Starting phenix.real_space_refine on Sat May 17 16:49:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz2_45051/05_2025/9bz2_45051_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz2_45051/05_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_45051/05_2025/9bz2_45051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz2_45051/05_2025/9bz2_45051.map" model { file = "/net/cci-nas-00/data/ceres_data/9bz2_45051/05_2025/9bz2_45051_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz2_45051/05_2025/9bz2_45051_neut.cif" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 8.64, per 1000 atoms: 0.54 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: 3.61 Conformation dependent library (CDL) restraints added in 1.8 seconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.984A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.954A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.665A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.694A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.627A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.073A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.958A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.677A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.645A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.730A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.027A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.068A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.514A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.669A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.360A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.478A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.478A pdb=" N LEU A 656 " --> pdb=" O ARG A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.185A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.049A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.62 Time building geometry restraints manager: 4.24 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: 0.010 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 33.140 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 16386 Z= 0.317 Angle : 0.750 12.283 22134 Z= 0.471 Chirality : 0.058 0.467 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.888 179.009 6154 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.40 % Allowed : 15.15 % Favored : 83.45 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.18), residues: 1932 helix: 0.58 (0.14), residues: 1151 sheet: 0.46 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 PHE 0.021 0.002 PHE C 168 TYR 0.020 0.002 TYR C 169 ARG 0.004 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.15423 ( 871) hydrogen bonds : angle 6.51784 ( 2571) covalent geometry : bond 0.00556 (16386) covalent geometry : angle 0.74994 (22134) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 809 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ILE cc_start: 0.9185 (mt) cc_final: 0.8938 (mt) REVERT: A 127 LEU cc_start: 0.9149 (mt) cc_final: 0.8859 (mt) REVERT: A 131 ASN cc_start: 0.8653 (t0) cc_final: 0.8379 (t0) REVERT: A 138 LYS cc_start: 0.8180 (mtpt) cc_final: 0.7846 (mtpp) REVERT: A 145 ILE cc_start: 0.9125 (tp) cc_final: 0.8906 (tp) REVERT: A 172 LEU cc_start: 0.9004 (mp) cc_final: 0.8770 (mp) REVERT: A 179 LEU cc_start: 0.8997 (tp) cc_final: 0.8450 (tp) REVERT: A 220 THR cc_start: 0.8806 (m) cc_final: 0.8511 (p) REVERT: A 227 MET cc_start: 0.7829 (mtp) cc_final: 0.7587 (mtp) REVERT: A 319 MET cc_start: 0.7850 (tpp) cc_final: 0.7398 (tpp) REVERT: A 367 VAL cc_start: 0.9098 (m) cc_final: 0.8773 (t) REVERT: A 380 ASN cc_start: 0.8968 (p0) cc_final: 0.8740 (p0) REVERT: A 446 ARG cc_start: 0.7519 (mmm-85) cc_final: 0.7241 (mtp85) REVERT: A 447 ASN cc_start: 0.7944 (m-40) cc_final: 0.7333 (m110) REVERT: A 546 LEU cc_start: 0.8855 (mt) cc_final: 0.8647 (mt) REVERT: A 550 MET cc_start: 0.8096 (mtm) cc_final: 0.7875 (mtt) REVERT: A 598 MET cc_start: 0.8373 (mtm) cc_final: 0.7780 (mtp) REVERT: B 51 LEU cc_start: 0.8213 (tp) cc_final: 0.7886 (tp) REVERT: B 67 GLU cc_start: 0.7746 (mp0) cc_final: 0.7141 (mp0) REVERT: B 106 LEU cc_start: 0.8835 (tp) cc_final: 0.7898 (tt) REVERT: B 127 LEU cc_start: 0.9042 (mt) cc_final: 0.8800 (mt) REVERT: B 129 PHE cc_start: 0.8421 (m-10) cc_final: 0.8064 (m-10) REVERT: B 180 ASN cc_start: 0.7535 (m-40) cc_final: 0.7327 (m110) REVERT: B 186 ILE cc_start: 0.9216 (mt) cc_final: 0.9013 (mt) REVERT: B 211 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7480 (mm-30) REVERT: B 286 ASP cc_start: 0.6894 (OUTLIER) cc_final: 0.6686 (m-30) REVERT: B 319 MET cc_start: 0.7902 (tpp) cc_final: 0.7658 (tpp) REVERT: B 348 MET cc_start: 0.7346 (tmm) cc_final: 0.7075 (ttm) REVERT: B 358 ILE cc_start: 0.9193 (mm) cc_final: 0.8937 (mm) REVERT: B 381 LEU cc_start: 0.9246 (tp) cc_final: 0.8968 (tp) REVERT: B 384 GLU cc_start: 0.8948 (pm20) cc_final: 0.8159 (pm20) REVERT: B 389 SER cc_start: 0.8046 (p) cc_final: 0.7835 (p) REVERT: B 458 MET cc_start: 0.8463 (mmm) cc_final: 0.8156 (mmm) REVERT: B 460 SER cc_start: 0.8912 (t) cc_final: 0.8712 (p) REVERT: B 471 TYR cc_start: 0.8260 (t80) cc_final: 0.7681 (t80) REVERT: B 500 ILE cc_start: 0.9095 (mt) cc_final: 0.8888 (mt) REVERT: B 585 SER cc_start: 0.9148 (p) cc_final: 0.8880 (p) REVERT: C 89 VAL cc_start: 0.5232 (t) cc_final: 0.3654 (t) REVERT: C 229 ILE cc_start: 0.5031 (mt) cc_final: 0.4266 (mm) REVERT: D 42 LEU cc_start: 0.1877 (mt) cc_final: 0.1438 (mt) REVERT: D 185 MET cc_start: 0.0973 (mmm) cc_final: 0.0575 (mmm) REVERT: D 282 ILE cc_start: 0.3799 (OUTLIER) cc_final: 0.3413 (pt) outliers start: 24 outliers final: 5 residues processed: 822 average time/residue: 0.2829 time to fit residues: 337.5072 Evaluate side-chains 570 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 563 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 365 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 14 ASN B 202 ASN B 312 GLN B 329 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN B 467 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 233 ASN D 71 ASN D 80 HIS D 91 ASN D 186 GLN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.154733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.106698 restraints weight = 30811.