Starting phenix.real_space_refine on Sat Jun 14 07:29:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz2_45051/06_2025/9bz2_45051_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz2_45051/06_2025/9bz2_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_45051/06_2025/9bz2_45051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz2_45051/06_2025/9bz2_45051.map" model { file = "/net/cci-nas-00/data/ceres_data/9bz2_45051/06_2025/9bz2_45051_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz2_45051/06_2025/9bz2_45051_neut.cif" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.38, per 1000 atoms: 0.58 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: 4.01 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.63 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: 4.75 Time building geometry restraints manager: 4.71 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=" 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=" C LEU D 41 " pdb=" N LEU D 42 " ideal model delta sigma weight residual 1.334 1.291 0.043 1.33e-02 5.65e+03 1.07e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.038 1.20e-02 6.94e+03 1.01e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.032 1.08e-02 8.57e+03 8.96e+00 bond pdb=" N THR D 43 " pdb=" CA THR D 43 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.26e-02 6.30e+03 8.46e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 21745 2.46 - 4.91: 365 4.91 - 7.37: 17 7.37 - 9.83: 5 9.83 - 12.28: 2 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 - 35.80: 9473 35.80 - 71.60: 334 71.60 - 107.41: 37 107.41 - 143.21: 3 143.21 - 179.01: 3 Dihedral angle restraints: 9850 sinusoidal: 4092 harmonic: 5758 Sorted by residual: dihedral pdb=" C2 TTP A 803 " pdb=" C1' TTP A 803 " pdb=" N1 TTP A 803 " pdb=" O4' TTP A 803 " ideal model delta sinusoidal sigma weight residual -58.32 120.69 -179.01 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 TTP B 801 " pdb=" C1' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " ideal model delta sinusoidal sigma weight residual 301.68 151.18 150.50 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" C5' TTP A 803 " pdb=" O5' TTP A 803 " pdb=" PA TTP A 803 " pdb=" O3A TTP A 803 " ideal model delta sinusoidal sigma weight residual 179.97 31.90 148.07 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 9847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2149 0.093 - 0.187: 179 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 36.080 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 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 0.060 16386 Z= 0.317 Angle : 0.750 12.283 22134 Z= 0.471 Chirality : 0.058 0.467 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.888 179.009 6154 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.20 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 PHE 0.021 0.002 PHE C 168 TYR 0.020 0.002 TYR C 169 ARG 0.004 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.15423 ( 871) hydrogen bonds : angle 6.51784 ( 2571) covalent geometry : bond 0.00556 (16386) covalent geometry : angle 0.74994 (22134) *********************** 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 : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ILE cc_start: 0.9185 (mt) cc_final: 0.8939 (mt) REVERT: A 127 LEU cc_start: 0.9149 (mt) cc_final: 0.8859 (mt) REVERT: A 131 ASN cc_start: 0.8653 (t0) cc_final: 0.8379 (t0) REVERT: A 138 LYS cc_start: 0.8180 (mtpt) cc_final: 0.7846 (mtpp) REVERT: A 145 ILE cc_start: 0.9125 (tp) cc_final: 0.8907 (tp) REVERT: A 172 LEU cc_start: 0.9004 (mp) cc_final: 0.8770 (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: 0.8511 (p) REVERT: A 227 MET cc_start: 0.7829 (mtp) cc_final: 0.7587 (mtp) REVERT: A 319 MET cc_start: 0.7850 (tpp) cc_final: 0.7398 (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: 0.8740 (p0) REVERT: A 446 ARG cc_start: 0.7519 (mmm-85) cc_final: 0.7241 (mtp85) REVERT: A 447 ASN cc_start: 0.7944 (m-40) cc_final: 0.7333 (m110) REVERT: A 546 LEU cc_start: 0.8855 (mt) cc_final: 0.8647 (mt) REVERT: A 550 MET cc_start: 0.8096 (mtm) cc_final: 0.7875 (mtt) REVERT: A 598 MET cc_start: 0.8373 (mtm) cc_final: 0.7780 (mtp) REVERT: B 51 LEU cc_start: 0.8213 (tp) cc_final: 0.7886 (tp) REVERT: B 67 GLU cc_start: 0.7746 (mp0) cc_final: 0.7141 (mp0) REVERT: B 106 LEU cc_start: 0.8835 (tp) cc_final: 0.7898 (tt) REVERT: B 127 LEU cc_start: 0.9042 (mt) cc_final: 0.8800 (mt) REVERT: B 129 PHE cc_start: 0.8421 (m-10) cc_final: 0.8064 (m-10) REVERT: B 180 ASN cc_start: 0.7535 (m-40) cc_final: 0.7326 (m110) REVERT: B 186 ILE cc_start: 0.9216 (mt) cc_final: 0.9013 (mt) REVERT: B 211 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7480 (mm-30) REVERT: B 286 ASP cc_start: 0.6894 (OUTLIER) cc_final: 0.6686 (m-30) REVERT: B 319 MET cc_start: 0.7902 (tpp) cc_final: 0.7659 (tpp) REVERT: B 348 MET cc_start: 0.7346 (tmm) cc_final: 0.7075 (ttm) REVERT: B 358 ILE cc_start: 0.9193 (mm) cc_final: 0.8937 (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: 0.8159 (pm20) REVERT: B 389 SER cc_start: 0.8046 (p) cc_final: 0.7835 (p) REVERT: B 458 MET cc_start: 0.8463 (mmm) cc_final: 0.8156 (mmm) REVERT: B 460 SER cc_start: 0.8912 (t) cc_final: 0.8711 (p) REVERT: B 471 TYR cc_start: 0.8260 (t80) cc_final: 0.7681 (t80) REVERT: B 500 ILE cc_start: 0.9095 (mt) cc_final: 0.8888 (mt) REVERT: B 585 SER cc_start: 0.9148 (p) cc_final: 0.8881 (p) REVERT: C 89 VAL cc_start: 0.5232 (t) cc_final: 0.3655 (t) REVERT: C 229 ILE cc_start: 0.5031 (mt) cc_final: 0.4266 (mm) REVERT: D 42 LEU cc_start: 0.1877 (mt) cc_final: 0.1438 (mt) REVERT: D 185 MET cc_start: 0.0973 (mmm) cc_final: 0.0575 (mmm) REVERT: D 282 ILE cc_start: 0.3799 (OUTLIER) cc_final: 0.3413 (pt) outliers start: 24 outliers final: 5 residues processed: 822 average time/residue: 0.2916 time to fit residues: 348.5967 Evaluate side-chains 570 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 563 time to evaluate : 1.686 ------------------------------------------------------------------------------- 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 162 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 239 GLN A 365 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 14 ASN B 202 ASN B 312 GLN B 329 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN B 467 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 233 ASN D 71 ASN D 80 HIS D 91 ASN D 186 GLN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.154480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.106321 restraints weight = 30845.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.109908 restraints weight = 15205.