Starting phenix.real_space_refine on Thu Sep 18 10:04:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz2_45051/09_2025/9bz2_45051_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz2_45051/09_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_45051/09_2025/9bz2_45051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz2_45051/09_2025/9bz2_45051.map" model { file = "/net/cci-nas-00/data/ceres_data/9bz2_45051/09_2025/9bz2_45051_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz2_45051/09_2025/9bz2_45051_neut.cif" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.22, per 1000 atoms: 0.20 Number of scatterers: 16038 At special positions: 0 Unit cell: (94.581, 131.193, 132.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 635.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.984A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.954A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.665A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.694A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.627A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.073A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.958A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.677A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.645A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.730A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.027A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.068A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.514A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.669A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.360A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.478A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.478A pdb=" N LEU A 656 " --> pdb=" O ARG A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.185A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.049A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 1.47 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.000 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.420 ------------------------------------------------------------------------------- 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 : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.40 % Allowed : 15.15 % Favored : 83.45 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.18), residues: 1932 helix: 0.58 (0.14), residues: 1151 sheet: 0.46 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 196 TYR 0.020 0.002 TYR C 169 PHE 0.021 0.002 PHE C 168 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00556 (16386) covalent geometry : angle 0.74994 (22134) hydrogen bonds : bond 0.15423 ( 871) hydrogen bonds : angle 6.51784 ( 2571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 809 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ILE cc_start: 0.9185 (mt) cc_final: 0.8940 (mt) REVERT: A 127 LEU cc_start: 0.9149 (mt) cc_final: 0.8851 (mt) REVERT: A 131 ASN cc_start: 0.8653 (t0) cc_final: 0.8375 (t0) REVERT: A 138 LYS cc_start: 0.8180 (mtpt) cc_final: 0.7826 (mtpp) REVERT: A 145 ILE cc_start: 0.9125 (tp) cc_final: 0.8904 (tp) REVERT: A 172 LEU cc_start: 0.9004 (mp) cc_final: 0.8771 (mp) REVERT: A 179 LEU cc_start: 0.8997 (tp) cc_final: 0.8451 (tp) REVERT: A 220 THR cc_start: 0.8806 (m) cc_final: 0.8515 (p) REVERT: A 227 MET cc_start: 0.7829 (mtp) cc_final: 0.7584 (mtp) REVERT: A 319 MET cc_start: 0.7850 (tpp) cc_final: 0.7399 (tpp) REVERT: A 367 VAL cc_start: 0.9098 (m) cc_final: 0.8773 (t) REVERT: A 380 ASN cc_start: 0.8968 (p0) cc_final: 0.8736 (p0) REVERT: A 446 ARG cc_start: 0.7519 (mmm-85) cc_final: 0.7225 (mtp85) REVERT: A 447 ASN cc_start: 0.7944 (m-40) cc_final: 0.7321 (m110) REVERT: A 546 LEU cc_start: 0.8855 (mt) cc_final: 0.8648 (mt) REVERT: A 550 MET cc_start: 0.8096 (mtm) cc_final: 0.7880 (mtt) REVERT: A 598 MET cc_start: 0.8373 (mtm) cc_final: 0.7776 (mtp) REVERT: B 51 LEU cc_start: 0.8213 (tp) cc_final: 0.7883 (tp) REVERT: B 67 GLU cc_start: 0.7746 (mp0) cc_final: 0.7137 (mp0) REVERT: B 106 LEU cc_start: 0.8835 (tp) cc_final: 0.7901 (tt) REVERT: B 127 LEU cc_start: 0.9042 (mt) cc_final: 0.8806 (mt) REVERT: B 129 PHE cc_start: 0.8421 (m-10) cc_final: 0.8054 (m-10) REVERT: B 180 ASN cc_start: 0.7535 (m-40) cc_final: 0.7323 (m110) REVERT: B 186 ILE cc_start: 0.9216 (mt) cc_final: 0.9013 (mt) REVERT: B 211 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7475 (mm-30) REVERT: B 286 ASP cc_start: 0.6894 (OUTLIER) cc_final: 0.6684 (m-30) REVERT: B 319 MET cc_start: 0.7902 (tpp) cc_final: 0.7651 (tpp) REVERT: B 348 MET cc_start: 0.7346 (tmm) cc_final: 0.7076 (ttm) REVERT: B 358 ILE cc_start: 0.9193 (mm) cc_final: 0.8933 (mm) REVERT: B 381 LEU cc_start: 0.9246 (tp) cc_final: 0.8968 (tp) REVERT: B 384 GLU cc_start: 0.8948 (pm20) cc_final: 0.8157 (pm20) REVERT: B 389 SER cc_start: 0.8046 (p) cc_final: 0.7833 (p) REVERT: B 458 MET cc_start: 0.8463 (mmm) cc_final: 0.8144 (mmm) REVERT: B 460 SER cc_start: 0.8912 (t) cc_final: 0.8699 (p) REVERT: B 471 TYR cc_start: 0.8260 (t80) cc_final: 0.7678 (t80) REVERT: B 491 PHE cc_start: 0.8630 (t80) cc_final: 0.8429 (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: 0.8861 (p) REVERT: C 89 VAL cc_start: 0.5232 (t) cc_final: 0.3665 (t) REVERT: C 229 ILE cc_start: 0.5031 (mt) cc_final: 0.4262 (mm) REVERT: D 42 LEU cc_start: 0.1877 (mt) cc_final: 0.1452 (mt) REVERT: D 185 MET cc_start: 0.0973 (mmm) cc_final: 0.0569 (mmm) REVERT: D 282 ILE cc_start: 0.3799 (OUTLIER) cc_final: 0.3395 (pt) outliers start: 24 outliers final: 5 residues processed: 822 average time/residue: 0.1297 time to fit residues: 156.6875 Evaluate side-chains 566 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 559 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 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 410 ASN B 467 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 233 ASN D 71 ASN D 80 HIS D 91 ASN D 186 GLN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.153618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.105493 restraints weight = 31425.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.109078 restraints weight = 15467.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.111245 restraints weight = 9371.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.112656 restraints weight = 6798.