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.110250 restraints weight = 15153.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.112503 restraints weight = 9284.543| |-----------------------------------------------------------------------------| 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) = 0.108 | | 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: 0.7597 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16386 Z= 0.241 Angle : 0.673 7.966 22134 Z= 0.353 Chirality : 0.045 0.291 2360 Planarity : 0.004 0.037 2818 Dihedral : 11.627 179.328 2254 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.08 % Allowed : 18.07 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.19), residues: 1932 helix: 1.43 (0.15), residues: 1133 sheet: -0.19 (0.46), residues: 114 loop : 0.70 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 44 HIS 0.006 0.001 HIS B 438 PHE 0.027 0.002 PHE B 261 TYR 0.031 0.002 TYR D 174 ARG 0.006 0.001 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.04804 ( 871) hydrogen bonds : angle 5.07255 ( 2571) covalent geometry : bond 0.00529 (16386) covalent geometry : angle 0.67284 (22134) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 582 time to evaluate : 1.642 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: 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: 0.8914 (p0) cc_final: 0.8570 (p0) REVERT: A 65 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7270 (mp0) REVERT: A 117 ARG cc_start: 0.8313 (mtp85) cc_final: 0.8057 (mtp85) REVERT: A 119 GLU cc_start: 0.8513 (mp0) cc_final: 0.8212 (mp0) REVERT: A 138 LYS cc_start: 0.9096 (mtpt) cc_final: 0.8823 (mtpp) REVERT: A 172 LEU cc_start: 0.9326 (mp) cc_final: 0.9005 (mp) REVERT: A 191 GLN cc_start: 0.8396 (mm-40) cc_final: 0.8027 (mm-40) REVERT: A 317 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7885 (ptp) REVERT: A 357 TYR cc_start: 0.8993 (m-10) cc_final: 0.8030 (m-10) REVERT: A 362 ASP cc_start: 0.8419 (m-30) cc_final: 0.8075 (m-30) REVERT: A 384 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.7656 (pm20) REVERT: A 402 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7320 (tm-30) REVERT: A 436 LEU cc_start: 0.9493 (mt) cc_final: 0.9278 (mm) REVERT: A 444 ASP cc_start: 0.8456 (t70) cc_final: 0.8247 (t70) REVERT: A 447 ASN cc_start: 0.8777 (m-40) cc_final: 0.8363 (m-40) REVERT: A 456 LYS cc_start: 0.8915 (mtmm) cc_final: 0.8548 (mtmm) REVERT: A 493 MET cc_start: 0.8910 (tmm) cc_final: 0.8514 (tmm) REVERT: A 548 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8333 (mm-30) REVERT: A 640 MET cc_start: 0.9314 (tpp) cc_final: 0.8886 (tpp) REVERT: A 663 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8067 (t) REVERT: B 52 LYS cc_start: 0.9416 (tppt) cc_final: 0.9118 (tppt) REVERT: B 53 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8397 (mt-10) REVERT: B 118 TYR cc_start: 0.9381 (t80) cc_final: 0.9169 (t80) REVERT: B 184 ARG cc_start: 0.9164 (tpp-160) cc_final: 0.8866 (tpp-160) REVERT: B 214 LYS cc_start: 0.8427 (ttmm) cc_final: 0.7877 (mmtm) REVERT: B 236 TYR cc_start: 0.9191 (t80) cc_final: 0.8947 (t80) REVERT: B 335 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7369 (mt-10) REVERT: B 362 ASP cc_start: 0.8007 (m-30) cc_final: 0.7715 (m-30) REVERT: B 420 MET cc_start: 0.9379 (mmm) cc_final: 0.9066 (mmm) REVERT: B 425 ILE cc_start: 0.9469 (mt) cc_final: 0.9162 (mt) REVERT: B 493 MET cc_start: 0.9506 (tmm) cc_final: 0.9281 (tmm) REVERT: B 570 MET cc_start: 0.8186 (mtp) cc_final: 0.7819 (mtt) REVERT: B 602 GLU cc_start: 0.8107 (pt0) cc_final: 0.7715 (pt0) REVERT: B 604 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8439 (mmt-90) REVERT: B 610 LYS cc_start: 0.9063 (ptpt) cc_final: 0.8666 (ptmm) REVERT: B 612 TYR cc_start: 0.9037 (m-80) cc_final: 0.8124 (m-80) REVERT: B 620 SER cc_start: 0.9507 (OUTLIER) cc_final: 0.9306 (p) REVERT: B 648 ILE cc_start: 0.9151 (mm) cc_final: 0.8910 (mt) REVERT: B 650 GLN cc_start: 0.8463 (mt0) cc_final: 0.8140 (mt0) REVERT: C 56 MET cc_start: 0.4633 (ptt) cc_final: 0.4133 (ppp) REVERT: C 90 LEU cc_start: 0.7565 (mt) cc_final: 0.6962 (mt) REVERT: C 146 GLN cc_start: 0.6380 (mm-40) cc_final: 0.6079 (mm110) REVERT: C 178 PHE cc_start: 0.7850 (m-80) cc_final: 0.7513 (m-80) REVERT: C 278 GLU cc_start: 0.8781 (tt0) cc_final: 0.8580 (tp30) REVERT: D 96 MET cc_start: 0.0057 (mmt) cc_final: -0.0256 (mmt) outliers start: 70 outliers final: 29 residues processed: 616 average time/residue: 0.2666 time to fit residues: 243.6733 Evaluate side-chains 515 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 480 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 216 GLN Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 3.9990 chunk 168 optimal weight: 30.0000 chunk 175 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 191 optimal weight: 0.0270 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 189 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 410 ASN A 645 GLN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3831 r_free = 0.3831 target = 0.150370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.105171 restraints weight = 31815.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.108589 restraints weight = 15287.