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.112147 restraints weight = 9241.837| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16386 Z= 0.245 Angle : 0.680 8.214 22134 Z= 0.356 Chirality : 0.045 0.326 2360 Planarity : 0.004 0.038 2818 Dihedral : 11.614 179.113 2254 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.20 % Allowed : 17.83 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.19), residues: 1932 helix: 1.43 (0.15), residues: 1133 sheet: -0.19 (0.46), residues: 114 loop : 0.69 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP D 44 HIS 0.006 0.001 HIS B 438 PHE 0.027 0.002 PHE B 261 TYR 0.034 0.002 TYR D 174 ARG 0.006 0.001 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.04660 ( 871) hydrogen bonds : angle 5.06718 ( 2571) covalent geometry : bond 0.00539 (16386) covalent geometry : angle 0.68042 (22134) *********************** 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 654 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 582 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8907 (p0) cc_final: 0.8552 (p0) REVERT: A 65 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7272 (mp0) REVERT: A 117 ARG cc_start: 0.8369 (mtp85) cc_final: 0.8124 (mtp85) REVERT: A 119 GLU cc_start: 0.8529 (mp0) cc_final: 0.8208 (mp0) REVERT: A 138 LYS cc_start: 0.9088 (mtpt) cc_final: 0.8813 (mtpp) REVERT: A 172 LEU cc_start: 0.9323 (mp) cc_final: 0.9000 (mp) REVERT: A 317 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7860 (ptp) REVERT: A 357 TYR cc_start: 0.9016 (m-10) cc_final: 0.8070 (m-10) REVERT: A 362 ASP cc_start: 0.8413 (m-30) cc_final: 0.8144 (m-30) REVERT: A 379 SER cc_start: 0.9385 (t) cc_final: 0.9179 (t) REVERT: A 384 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.7590 (pm20) REVERT: A 402 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7346 (tm-30) REVERT: A 436 LEU cc_start: 0.9494 (mt) cc_final: 0.9287 (mm) REVERT: A 456 LYS cc_start: 0.8931 (mtmm) cc_final: 0.8551 (mtmm) REVERT: A 493 MET cc_start: 0.8941 (tmm) cc_final: 0.8524 (tmm) REVERT: A 548 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8338 (mm-30) REVERT: A 602 GLU cc_start: 0.7710 (pt0) cc_final: 0.7138 (pt0) REVERT: A 640 MET cc_start: 0.9316 (tpp) cc_final: 0.8860 (tpp) REVERT: A 663 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8111 (t) REVERT: B 52 LYS cc_start: 0.9415 (tppt) cc_final: 0.9101 (tppt) REVERT: B 71 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9321 (mt) REVERT: B 118 TYR cc_start: 0.9378 (t80) cc_final: 0.9172 (t80) REVERT: B 236 TYR cc_start: 0.9207 (t80) cc_final: 0.8979 (t80) REVERT: B 362 ASP cc_start: 0.8019 (m-30) cc_final: 0.7722 (m-30) REVERT: B 420 MET cc_start: 0.9390 (mmm) cc_final: 0.9142 (mmm) REVERT: B 425 ILE cc_start: 0.9474 (mt) cc_final: 0.9171 (mt) REVERT: B 493 MET cc_start: 0.9505 (tmm) cc_final: 0.9287 (tmm) REVERT: B 570 MET cc_start: 0.8253 (mtp) cc_final: 0.7925 (mtt) REVERT: B 602 GLU cc_start: 0.8087 (pt0) cc_final: 0.7630 (pt0) REVERT: B 604 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8439 (mmt-90) REVERT: B 610 LYS cc_start: 0.9071 (ptpt) cc_final: 0.8677 (ptmm) REVERT: B 612 TYR cc_start: 0.9033 (m-80) cc_final: 0.8143 (m-80) REVERT: B 620 SER cc_start: 0.9513 (OUTLIER) cc_final: 0.9311 (p) REVERT: B 648 ILE cc_start: 0.9154 (mm) cc_final: 0.8886 (mt) REVERT: B 650 GLN cc_start: 0.8492 (mt0) cc_final: 0.8165 (mt0) REVERT: B 656 LEU cc_start: 0.9560 (mt) cc_final: 0.9359 (mt) REVERT: C 56 MET cc_start: 0.4623 (ptt) cc_final: 0.4175 (ppp) REVERT: C 90 LEU cc_start: 0.7632 (mt) cc_final: 0.6906 (mt) REVERT: C 146 GLN cc_start: 0.6413 (mm-40) cc_final: 0.6116 (mm110) REVERT: C 178 PHE cc_start: 0.7867 (m-80) cc_final: 0.7516 (m-80) REVERT: C 278 GLU cc_start: 0.8791 (tt0) cc_final: 0.8589 (tp30) REVERT: D 96 MET cc_start: 0.0075 (mmt) cc_final: -0.0232 (mmt) outliers start: 72 outliers final: 26 residues processed: 621 average time/residue: 0.2803 time to fit residues: 260.2479 Evaluate side-chains 521 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 488 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 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 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 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN 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 B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 136 GLN 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 8 optimal weight: 2.9990 chunk 168 optimal weight: 30.0000 chunk 175 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 191 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 189 optimal weight: 20.0000 chunk 141 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 410 ASN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 232 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 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 69 GLN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 288 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.149304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.102841 restraints weight = 32212.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.106152 restraints weight = 15857.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.108208 restraints weight = 9627.182| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 16386 Z= 0.270 Angle : 0.676 10.708 22134 Z= 0.353 Chirality : 0.046 0.258 2360 Planarity : 0.004 0.041 2818 Dihedral : 11.455 173.471 2248 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.60 % Allowed : 21.10 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.19), residues: 1932 helix: 1.32 (0.15), residues: 1127 sheet: -0.47 (0.46), residues: 118 loop : 0.52 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 9 HIS 0.007 0.001 HIS A 647 PHE 0.032 0.002 PHE A 492 TYR 0.043 0.002 TYR D 174 ARG 0.005 0.001 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 871) hydrogen bonds : angle 5.08042 ( 2571) covalent geometry : bond 0.00588 (16386) covalent geometry : angle 0.67577 (22134) *********************** 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 604 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 525 time to evaluate : 1.777 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: 0.8983 (p0) cc_final: 0.8725 (p0) REVERT: A 65 GLU cc_start: 0.8440 (mm-30) cc_final: 0.7964 (mp0) REVERT: A 95 MET cc_start: 0.9185 (mmm) cc_final: 0.8938 (mmm) REVERT: A 117 ARG cc_start: 0.8644 (mtp85) cc_final: 0.8378 (mtp85) REVERT: A 119 GLU cc_start: 0.8492 (mp0) cc_final: 0.8079 (mp0) REVERT: A 150 GLN cc_start: 0.9117 (tm-30) cc_final: 0.8750 (tm-30) REVERT: A 172 LEU cc_start: 0.9392 (mp) cc_final: 0.9078 (mp) REVERT: A 317 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7987 (ptp) REVERT: A 346 LEU cc_start: 0.9464 (mp) cc_final: 0.9248 (mp) REVERT: A 348 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7395 (ptm) REVERT: A 357 TYR cc_start: 0.9045 (m-10) cc_final: 0.8211 (m-10) REVERT: A 362 ASP cc_start: 0.8431 (m-30) cc_final: 0.8028 (m-30) REVERT: A 384 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.7466 (pm20) REVERT: A 402 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7277 (tm-30) REVERT: A 436 LEU cc_start: 0.9534 (mt) cc_final: 0.9228 (mm) REVERT: A 453 ARG cc_start: 0.9214 (OUTLIER) cc_final: 0.9004 (ttt90) REVERT: A 456 LYS cc_start: 0.8945 (mtmm) cc_final: 0.8682 (mtmm) REVERT: A 493 MET cc_start: 0.8923 (tmm) cc_final: 0.8281 (tmm) REVERT: A 515 ASP cc_start: 0.8839 (m-30) cc_final: 0.8585 (m-30) REVERT: A 570 MET cc_start: 0.8853 (mtp) cc_final: 0.8520 (mtp) REVERT: A 588 GLN cc_start: 0.9022 (mm-40) cc_final: 0.8374 (mm-40) REVERT: A 645 GLN cc_start: 0.9145 (tp40) cc_final: 0.8891 (tp-100) REVERT: A 663 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8445 (t) REVERT: B 52 LYS cc_start: 0.9392 (tppt) cc_final: 0.9067 (tppt) REVERT: B 79 GLU cc_start: 0.8908 (tp30) cc_final: 0.8257 (tp30) REVERT: B 184 ARG cc_start: 0.9179 (tpp-160) cc_final: 0.8974 (tpp-160) REVERT: B 214 LYS cc_start: 0.8410 (ttmm) cc_final: 0.8032 (mmtm) REVERT: B 217 GLU cc_start: 0.8426 (mp0) cc_final: 0.8213 (mp0) REVERT: B 315 ASP cc_start: 0.8972 (p0) cc_final: 0.8739 (p0) REVERT: B 362 ASP cc_start: 0.7760 (m-30) cc_final: 0.7518 (m-30) REVERT: B 384 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8697 (pp20) REVERT: B 420 MET cc_start: 0.9357 (mmm) cc_final: 0.9126 (mmm) REVERT: B 458 MET cc_start: 0.9065 (mmm) cc_final: 0.8840 (mmm) REVERT: B 467 ASN cc_start: 0.9315 (t0) cc_final: 0.8722 (t0) REVERT: B 493 MET cc_start: 0.9452 (tmm) cc_final: 0.9224 (tmm) REVERT: B 526 GLU cc_start: 0.8685 (mp0) cc_final: 0.8416 (mp0) REVERT: B 599 GLU cc_start: 0.8809 (pm20) cc_final: 0.8522 (pm20) REVERT: B 602 GLU cc_start: 0.7987 (pt0) cc_final: 0.7400 (pt0) REVERT: B 604 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8644 (mmt-90) REVERT: B 610 LYS cc_start: 0.9207 (ptpt) cc_final: 0.8821 (ptmm) REVERT: B 620 SER cc_start: 0.9498 (OUTLIER) cc_final: 0.9267 (p) REVERT: B 667 LEU cc_start: 0.8798 (tp) cc_final: 0.8582 (tp) REVERT: C 56 MET cc_start: 0.5034 (ptt) cc_final: 0.4510 (ppp) REVERT: C 95 MET cc_start: 0.7727 (ppp) cc_final: 0.7458 (ppp) REVERT: C 105 TYR cc_start: 0.7665 (m-80) cc_final: 0.7317 (m-80) REVERT: C 149 ASP cc_start: 0.8208 (m-30) cc_final: 0.7958 (m-30) REVERT: C 157 MET cc_start: 0.8671 (mtp) cc_final: 0.8224 (ttt) REVERT: C 168 PHE cc_start: 0.8611 (m-80) cc_final: 0.8371 (m-80) REVERT: C 169 TYR cc_start: 0.8641 (m-80) cc_final: 0.8417 (m-80) REVERT: C 178 PHE cc_start: 0.7981 (m-80) cc_final: 0.7629 (m-80) REVERT: C 278 GLU cc_start: 0.8850 (tt0) cc_final: 0.8606 (tp30) REVERT: D 47 LEU cc_start: 0.8497 (mp) cc_final: 0.7998 (tp) REVERT: D 124 TRP cc_start: 0.6856 (t60) cc_final: 0.6625 (t60) REVERT: D 268 LEU cc_start: 0.4165 (mt) cc_final: 0.3899 (mp) outliers start: 79 outliers final: 41 residues processed: 564 average time/residue: 0.2638 time to fit residues: 221.5787 Evaluate side-chains 504 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 455 time to evaluate : 1.663 ------------------------------------------------------------------------------- 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 153 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU 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 453 ARG Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 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 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 620 SER 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 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 136 GLN 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 203 VAL Chi-restraints excluded: chain D residue 242 TYR 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 180 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3871 r_free = 0.3871 target = 0.153190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107735 restraints weight = 31760.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.111303 restraints weight = 15158.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.113595 restraints weight = 9021.718| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16386 Z= 0.138 Angle : 0.609 8.617 22134 Z= 0.316 Chirality : 0.042 0.227 2360 Planarity : 0.003 0.040 2818 Dihedral : 10.954 173.048 2246 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.44 % Allowed : 23.14 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.19), residues: 1932 helix: 1.39 (0.15), residues: 1129 sheet: -0.18 (0.49), residues: 106 loop : 0.42 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 124 HIS 0.011 0.001 HIS C 201 PHE 0.021 0.001 PHE A 492 TYR 0.025 0.001 TYR D 174 ARG 0.004 0.000 ARG A 350 Details of bonding type rmsd hydrogen bonds : bond 0.03947 ( 871) hydrogen bonds : angle 4.89488 ( 2571) covalent geometry : bond 0.00308 (16386) covalent geometry : angle 0.60874 (22134) *********************** 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 600 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 541 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8980 (p0) cc_final: 0.8764 (p0) REVERT: A 64 TYR cc_start: 0.8502 (m-10) cc_final: 0.7429 (m-10) REVERT: A 65 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7845 (mp0) REVERT: A 119 GLU cc_start: 0.8410 (mp0) cc_final: 0.8088 (mp0) REVERT: A 150 GLN cc_start: 0.9043 (tm-30) cc_final: 0.8781 (tm-30) REVERT: A 158 ASN cc_start: 0.8848 (m-40) cc_final: 0.8576 (m-40) REVERT: A 172 LEU cc_start: 0.9331 (mp) cc_final: 0.8984 (mp) REVERT: A 317 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7781 (ptp) REVERT: A 357 TYR cc_start: 0.8988 (m-10) cc_final: 0.7956 (m-10) REVERT: A 362 ASP cc_start: 0.8310 (m-30) cc_final: 0.8040 (m-30) REVERT: A 384 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7490 (pm20) REVERT: A 402 GLU cc_start: 0.7493 (tm-30) cc_final: 0.7238 (tm-30) REVERT: A 411 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7599 (mp) REVERT: A 456 LYS cc_start: 0.8954 (mtmm) cc_final: 0.8715 (mtmm) REVERT: A 505 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8152 (mt-10) REVERT: A 515 ASP cc_start: 0.8832 (m-30) cc_final: 0.8565 (m-30) REVERT: A 546 LEU cc_start: 0.9433 (mt) cc_final: 0.9190 (mt) REVERT: A 571 TYR cc_start: 0.9257 (t80) cc_final: 0.8625 (t80) REVERT: A 640 MET cc_start: 0.9290 (OUTLIER) cc_final: 0.8698 (tpp) REVERT: A 645 GLN cc_start: 0.9094 (tp40) cc_final: 0.8575 (tp-100) REVERT: A 663 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8506 (t) REVERT: B 52 LYS cc_start: 0.9396 (tppt) cc_final: 0.9089 (tppt) REVERT: B 71 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9270 (mp) REVERT: B 79 GLU cc_start: 0.8930 (tp30) cc_final: 0.8277 (tp30) REVERT: B 104 TYR cc_start: 0.8610 (m-80) cc_final: 0.8365 (m-80) REVERT: B 184 ARG cc_start: 0.9153 (tpp-160) cc_final: 0.8842 (tpp-160) REVERT: B 232 ASN cc_start: 0.8876 (OUTLIER) cc_final: 0.8644 (m110) REVERT: B 257 ASP cc_start: 0.8928 (m-30) cc_final: 0.8695 (m-30) REVERT: B 290 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8099 (pp20) REVERT: B 314 MET cc_start: 0.9142 (ttp) cc_final: 0.8916 (tmm) REVERT: B 315 ASP cc_start: 0.8929 (p0) cc_final: 0.8686 (p0) REVERT: B 467 ASN cc_start: 0.9117 (t0) cc_final: 0.8487 (t0) REVERT: B 526 GLU cc_start: 0.8675 (mp0) cc_final: 0.8394 (mm-30) REVERT: B 586 TYR cc_start: 0.8491 (m-80) cc_final: 0.8039 (m-80) REVERT: B 599 GLU cc_start: 0.8746 (pm20) cc_final: 0.8245 (pm20) REVERT: B 602 GLU cc_start: 0.7780 (pt0) cc_final: 0.6501 (pt0) REVERT: B 604 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8748 (mmt-90) REVERT: B 610 LYS cc_start: 0.9226 (ptpt) cc_final: 0.8929 (ptmm) REVERT: B 620 SER cc_start: 0.9484 (OUTLIER) cc_final: 0.9261 (p) REVERT: C 95 MET cc_start: 0.7470 (ppp) cc_final: 0.7095 (ppp) REVERT: C 149 ASP cc_start: 0.8193 (m-30) cc_final: 0.7988 (m-30) REVERT: C 157 MET cc_start: 0.8711 (mtp) cc_final: 0.8341 (ttt) REVERT: C 169 TYR cc_start: 0.8734 (m-80) cc_final: 0.8453 (m-80) REVERT: C 178 PHE cc_start: 0.7921 (m-10) cc_final: 0.7634 (m-80) REVERT: C 227 PHE cc_start: 0.6255 (m-80) cc_final: 0.6025 (m-80) REVERT: C 238 ASN cc_start: 0.6964 (m-40) cc_final: 0.6481 (m-40) REVERT: C 240 LEU cc_start: 0.6271 (OUTLIER) cc_final: 0.5974 (mm) outliers start: 59 outliers final: 25 residues processed: 571 average time/residue: 0.2709 time to fit residues: 230.8598 Evaluate side-chains 510 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 475 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 640 MET 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 143 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 136 GLN 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 C residue 240 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 67 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 175 optimal weight: 9.9990 chunk 182 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 150 GLN ** 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** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.152597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.108111 restraints weight = 31984.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.111435 restraints weight = 15079.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113644 restraints weight = 8906.312| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 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 = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16386 Z= 0.151 Angle : 0.625 11.515 22134 Z= 0.322 Chirality : 0.043 0.202 2360 Planarity : 0.003 0.040 2818 Dihedral : 10.835 179.853 2245 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.61 % Allowed : 23.43 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.19), residues: 1932 helix: 1.35 (0.15), residues: 1122 sheet: -0.12 (0.50), residues: 110 loop : 0.41 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 44 HIS 0.007 0.001 HIS C 201 PHE 0.025 0.002 PHE C 168 TYR 0.022 0.001 TYR C 204 ARG 0.004 0.000 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 871) hydrogen bonds : angle 4.93096 ( 2571) covalent geometry : bond 0.00344 (16386) covalent geometry : angle 0.62475 (22134) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 504 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8974 (p0) cc_final: 0.8743 (p0) REVERT: A 65 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7444 (mp0) REVERT: A 119 GLU cc_start: 0.8279 (mp0) cc_final: 0.8029 (mp0) REVERT: A 158 ASN cc_start: 0.8772 (m-40) cc_final: 0.8530 (m-40) REVERT: A 172 LEU cc_start: 0.9326 (mp) cc_final: 0.9000 (mp) REVERT: A 317 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7612 (ptp) REVERT: A 357 TYR cc_start: 0.9006 (m-10) cc_final: 0.7986 (m-10) REVERT: A 361 GLN cc_start: 0.8854 (tp40) cc_final: 0.8642 (tp40) REVERT: A 384 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7477 (pm20) REVERT: A 402 GLU cc_start: 0.7474 (tm-30) cc_final: 0.7199 (tm-30) REVERT: A 411 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7466 (mp) REVERT: A 444 ASP cc_start: 0.8606 (t70) cc_final: 0.8193 (t70) REVERT: A 453 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8261 (ttt-90) REVERT: A 456 LYS cc_start: 0.8976 (mtmm) cc_final: 0.8743 (mtmm) REVERT: A 505 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8143 (mt-10) REVERT: A 515 ASP cc_start: 0.8817 (m-30) cc_final: 0.8558 (m-30) REVERT: A 546 LEU cc_start: 0.9461 (mt) cc_final: 0.9239 (mt) REVERT: A 571 TYR cc_start: 0.9251 (t80) cc_final: 0.8692 (t80) REVERT: A 640 MET cc_start: 0.9284 (OUTLIER) cc_final: 0.8693 (tpp) REVERT: A 645 GLN cc_start: 0.9059 (tp40) cc_final: 0.8533 (tp-100) REVERT: B 18 ILE cc_start: 0.9441 (mm) cc_final: 0.9174 (mp) REVERT: B 27 ASP cc_start: 0.8815 (p0) cc_final: 0.8603 (p0) REVERT: B 52 LYS cc_start: 0.9400 (tppt) cc_final: 0.9084 (tppt) REVERT: B 71 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9265 (mp) REVERT: B 79 GLU cc_start: 0.8893 (tp30) cc_final: 0.8242 (tp30) REVERT: B 232 ASN cc_start: 0.8905 (OUTLIER) cc_final: 0.8679 (m-40) REVERT: B 257 ASP cc_start: 0.8914 (m-30) cc_final: 0.8712 (m-30) REVERT: B 314 MET cc_start: 0.9154 (ttp) cc_final: 0.8906 (tmm) REVERT: B 315 ASP cc_start: 0.8888 (p0) cc_final: 0.8664 (p0) REVERT: B 319 MET cc_start: 0.8917 (tpp) cc_final: 0.8620 (tpp) REVERT: B 338 ASN cc_start: 0.9362 (OUTLIER) cc_final: 0.9085 (t0) REVERT: B 416 ILE cc_start: 0.9178 (mm) cc_final: 0.8903 (mm) REVERT: B 467 ASN cc_start: 0.9145 (t0) cc_final: 0.8556 (t0) REVERT: B 526 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8360 (mm-30) REVERT: B 586 TYR cc_start: 0.8498 (m-80) cc_final: 0.8080 (m-80) REVERT: B 599 GLU cc_start: 0.8742 (pm20) cc_final: 0.8279 (pm20) REVERT: B 602 GLU cc_start: 0.7737 (pt0) cc_final: 0.6503 (pt0) REVERT: B 604 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8758 (mmt-90) REVERT: B 610 LYS cc_start: 0.9355 (ptpt) cc_final: 0.8973 (ptmm) REVERT: B 612 TYR cc_start: 0.8805 (m-80) cc_final: 0.7781 (m-80) REVERT: B 620 SER cc_start: 0.9474 (OUTLIER) cc_final: 0.9246 (p) REVERT: C 56 MET cc_start: 0.5815 (ppp) cc_final: 0.5233 (ppp) REVERT: C 95 MET cc_start: 0.7261 (ppp) cc_final: 0.6884 (ppp) REVERT: C 149 ASP cc_start: 0.8132 (m-30) cc_final: 0.7907 (m-30) REVERT: C 157 MET cc_start: 0.8722 (mtp) cc_final: 0.8341 (ttt) REVERT: C 169 TYR cc_start: 0.8778 (m-80) cc_final: 0.8505 (m-80) REVERT: C 178 PHE cc_start: 0.7916 (m-10) cc_final: 0.7632 (m-80) REVERT: C 189 GLU cc_start: 0.3450 (OUTLIER) cc_final: 0.2456 (mt-10) REVERT: C 227 PHE cc_start: 0.6286 (m-80) cc_final: 0.5987 (m-80) REVERT: C 238 ASN cc_start: 0.6755 (m-40) cc_final: 0.6289 (m-40) REVERT: D 185 MET cc_start: -0.0993 (mmm) cc_final: -0.1429 (mmm) outliers start: 62 outliers final: 36 residues processed: 535 average time/residue: 0.2618 time to fit residues: 210.4816 Evaluate side-chains 516 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 468 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 134 THR 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 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 390 GLN 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 565 VAL Chi-restraints excluded: chain A residue 640 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 71 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 200 SER 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 B residue 526 GLU Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 136 GLN 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 203 VAL Chi-restraints excluded: chain D residue 242 TYR 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 31 optimal weight: 6.9990 chunk 126 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 156 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 169 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 191 GLN B 232 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN D 25 ASN ** 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 = 0.3767 r_free = 0.3767 target = 0.144910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.100473 restraints weight = 32739.