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.113393 restraints weight = 5528.174| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 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 = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 16386 Z= 0.296 Angle : 0.720 7.577 22134 Z= 0.379 Chirality : 0.046 0.298 2360 Planarity : 0.004 0.042 2818 Dihedral : 11.772 178.184 2254 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.37 % Allowed : 18.30 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.19), residues: 1932 helix: 1.30 (0.15), residues: 1135 sheet: -0.22 (0.46), residues: 114 loop : 0.66 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 164 TYR 0.032 0.002 TYR D 174 PHE 0.029 0.002 PHE B 261 TRP 0.016 0.003 TRP D 124 HIS 0.006 0.002 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00642 (16386) covalent geometry : angle 0.72012 (22134) hydrogen bonds : bond 0.04781 ( 871) hydrogen bonds : angle 5.15989 ( 2571) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 565 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8848 (p0) cc_final: 0.8491 (p0) REVERT: A 65 GLU cc_start: 0.8428 (mm-30) cc_final: 0.7923 (mp0) REVERT: A 117 ARG cc_start: 0.8445 (mtp85) cc_final: 0.8171 (mtp85) REVERT: A 119 GLU cc_start: 0.8507 (mp0) cc_final: 0.8196 (mp0) REVERT: A 138 LYS cc_start: 0.9059 (mtpt) cc_final: 0.8827 (mtpp) REVERT: A 172 LEU cc_start: 0.9346 (mp) cc_final: 0.9047 (mp) REVERT: A 179 LEU cc_start: 0.9235 (tp) cc_final: 0.9028 (tt) REVERT: A 317 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7951 (ptp) REVERT: A 346 LEU cc_start: 0.9396 (mt) cc_final: 0.9184 (mp) REVERT: A 357 TYR cc_start: 0.9043 (m-10) cc_final: 0.8087 (m-10) REVERT: A 362 ASP cc_start: 0.8469 (m-30) cc_final: 0.8164 (m-30) REVERT: A 379 SER cc_start: 0.9341 (t) cc_final: 0.9139 (t) REVERT: A 384 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7526 (pm20) REVERT: A 402 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7288 (tm-30) REVERT: A 493 MET cc_start: 0.8894 (tmm) cc_final: 0.8460 (tmm) REVERT: A 515 ASP cc_start: 0.8849 (m-30) cc_final: 0.8602 (m-30) REVERT: A 588 GLN cc_start: 0.9113 (mm-40) cc_final: 0.8616 (mm-40) REVERT: A 602 GLU cc_start: 0.7670 (pt0) cc_final: 0.7211 (pt0) REVERT: A 640 MET cc_start: 0.9328 (tpp) cc_final: 0.8903 (tpp) REVERT: A 663 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8196 (t) REVERT: B 52 LYS cc_start: 0.9400 (tppt) cc_final: 0.9073 (tppt) REVERT: B 53 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8410 (mt-10) REVERT: B 79 GLU cc_start: 0.8953 (tp30) cc_final: 0.8238 (tp30) REVERT: B 118 TYR cc_start: 0.9400 (t80) cc_final: 0.9195 (t80) REVERT: B 344 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8458 (mt-10) REVERT: B 362 ASP cc_start: 0.8061 (m-30) cc_final: 0.7792 (m-30) REVERT: B 420 MET cc_start: 0.9371 (mmm) cc_final: 0.9107 (mmm) REVERT: B 425 ILE cc_start: 0.9508 (mt) cc_final: 0.9229 (mt) REVERT: B 515 ASP cc_start: 0.9034 (m-30) cc_final: 0.8813 (m-30) REVERT: B 570 MET cc_start: 0.8211 (mtp) cc_final: 0.7943 (mtt) REVERT: B 602 GLU cc_start: 0.8129 (pt0) cc_final: 0.7614 (pt0) REVERT: B 604 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8388 (mmt-90) REVERT: B 610 LYS cc_start: 0.9091 (ptpt) cc_final: 0.8633 (ptmm) REVERT: B 620 SER cc_start: 0.9519 (OUTLIER) cc_final: 0.9306 (p) REVERT: B 632 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8263 (mtm) REVERT: B 648 ILE cc_start: 0.9113 (mm) cc_final: 0.8815 (mt) REVERT: B 650 GLN cc_start: 0.8478 (mt0) cc_final: 0.8166 (mt0) REVERT: C 56 MET cc_start: 0.4925 (ptt) cc_final: 0.4342 (ppp) REVERT: C 90 LEU cc_start: 0.7524 (mt) cc_final: 0.6953 (mt) REVERT: C 168 PHE cc_start: 0.8521 (m-80) cc_final: 0.8303 (m-80) REVERT: C 178 PHE cc_start: 0.7724 (m-80) cc_final: 0.7472 (m-80) REVERT: C 278 GLU cc_start: 0.8838 (tt0) cc_final: 0.8615 (tp30) REVERT: D 96 MET cc_start: 0.0600 (mmt) cc_final: 0.0322 (mmt) REVERT: D 268 LEU cc_start: 0.4022 (mt) cc_final: 0.3800 (mp) outliers start: 75 outliers final: 30 residues processed: 606 average time/residue: 0.1316 time to fit residues: 119.1611 Evaluate side-chains 512 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 476 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 664 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 D residue 312 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 20.0000 chunk 131 optimal weight: 0.9990 chunk 164 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 182 optimal weight: 5.9990 chunk 159 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.152971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.106672 restraints weight = 31999.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.110152 restraints weight = 15262.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.112427 restraints weight = 9150.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.113876 restraints weight = 6510.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.114655 restraints weight = 5226.376| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16386 Z= 0.170 Angle : 0.632 11.119 22134 Z= 0.328 Chirality : 0.044 0.295 2360 Planarity : 0.003 0.042 2818 Dihedral : 11.279 174.960 2246 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.26 % Allowed : 21.85 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.19), residues: 1932 helix: 1.37 (0.15), residues: 1127 sheet: -0.10 (0.48), residues: 106 loop : 0.46 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 350 TYR 0.042 0.002 TYR D 174 PHE 0.027 0.002 PHE A 492 TRP 0.014 0.002 TRP D 124 HIS 0.006 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00380 (16386) covalent geometry : angle 0.63184 (22134) hydrogen bonds : bond 0.04272 ( 871) hydrogen bonds : angle 4.99424 ( 2571) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 533 time to evaluate : 0.614 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: 0.8941 (p0) cc_final: 0.8653 (p0) REVERT: A 64 TYR cc_start: 0.8466 (m-10) cc_final: 0.7448 (m-10) REVERT: A 65 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7285 (mp0) REVERT: A 117 ARG cc_start: 0.8472 (mtp85) cc_final: 0.8266 (mtp85) REVERT: A 119 GLU cc_start: 0.8486 (mp0) cc_final: 0.8091 (mp0) REVERT: A 150 GLN cc_start: 0.9028 (tm-30) cc_final: 0.8795 (tm-30) REVERT: A 161 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7338 (ttm-80) REVERT: A 172 LEU cc_start: 0.9281 (mp) cc_final: 0.8974 (mp) REVERT: A 317 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7900 (ptp) REVERT: A 346 LEU cc_start: 0.9374 (mt) cc_final: 0.9158 (mp) REVERT: A 348 MET cc_start: 0.7513 (ptp) cc_final: 0.7296 (ptm) REVERT: A 357 TYR cc_start: 0.9004 (m-10) cc_final: 0.7976 (m-10) REVERT: A 361 GLN cc_start: 0.8725 (tp40) cc_final: 0.8503 (tp40) REVERT: A 362 ASP cc_start: 0.8380 (m-30) cc_final: 0.7992 (m-30) REVERT: A 384 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.7469 (pm20) REVERT: A 402 GLU cc_start: 0.7411 (tm-30) cc_final: 0.7176 (tm-30) REVERT: A 415 ASN cc_start: 0.8924 (t0) cc_final: 0.8709 (t0) REVERT: A 456 LYS cc_start: 0.8934 (mtmm) cc_final: 0.8627 (mtmm) REVERT: A 493 MET cc_start: 0.8927 (tmm) cc_final: 0.8302 (tmm) REVERT: A 505 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8107 (mt-10) REVERT: A 515 ASP cc_start: 0.8847 (m-30) cc_final: 0.8580 (m-30) REVERT: A 570 MET cc_start: 0.8877 (mtp) cc_final: 0.8633 (mtp) REVERT: A 571 TYR cc_start: 0.9207 (t80) cc_final: 0.8626 (t80) REVERT: A 588 GLN cc_start: 0.9030 (mm-40) cc_final: 0.8741 (mm-40) REVERT: A 640 MET cc_start: 0.9266 (tpp) cc_final: 0.8739 (tpp) REVERT: A 663 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8388 (t) REVERT: B 52 LYS cc_start: 0.9442 (tppt) cc_final: 0.9152 (tppt) REVERT: B 79 GLU cc_start: 0.8836 (tp30) cc_final: 0.8177 (tp30) REVERT: B 118 TYR cc_start: 0.9299 (t80) cc_final: 0.9082 (t80) REVERT: B 184 ARG cc_start: 0.9148 (tpp-160) cc_final: 0.8901 (tpp-160) REVERT: B 209 LYS cc_start: 0.8293 (ttmm) cc_final: 0.7914 (ttmm) REVERT: B 214 LYS cc_start: 0.8285 (ttmm) cc_final: 0.7911 (mmtm) REVERT: B 234 PHE cc_start: 0.8951 (m-80) cc_final: 0.8720 (m-80) REVERT: B 290 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8175 (pp20) REVERT: B 352 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8226 (mt-10) REVERT: B 362 ASP cc_start: 0.7805 (m-30) cc_final: 0.7531 (m-30) REVERT: B 425 ILE cc_start: 0.9499 (mt) cc_final: 0.9263 (mt) REVERT: B 446 ARG cc_start: 0.8512 (ttm-80) cc_final: 0.8257 (ttm-80) REVERT: B 467 ASN cc_start: 0.9161 (t0) cc_final: 0.8347 (t0) REVERT: B 522 TYR cc_start: 0.8986 (m-80) cc_final: 0.8770 (m-10) REVERT: B 570 MET cc_start: 0.8120 (mtp) cc_final: 0.7770 (mtt) REVERT: B 571 TYR cc_start: 0.8950 (t80) cc_final: 0.8744 (t80) REVERT: B 586 TYR cc_start: 0.8612 (m-80) cc_final: 0.8411 (m-80) REVERT: B 599 GLU cc_start: 0.8740 (pm20) cc_final: 0.8451 (pm20) REVERT: B 602 GLU cc_start: 0.7709 (pt0) cc_final: 0.7043 (pt0) REVERT: B 604 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8653 (mmt-90) REVERT: B 610 LYS cc_start: 0.9172 (ptpt) cc_final: 0.8849 (ptmm) REVERT: B 612 TYR cc_start: 0.8857 (m-80) cc_final: 0.7976 (m-80) REVERT: C 157 MET cc_start: 0.8757 (mtp) cc_final: 0.8268 (ttt) REVERT: C 178 PHE cc_start: 0.7593 (m-80) cc_final: 0.7368 (m-80) REVERT: C 278 GLU cc_start: 0.8838 (tt0) cc_final: 0.8607 (tp30) REVERT: D 93 MET cc_start: 0.8042 (mtp) cc_final: 0.7815 (mtp) outliers start: 56 outliers final: 29 residues processed: 563 average time/residue: 0.1225 time to fit residues: 103.1690 Evaluate side-chains 500 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 467 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 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 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 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 287 LEU Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 168 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 185 optimal weight: 6.9990 chunk 191 optimal weight: 20.0000 chunk 159 optimal weight: 9.9990 chunk 182 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 232 ASN B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 146 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.153569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.107354 restraints weight = 32155.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.110678 restraints weight = 15427.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.112935 restraints weight = 9279.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.114224 restraints weight = 6669.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.115110 restraints weight = 5408.925| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16386 Z= 0.188 Angle : 0.629 10.782 22134 Z= 0.327 Chirality : 0.043 0.261 2360 Planarity : 0.003 0.043 2818 Dihedral : 11.004 176.688 2245 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.79 % Allowed : 22.26 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.19), residues: 1932 helix: 1.36 (0.15), residues: 1125 sheet: -0.11 (0.49), residues: 106 loop : 0.42 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 235 TYR 0.027 0.002 TYR D 174 PHE 0.027 0.002 PHE A 492 TRP 0.015 0.002 TRP D 124 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00416 (16386) covalent geometry : angle 0.62856 (22134) hydrogen bonds : bond 0.04086 ( 871) hydrogen bonds : angle 4.97507 ( 2571) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 497 time to evaluate : 0.642 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: 0.8956 (p0) cc_final: 0.8727 (p0) REVERT: A 65 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7457 (mp0) REVERT: A 109 ASN cc_start: 0.9362 (m-40) cc_final: 0.9135 (m-40) REVERT: A 119 GLU cc_start: 0.8292 (mp0) cc_final: 0.7967 (mp0) REVERT: A 150 GLN cc_start: 0.9027 (tm-30) cc_final: 0.8807 (tm-30) REVERT: A 161 ARG cc_start: 0.8184 (ttm-80) cc_final: 0.7537 (ttm-80) REVERT: A 172 LEU cc_start: 0.9307 (mp) cc_final: 0.8984 (mp) REVERT: A 317 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7978 (ptp) REVERT: A 346 LEU cc_start: 0.9396 (mt) cc_final: 0.9189 (mp) REVERT: A 348 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.7326 (ptm) REVERT: A 357 TYR cc_start: 0.9028 (m-10) cc_final: 0.8149 (m-10) REVERT: A 361 GLN cc_start: 0.8754 (tp40) cc_final: 0.8522 (tp40) REVERT: A 362 ASP cc_start: 0.8404 (m-30) cc_final: 0.8036 (m-30) REVERT: A 384 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7336 (pm20) REVERT: A 402 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7255 (tm-30) REVERT: A 415 ASN cc_start: 0.8932 (t0) cc_final: 0.8705 (t0) REVERT: A 444 ASP cc_start: 0.8357 (t70) cc_final: 0.8106 (t70) REVERT: A 505 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8107 (mt-10) REVERT: A 515 ASP cc_start: 0.8833 (m-30) cc_final: 0.8532 (m-30) REVERT: A 588 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8819 (mm-40) REVERT: A 640 MET cc_start: 0.9265 (tpp) cc_final: 0.8670 (tpp) REVERT: A 645 GLN cc_start: 0.9056 (tp-100) cc_final: 0.8775 (tp-100) REVERT: A 