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.110826 restraints weight = 9256.984| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16386 Z= 0.220 Angle : 0.647 12.149 22134 Z= 0.337 Chirality : 0.044 0.271 2360 Planarity : 0.004 0.039 2818 Dihedral : 11.337 173.867 2248 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.02 % Allowed : 21.45 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.19), residues: 1932 helix: 1.38 (0.15), residues: 1132 sheet: -0.21 (0.42), residues: 146 loop : 0.67 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 124 HIS 0.005 0.001 HIS B 438 PHE 0.028 0.002 PHE A 492 TYR 0.041 0.002 TYR D 174 ARG 0.005 0.001 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.04331 ( 871) hydrogen bonds : angle 5.00317 ( 2571) covalent geometry : bond 0.00484 (16386) covalent geometry : angle 0.64673 (22134) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 524 time to evaluate : 1.856 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: 0.8934 (p0) cc_final: 0.8651 (p0) REVERT: A 65 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7345 (mp0) REVERT: A 117 ARG cc_start: 0.8552 (mtp85) cc_final: 0.8328 (mtp85) REVERT: A 119 GLU cc_start: 0.8491 (mp0) cc_final: 0.8108 (mp0) REVERT: A 138 LYS cc_start: 0.9069 (mtpt) cc_final: 0.8829 (mtpp) REVERT: A 145 ILE cc_start: 0.9564 (tp) cc_final: 0.9334 (tp) REVERT: A 150 GLN cc_start: 0.9079 (tm-30) cc_final: 0.8686 (tm-30) REVERT: A 172 LEU cc_start: 0.9359 (mp) cc_final: 0.9034 (mp) REVERT: A 317 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7902 (ptp) REVERT: A 346 LEU cc_start: 0.9416 (mp) cc_final: 0.9169 (mp) REVERT: A 357 TYR cc_start: 0.9038 (m-10) cc_final: 0.8180 (m-10) REVERT: A 362 ASP cc_start: 0.8377 (m-30) cc_final: 0.8010 (m-30) REVERT: A 384 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.7479 (pm20) REVERT: A 402 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7208 (tm-30) REVERT: A 436 LEU cc_start: 0.9511 (mt) cc_final: 0.9310 (mm) REVERT: A 447 ASN cc_start: 0.8730 (m-40) cc_final: 0.8123 (m-40) REVERT: A 453 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.8333 (ttt-90) REVERT: A 456 LYS cc_start: 0.8936 (mtmm) cc_final: 0.8669 (mtmm) REVERT: A 493 MET cc_start: 0.8893 (tmm) cc_final: 0.8253 (tmm) REVERT: A 505 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8134 (mt-10) REVERT: A 515 ASP cc_start: 0.8836 (m-30) cc_final: 0.8583 (m-30) REVERT: A 548 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8335 (mm-30) REVERT: A 570 MET cc_start: 0.8983 (mtp) cc_final: 0.8670 (mtp) REVERT: A 588 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8319 (mm-40) REVERT: A 590 SER cc_start: 0.9309 (t) cc_final: 0.9087 (t) REVERT: A 640 MET cc_start: 0.9284 (tpp) cc_final: 0.8746 (tpp) REVERT: A 663 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8356 (t) REVERT: B 52 LYS cc_start: 0.9439 (tppt) cc_final: 0.9142 (tppt) REVERT: B 184 ARG cc_start: 0.9147 (tpp-160) cc_final: 0.8866 (tpp-160) REVERT: B 214 LYS cc_start: 0.8350 (ttmm) cc_final: 0.7815 (mmtm) REVERT: B 362 ASP cc_start: 0.7768 (m-30) cc_final: 0.7525 (m-30) REVERT: B 420 MET cc_start: 0.9362 (mmm) cc_final: 0.9118 (mmm) REVERT: B 493 MET cc_start: 0.9476 (tmm) cc_final: 0.9245 (tmm) REVERT: B 570 MET cc_start: 0.8197 (mtp) cc_final: 0.7995 (mtt) REVERT: B 599 GLU cc_start: 0.8762 (pm20) cc_final: 0.8457 (pm20) REVERT: B 602 GLU cc_start: 0.7864 (pt0) cc_final: 0.7371 (pt0) REVERT: B 604 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8655 (mmt-90) REVERT: B 610 LYS cc_start: 0.9200 (ptpt) cc_final: 0.8796 (ptmm) REVERT: B 620 SER cc_start: 0.9519 (OUTLIER) cc_final: 0.9301 (p) REVERT: C 56 MET cc_start: 0.4805 (ptt) cc_final: 0.4279 (ppp) REVERT: C 95 MET cc_start: 0.7460 (ppp) cc_final: 0.7214 (ppp) REVERT: C 149 ASP cc_start: 0.8122 (m-30) cc_final: 0.7862 (m-30) REVERT: C 157 MET cc_start: 0.8552 (mtp) cc_final: 0.8043 (ttt) REVERT: C 168 PHE cc_start: 0.8599 (m-80) cc_final: 0.8353 (m-80) REVERT: C 169 TYR cc_start: 0.8576 (m-80) cc_final: 0.8337 (m-80) REVERT: C 178 PHE cc_start: 0.7873 (m-80) cc_final: 0.7532 (m-80) REVERT: C 238 ASN cc_start: 0.7937 (t0) cc_final: 0.7383 (m-40) REVERT: C 278 GLU cc_start: 0.8859 (tt0) cc_final: 0.8619 (tp30) REVERT: D 47 LEU cc_start: 0.8260 (mm) cc_final: 0.7888 (tp) REVERT: D 124 TRP cc_start: 0.6840 (t60) cc_final: 0.6609 (t60) REVERT: D 185 MET cc_start: -0.1535 (mmm) cc_final: -0.2000 (mmm) outliers start: 69 outliers final: 36 residues processed: 560 average time/residue: 0.2629 time to fit residues: 219.8032 Evaluate side-chains 509 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 466 time to evaluate : 1.755 ------------------------------------------------------------------------------- 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 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 180 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN ** 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 410 ASN B 467 ASN B 645 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN D 288 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.150747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.103885 restraints weight = 32076.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107308 restraints weight = 15635.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.109518 restraints weight = 9500.921| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16386 Z= 0.218 Angle : 0.641 9.866 22134 Z= 0.335 Chirality : 0.044 0.271 2360 Planarity : 0.003 0.043 2818 Dihedral : 11.145 177.430 2246 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.25 % Allowed : 22.14 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.19), residues: 1932 helix: 1.33 (0.15), residues: 1127 sheet: -0.66 (0.47), residues: 118 loop : 0.50 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 44 HIS 0.008 0.001 HIS C 201 PHE 0.027 0.002 PHE A 492 TYR 0.026 0.002 TYR D 174 ARG 0.004 0.001 ARG A 350 Details of bonding type rmsd hydrogen bonds : bond 0.04170 ( 871) hydrogen bonds : angle 5.01801 ( 2571) covalent geometry : bond 0.00482 (16386) covalent geometry : angle 0.64093 (22134) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 519 time to evaluate : 1.753 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: symmetry clash REVERT: A 27 ASP cc_start: 0.8950 (p0) cc_final: 0.8735 (p0) REVERT: A 65 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7409 (mp0) REVERT: A 119 GLU cc_start: 0.8400 (mp0) cc_final: 0.7982 (mp0) REVERT: A 138 LYS cc_start: 0.9070 (mtpt) cc_final: 0.8850 (mtpp) REVERT: A 145 ILE cc_start: 0.9546 (tp) cc_final: 0.9343 (tp) REVERT: A 150 GLN cc_start: 0.9083 (tm-30) cc_final: 0.8796 (tm-30) REVERT: A 161 ARG cc_start: 0.7974 (ttm-80) cc_final: 0.7423 (ttm-80) REVERT: A 172 LEU cc_start: 0.9376 (mp) cc_final: 0.9054 (mp) REVERT: A 191 GLN cc_start: 0.8287 (mm-40) cc_final: 0.8053 (mm-40) REVERT: A 346 LEU cc_start: 0.9483 (mp) cc_final: 0.9228 (mp) REVERT: A 357 TYR cc_start: 0.9091 (m-10) cc_final: 0.8272 (m-10) REVERT: A 362 ASP cc_start: 0.8438 (m-30) cc_final: 0.8039 (m-30) REVERT: A 384 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7311 (pm20) REVERT: A 402 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7229 (tm-30) REVERT: A 447 ASN cc_start: 0.8584 (m-40) cc_final: 0.7776 (m-40) REVERT: A 456 LYS cc_start: 0.8945 (mtmm) cc_final: 0.8709 (mtmm) REVERT: A 505 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8147 (mt-10) REVERT: A 515 ASP cc_start: 0.8854 (m-30) cc_final: 0.8590 (m-30) REVERT: A 546 LEU cc_start: 0.9418 (mt) cc_final: 0.9157 (mt) REVERT: A 571 TYR cc_start: 0.9235 (t80) cc_final: 0.8652 (t80) REVERT: A 654 PHE cc_start: 0.9296 (t80) cc_final: 0.9090 (t80) REVERT: B 52 LYS cc_start: 0.9412 (tppt) cc_final: 0.9086 (tppt) REVERT: B 79 GLU cc_start: 0.8936 (tp30) cc_final: 0.8270 (tp30) REVERT: B 232 ASN cc_start: 0.8953 (OUTLIER) cc_final: 0.8684 (m110) REVERT: B 257 ASP cc_start: 0.8979 (m-30) cc_final: 0.8740 (m-30) REVERT: B 314 MET cc_start: 0.9185 (ttp) cc_final: 0.8971 (tmm) REVERT: B 335 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7224 (mt-10) REVERT: B 384 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.7421 (pm20) REVERT: B 493 MET cc_start: 0.9433 (tmm) cc_final: 0.9213 (tmm) REVERT: B 570 MET cc_start: 0.8118 (mtp) cc_final: 0.7775 (mtt) REVERT: B 586 TYR cc_start: 0.8566 (m-80) cc_final: 0.8303 (m-80) REVERT: B 599 GLU cc_start: 0.8770 (pm20) cc_final: 0.8297 (pm20) REVERT: B 602 GLU cc_start: 0.7813 (pt0) cc_final: 0.6909 (pt0) REVERT: B 604 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8708 (mmt-90) REVERT: B 610 LYS cc_start: 0.9228 (ptpt) cc_final: 0.8818 (ptmm) REVERT: B 620 SER cc_start: 0.9494 (OUTLIER) cc_final: 0.9265 (p) REVERT: C 56 MET cc_start: 0.4978 (ptt) cc_final: 0.4469 (ppp) REVERT: C 149 ASP cc_start: 0.8125 (m-30) cc_final: 0.7916 (m-30) REVERT: C 157 MET cc_start: 0.8663 (mtp) cc_final: 0.8268 (ttt) REVERT: C 169 TYR cc_start: 0.8721 (m-80) cc_final: 0.8489 (m-80) REVERT: C 178 PHE cc_start: 0.7938 (m-10) cc_final: 0.7640 (m-80) REVERT: C 179 TYR cc_start: 0.5382 (t80) cc_final: 0.5169 (t80) REVERT: C 238 ASN cc_start: 0.7785 (t0) cc_final: 0.7294 (m-40) REVERT: D 96 MET cc_start: 0.1117 (mmt) cc_final: 0.0820 (mmt) REVERT: D 185 MET cc_start: -0.1526 (mmm) cc_final: -0.2176 (mmm) outliers start: 73 outliers final: 42 residues processed: 553 average time/residue: 0.2552 time to fit residues: 210.9352 Evaluate side-chains 521 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 474 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 260 ASP 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 598 MET Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 67 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 175 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN D 233 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.152309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.107619 restraints weight = 32257.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.111092 restraints weight = 15361.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.113356 restraints weight = 9211.764| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.5199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16386 Z= 0.142 Angle : 0.611 9.393 22134 Z= 0.318 Chirality : 0.042 0.241 2360 Planarity : 0.003 0.044 2818 Dihedral : 10.837 176.813 2245 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.44 % Allowed : 23.48 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.19), residues: 1932 helix: 1.33 (0.15), residues: 1128 sheet: -0.27 (0.49), residues: 106 loop : 0.37 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 124 HIS 0.012 0.001 HIS C 201 PHE 0.022 0.001 PHE C 168 TYR 0.023 0.001 TYR A 571 ARG 0.004 0.000 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 871) hydrogen bonds : angle 4.96100 ( 2571) covalent geometry : bond 0.00318 (16386) covalent geometry : angle 0.61137 (22134) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 544 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8916 (p0) cc_final: 0.8667 (p0) REVERT: A 65 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7363 (mp0) REVERT: A 119 GLU cc_start: 0.8381 (mp0) cc_final: 0.8047 (mp0) REVERT: A 138 LYS cc_start: 0.9049 (mtpt) cc_final: 0.8838 (mtpp) REVERT: A 162 LYS cc_start: 0.8775 (ttpt) cc_final: 0.8263 (ttpt) REVERT: A 172 LEU cc_start: 0.9324 (mp) cc_final: 0.8976 (mp) REVERT: A 346 LEU cc_start: 0.9458 (mt) cc_final: 0.9207 (mp) REVERT: A 357 TYR cc_start: 0.9057 (m-10) cc_final: 0.7932 (m-10) REVERT: A 361 GLN cc_start: 0.8722 (tp40) cc_final: 0.8491 (tp40) REVERT: A 362 ASP cc_start: 0.8257 (m-30) cc_final: 0.7915 (m-30) REVERT: A 384 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7347 (pm20) REVERT: A 402 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7264 (tm-30) REVERT: A 411 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7462 (mp) REVERT: A 415 ASN cc_start: 0.8840 (t0) cc_final: 0.8593 (t0) REVERT: A 444 ASP cc_start: 0.8590 (t70) cc_final: 0.8025 (t70) REVERT: A 446 ARG cc_start: 0.7959 (mtp85) cc_final: 0.7703 (mmm-85) REVERT: A 447 ASN cc_start: 0.8381 (m-40) cc_final: 0.7680 (m-40) REVERT: A 456 LYS cc_start: 0.8988 (mtmm) cc_final: 0.8783 (mtmm) REVERT: A 505 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8084 (mt-10) REVERT: A 515 ASP cc_start: 0.8809 (m-30) cc_final: 0.8547 (m-30) REVERT: A 571 TYR cc_start: 0.9226 (t80) cc_final: 0.8829 (t80) REVERT: A 640 MET cc_start: 0.9292 (OUTLIER) cc_final: 0.8689 (tpp) REVERT: B 27 ASP cc_start: 0.8914 (p0) cc_final: 0.8523 (p0) REVERT: B 31 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7934 (mt-10) REVERT: B 52 