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.103721 restraints weight = 15880.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.105807 restraints weight = 9730.227| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 16386 Z= 0.341 Angle : 0.758 12.961 22134 Z= 0.394 Chirality : 0.048 0.403 2360 Planarity : 0.004 0.046 2818 Dihedral : 10.996 166.078 2245 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.66 % Allowed : 22.73 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.19), residues: 1932 helix: 0.99 (0.15), residues: 1139 sheet: -0.79 (0.47), residues: 122 loop : 0.45 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP D 44 HIS 0.009 0.002 HIS A 647 PHE 0.033 0.002 PHE A 492 TYR 0.025 0.002 TYR C 204 ARG 0.005 0.001 ARG A 163 Details of bonding type rmsd hydrogen bonds : bond 0.04438 ( 871) hydrogen bonds : angle 5.28138 ( 2571) covalent geometry : bond 0.00751 (16386) covalent geometry : angle 0.75828 (22134) *********************** 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 545 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 465 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8437 (mm-30) cc_final: 0.7432 (mp0) REVERT: A 117 ARG cc_start: 0.8596 (mtp85) cc_final: 0.8390 (mtp85) REVERT: A 119 GLU cc_start: 0.8395 (mp0) cc_final: 0.8104 (mp0) REVERT: A 172 LEU cc_start: 0.9348 (mp) cc_final: 0.9141 (mp) REVERT: A 188 ILE cc_start: 0.9537 (mt) cc_final: 0.9299 (mm) REVERT: A 357 TYR cc_start: 0.9095 (m-10) cc_final: 0.8155 (m-10) REVERT: A 384 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8038 (pp20) REVERT: A 402 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7363 (tm-30) REVERT: A 453 ARG cc_start: 0.9263 (OUTLIER) cc_final: 0.8460 (ttt-90) REVERT: A 456 LYS cc_start: 0.8967 (mtmm) cc_final: 0.8744 (mtmm) REVERT: A 505 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8078 (mt-10) REVERT: A 515 ASP cc_start: 0.8894 (m-30) cc_final: 0.8654 (m-30) REVERT: A 640 MET cc_start: 0.9316 (OUTLIER) cc_final: 0.8778 (tpp) REVERT: A 684 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.7536 (m-80) REVERT: B 52 LYS cc_start: 0.9391 (tppt) cc_final: 0.9070 (tppt) REVERT: B 79 GLU cc_start: 0.8970 (tp30) cc_final: 0.8290 (tp30) REVERT: B 104 TYR cc_start: 0.8812 (m-80) cc_final: 0.8606 (m-80) REVERT: B 184 ARG cc_start: 0.9067 (tpp-160) cc_final: 0.8850 (tpp-160) REVERT: B 214 LYS cc_start: 0.8247 (ttmm) cc_final: 0.7916 (mmtm) REVERT: B 232 ASN cc_start: 0.9067 (OUTLIER) cc_final: 0.8804 (m-40) REVERT: B 257 ASP cc_start: 0.9063 (m-30) cc_final: 0.8790 (m-30) REVERT: B 384 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.7370 (pm20) REVERT: B 599 GLU cc_start: 0.8801 (pm20) cc_final: 0.8359 (pm20) REVERT: B 602 GLU cc_start: 0.8014 (pt0) cc_final: 0.7575 (pt0) REVERT: B 604 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8731 (mmt-90) REVERT: B 610 LYS cc_start: 0.9392 (ptpt) cc_final: 0.8909 (ptmm) REVERT: B 620 SER cc_start: 0.9520 (OUTLIER) cc_final: 0.9304 (p) REVERT: C 149 ASP cc_start: 0.8255 (m-30) cc_final: 0.8021 (m-30) REVERT: C 157 MET cc_start: 0.8760 (mtp) cc_final: 0.8391 (ttt) REVERT: C 169 TYR cc_start: 0.8768 (m-80) cc_final: 0.8508 (m-80) REVERT: C 178 PHE cc_start: 0.8041 (m-10) cc_final: 0.7736 (m-80) REVERT: D 174 TYR cc_start: 0.6342 (OUTLIER) cc_final: 0.5965 (t80) REVERT: D 185 MET cc_start: -0.0595 (mmm) cc_final: -0.0973 (mmm) outliers start: 80 outliers final: 49 residues processed: 504 average time/residue: 0.2654 time to fit residues: 200.5362 Evaluate side-chains 502 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 444 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 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 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 640 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 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 260 ASP Chi-restraints excluded: chain B residue 276 LYS 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 B residue 598 MET Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 39 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 175 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** 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 270 ASN D 24 GLN D 28 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.152379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.107834 restraints weight = 32335.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.111346 restraints weight = 15431.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.113633 restraints weight = 9264.920| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16386 Z= 0.143 Angle : 0.672 14.285 22134 Z= 0.342 Chirality : 0.045 0.396 2360 Planarity : 0.003 0.047 2818 Dihedral : 10.524 152.499 2245 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.38 % Allowed : 25.23 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.19), residues: 1932 helix: 1.11 (0.15), residues: 1137 sheet: -0.00 (0.53), residues: 106 loop : 0.31 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 44 HIS 0.014 0.001 HIS C 201 PHE 0.031 0.002 PHE C 92 TYR 0.025 0.001 TYR C 105 ARG 0.005 0.001 ARG A 350 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 871) hydrogen bonds : angle 5.06518 ( 2571) covalent geometry : bond 0.00321 (16386) covalent geometry : angle 0.67242 (22134) *********************** 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 557 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 499 time to evaluate : 1.875 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 64 TYR cc_start: 0.8135 (m-10) cc_final: 0.7762 (m-10) REVERT: A 65 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7394 (mp0) REVERT: A 119 GLU cc_start: 0.8277 (mp0) cc_final: 0.7967 (mp0) REVERT: A 158 ASN cc_start: 0.8716 (m-40) cc_final: 0.8468 (m-40) REVERT: A 172 LEU cc_start: 0.9374 (mp) cc_final: 0.9103 (mp) REVERT: A 232 ASN cc_start: 0.8805 (m110) cc_final: 0.8335 (m-40) REVERT: A 350 ARG cc_start: 0.8458 (mtp85) cc_final: 0.8034 (mtp180) REVERT: A 357 TYR cc_start: 0.9001 (m-10) cc_final: 0.7935 (m-10) REVERT: A 359 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8508 (ttp) REVERT: A 361 GLN cc_start: 0.8773 (tp40) cc_final: 0.8250 (tp40) REVERT: A 384 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7303 (pm20) REVERT: A 402 GLU cc_start: 0.7404 (tm-30) cc_final: 0.7166 (tm-30) REVERT: A 411 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7102 (mp) REVERT: A 456 LYS cc_start: 0.8957 (mtmm) cc_final: 0.8713 (mtmm) REVERT: A 505 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8034 (mt-10) REVERT: A 515 ASP cc_start: 0.8827 (m-30) cc_final: 0.8561 (m-30) REVERT: A 571 TYR cc_start: 0.9237 (t80) cc_final: 0.8690 (t80) REVERT: A 588 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8637 (mm-40) REVERT: A 628 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8521 (mt-10) REVERT: A 640 MET cc_start: 0.9323 (OUTLIER) cc_final: 0.8782 (tpp) REVERT: A 645 GLN cc_start: 0.9144 (tp40) cc_final: 0.8506 (tp-100) REVERT: B 27 ASP cc_start: 0.8783 (p0) cc_final: 0.8388 (p0) REVERT: B 52 LYS cc_start: 0.9433 (tppt) cc_final: 0.9128 (tppt) REVERT: B 79 GLU cc_start: 0.8936 (tp30) cc_final: 0.8292 (tp30) REVERT: B 111 LYS cc_start: 0.9388 (mmtp) cc_final: 0.9065 (mmtt) REVERT: B 232 ASN cc_start: 0.8882 (OUTLIER) cc_final: 0.8636 (m-40) REVERT: B 257 ASP cc_start: 0.8938 (m-30) cc_final: 0.8693 (m-30) REVERT: B 344 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8279 (mt-10) REVERT: B 384 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.7229 (pm20) REVERT: B 586 TYR cc_start: 0.8487 (m-80) cc_final: 0.8029 (m-10) REVERT: B 589 SER cc_start: 0.9677 (t) cc_final: 0.9406 (t) REVERT: B 599 GLU cc_start: 0.8688 (pm20) cc_final: 0.8218 (pm20) REVERT: B 602 GLU cc_start: 0.7681 (pt0) cc_final: 0.6143 (pt0) REVERT: B 604 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8719 (mmt-90) REVERT: B 610 LYS cc_start: 0.9419 (ptpt) cc_final: 0.9037 (ptmm) REVERT: B 620 SER cc_start: 0.9500 (OUTLIER) cc_final: 0.9282 (p) REVERT: C 95 MET cc_start: 0.7568 (ppp) cc_final: 0.7221 (ppp) REVERT: C 149 ASP cc_start: 0.8331 (m-30) cc_final: 0.8095 (m-30) REVERT: C 157 MET cc_start: 0.8801 (mtp) cc_final: 0.8376 (ttt) REVERT: C 169 TYR cc_start: 0.8837 (m-80) cc_final: 0.8557 (m-80) REVERT: C 178 PHE cc_start: 0.7927 (m-10) cc_final: 0.7635 (m-80) REVERT: C 238 ASN cc_start: 0.6820 (m-40) cc_final: 0.6129 (m-40) REVERT: D 185 MET cc_start: -0.0978 (mmm) cc_final: -0.1233 (mmm) outliers start: 58 outliers final: 35 residues processed: 525 average time/residue: 0.2668 time to fit residues: 210.2030 Evaluate side-chains 514 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 471 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 640 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 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER 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 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 189 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 242 TYR 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 96 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 159 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 108 optimal weight: 0.4980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.150041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.106136 restraints weight = 32251.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.109539 restraints weight = 15488.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.111690 restraints weight = 9337.892| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.6016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16386 Z= 0.180 Angle : 0.691 15.246 22134 Z= 0.354 Chirality : 0.046 0.374 2360 Planarity : 0.004 0.047 2818 Dihedral : 10.350 154.321 2245 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.67 % Allowed : 26.22 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.19), residues: 1932 helix: 1.09 (0.15), residues: 1138 sheet: -0.26 (0.44), residues: 132 loop : 0.36 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 44 HIS 0.015 0.001 HIS C 201 PHE 0.032 0.002 PHE A 654 TYR 0.044 0.002 TYR B 36 ARG 0.008 0.001 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.04001 ( 871) hydrogen bonds : angle 5.10082 ( 2571) covalent geometry : bond 0.00408 (16386) covalent geometry : angle 0.69093 (22134) *********************** 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 545 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 482 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7387 (mp0) REVERT: A 119 GLU cc_start: 0.8313 (mp0) cc_final: 0.8022 (mp0) REVERT: A 158 ASN cc_start: 0.8723 (m-40) cc_final: 0.8464 (m-40) REVERT: A 172 LEU cc_start: 0.9376 (mp) cc_final: 0.9138 (mp) REVERT: A 214 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7529 (mmtm) REVERT: A 357 TYR cc_start: 0.9002 (m-10) cc_final: 0.7998 (m-10) REVERT: A 359 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8491 (ttp) REVERT: A 361 GLN cc_start: 0.8751 (tp40) cc_final: 0.8233 (tp40) REVERT: A 384 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7323 (pm20) REVERT: A 402 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7217 (tm-30) REVERT: A 456 LYS cc_start: 0.8968 (mtmm) cc_final: 0.8727 (mtmm) REVERT: A 505 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8150 (mt-10) REVERT: A 515 ASP cc_start: 0.8832 (m-30) cc_final: 0.8596 (m-30) REVERT: A 571 TYR cc_start: 0.9224 (t80) cc_final: 0.8706 (t80) REVERT: A 588 GLN cc_start: 0.9138 (mm-40) cc_final: 0.8597 (mm-40) REVERT: A 640 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8589 (tpp) REVERT: A 645 GLN cc_start: 0.9153 (tp40) cc_final: 0.8520 (tp-100) REVERT: A 686 ARG cc_start: 0.8071 (mmt180) cc_final: 0.7835 (mmt-90) REVERT: B 52 LYS cc_start: 0.9439 (tppt) cc_final: 0.9142 (tppt) REVERT: B 79 GLU cc_start: 0.8940 (tp30) cc_final: 0.8270 (tp30) REVERT: B 104 TYR cc_start: 0.8759 (m-80) cc_final: 0.8211 (m-80) REVERT: B 111 LYS cc_start: 0.9387 (mmtp) cc_final: 0.9133 (mmtt) REVERT: B 232 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8669 (m-40) REVERT: B 257 ASP cc_start: 0.8974 (m-30) cc_final: 0.8721 (m-30) REVERT: B 312 GLN cc_start: 0.8972 (mt0) cc_final: 0.8545 (mt0) REVERT: B 344 GLU cc_start: 0.8620 (mt-10) cc_final: 0.7992 (mt-10) REVERT: B 384 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.7282 (pm20) REVERT: B 467 ASN cc_start: 0.9265 (t0) cc_final: 0.8448 (t0) REVERT: B 526 GLU cc_start: 0.8607 (mp0) cc_final: 0.8338 (mm-30) REVERT: B 586 TYR cc_start: 0.8520 (m-80) cc_final: 0.8108 (m-80) REVERT: B 589 SER cc_start: 0.9638 (t) cc_final: 0.9405 (t) REVERT: B 599 GLU cc_start: 0.8718 (pm20) cc_final: 0.8351 (pm20) REVERT: B 602 GLU cc_start: 0.7721 (pt0) cc_final: 0.6533 (pt0) REVERT: B 610 LYS cc_start: 0.9432 (ptpt) cc_final: 0.9085 (ptmm) REVERT: B 612 