663 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8500 (t) REVERT: B 27 ASP cc_start: 0.8907 (p0) cc_final: 0.8334 (p0) REVERT: B 31 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8001 (mt-10) REVERT: B 79 GLU cc_start: 0.8846 (tp30) cc_final: 0.8214 (tp30) REVERT: B 116 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8354 (mp0) REVERT: B 214 LYS cc_start: 0.8071 (ttmm) cc_final: 0.7741 (mmtm) REVERT: B 257 ASP cc_start: 0.8928 (m-30) cc_final: 0.8720 (m-30) REVERT: B 314 MET cc_start: 0.9139 (ttp) cc_final: 0.8935 (tmm) REVERT: B 352 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8177 (mt-10) REVERT: B 384 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.7276 (pm20) REVERT: B 467 ASN cc_start: 0.9183 (t0) cc_final: 0.8546 (t0) REVERT: B 515 ASP cc_start: 0.8892 (m-30) cc_final: 0.8639 (m-30) REVERT: B 570 MET cc_start: 0.8158 (mtp) cc_final: 0.7787 (mtt) REVERT: B 586 TYR cc_start: 0.8582 (m-80) cc_final: 0.8341 (m-80) REVERT: B 595 MET cc_start: 0.8712 (mmm) cc_final: 0.8398 (mmm) REVERT: B 599 GLU cc_start: 0.8774 (pm20) cc_final: 0.8336 (pm20) REVERT: B 602 GLU cc_start: 0.7763 (pt0) cc_final: 0.6844 (pt0) REVERT: B 604 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8705 (mmt-90) REVERT: B 610 LYS cc_start: 0.9187 (ptpt) cc_final: 0.8859 (ptmm) REVERT: C 56 MET cc_start: 0.5350 (ptt) cc_final: 0.4855 (ppp) REVERT: C 95 MET cc_start: 0.7928 (ppp) cc_final: 0.7674 (ppp) REVERT: C 157 MET cc_start: 0.8768 (mtp) cc_final: 0.8412 (ttt) REVERT: C 178 PHE cc_start: 0.7575 (m-80) cc_final: 0.7329 (m-80) REVERT: C 238 ASN cc_start: 0.7895 (t0) cc_final: 0.7612 (m-40) REVERT: D 268 LEU cc_start: 0.4214 (mt) cc_final: 0.3951 (mp) outliers start: 65 outliers final: 37 residues processed: 528 average time/residue: 0.1238 time to fit residues: 99.1910 Evaluate side-chains 506 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 463 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 194 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 425 ILE 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 33 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 37 optimal weight: 0.0000 chunk 126 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- 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 ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN ** C 238 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 = 0.3883 r_free = 0.3883 target = 0.154960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.109312 restraints weight = 32230.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.112809 restraints weight = 15373.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.115148 restraints weight = 9200.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.116539 restraints weight = 6535.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.117408 restraints weight = 5266.440| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.5302 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 10.008 22134 Z= 0.317 Chirality : 0.043 0.248 2360 Planarity : 0.003 0.043 2818 Dihedral : 10.703 177.690 2245 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.09 % Allowed : 22.84 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.19), residues: 1932 helix: 1.41 (0.15), residues: 1120 sheet: -0.14 (0.49), residues: 106 loop : 0.36 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 350 TYR 0.021 0.001 TYR A 118 PHE 0.028 0.002 PHE C 168 TRP 0.011 0.001 TRP B 9 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00311 (16386) covalent geometry : angle 0.60851 (22134) hydrogen bonds : bond 0.03903 ( 871) hydrogen bonds : angle 4.92700 ( 2571) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 512 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8938 (p0) cc_final: 0.8695 (p0) REVERT: A 65 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7391 (mp0) REVERT: A 119 GLU cc_start: 0.8293 (mp0) cc_final: 0.8032 (mp0) REVERT: A 158 ASN cc_start: 0.8902 (m-40) cc_final: 0.8585 (m-40) REVERT: A 172 LEU cc_start: 0.9245 (mp) cc_final: 0.8912 (mp) REVERT: A 214 LYS cc_start: 0.7756 (mptt) cc_final: 0.7541 (mptt) REVERT: A 232 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.8152 (m-40) REVERT: A 317 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7602 (ptp) REVERT: A 346 LEU cc_start: 0.9331 (mt) cc_final: 0.9120 (mp) REVERT: A 348 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7322 (ptm) REVERT: A 357 TYR cc_start: 0.9003 (m-10) cc_final: 0.7980 (m-10) REVERT: A 361 GLN cc_start: 0.8720 (tp40) cc_final: 0.8487 (tp40) REVERT: A 362 ASP cc_start: 0.8228 (m-30) cc_final: 0.7883 (m-30) REVERT: A 384 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7406 (pm20) REVERT: A 402 GLU cc_start: 0.7408 (tm-30) cc_final: 0.7160 (tm-30) REVERT: A 415 ASN cc_start: 0.8905 (t0) cc_final: 0.8694 (t0) REVERT: A 444 ASP cc_start: 0.8303 (t70) cc_final: 0.8035 (t70) REVERT: A 446 ARG cc_start: 0.7621 (mmm-85) cc_final: 0.7389 (mmm-85) REVERT: A 505 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8006 (mt-10) REVERT: A 515 ASP cc_start: 0.8796 (m-30) cc_final: 0.8514 (m-30) REVERT: A 571 TYR cc_start: 0.9245 (t80) cc_final: 0.8743 (t80) REVERT: A 640 MET cc_start: 0.9285 (OUTLIER) cc_final: 0.8698 (tpp) REVERT: A 645 GLN cc_start: 0.8871 (tp-100) cc_final: 0.8561 (tp-100) REVERT: B 79 GLU cc_start: 0.8830 (tp30) cc_final: 0.8237 (tp30) REVERT: B 104 TYR cc_start: 0.8724 (m-80) cc_final: 0.8389 (m-80) REVERT: B 116 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8334 (mp0) REVERT: B 319 MET cc_start: 0.8780 (tpp) cc_final: 0.8552 (tpp) REVERT: B 338 ASN cc_start: 0.9345 (OUTLIER) cc_final: 0.9031 (t0) REVERT: B 384 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.7277 (pm20) REVERT: B 441 GLU cc_start: 0.8414 (pt0) cc_final: 0.8174 (pt0) REVERT: B 467 ASN cc_start: 0.9025 (t0) cc_final: 0.8542 (t0) REVERT: B 515 ASP cc_start: 0.8964 (m-30) cc_final: 0.8697 (m-30) REVERT: B 526 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8345 (mm-30) REVERT: B 586 TYR cc_start: 0.8545 (m-80) cc_final: 0.8207 (m-80) REVERT: B 595 MET cc_start: 0.8632 (mmm) cc_final: 0.8267 (mmm) REVERT: B 599 GLU cc_start: 0.8765 (pm20) cc_final: 0.8334 (pm20) REVERT: B 602 GLU cc_start: 0.7770 (pt0) cc_final: 0.6608 (pt0) REVERT: B 610 LYS cc_start: 0.9340 (ptpt) cc_final: 0.8968 (ptmm) REVERT: B 612 TYR cc_start: 0.8838 (m-80) cc_final: 0.7803 (m-80) REVERT: C 56 MET cc_start: 0.5204 (ptt) cc_final: 0.4770 (ppp) REVERT: C 157 MET cc_start: 0.8777 (mtp) cc_final: 0.8402 (ttt) REVERT: C 178 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.7393 (m-80) REVERT: C 233 ASN cc_start: 0.8333 (m-40) cc_final: 0.8069 (m110) REVERT: C 311 THR cc_start: 0.8459 (OUTLIER) cc_final: 0.8169 (t) REVERT: D 259 PHE cc_start: 0.4100 (m-80) cc_final: 0.3654 (m-80) outliers start: 53 outliers final: 30 residues processed: 534 average time/residue: 0.1196 time to fit residues: 96.3806 Evaluate side-chains 500 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 460 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER 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 96 SER Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** 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 = 0.3878 r_free = 0.3878 target = 0.153444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.108046 restraints weight = 32245.