LYS cc_start: 0.9411 (tppt) cc_final: 0.9157 (tppt) REVERT: B 79 GLU cc_start: 0.8913 (tp30) cc_final: 0.8267 (tp30) REVERT: B 87 LYS cc_start: 0.8704 (mmmm) cc_final: 0.8503 (tttt) REVERT: B 116 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8676 (mp0) REVERT: B 180 ASN cc_start: 0.8112 (m-40) cc_final: 0.7859 (m110) REVERT: B 191 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8627 (mm-40) REVERT: B 214 LYS cc_start: 0.8052 (ttmm) cc_final: 0.7683 (mmtm) REVERT: B 232 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8631 (m110) REVERT: B 257 ASP cc_start: 0.8866 (m-30) cc_final: 0.8639 (m-30) REVERT: B 319 MET cc_start: 0.8783 (tpp) cc_final: 0.8513 (tpp) REVERT: B 335 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7222 (mt-10) REVERT: B 384 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.7229 (pm20) REVERT: B 493 MET cc_start: 0.9416 (tmm) cc_final: 0.9208 (tmm) REVERT: B 526 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8360 (mm-30) REVERT: B 586 TYR cc_start: 0.8528 (m-80) cc_final: 0.8103 (m-80) REVERT: B 599 GLU cc_start: 0.8736 (pm20) cc_final: 0.8273 (pm20) REVERT: B 602 GLU cc_start: 0.7817 (pt0) cc_final: 0.6594 (pt0) REVERT: B 610 LYS cc_start: 0.9285 (ptpt) cc_final: 0.8951 (ptmm) REVERT: B 620 SER cc_start: 0.9479 (OUTLIER) cc_final: 0.9251 (p) REVERT: C 56 MET cc_start: 0.5092 (ptt) cc_final: 0.4606 (ppp) REVERT: C 95 MET cc_start: 0.7199 (ppp) cc_final: 0.6875 (ppp) REVERT: C 149 ASP cc_start: 0.8161 (m-30) cc_final: 0.7939 (m-30) REVERT: C 157 MET cc_start: 0.8676 (mtp) cc_final: 0.8227 (ttt) REVERT: C 169 TYR cc_start: 0.8825 (m-80) cc_final: 0.8607 (m-80) REVERT: C 178 PHE cc_start: 0.7879 (m-10) cc_final: 0.7602 (m-80) REVERT: C 238 ASN cc_start: 0.7588 (OUTLIER) cc_final: 0.7206 (m-40) REVERT: D 185 MET cc_start: -0.1650 (mmm) cc_final: -0.2327 (mmm) outliers start: 59 outliers final: 35 residues processed: 568 average time/residue: 0.2558 time to fit residues: 218.8406 Evaluate side-chains 527 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 484 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 207 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 31 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 156 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 177 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN A 239 GLN ** A 568 HIS ** 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** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 233 ASN D 91 ASN D 283 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.149611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.103504 restraints weight = 32685.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106834 restraints weight = 15805.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.108958 restraints weight = 9996.019| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16386 Z= 0.243 Angle : 0.669 8.037 22134 Z= 0.352 Chirality : 0.045 0.201 2360 Planarity : 0.004 0.044 2818 Dihedral : 10.816 167.138 2245 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.08 % Allowed : 23.83 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.19), residues: 1932 helix: 1.13 (0.15), residues: 1140 sheet: -0.63 (0.48), residues: 118 loop : 0.39 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 44 HIS 0.008 0.001 HIS C 201 PHE 0.025 0.002 PHE A 492 TYR 0.023 0.002 TYR A 571 ARG 0.004 0.001 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.04191 ( 871) hydrogen bonds : angle 5.15783 ( 2571) covalent geometry : bond 0.00538 (16386) covalent geometry : angle 0.66931 (22134) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 490 time to evaluate : 1.685 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: 0.8403 (mm-30) cc_final: 0.7446 (mp0) REVERT: A 108 THR cc_start: 0.9000 (OUTLIER) cc_final: 0.8632 (p) REVERT: A 119 GLU cc_start: 0.8355 (mp0) cc_final: 0.8044 (mp0) REVERT: A 121 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.7975 (tpm-80) REVERT: A 150 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8629 (tm-30) REVERT: A 172 LEU cc_start: 0.9355 (mp) cc_final: 0.9104 (mp) REVERT: A 188 ILE cc_start: 0.9526 (mt) cc_final: 0.9247 (mm) REVERT: A 346 LEU cc_start: 0.9491 (mt) cc_final: 0.9189 (mp) REVERT: A 357 TYR cc_start: 0.9110 (m-10) cc_final: 0.8226 (m-10) REVERT: A 384 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7425 (pm20) REVERT: A 402 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7344 (tm-30) REVERT: A 456 LYS cc_start: 0.8968 (mtmm) cc_final: 0.8726 (mtmm) REVERT: A 505 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8136 (mt-10) REVERT: A 515 ASP cc_start: 0.8841 (m-30) cc_final: 0.8603 (m-30) REVERT: A 571 TYR cc_start: 0.9232 (t80) cc_final: 0.8713 (t80) REVERT: A 640 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.8689 (tpp) REVERT: B 52 LYS cc_start: 0.9411 (tppt) cc_final: 0.9096 (tppt) REVERT: B 79 GLU cc_start: 0.8913 (tp30) cc_final: 0.8243 (tp30) REVERT: B 87 LYS cc_start: 0.8829 (mmmm) cc_final: 0.8590 (tttt) REVERT: B 116 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8715 (mt-10) REVERT: B 214 LYS cc_start: 0.8182 (ttmm) cc_final: 0.7857 (mmtm) REVERT: B 232 ASN cc_start: 0.9006 (OUTLIER) cc_final: 0.8713 (m-40) REVERT: B 257 ASP cc_start: 0.9004 (m-30) cc_final: 0.8763 (m-30) REVERT: B 384 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.7431 (pm20) REVERT: B 493 MET cc_start: 0.9435 (tmm) cc_final: 0.9165 (tmm) REVERT: B 586 TYR cc_start: 0.8649 (m-80) cc_final: 0.8381 (m-80) REVERT: B 599 GLU cc_start: 0.8757 (pm20) cc_final: 0.8286 (pm20) REVERT: B 610 LYS cc_start: 0.9402 (ptpt) cc_final: 0.9005 (ptmm) REVERT: B 620 SER cc_start: 0.9484 (OUTLIER) cc_final: 0.9256 (p) REVERT: B 668 ASN cc_start: 0.8804 (m-40) cc_final: 0.8594 (m-40) REVERT: C 56 MET cc_start: 0.5236 (ptt) cc_final: 0.4677 (ppp) REVERT: C 95 MET cc_start: 0.7687 (ppp) cc_final: 0.7328 (ppp) REVERT: C 122 PHE cc_start: 0.6932 (m-80) cc_final: 0.6230 (m-80) REVERT: C 149 ASP cc_start: 0.8274 (m-30) cc_final: 0.8048 (m-30) REVERT: C 157 MET