TYR cc_start: 0.8805 (m-80) cc_final: 0.7444 (m-80) REVERT: B 620 SER cc_start: 0.9506 (OUTLIER) cc_final: 0.9290 (p) REVERT: C 95 MET cc_start: 0.7613 (ppp) cc_final: 0.7305 (ppp) REVERT: C 149 ASP cc_start: 0.8291 (m-30) cc_final: 0.8033 (m-30) REVERT: C 157 MET cc_start: 0.8761 (mtp) cc_final: 0.8363 (ttt) REVERT: C 169 TYR cc_start: 0.8868 (m-80) cc_final: 0.8563 (m-80) REVERT: C 178 PHE cc_start: 0.7910 (m-10) cc_final: 0.7625 (m-80) REVERT: D 204 TYR cc_start: 0.7157 (OUTLIER) cc_final: 0.6592 (t80) REVERT: D 259 PHE cc_start: 0.5288 (OUTLIER) cc_final: 0.4946 (t80) outliers start: 63 outliers final: 45 residues processed: 508 average time/residue: 0.2605 time to fit residues: 200.4225 Evaluate side-chains 520 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 466 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 640 MET 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 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 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 B residue 620 SER 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 72 THR 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 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 D residue 204 TYR Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 283 ASN 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 111 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 182 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 127 optimal weight: 0.4980 chunk 188 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN D 80 HIS ** 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 = 0.3837 r_free = 0.3837 target = 0.151261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.107100 restraints weight = 32460.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.110532 restraints weight = 15442.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.112716 restraints weight = 9498.780| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.6173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 16386 Z= 0.191 Angle : 0.701 14.913 22134 Z= 0.359 Chirality : 0.046 0.370 2360 Planarity : 0.004 0.047 2818 Dihedral : 10.095 150.833 2245 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.55 % Allowed : 26.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.19), residues: 1932 helix: 1.00 (0.15), residues: 1141 sheet: -0.52 (0.50), residues: 106 loop : 0.30 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 44 HIS 0.017 0.001 HIS C 201 PHE 0.028 0.002 PHE B 261 TYR 0.042 0.002 TYR B 36 ARG 0.007 0.001 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 871) hydrogen bonds : angle 5.10782 ( 2571) covalent geometry : bond 0.00429 (16386) covalent geometry : angle 0.70080 (22134) *********************** 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 532 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 471 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7442 (mp0) REVERT: A 117 ARG cc_start: 0.8612 (mtp85) cc_final: 0.8118 (mtp85) REVERT: A 119 GLU cc_start: 0.8329 (mp0) cc_final: 0.8042 (mp0) REVERT: A 121 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.7849 (tpm-80) REVERT: A 158 ASN cc_start: 0.8698 (m-40) cc_final: 0.8458 (m-40) REVERT: A 172 LEU cc_start: 0.9395 (mp) cc_final: 0.9136 (mp) REVERT: A 348 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7580 (ptt) REVERT: A 350 ARG cc_start: 0.8578 (mtp85) cc_final: 0.8114 (mtp85) REVERT: A 357 TYR cc_start: 0.9013 (m-10) cc_final: 0.7983 (m-10) REVERT: A 361 GLN cc_start: 0.8751 (tp40) cc_final: 0.8530 (tp40) REVERT: A 384 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7261 (pm20) REVERT: A 389 SER cc_start: 0.9209 (OUTLIER) cc_final: 0.8905 (p) REVERT: A 402 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7410 (tm-30) REVERT: A 456 LYS cc_start: 0.8979 (mtmm) cc_final: 0.8738 (mtmm) REVERT: A 505 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8205 (mt-10) REVERT: A 515 ASP cc_start: 0.8840 (m-30) cc_final: 0.8608 (m-30) REVERT: A 571 TYR cc_start: 0.9234 (t80) cc_final: 0.8710 (t80) REVERT: A 640 MET cc_start: 0.9284 (OUTLIER) cc_final: 0.8664 (tpp) REVERT: A 645 GLN cc_start: 0.9161 (tp40) cc_final: 0.8539 (tp-100) REVERT: B 27 ASP cc_start: 0.8853 (p0) cc_final: 0.8495 (p0) REVERT: B 52 LYS cc_start: 0.9420 (tppt) cc_final: 0.9197 (tppt) REVERT: B 79 GLU cc_start: 0.8972 (tp30) cc_final: 0.8287 (tp30) REVERT: B 111 LYS cc_start: 0.9381 (mmtp) cc_final: 0.9133 (mmtt) REVERT: B 232 ASN cc_start: 0.8896 (OUTLIER) cc_final: 0.8627 (m110) REVERT: B 257 ASP cc_start: 0.8973 (m-30) cc_final: 0.8725 (m-30) REVERT: B 312 GLN cc_start: 0.8989 (mt0) cc_final: 0.8548 (mt0) REVERT: B 344 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8012 (mt-10) REVERT: B 384 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.7206 (pm20) REVERT: B 467 ASN cc_start: 0.9257 (t0) cc_final: 0.8464 (t0) REVERT: B 526 GLU cc_start: 0.8604 (mp0) cc_final: 0.8324 (mm-30) REVERT: B 586 TYR cc_start: 0.8507 (m-80) cc_final: 0.8075 (m-80) REVERT: B 599 GLU cc_start: 0.8695 (pm20) cc_final: 0.8318 (pm20) REVERT: B 602 GLU cc_start: 0.7664 (pt0) cc_final: 0.6283 (pt0) REVERT: B 610 LYS cc_start: 0.9445 (ptpt) cc_final: 0.9063 (ptmm) REVERT: B 620 SER cc_start: 0.9504 (OUTLIER) cc_final: 0.9284 (p) REVERT: C 95 MET cc_start: 0.7718 (ppp) cc_final: 0.7439 (ppp) REVERT: C 149 ASP cc_start: 0.8251 (m-30) cc_final: 0.7989 (m-30) REVERT: C 157 MET cc_start: 0.8794 (mtp) cc_final: 0.8380 (ttt) REVERT: C 178 PHE cc_start: 0.7991 (m-10) cc_final: 0.7726 (m-80) REVERT: D 157 MET cc_start: 0.0365 (ppp) cc_final: -0.0088 (ppp) REVERT: D 204 TYR cc_start: 0.7173 (OUTLIER) cc_final: 0.6712 (t80) outliers start: 61 outliers final: 43 residues processed: 498 average time/residue: 0.3127 time to fit residues: 235.0092 Evaluate side-chains 508 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 456 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 121 ARG 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 289 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 640 MET 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 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 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 B residue 620 SER 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 72 THR 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 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 D residue 204 TYR Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 283 ASN 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 137 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 160 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 148 optimal weight: 9.9990 chunk 127 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** 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 25 ASN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN D 283 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.148781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.105124 restraints weight = 32696.