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.111448 restraints weight = 15595.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.113789 restraints weight = 9373.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.115200 restraints weight = 6671.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.116082 restraints weight = 5378.041| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16386 Z= 0.146 Angle : 0.626 10.473 22134 Z= 0.326 Chirality : 0.043 0.217 2360 Planarity : 0.003 0.041 2818 Dihedral : 10.604 176.923 2245 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.38 % Allowed : 23.72 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.19), residues: 1932 helix: 1.31 (0.15), residues: 1134 sheet: -0.13 (0.50), residues: 106 loop : 0.27 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 604 TYR 0.032 0.001 TYR B 36 PHE 0.028 0.002 PHE C 168 TRP 0.018 0.002 TRP D 44 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00330 (16386) covalent geometry : angle 0.62608 (22134) hydrogen bonds : bond 0.03837 ( 871) hydrogen bonds : angle 4.94112 ( 2571) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 486 time to evaluate : 0.613 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: 0.8317 (mm-30) cc_final: 0.7307 (mp0) REVERT: A 119 GLU cc_start: 0.8275 (mp0) cc_final: 0.8067 (mp0) REVERT: A 150 GLN cc_start: 0.9164 (tm-30) cc_final: 0.8759 (tm-30) REVERT: A 158 ASN cc_start: 0.8831 (m-40) cc_final: 0.8529 (m-40) REVERT: A 172 LEU cc_start: 0.9258 (mp) cc_final: 0.8928 (mp) REVERT: A 232 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8159 (m-40) REVERT: A 317 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7611 (ptp) REVERT: A 348 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.7274 (ptm) REVERT: A 357 TYR cc_start: 0.9015 (m-10) cc_final: 0.7944 (m-10) REVERT: A 361 GLN cc_start: 0.8627 (tp40) cc_final: 0.8391 (tp40) REVERT: A 384 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7353 (pm20) REVERT: A 402 GLU cc_start: 0.7429 (tm-30) cc_final: 0.7173 (tm-30) REVERT: A 444 ASP cc_start: 0.8426 (t70) cc_final: 0.8010 (t70) REVERT: A 446 ARG cc_start: 0.7747 (mmm-85) cc_final: 0.7472 (mmm-85) REVERT: A 456 LYS cc_start: 0.9015 (mtmm) cc_final: 0.8801 (mtmm) REVERT: A 505 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8096 (mt-10) REVERT: A 515 ASP cc_start: 0.8787 (m-30) cc_final: 0.8512 (m-30) REVERT: A 571 TYR cc_start: 0.9197 (t80) cc_final: 0.8724 (t80) REVERT: A 640 MET cc_start: 0.9284 (OUTLIER) cc_final: 0.8692 (tpp) REVERT: A 645 GLN cc_start: 0.8862 (tp-100) cc_final: 0.8547 (tp-100) REVERT: A 648 ILE cc_start: 0.9164 (mm) cc_final: 0.8941 (mm) REVERT: B 27 ASP cc_start: 0.8838 (p0) cc_final: 0.8511 (p0) REVERT: B 79 GLU cc_start: 0.8840 (tp30) cc_final: 0.8239 (tp30) REVERT: B 104 TYR cc_start: 0.8664 (m-80) cc_final: 0.8175 (m-80) REVERT: B 116 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8363 (mp0) REVERT: B 191 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8513 (mm-40) REVERT: B 338 ASN cc_start: 0.9338 (OUTLIER) cc_final: 0.9032 (t0) REVERT: B 344 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8272 (mt-10) REVERT: B 384 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.7244 (pm20) REVERT: B 447 ASN cc_start: 0.8292 (m-40) cc_final: 0.7906 (m-40) REVERT: B 467 ASN cc_start: 0.9082 (t0) cc_final: 0.8293 (t0) REVERT: B 515 ASP cc_start: 0.8960 (m-30) cc_final: 0.8710 (m-30) REVERT: B 586 TYR cc_start: 0.8557 (m-80) cc_final: 0.8237 (m-80) REVERT: B 595 MET cc_start: 0.8626 (mmm) cc_final: 0.8321 (mmm) REVERT: B 599 GLU cc_start: 0.8751 (pm20) cc_final: 0.8354 (pm20) REVERT: B 610 LYS cc_start: 0.9391 (ptpt) cc_final: 0.9039 (ptmm) REVERT: B 612 TYR cc_start: 0.8825 (m-80) cc_final: 0.7584 (m-80) REVERT: C 56 MET cc_start: 0.5414 (ptt) cc_final: 0.5044 (ppp) REVERT: C 64 LEU cc_start: 0.8151 (tp) cc_final: 0.7905 (pp) REVERT: C 157 MET cc_start: 0.8778 (mtp) cc_final: 0.8259 (ttt) REVERT: C 178 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.7393 (m-80) REVERT: D 174 TYR cc_start: 0.5921 (OUTLIER) cc_final: 0.5396 (t80) REVERT: D 259 PHE cc_start: 0.4241 (m-80) cc_final: 0.3735 (m-80) outliers start: 58 outliers final: 39 residues processed: 511 average time/residue: 0.1155 time to fit residues: 90.5727 Evaluate side-chains 508 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 460 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 186 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN D 25 ASN D 69 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.153856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.108915 restraints weight = 32088.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.112468 restraints weight = 15621.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.114652 restraints weight = 9450.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.116073 restraints weight = 6737.