cc_start: 0.8764 (mtp) cc_final: 0.8297 (ttt) REVERT: C 169 TYR cc_start: 0.8826 (m-80) cc_final: 0.8557 (m-80) REVERT: C 178 PHE cc_start: 0.7966 (m-10) cc_final: 0.7633 (m-80) REVERT: C 189 GLU cc_start: 0.3041 (OUTLIER) cc_final: 0.2124 (mt-10) REVERT: C 238 ASN cc_start: 0.7898 (OUTLIER) cc_final: 0.7359 (m-40) REVERT: D 19 GLN cc_start: 0.7437 (pm20) cc_final: 0.6804 (mm110) REVERT: D 174 TYR cc_start: 0.6247 (OUTLIER) cc_final: 0.5822 (t80) REVERT: D 185 MET cc_start: -0.1153 (mmm) cc_final: -0.1721 (mmm) outliers start: 70 outliers final: 45 residues processed: 521 average time/residue: 0.2614 time to fit residues: 204.4867 Evaluate side-chains 511 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 456 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 667 LEU 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 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 285 ILE 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 242 TYR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 39 optimal weight: 8.9990 chunk 85 optimal weight: 0.7980 chunk 161 optimal weight: 10.0000 chunk 23 optimal weight: 0.0570 chunk 40 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 184 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 175 optimal weight: 30.0000 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN D 25 ASN ** D 283 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 = 0.3876 r_free = 0.3876 target = 0.154072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.108714 restraints weight = 32446.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.112339 restraints weight = 15540.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.114651 restraints weight = 9375.724| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3287 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16386 Z= 0.141 Angle : 0.636 10.005 22134 Z= 0.331 Chirality : 0.043 0.234 2360 Planarity : 0.003 0.046 2818 Dihedral : 10.482 156.809 2245 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.61 % Allowed : 24.77 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.19), residues: 1932 helix: 1.16 (0.15), residues: 1139 sheet: 0.01 (0.52), residues: 102 loop : 0.29 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 44 HIS 0.013 0.001 HIS C 201 PHE 0.030 0.002 PHE B 261 TYR 0.017 0.001 TYR C 179 ARG 0.004 0.000 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 871) hydrogen bonds : angle 5.08747 ( 2571) covalent geometry : bond 0.00319 (16386) covalent geometry : angle 0.63583 (22134) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 494 time to evaluate : 1.642 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: A 65 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7396 (mp0) REVERT: A 119 GLU cc_start: 0.8303 (mp0) cc_final: 0.8048 (mp0) REVERT: A 138 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8794 (mttm) REVERT: A 161 ARG cc_start: 0.7751 (ttm-80) cc_final: 0.7192 (ttm-80) REVERT: A 162 LYS cc_start: 0.8732 (ttpt) cc_final: 0.8276 (ttpt) REVERT: A 172 LEU cc_start: 0.9331 (mp) cc_final: 0.9080 (mp) REVERT: A 232 ASN cc_start: 0.8926 (OUTLIER) cc_final: 0.8379 (m-40) REVERT: A 346 LEU cc_start: 0.9446 (mt) cc_final: 0.9163 (mp) REVERT: A 357 TYR cc_start: 0.9050 (m-10) cc_final: 0.8025 (m-10) REVERT: A 361 GLN cc_start: 0.8579 (tp40) cc_final: 0.8360 (tp40) REVERT: A 384 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7240 (pm20) REVERT: A 402 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7294 (tm-30) REVERT: A 447 ASN cc_start: 0.8306 (m-40) cc_final: 0.7913 (m-40) REVERT: A 456 LYS cc_start: 0.9029 (mtmm) cc_final: 0.8796 (mtmm) REVERT: A 466 MET cc_start: 0.8680 (ptt) cc_final: 0.8388 (ptt) REVERT: A 505 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8175 (mt-10) REVERT: A 515 ASP cc_start: 0.8803 (m-30) cc_final: 0.8568 (m-30) REVERT: A 571 TYR cc_start: 0.9193 (t80) cc_final: 0.8746 (t80) REVERT: A 628 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8484 (mt-10) REVERT: A 640 MET cc_start: 0.9324 (OUTLIER) cc_final: 0.8803 (tpp) REVERT: B 52 LYS cc_start: 0.9432 (tppt) cc_final: 0.9142 (tppt) REVERT: B 79 GLU cc_start: 0.8876 (tp30) cc_final: 0.8228 (tp30) REVERT: B 87 LYS cc_start: 0.8739 (mmmm) cc_final: 0.8516 (tttt) REVERT: B 116 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8651 (mp0) REVERT: B 232 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8552 (m110) REVERT: B 257 ASP cc_start: 0.8933 (m-30) cc_final: 0.8692 (m-30) REVERT: B 344 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8251 (mt-10) REVERT: B 384 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.7318 (pm20) REVERT: B 493 MET cc_start: 0.9376 (tmm) cc_final: 0.9165 (tmm) REVERT: B 586 TYR cc_start: 0.8583 (m-80) cc_final: 0.8203 (m-80) REVERT: B 589 SER cc_start: 0.9656 (t) cc_final: 0.9404 (t) REVERT: B 594 VAL cc_start: 0.9253 (m) cc_final: 0.8987 (p) REVERT: B 599 GLU cc_start: 0.8683 (pm20) cc_final: 0.8181 (pm20) REVERT: B 610 LYS cc_start: 0.9413 (ptpt) cc_final: 0.9047 (ptmm) REVERT: B 620 SER cc_start: 0.9486 (OUTLIER) cc_final: 0.9261 (p) REVERT: C 56 MET cc_start: 0.5175 (ptt) cc_final: 0.4671 (ppp) REVERT: C 95 MET cc_start: 0.7678 (ppp) cc_final: 0.7310 (ppp) REVERT: C 149 ASP cc_start: 0.8357 (m-30) cc_final: 0.8133 (m-30) REVERT: C 157 MET cc_start: 0.8708 (mtp) cc_final: 0.8282 (ttt) REVERT: C 169 TYR cc_start: 0.8864 (m-80) cc_final: 0.8616 (m-80) REVERT: C 178 PHE cc_start: 0.7885 (m-10) cc_final: 0.7613 (m-80) REVERT: C 238 ASN cc_start: 0.7836 (OUTLIER) cc_final: 0.7408 (m-40) REVERT: D 174 TYR cc_start: 0.6025 (OUTLIER) cc_final: 0.5538 (t80) REVERT: D 185 MET cc_start: -0.1321 (mmm) cc_final: -0.1868 (mmm) REVERT: D 259 PHE cc_start: 0.4902 (OUTLIER) cc_final: 0.4623 (t80) REVERT: D 268 LEU cc_start: 0.2990 (mm) cc_final: 0.2769 (mm) REVERT: D 286 VAL cc_start: 0.6336 (OUTLIER) cc_final: 0.6133 (t) outliers start: 62 outliers final: 32 residues processed: 518 average time/residue: 0.2605 time to fit residues: 202.7148 Evaluate side-chains 513 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 470 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 138 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 344 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 425 ILE 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 640 MET Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 620 SER 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 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 238 ASN Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 180 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 646 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 132 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.153464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.108960 restraints weight = 32160.