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.108536 restraints weight = 15795.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.110683 restraints weight = 9626.340| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.6317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 16386 Z= 0.246 Angle : 0.753 14.998 22134 Z= 0.385 Chirality : 0.047 0.406 2360 Planarity : 0.004 0.047 2818 Dihedral : 10.113 149.496 2245 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.61 % Allowed : 27.21 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.19), residues: 1932 helix: 0.93 (0.15), residues: 1136 sheet: -1.01 (0.47), residues: 118 loop : 0.32 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP D 44 HIS 0.019 0.002 HIS C 201 PHE 0.028 0.002 PHE B 261 TYR 0.039 0.002 TYR B 36 ARG 0.006 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04172 ( 871) hydrogen bonds : angle 5.22963 ( 2571) covalent geometry : bond 0.00551 (16386) covalent geometry : angle 0.75282 (22134) ********************** 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 517 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 455 time to evaluate : 1.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7488 (mp0) REVERT: A 117 ARG cc_start: 0.8626 (mtp85) cc_final: 0.8127 (mtp85) REVERT: A 119 GLU cc_start: 0.8341 (mp0) cc_final: 0.8054 (mp0) REVERT: A 121 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.7970 (tpm-80) REVERT: A 158 ASN cc_start: 0.8772 (m-40) cc_final: 0.8509 (m-40) REVERT: A 172 LEU cc_start: 0.9402 (mp) cc_final: 0.9157 (mp) REVERT: A 174 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7788 (mt-10) REVERT: A 188 ILE cc_start: 0.9502 (mt) cc_final: 0.9257 (mm) REVERT: A 348 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7627 (ptt) REVERT: A 357 TYR cc_start: 0.9000 (m-10) cc_final: 0.8036 (m-10) REVERT: A 361 GLN cc_start: 0.8793 (tp40) cc_final: 0.8569 (tp40) REVERT: A 384 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7212 (pm20) REVERT: A 389 SER cc_start: 0.9243 (OUTLIER) cc_final: 0.8557 (p) REVERT: A 402 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7408 (tm-30) REVERT: A 456 LYS cc_start: 0.8996 (mtmm) cc_final: 0.8759 (mtmm) REVERT: A 505 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8159 (mt-10) REVERT: A 515 ASP cc_start: 0.8845 (m-30) cc_final: 0.8627 (m-30) REVERT: A 571 TYR cc_start: 0.9260 (t80) cc_final: 0.8661 (t80) REVERT: A 640 MET cc_start: 0.9257 (OUTLIER) cc_final: 0.8580 (tpp) REVERT: A 645 GLN cc_start: 0.9200 (tp40) cc_final: 0.8566 (tp-100) REVERT: B 52 LYS cc_start: 0.9405 (tppt) cc_final: 0.9094 (tppt) REVERT: B 79 GLU cc_start: 0.8952 (tp30) cc_final: 0.8298 (tp30) REVERT: B 111 LYS cc_start: 0.9391 (mmtp) cc_final: 0.9142 (mmtt) REVERT: B 184 ARG cc_start: 0.9110 (tpp-160) cc_final: 0.8904 (tpp-160) REVERT: B 191 GLN cc_start: 0.8368 (mt0) cc_final: 0.8051 (mt0) REVERT: B 232 ASN cc_start: 0.8922 (OUTLIER) cc_final: 0.8663 (m110) REVERT: B 257 ASP cc_start: 0.8995 (m-30) cc_final: 0.8710 (m-30) REVERT: B 312 GLN cc_start: 0.8973 (mt0) cc_final: 0.8536 (mt0) REVERT: B 344 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8019 (mt-10) REVERT: B 384 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.7243 (pm20) REVERT: B 447 ASN cc_start: 0.8563 (m-40) cc_final: 0.7658 (m-40) REVERT: B 467 ASN cc_start: 0.9324 (t0) cc_final: 0.8572 (t0) REVERT: B 526 GLU cc_start: 0.8655 (mp0) cc_final: 0.8369 (mm-30) REVERT: B 586 TYR cc_start: 0.8559 (m-80) cc_final: 0.8245 (m-80) REVERT: B 589 SER cc_start: 0.9640 (t) cc_final: 0.9380 (t) REVERT: B 599 GLU cc_start: 0.8751 (pm20) cc_final: 0.8361 (pm20) REVERT: B 602 GLU cc_start: 0.7756 (pt0) cc_final: 0.6743 (pt0) REVERT: B 610 LYS cc_start: 0.9446 (ptpt) cc_final: 0.9057 (ptmm) REVERT: B 620 SER cc_start: 0.9518 (OUTLIER) cc_final: 0.9312 (p) REVERT: B 686 ARG cc_start: 0.8121 (mmt-90) cc_final: 0.7831 (mpt90) REVERT: C 95 MET cc_start: 0.7851 (ppp) cc_final: 0.7590 (ppp) REVERT: C 149 ASP cc_start: 0.8203 (m-30) cc_final: 0.7931 (m-30) REVERT: C 157 MET cc_start: 0.8821 (mtp) cc_final: 0.8386 (ttt) REVERT: C 178 PHE cc_start: 0.7880 (m-10) cc_final: 0.7634 (m-80) REVERT: C 233 ASN cc_start: 0.8813 (m-40) cc_final: 0.8592 (t0) REVERT: D 204 TYR cc_start: 0.7256 (OUTLIER) cc_final: 0.6809 (t80) outliers start: 62 outliers final: 43 residues processed: 483 average time/residue: 0.2599 time to fit residues: 188.6367 Evaluate side-chains 497 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 445 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 121 ARG 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 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 344 GLU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 653 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 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 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 B residue 620 SER 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 64 LEU Chi-restraints excluded: chain C residue 72 THR 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 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 D residue 204 TYR Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 81 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 179 optimal weight: 20.0000 chunk 190 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 180 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN B 61 ASN ** 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 132 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.152636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.109308 restraints weight = 32208.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.112729 restraints weight = 15538.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.114943 restraints weight = 9290.090| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 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 = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.6479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16386 Z= 0.146 Angle : 0.733 15.283 22134 Z= 0.369 Chirality : 0.046 0.423 2360 Planarity : 0.004 0.046 2818 Dihedral : 9.862 138.179 2245 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.09 % Allowed : 27.86 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.19), residues: 1932 helix: 0.94 (0.15), residues: 1139 sheet: -0.49 (0.50), residues: 106 loop : 0.19 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 44 HIS 0.019 0.001 HIS C 201 PHE 0.040 0.002 PHE C 92 TYR 0.034 0.002 TYR B 36 ARG 0.008 0.001 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.03967 ( 871) hydrogen bonds : angle 5.14547 ( 2571) covalent geometry : bond 0.00331 (16386) covalent geometry : angle 0.73329 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6359.13 seconds wall clock time: 111 minutes 57.92 seconds (6717.92 seconds total)