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.116927 restraints weight = 5454.378| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.5730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16386 Z= 0.182 Angle : 0.660 11.283 22134 Z= 0.342 Chirality : 0.044 0.315 2360 Planarity : 0.003 0.044 2818 Dihedral : 10.644 178.845 2245 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.90 % Allowed : 23.89 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.19), residues: 1932 helix: 1.22 (0.15), residues: 1134 sheet: -0.46 (0.48), residues: 114 loop : 0.40 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 604 TYR 0.029 0.002 TYR C 55 PHE 0.027 0.002 PHE C 168 TRP 0.023 0.002 TRP D 44 HIS 0.010 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00409 (16386) covalent geometry : angle 0.66022 (22134) hydrogen bonds : bond 0.03967 ( 871) hydrogen bonds : angle 5.06144 ( 2571) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 470 time to evaluate : 0.750 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 51 LEU cc_start: 0.9112 (mt) cc_final: 0.8843 (mt) REVERT: A 64 TYR cc_start: 0.7970 (m-10) cc_final: 0.7440 (m-10) REVERT: A 65 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7309 (mp0) REVERT: A 119 GLU cc_start: 0.8251 (mp0) cc_final: 0.7934 (mp0) REVERT: A 158 ASN cc_start: 0.8867 (m-40) cc_final: 0.8600 (m-40) REVERT: A 172 LEU cc_start: 0.9303 (mp) cc_final: 0.8959 (mp) REVERT: A 232 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8205 (m-40) REVERT: A 348 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7302 (ptt) REVERT: A 357 TYR cc_start: 0.8967 (m-10) cc_final: 0.7933 (m-10) REVERT: A 361 GLN cc_start: 0.8667 (tp40) cc_final: 0.8441 (tp40) REVERT: A 384 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7410 (pm20) REVERT: A 402 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7167 (tm-30) REVERT: A 444 ASP cc_start: 0.8454 (t70) cc_final: 0.8018 (t70) REVERT: A 446 ARG cc_start: 0.7932 (mmm-85) cc_final: 0.7700 (mmm-85) REVERT: A 505 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8075 (mt-10) REVERT: A 515 ASP cc_start: 0.8820 (m-30) cc_final: 0.8560 (m-30) REVERT: A 571 TYR cc_start: 0.9214 (t80) cc_final: 0.8735 (t80) REVERT: A 640 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8606 (tpp) REVERT: A 645 GLN cc_start: 0.8927 (tp-100) cc_final: 0.8554 (tp-100) REVERT: A 648 ILE cc_start: 0.9194 (mm) cc_final: 0.8991 (mm) REVERT: B 27 ASP cc_start: 0.8707 (p0) cc_final: 0.8199 (p0) REVERT: B 79 GLU cc_start: 0.8806 (tp30) cc_final: 0.8230 (tp30) REVERT: B 104 TYR cc_start: 0.8574 (m-80) cc_final: 0.8353 (m-80) REVERT: B 116 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8405 (mp0) REVERT: B 191 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8467 (mm-40) REVERT: B 338 ASN cc_start: 0.9354 (OUTLIER) cc_final: 0.9075 (t0) REVERT: B 384 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.7268 (pm20) REVERT: B 447 ASN cc_start: 0.8361 (m-40) cc_final: 0.8160 (m-40) REVERT: B 467 ASN cc_start: 0.9203 (t0) cc_final: 0.8625 (t0) REVERT: B 515 ASP cc_start: 0.8946 (m-30) cc_final: 0.8704 (m-30) REVERT: B 586 TYR cc_start: 0.8589 (m-80) cc_final: 0.8278 (m-80) REVERT: B 595 MET cc_start: 0.8624 (mmm) cc_final: 0.8337 (mmm) REVERT: B 599 GLU cc_start: 0.8741 (pm20) cc_final: 0.8307 (pm20) REVERT: B 610 LYS cc_start: 0.9389 (ptpt) cc_final: 0.9076 (ptmm) REVERT: B 612 TYR cc_start: 0.8768 (m-80) cc_final: 0.7350 (m-80) REVERT: C 64 LEU cc_start: 0.8139 (tp) cc_final: 0.7873 (pp) REVERT: C 157 MET cc_start: 0.8702 (mtp) cc_final: 0.8173 (ttt) REVERT: C 178 PHE cc_start: 0.7696 (m-80) cc_final: 0.7445 (m-80) REVERT: D 19 GLN cc_start: 0.7152 (pm20) cc_final: 0.6283 (mt0) REVERT: D 20 MET cc_start: 0.8110 (ttp) cc_final: 0.7837 (ttp) REVERT: D 174 TYR cc_start: 0.5984 (OUTLIER) cc_final: 0.5396 (t80) REVERT: D 259 PHE cc_start: 0.4199 (m-80) cc_final: 0.3783 (m-80) outliers start: 67 outliers final: 46 residues processed: 497 average time/residue: 0.1205 time to fit residues: 91.5798 Evaluate side-chains 512 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 459 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 ASN 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 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 583 SER 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 33 VAL 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 338 ASN Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 632 MET 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 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 237 GLU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.155211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.110752 restraints weight = 32412.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.114184 restraints weight = 15574.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.116436 restraints weight = 9339.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.117830 restraints weight = 6654.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.118636 restraints weight = 5349.117| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.5926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16386 Z= 0.141 Angle : 0.663 15.496 22134 Z= 0.339 Chirality : 0.044 0.269 2360 Planarity : 0.003 0.045 2818 Dihedral : 10.434 169.641 2245 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.26 % Allowed : 24.94 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.19), residues: 1932 helix: 1.11 (0.15), residues: 1141 sheet: -0.21 (0.50), residues: 102 loop : 0.30 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 686 TYR 0.026 0.001 TYR C 55 PHE 0.030 0.001 PHE C 168 TRP 0.038 0.002 TRP D 44 HIS 0.012 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00319 (16386) covalent geometry : angle 0.66253 (22134) hydrogen bonds : bond 0.03884 ( 871) hydrogen bonds : angle 5.04333 ( 2571) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 480 time to evaluate : 0.753 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 65 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7351 (mp0) REVERT: A 116 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7594 (mm-30) REVERT: A 119 GLU cc_start: 0.8295 (mp0) cc_final: 0.8040 (mp0) REVERT: A 158 ASN cc_start: 0.8768 (m-40) cc_final: 0.8485 (m-40) REVERT: A 161 ARG cc_start: 0.7970 (ttm-80) cc_final: 0.7165 (ttm-80) REVERT: A 172 LEU cc_start: 0.9244 (mp) cc_final: 0.8877 (mp) REVERT: A 232 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.8174 (m-40) REVERT: A 357 TYR cc_start: 0.8863 (m-10) cc_final: 0.7760 (m-10) REVERT: A 361 GLN cc_start: 0.8595 (tp40) cc_final: 0.8377 (tp40) REVERT: A 384 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7278 (pm20) REVERT: A 402 GLU cc_start: 0.7368 (tm-30) cc_final: 0.7111 (tm-30) REVERT: A 444 ASP cc_start: 0.8488 (t70) cc_final: 0.8053 (t70) REVERT: A 446 ARG cc_start: 0.7949 (mmm-85) cc_final: 0.7703 (mmm-85) REVERT: A 505 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8197 (mt-10) REVERT: A 515 ASP cc_start: 0.8782 (m-30) cc_final: 0.8526 (m-30) REVERT: A 571 TYR cc_start: 0.9187 (t80) cc_final: 