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.112372 restraints weight = 15473.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114475 restraints weight = 9374.060| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 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 = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.5906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16386 Z= 0.144 Angle : 0.647 8.743 22134 Z= 0.336 Chirality : 0.044 0.256 2360 Planarity : 0.003 0.045 2818 Dihedral : 10.290 153.962 2245 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.26 % Allowed : 25.47 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.19), residues: 1932 helix: 1.13 (0.15), residues: 1141 sheet: -0.27 (0.51), residues: 106 loop : 0.24 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 44 HIS 0.014 0.001 HIS C 201 PHE 0.029 0.002 PHE B 261 TYR 0.023 0.001 TYR A 118 ARG 0.004 0.000 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 871) hydrogen bonds : angle 5.10260 ( 2571) covalent geometry : bond 0.00328 (16386) covalent geometry : angle 0.64684 (22134) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 483 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7759 (mp0) REVERT: A 119 GLU cc_start: 0.8257 (mp0) cc_final: 0.7992 (mp0) REVERT: A 162 LYS cc_start: 0.8747 (ttpt) cc_final: 0.8494 (ttpt) REVERT: A 172 LEU cc_start: 0.9314 (mp) cc_final: 0.9051 (mp) REVERT: A 232 ASN cc_start: 0.8856 (OUTLIER) cc_final: 0.8339 (m-40) REVERT: A 346 LEU cc_start: 0.9436 (mt) cc_final: 0.9153 (mp) REVERT: A 357 TYR cc_start: 0.8919 (m-10) cc_final: 0.7966 (m-10) REVERT: A 361 GLN cc_start: 0.8593 (tp40) cc_final: 0.8374 (tp40) REVERT: A 384 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7317 (pm20) REVERT: A 402 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7353 (tm-30) REVERT: A 466 MET cc_start: 0.8683 (ptt) cc_final: 0.8409 (ptt) REVERT: A 505 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8223 (mt-10) REVERT: A 515 ASP cc_start: 0.8798 (m-30) cc_final: 0.8558 (m-30) REVERT: A 546 LEU cc_start: 0.9396 (mt) cc_final: 0.9186 (tp) REVERT: A 571 TYR cc_start: 0.9163 (t80) cc_final: 0.8824 (t80) REVERT: A 598 MET cc_start: 0.8239 (mtt) cc_final: 0.7953 (mtt) REVERT: A 628 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8501 (mt-10) REVERT: A 640 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.8665 (tpp) REVERT: B 27 ASP cc_start: 0.8847 (p0) cc_final: 0.8368 (p0) REVERT: B 52 LYS cc_start: 0.9402 (tppt) cc_final: 0.9188 (tppt) REVERT: B 79 GLU cc_start: 0.8900 (tp30) cc_final: 0.8249 (tp30) REVERT: B 87 LYS cc_start: 0.8757 (mmmm) cc_final: 0.8528 (tttt) REVERT: B 116 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8635 (mp0) REVERT: B 232 ASN cc_start: 0.8844 (OUTLIER) cc_final: 0.8484 (m110) REVERT: B 257 ASP cc_start: 0.8921 (m-30) cc_final: 0.8700 (m-30) REVERT: B 312 GLN cc_start: 0.8934 (mt0) cc_final: 0.8675 (mt0) REVERT: B 344 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8291 (mt-10) REVERT: B 384 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.7201 (pm20) REVERT: B 467 ASN cc_start: 0.9135 (m-40) cc_final: 0.8895 (m-40) REVERT: B 471 TYR cc_start: 0.8871 (t80) cc_final: 0.8359 (t80) REVERT: B 493 MET cc_start: 0.9384 (tmm) cc_final: 0.9166 (tmm) REVERT: B 526 GLU cc_start: 0.8564 (mp0) cc_final: 0.8304 (mm-30) REVERT: B 586 TYR cc_start: 0.8577 (m-80) cc_final: 0.8156 (m-10) REVERT: B 599 GLU cc_start: 0.8706 (pm20) cc_final: 0.8233 (pm20) REVERT: B 604 ARG cc_start: 0.8952 (mmt-90) cc_final: 0.8658 (mmt-90) REVERT: B 610 LYS cc_start: 0.9442 (ptpt) cc_final: 0.9098 (ptmm) REVERT: B 612 TYR cc_start: 0.8794 (m-80) cc_final: 0.7476 (m-80) REVERT: B 620 SER cc_start: 0.9529 (OUTLIER) cc_final: 0.9306 (p) REVERT: C 56 MET cc_start: 0.5220 (ptt) cc_final: 0.4702 (ppp) REVERT: C 95 MET cc_start: 0.7420 (ppp) cc_final: 0.7059 (ppp) REVERT: C 157 MET cc_start: 0.8652 (mtp) cc_final: 0.8228 (ttt) REVERT: C 169 TYR cc_start: 0.8844 (m-80) cc_final: 0.8587 (m-80) REVERT: C 178 PHE cc_start: 0.7870 (m-10) cc_final: 0.7580 (m-80) REVERT: C 238 ASN cc_start: 0.7875 (OUTLIER) cc_final: 0.7529 (m-40) REVERT: D 157 MET cc_start: -0.0414 (ppp) cc_final: -0.0827 (ppp) REVERT: D 185 MET cc_start: -0.1677 (mmm) cc_final: -0.2209 (mmm) REVERT: D 204 TYR cc_start: 0.7518 (OUTLIER) cc_final: 0.7098 (t80) REVERT: D 259 PHE cc_start: 0.4916 (OUTLIER) cc_final: 0.4650 (t80) REVERT: D 268 LEU cc_start: 0.2563 (mm) cc_final: 0.2358 (mm) REVERT: D 286 VAL cc_start: 0.6384 (OUTLIER) cc_final: 0.6145 (t) outliers start: 56 outliers final: 35 residues processed: 511 average time/residue: 0.2586 time to fit residues: 199.8070 Evaluate side-chains 505 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 460 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 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 317 MET 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 565 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 646 GLN Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 111 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 182 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 188 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.149488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.105424 restraints weight = 32431.