tppt) REVERT: B 79 GLU cc_start: 0.8862 (tp30) cc_final: 0.8262 (tp30) REVERT: B 232 ASN cc_start: 0.8860 (OUTLIER) cc_final: 0.8585 (m110) REVERT: B 312 GLN cc_start: 0.8964 (mt0) cc_final: 0.8534 (mt0) REVERT: B 338 ASN cc_start: 0.9332 (OUTLIER) cc_final: 0.9060 (t0) REVERT: B 344 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8206 (mt-10) REVERT: B 384 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.7294 (pm20) REVERT: B 493 MET cc_start: 0.9403 (tmm) cc_final: 0.9116 (tmm) REVERT: B 586 TYR cc_start: 0.8506 (m-80) cc_final: 0.8162 (m-80) REVERT: B 599 GLU cc_start: 0.8687 (pm20) cc_final: 0.8328 (pm20) REVERT: B 602 GLU cc_start: 0.7576 (pt0) cc_final: 0.6351 (pt0) REVERT: B 604 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8626 (mmt-90) REVERT: B 610 LYS cc_start: 0.9408 (ptpt) cc_final: 0.9045 (ptmm) REVERT: C 56 MET cc_start: 0.6493 (ppp) cc_final: 0.6141 (ppp) REVERT: C 95 MET cc_start: 0.8665 (ppp) cc_final: 0.8437 (ppp) REVERT: C 157 MET cc_start: 0.8863 (mtp) cc_final: 0.8393 (ttt) REVERT: C 169 TYR cc_start: 0.8813 (m-80) cc_final: 0.8531 (m-80) REVERT: C 178 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.7383 (m-80) REVERT: D 93 MET cc_start: 0.7910 (mtp) cc_final: 0.7643 (mtp) REVERT: D 157 MET cc_start: 0.0168 (ppp) cc_final: -0.0274 (ppp) REVERT: D 174 TYR cc_start: 0.5774 (OUTLIER) cc_final: 0.5293 (t80) REVERT: D 204 TYR cc_start: 0.7083 (OUTLIER) cc_final: 0.6582 (t80) REVERT: D 259 PHE cc_start: 0.5131 (OUTLIER) cc_final: 0.4722 (t80) outliers start: 69 outliers final: 51 residues processed: 514 average time/residue: 0.1242 time to fit residues: 96.9726 Evaluate side-chains 512 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 450 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 216 VAL 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 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 662 MET 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 155 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 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 661 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 195 LEU 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 42 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 259 PHE 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: 1.9990 chunk 133 optimal weight: 0.1980 chunk 149 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** 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 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 132 GLN ** D 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.154457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.111031 restraints weight = 32472.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.114287 restraints weight = 16003.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.116337 restraints weight = 9763.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.117708 restraints weight = 7003.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.118610 restraints weight = 5653.075| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.6256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16386 Z= 0.142 Angle : 0.698 13.673 22134 Z= 0.361 Chirality : 0.045 0.277 2360 Planarity : 0.003 0.043 2818 Dihedral : 8.621 137.310 2293 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.55 % Allowed : 26.40 % Favored : 70.05 % 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: 0.93 (0.19), residues: 1932 helix: 1.05 (0.15), residues: 1142 sheet: -0.26 (0.44), residues: 134 loop : 0.25 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 117 TYR 0.031 0.001 TYR B 36 PHE 0.025 0.002 PHE C 168 TRP 0.014 0.001 TRP D 124 HIS 0.015 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (16386) covalent geometry : angle 0.69804 / 0.36 (22134) hydrogen bonds : bond 0.04057 / 2.54 ( 871) hydrogen bonds : angle 5.13168 / 3.71 ( 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 536 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 475 time to evaluate : 0.596 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: 0.8226 (mm-30) cc_final: 0.7434 (mp0) REVERT: A 117 ARG cc_start: 0.8497 (mtp85) cc_final: 0.8082 (mtp85) REVERT: A 119 GLU cc_start: 0.8342 (mp0) cc_final: 0.8078 (mp0) REVERT: A 158 ASN cc_start: 0.8647 (m-40) cc_final: 0.8359 (m-40) REVERT: A 161 ARG cc_start: 0.8015 (ttm-80) cc_final: 0.7654 (ttm110) REVERT: A 172 LEU cc_start: 0.9312 (mp) cc_final: 0.9006 (mp) REVERT: A 214 LYS cc_start: 0.7892 (mmtt) cc_final: 0.7608 (mptt) REVERT: A 232 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8200 (m-40) REVERT: A 357 TYR cc_start: 0.8875 (m-10) cc_final: 0.7832 (m-10) REVERT: A 361 GLN cc_start: 0.8536 (tp40) cc_final: 0.8287 (tp40) REVERT: A 384 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7387 (pm20) REVERT: A 420 MET cc_start: 0.8550 (mmm) cc_final: 0.8275 (mmm) REVERT: A 