0.8757 (t80) REVERT: A 640 MET cc_start: 0.9273 (OUTLIER) cc_final: 0.8640 (tpp) REVERT: A 645 GLN cc_start: 0.8784 (tp-100) cc_final: 0.8445 (tp-100) REVERT: A 648 ILE cc_start: 0.9168 (mm) cc_final: 0.8941 (mm) REVERT: B 79 GLU cc_start: 0.8839 (tp30) cc_final: 0.8264 (tp30) REVERT: B 312 GLN cc_start: 0.8901 (mt0) cc_final: 0.8530 (mt0) REVERT: B 338 ASN cc_start: 0.9312 (OUTLIER) cc_final: 0.8990 (t0) REVERT: B 344 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8154 (mt-10) REVERT: B 384 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.7226 (pm20) REVERT: B 447 ASN cc_start: 0.8255 (m-40) cc_final: 0.7192 (m-40) REVERT: B 467 ASN cc_start: 0.9060 (t0) cc_final: 0.8381 (t0) REVERT: B 515 ASP cc_start: 0.8964 (m-30) cc_final: 0.8735 (m-30) REVERT: B 586 TYR cc_start: 0.8512 (m-80) cc_final: 0.8096 (m-80) REVERT: B 595 MET cc_start: 0.8572 (mmm) cc_final: 0.8291 (mmm) REVERT: B 599 GLU cc_start: 0.8726 (pm20) cc_final: 0.8287 (pm20) REVERT: B 604 ARG cc_start: 0.8925 (mmt-90) cc_final: 0.8624 (mmt-90) REVERT: B 610 LYS cc_start: 0.9406 (ptpt) cc_final: 0.9067 (ptmm) REVERT: B 612 TYR cc_start: 0.8772 (m-80) cc_final: 0.7490 (m-80) REVERT: C 64 LEU cc_start: 0.8126 (tp) cc_final: 0.7874 (pp) REVERT: C 157 MET cc_start: 0.8688 (mtp) cc_final: 0.8222 (ttt) REVERT: C 178 PHE cc_start: 0.7727 (OUTLIER) cc_final: 0.7437 (m-80) REVERT: D 19 GLN cc_start: 0.7132 (pm20) cc_final: 0.6335 (mp10) REVERT: D 174 TYR cc_start: 0.5835 (OUTLIER) cc_final: 0.5276 (t80) REVERT: D 185 MET cc_start: -0.1118 (mmm) cc_final: -0.1561 (mmm) REVERT: D 259 PHE cc_start: 0.4324 (m-80) cc_final: 0.3964 (m-80) outliers start: 56 outliers final: 42 residues processed: 500 average time/residue: 0.1295 time to fit residues: 98.6566 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 : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER 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 143 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.151619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107828 restraints weight = 32194.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.111147 restraints weight = 15614.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.113430 restraints weight = 9227.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.114706 restraints weight = 6559.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.115574 restraints weight = 5305.130| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3314 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.6094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16386 Z= 0.166 Angle : 0.673 14.853 22134 Z= 0.346 Chirality : 0.044 0.244 2360 Planarity : 0.003 0.041 2818 Dihedral : 10.396 173.592 2244 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.09 % Allowed : 25.70 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.19), residues: 1932 helix: 1.12 (0.15), residues: 1141 sheet: -0.55 (0.42), residues: 142 loop : 0.39 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 117 TYR 0.023 0.001 TYR C 55 PHE 0.021 0.002 PHE B 491 TRP 0.035 0.002 TRP D 44 HIS 0.016 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00375 (16386) covalent geometry : angle 0.67285 (22134) hydrogen bonds : bond 0.03962 ( 871) hydrogen bonds : angle 5.05711 ( 2571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 464 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7358 (mp0) REVERT: A 119 GLU cc_start: 0.8289 (mp0) cc_final: 0.8031 (mp0) REVERT: A 150 GLN cc_start: 0.9105 (tm-30) cc_final: 0.8827 (tm-30) REVERT: A 158 ASN cc_start: 0.8702 (m-40) cc_final: 0.8456 (m-40) REVERT: A 162 LYS cc_start: 0.8720 (ttpt) cc_final: 0.8384 (ttpt) REVERT: A 172 LEU cc_start: 0.9248 (mp) cc_final: 0.8912 (mp) REVERT: A 232 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8162 (m-40) REVERT: A 277 THR cc_start: 0.9180 (p) cc_final: 0.8843 (t) REVERT: A 357 TYR cc_start: 0.8914 (m-10) cc_final: 0.7805 (m-10) REVERT: A 361 GLN cc_start: 0.8612 (tp40) cc_final: 0.8303 (tp40) REVERT: A 384 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7289 (pm20) REVERT: A 402 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7170 (tm-30) REVERT: A 456 LYS cc_start: 0.8970 (mtmm) cc_final: 0.8676 (mtmm) REVERT: A 505 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8162 (mt-10) REVERT: A 515 ASP cc_start: 0.8826 (m-30) cc_final: 0.8569 (m-30) REVERT: A 571 TYR cc_start: 0.9226 (t80) cc_final: 0.8752 (t80) REVERT: A 640 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.8663 (tpp) REVERT: A 645 GLN cc_start: 0.8890 (tp-100) cc_final: 0.8544 (tp-100) REVERT: A 648 ILE cc_start: 0.9164 (mm) cc_final: 0.8941 (mm) REVERT: B 27 ASP cc_start: 0.8739 (p0) cc_final: 0.8348 (p0) REVERT: B 79 GLU cc_start: 0.8927 (tp30) cc_final: 0.8333 (tp30) REVERT: B 312 GLN cc_start: 0.8934 (mt0) cc_final: 0.8504 (mt0) REVERT: B 338 ASN cc_start: 0.9353 (OUTLIER) cc_final: 0.9027 (t0) REVERT: B 344 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8250 (mt-10) REVERT: B 384 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.7188 (pm20) REVERT: B 467 ASN cc_start: 0.9138 (t0) cc_final: 0.8640 (t0) REVERT: B 522 TYR cc_start: 0.8900 (m-80) cc_final: 0.8642 (m-80) REVERT: B 526 GLU cc_start: 0.8569 (mp0) cc_final: 0.8296 (mm-30) REVERT: B 586 TYR cc_start: 0.8531 (m-80) cc_final: 0.8043 (m-80) REVERT: B 595 MET cc_start: 0.8613 (mmm) cc_final: 0.8339 (mmm) REVERT: B 599 GLU cc_start: 0.8767 (pm20) cc_final: 0.8353 (pm20) REVERT: B 604 ARG cc_start: 0.8976 (mmt-90) cc_final: 0.8634 (mmt-90) REVERT: B 610 LYS cc_start: 0.9431 (ptpt) cc_final: 0.9091 (ptmm) REVERT: B 612 TYR cc_start: 0.8776 (m-80) cc_final: 0.7357 (m-80) REVERT: C 64 LEU cc_start: 0.8032 (tp) cc_final: 0.7750 (pp) REVERT: C 157 MET cc_start: 0.8643 (mtp) cc_final: 0.8148 (ttt) REVERT: C 178 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.7377 (m-80) REVERT: D 19 GLN cc_start: 0.7150 (pm20) cc_final: 0.6319 (mt0) REVERT: D 174 TYR cc_start: 0.5866 (OUTLIER) cc_final: 0.5332 (t80) REVERT: D 185 MET cc_start: -0.1377 (mmm) cc_final: -0.1579 (mmm) REVERT: D 259 PHE cc_start: 0.4309 (m-80) cc_final: 0.3986 (m-80) outliers start: 53 outliers final: 43 residues processed: 482 average time/residue: 0.1217 time to fit residues: 89.6413 Evaluate side-chains 504 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 454 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER 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 143 LEU Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 231 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 189 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.152422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.108405 restraints weight = 32361.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.111782 restraints weight = 15784.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.113988 restraints weight = 9582.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.115397 restraints weight = 6853.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.116049 restraints weight = 5483.437| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.6240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 16386 Z= 0.171 Angle : 0.696 16.543 22134 Z= 0.358 Chirality : 0.045 0.267 2360 Planarity : 0.004 0.042 2818 Dihedral : 10.332 171.712 2244 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.03 % Allowed : 25.82 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.19), residues: 1932 helix: 1.04 (0.15), residues: 1140 sheet: -0.76 (0.48), residues: 114 loop : 0.27 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 686 TYR 0.029 0.002 TYR C 55 PHE 0.024 0.002 PHE B 288 TRP 0.035 0.002 TRP D 44 HIS 0.018 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00387 (16386) covalent geometry : angle 0.69600 (22134) hydrogen bonds : bond 0.04017 ( 871) hydrogen bonds : angle 5.10975 ( 2571) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 466 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7396 (mp0) REVERT: A 119 GLU cc_start: 0.8252 (mp0) cc_final: 0.7999 (mp0) REVERT: A 150 GLN cc_start: 0.9096 (tm-30) cc_final: 0.8813 (tm-30) REVERT: A 158 ASN cc_start: 0.8684 (m-40) cc_final: 0.8432 (m-40) REVERT: A 162 LYS cc_start: 0.8708 (ttpt) cc_final: 0.8215 (ttpt) REVERT: A 172 LEU cc_start: 0.9259 (mp) cc_final: 0.8906 (mp) REVERT: A 232 ASN cc_start: 0.8582 (OUTLIER) cc_final: 0.8139 (m-40) REVERT: A 239 GLN cc_start: 0.7450 (tt0) cc_final: 0.7180 (pp30) REVERT: A 277 THR cc_start: 0.9163 (p) cc_final: 0.8831 (t) REVERT: A 357 TYR cc_start: 0.8928 (m-10) cc_final: 0.7932 (m-10) REVERT: A 361 GLN cc_start: 0.8582 (tp40) cc_final: 0.8279 (tp40) REVERT: A 384 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7278 (pm20) REVERT: A 402 GLU cc_start: 0.7445 (tm-30) cc_final: 0.7207 (tm-30) REVERT: A 456 LYS cc_start: 0.8979 (mtmm) cc_final: 0.8666 (mtmm) REVERT: A 505 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8139 (mt-10) REVERT: A 515 ASP cc_start: 0.8812 (m-30) cc_final: 0.8550 (m-30) REVERT: A 571 TYR cc_start: 0.9216 (t80) cc_final: 0.8728 (t80) REVERT: A 640 MET cc_start: 0.9303 (OUTLIER) cc_final: 0.8692 (tpp) REVERT: A 645 GLN cc_start: 0.8928 (tp-100) cc_final: 0.8568 (tp-100) REVERT: A 648 ILE cc_start: 0.9183 (mm) cc_final: 0.8953 (mm) REVERT: B 27 ASP cc_start: 0.8731 (p0) cc_final: 0.8312 (p0) REVERT: B 79 GLU cc_start: 0.8879 (tp30) cc_final: 0.8298 (tp30) REVERT: B 111 LYS cc_start: 0.9309 (mmtp) cc_final: 0.9066 (mmtt) REVERT: B 312 GLN cc_start: 0.8907 (mt0) cc_final: 0.8483 (mt0) REVERT: B 338 ASN cc_start: 0.9366 (OUTLIER) cc_final: 0.9046 (t0) REVERT: B 344 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8236 (mt-10) REVERT: B 384 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.7169 (pm20) REVERT: B 467 ASN cc_start: 0.9136 (t0) cc_final: 0.8667 (t0) REVERT: B 522 TYR cc_start: 0.8884 (m-80) cc_final: 0.8639 (m-80) REVERT: B 526 GLU cc_start: 0.8565 (mp0) cc_final: 0.8308 (mm-30) REVERT: B 586 TYR cc_start: 0.8520 (m-80) cc_final: 0.8036 (m-80) REVERT: B 589 SER cc_start: 0.9621 (t) cc_final: 0.9376 (t) REVERT: B 595 MET cc_start: 0.8608 (mmm) cc_final: 0.8331 (mmm) REVERT: B 599 GLU cc_start: 0.8767 (pm20) cc_final: 0.8340 (pm20) REVERT: B 604 ARG cc_start: 0.9009 (mmt-90) cc_final: 0.8665 (mmt-90) REVERT: B 610 LYS cc_start: 0.9426 (ptpt) cc_final: 0.9088 (ptmm) REVERT: B 612 TYR cc_start: 0.8759 (m-80) cc_final: 0.7319 (m-80) REVERT: C 64 LEU cc_start: 0.8131 (tp) cc_final: 0.7777 (pp) REVERT: C 157 MET cc_start: 0.8577 (mtp) cc_final: 0.8103 (ttt) REVERT: C 178 PHE cc_start: 0.7774 (OUTLIER) cc_final: 0.7385 (m-80) REVERT: D 174 TYR cc_start: 0.5790 (OUTLIER) cc_final: 0.5280 (t80) REVERT: D 185 MET cc_start: -0.1319 (mmm) cc_final: -0.1541 (mmm) REVERT: D 259 PHE cc_start: 0.4308 (m-80) cc_final: 0.4045 (m-80) outliers start: 52 outliers final: 39 residues processed: 483 average time/residue: 0.1162 time to fit residues: 86.3104 Evaluate side-chains 496 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 450 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER 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 33 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 148 optimal weight: 9.9990 chunk 125 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** A 646 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** 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 = 0.3890 r_free = 0.3890 target = 0.157234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.113354 restraints weight = 32167.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.117067 restraints weight = 15334.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.119421 restraints weight = 9124.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.120757 restraints weight = 6468.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.121710 restraints weight = 5186.503| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3364 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3364 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.6451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 16386 Z= 0.142 Angle : 0.704 18.327 22134 Z= 0.358 Chirality : 0.045 0.389 2360 Planarity : 0.004 0.043 2818 Dihedral : 10.107 163.785 2244 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.86 % Allowed : 26.63 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.19), residues: 1932 helix: 0.99 (0.15), residues: 1143 sheet: -0.76 (0.48), residues: 106 loop : 0.17 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 117 TYR 0.025 0.001 TYR C 55 PHE 0.061 0.002 PHE C 92 TRP 0.032 0.002 TRP D 44 HIS 0.015 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00326 (16386) covalent geometry : angle 0.70364 (22134) hydrogen bonds : bond 0.04020 ( 871) hydrogen bonds : angle 5.07676 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3314.46 seconds wall clock time: 58 minutes 8.79 seconds (3488.79 seconds total)