453 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8359 (ttt-90) REVERT: A 456 LYS cc_start: 0.8985 (mtmm) cc_final: 0.8731 (mtmm) REVERT: A 505 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8224 (mt-10) REVERT: A 515 ASP cc_start: 0.8757 (m-30) cc_final: 0.8523 (m-30) REVERT: A 571 TYR cc_start: 0.9093 (t80) cc_final: 0.8875 (t80) REVERT: A 640 MET cc_start: 0.9149 (tpp) cc_final: 0.8670 (tpt) REVERT: B 27 ASP cc_start: 0.8646 (p0) cc_final: 0.8259 (p0) REVERT: B 52 LYS cc_start: 0.9405 (tppt) cc_final: 0.9168 (tppt) REVERT: B 79 GLU cc_start: 0.8774 (tp30) cc_final: 0.8223 (tp30) REVERT: B 232 ASN cc_start: 0.8778 (m-40) cc_final: 0.8470 (m-40) REVERT: B 312 GLN cc_start: 0.8838 (mt0) cc_final: 0.8476 (mt0) REVERT: B 338 ASN cc_start: 0.9351 (OUTLIER) cc_final: 0.9046 (t0) REVERT: B 344 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8111 (mt-10) REVERT: B 384 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.7300 (pm20) REVERT: B 493 MET cc_start: 0.9338 (tmm) cc_final: 0.9103 (tmm) REVERT: B 570 MET cc_start: 0.8622 (mmm) cc_final: 0.7731 (mtt) REVERT: B 586 TYR cc_start: 0.8414 (m-80) cc_final: 0.8001 (m-10) REVERT: B 594 VAL cc_start: 0.9216 (m) cc_final: 0.8983 (p) REVERT: B 599 GLU cc_start: 0.8667 (pm20) cc_final: 0.8329 (pm20) REVERT: B 610 LYS cc_start: 0.9422 (ptpt) cc_final: 0.9109 (ptmm) REVERT: C 56 MET cc_start: 0.6484 (ppp) cc_final: 0.5960 (ppp) REVERT: C 169 TYR cc_start: 0.8785 (m-80) cc_final: 0.8535 (m-80) REVERT: C 178 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7413 (m-80) REVERT: C 208 LEU cc_start: 0.8436 (tp) cc_final: 0.8098 (pp) REVERT: D 93 MET cc_start: 0.7790 (mtp) cc_final: 0.7532 (mtp) REVERT: D 157 MET cc_start: -0.0169 (ppp) cc_final: -0.0639 (ppp) REVERT: D 174 TYR cc_start: 0.5835 (OUTLIER) cc_final: 0.5411 (t80) REVERT: D 204 TYR cc_start: 0.7076 (OUTLIER) cc_final: 0.6696 (t80) REVERT: D 259 PHE cc_start: 0.5256 (OUTLIER) cc_final: 0.4685 (t80) outliers start: 61 outliers final: 38 residues processed: 501 average time/residue: 0.1213 time to fit residues: 92.7872 Evaluate side-chains 502 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 455 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 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 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 684 TYR 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 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 495 VAL 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 55 TYR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 74 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 256 VAL Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 189 optimal weight: 20.0000 chunk 181 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 132 optimal weight: 0.5980 chunk 50 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN B 180 ASN B 232 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 HIS ** 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 283 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 = 0.3854 r_free = 0.3854 target = 0.152304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.108723 restraints weight = 32490.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.112219 restraints weight = 15644.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.114456 restraints weight = 9420.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.115753 restraints weight = 6741.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.116663 restraints weight = 5442.945| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.6384 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= 0.173 Angle : 0.716 13.292 22134 Z= 0.371 Chirality : 0.046 0.302 2360 Planarity : 0.004 0.040 2818 Dihedral : 8.646 139.393 2293 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.32 % Allowed : 27.16 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.19), residues: 1932 helix: 1.01 (0.15), residues: 1141 sheet: -0.46 (0.43), residues: 134 loop : 0.26 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 261 TYR 0.032 0.002 TYR B 36 PHE 0.027 0.002 PHE B 156 TRP 0.021 0.002 TRP D 44 HIS 0.014 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (16386) covalent geometry : angle 0.71603 / 0.37 (22134) hydrogen bonds : bond 0.04124 / 2.58 ( 871) hydrogen bonds : angle 5.18724 / 3.75 ( 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 516 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 459 time to evaluate : 0.592 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: 0.8325 (mm-30) cc_final: 0.7454 (mp0) REVERT: A 117 ARG cc_start: 0.8535 (mtp85) cc_final: 0.8070 (mtp85) REVERT: A 119 GLU cc_start: 0.8381 (mp0) cc_final: 0.8072 (mp0) REVERT: A 158 ASN cc_start: 0.8656 (m-40) cc_final: 0.8405 (m-40) REVERT: A 172 LEU cc_start: 0.9319 (mp) cc_final: 0.9007 (mp) REVERT: A 214 LYS cc_start: 0.7940 (mmtt) cc_final: 0.7718 (mptt) REVERT: A 232 ASN cc_start: 0.8876 (OUTLIER) cc_final: 0.8188 (m-40) REVERT: A 357 TYR cc_start: 0.8997 (m-10) cc_final: 0.7941 (m-10) REVERT: A 361 GLN cc_start: 0.8567 (tp40) cc_final: 0.8296 (tp40) REVERT: A 384 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7317 (pm20) REVERT: A 453 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.8373 (ttt-90) REVERT: A 456 LYS cc_start: 0.8991 (mtmm) cc_final: 0.8734 (mtmm) REVERT: A 493 MET cc_start: 0.8690 (tmm) cc_final: 0.8379 (tmm) REVERT: A 505 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8176 (mt-10) REVERT: A 515 ASP cc_start: 0.8794 (m-30) cc_final: 0.8552 (m-30) REVERT: A 571 TYR cc_start: 0.9123 (t80) cc_final: 0.8856 (t80) REVERT: A 640 MET cc_start: 0.9154 (tpp) cc_final: 0.8716 (tpt) REVERT: A 646 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8579 (pm20) REVERT: B 27 ASP cc_start: 0.8761 (p0) cc_final: 0.8350 (p0) REVERT: B 79 GLU cc_start: 0.8898 (tp30) cc_final: 0.8279 (tp30) REVERT: B 205 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7815 (mttp) REVERT: B 232 ASN cc_start: 0.8825 (OUTLIER) cc_final: 0.8479 (m110) REVERT: B 312 GLN cc_start: 0.8890 (mt0) cc_final: 0.8479 (mt0) REVERT: B 338 ASN cc_start: 0.9376 (OUTLIER) cc_final: 0.9040 (t0) REVERT: B 344 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8251 (mt-10) REVERT: B 471 TYR cc_start: 0.8878 (t80) cc_final: 0.8387 (t80) REVERT: B 493 MET cc_start: 0.9418 (tmm) cc_final: 0.9131 (tmm) REVERT: B 586 TYR cc_start: 0.8405 (m-80) cc_final: 0.7821 (m-80) REVERT: B 599 GLU cc_start: 0.8721 (pm20) cc_final: 0.8287 (pm20) REVERT: B 610 LYS cc_start: 0.9469 (ptpt) cc_final: 0.9106 (ptmm) REVERT: C 56 MET cc_start: 0.6424 (ppp) cc_final: 0.5844 (ppp) REVERT: C 169 TYR cc_start: 0.8840 (m-80) cc_final: 0.8587 (m-80) REVERT: C 178 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.7399 (m-80) REVERT: C 208 LEU cc_start: 0.8402 (tp) cc_final: 0.8080 (pp) REVERT: D 93 MET cc_start: 0.7811 (mtp) cc_final: 0.7551 (mtp) REVERT: D 157 MET cc_start: -0.0136 (ppp) cc_final: -0.0598 (ppp) REVERT: D 174 TYR cc_start: 0.5728 (OUTLIER) cc_final: 0.5276 (t80) REVERT: D 204 TYR cc_start: 0.7082 (OUTLIER) cc_final: 0.6647 (t80) REVERT: D 259 PHE cc_start: 0.5238 (OUTLIER) cc_final: 0.4697 (t80) outliers start: 57 outliers final: 41 residues processed: 484 average time/residue: 0.1072 time to fit residues: 79.5993 Evaluate side-chains 498 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 446 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 216 VAL 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 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 646 GLN Chi-restraints excluded: chain A residue 662 MET 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 205 LYS Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 348 MET 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 495 VAL 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 55 TYR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 74 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 259 PHE Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 0.0870 chunk 148 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 ASN ** A 418 ASN ** 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 107 ASN ** D 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.154574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.111611 restraints weight = 31919.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.115047 restraints weight = 15346.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.117222 restraints weight = 9195.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.118592 restraints weight = 6533.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.119287 restraints weight = 5232.304| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3364 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3364 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.6522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16386 Z= 0.143 Angle : 0.725 13.521 22134 Z= 0.373 Chirality : 0.046 0.297 2360 Planarity : 0.004 0.041 2818 Dihedral : 8.605 138.803 2293 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.97 % Allowed : 27.74 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.19), residues: 1932 helix: 0.95 (0.15), residues: 1141 sheet: -0.56 (0.43), residues: 134 loop : 0.22 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 261 TYR 0.029 0.001 TYR B 36 PHE 0.025 0.002 PHE C 168 TRP 0.021 0.002 TRP D 44 HIS 0.016 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (16386) covalent geometry : angle 0.72547 / 0.37 (22134) hydrogen bonds : bond 0.04069 / 2.56 ( 871) hydrogen bonds : angle 5.17472 / 3.74 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3102.32 seconds wall clock time: 54 minutes 30.15 seconds (3270.15 seconds total)