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.108813 restraints weight = 15578.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110986 restraints weight = 9360.917| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.6055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 16386 Z= 0.223 Angle : 0.691 9.143 22134 Z= 0.360 Chirality : 0.045 0.304 2360 Planarity : 0.004 0.045 2818 Dihedral : 10.281 156.693 2245 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.21 % Allowed : 25.87 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.19), residues: 1932 helix: 1.10 (0.15), residues: 1143 sheet: -0.62 (0.50), residues: 114 loop : 0.36 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 44 HIS 0.015 0.001 HIS C 201 PHE 0.044 0.002 PHE C 92 TYR 0.035 0.002 TYR B 36 ARG 0.005 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04070 ( 871) hydrogen bonds : angle 5.19028 ( 2571) covalent geometry : bond 0.00501 (16386) covalent geometry : angle 0.69127 (22134) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 472 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8326 (mp0) cc_final: 0.7948 (mp0) REVERT: A 162 LYS cc_start: 0.8723 (ttpt) cc_final: 0.8387 (ttpt) REVERT: A 172 LEU cc_start: 0.9348 (mp) cc_final: 0.9110 (mp) REVERT: A 232 ASN cc_start: 0.8921 (OUTLIER) cc_final: 0.8391 (m-40) REVERT: A 346 LEU cc_start: 0.9461 (mt) cc_final: 0.9153 (mp) REVERT: A 357 TYR cc_start: 0.9042 (m-10) cc_final: 0.8160 (m-10) REVERT: A 361 GLN cc_start: 0.8662 (tp40) cc_final: 0.8415 (tp40) REVERT: A 384 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7214 (pm20) REVERT: A 402 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7356 (tm-30) REVERT: A 456 LYS cc_start: 0.8964 (mtmm) cc_final: 0.8612 (mtmm) REVERT: A 505 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8228 (mt-10) REVERT: A 515 ASP cc_start: 0.8858 (m-30) cc_final: 0.8628 (m-30) REVERT: A 571 TYR cc_start: 0.9223 (t80) cc_final: 0.8803 (t80) REVERT: A 640 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.8705 (tpp) REVERT: B 41 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8416 (mm) REVERT: B 79 GLU cc_start: 0.8961 (tp30) cc_final: 0.8283 (tp30) REVERT: B 87 LYS cc_start: 0.8823 (mmmm) cc_final: 0.8576 (tttt) REVERT: B 116 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8656 (mt-10) REVERT: B 232 ASN cc_start: 0.8927 (OUTLIER) cc_final: 0.8580 (m110) REVERT: B 257 ASP cc_start: 0.9047 (m-30) cc_final: 0.8736 (m-30) REVERT: B 344 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8269 (mt-10) REVERT: B 384 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.7255 (pm20) REVERT: B 467 ASN cc_start: 0.9246 (m-40) cc_final: 0.8929 (m-40) REVERT: B 526 GLU cc_start: 0.8664 (mp0) cc_final: 0.8390 (mm-30) REVERT: B 586 TYR cc_start: 0.8586 (m-80) cc_final: 0.8200 (m-80) REVERT: B 599 GLU cc_start: 0.8726 (pm20) cc_final: 0.8304 (pm20) REVERT: B 604 ARG cc_start: 0.9008 (mmt-90) cc_final: 0.8672 (mmt-90) REVERT: B 610 LYS cc_start: 0.9447 (ptpt) cc_final: 0.9041 (ptmm) REVERT: B 620 SER cc_start: 0.9509 (OUTLIER) cc_final: 0.9282 (p) REVERT: B 668 ASN cc_start: 0.8883 (m110) cc_final: 0.8578 (m110) REVERT: C 56 MET cc_start: 0.5297 (ptt) cc_final: 0.4720 (ppp) REVERT: C 95 MET cc_start: 0.7735 (ppp) cc_final: 0.7388 (ppp) REVERT: C 157 MET cc_start: 0.8708 (mtp) cc_final: 0.8271 (ttt) REVERT: C 169 TYR cc_start: 0.8902 (m-80) cc_final: 0.8610 (m-80) REVERT: C 178 PHE cc_start: 0.7900 (m-10) cc_final: 0.7509 (m-80) REVERT: C 238 ASN cc_start: 0.8013 (OUTLIER) cc_final: 0.7666 (m-40) REVERT: D 157 MET cc_start: 0.0180 (ppp) cc_final: -0.0286 (ppp) REVERT: D 174 TYR cc_start: 0.6193 (OUTLIER) cc_final: 0.5676 (t80) REVERT: D 185 MET cc_start: -0.1311 (mmm) cc_final: -0.1661 (mmm) REVERT: D 204 TYR cc_start: 0.7422 (OUTLIER) cc_final: 0.7065 (t80) REVERT: D 259 PHE cc_start: 0.5041 (OUTLIER) cc_final: 0.4710 (t80) outliers start: 55 outliers final: 36 residues processed: 495 average time/residue: 0.2505 time to fit residues: 187.2176 Evaluate side-chains 496 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 449 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 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 317 MET Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 620 SER 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 81 VAL Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 283 ASN 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 137 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 160 optimal weight: 7.9990 chunk 106 optimal weight: 0.6980 chunk 120 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 127 optimal weight: 0.0980 chunk 68 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.152604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.108242 restraints weight = 32485.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111702 restraints weight = 15548.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.113937 restraints weight = 9373.353| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.6185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 16386 Z= 0.176 Angle : 0.702 9.924 22134 Z= 0.360 Chirality : 0.045 0.299 2360 Planarity : 0.004 0.044 2818 Dihedral : 10.002 150.515 2245 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.09 % Allowed : 26.28 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.19), residues: 1932 helix: 1.01 (0.15), residues: 1151 sheet: -0.30 (0.52), residues: 102 loop : 0.26 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 44 HIS 0.014 0.001 HIS C 201 PHE 0.028 0.002 PHE B 261 TYR 0.032 0.002 TYR B 36 ARG 0.007 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03980 ( 871) hydrogen bonds : angle 5.19617 ( 2571) covalent geometry : bond 0.00402 (16386) covalent geometry : angle 0.70169 (22134) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 454 time to evaluate : 1.659 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 119 GLU cc_start: 0.8310 (mp0) cc_final: 0.7953 (mp0) REVERT: A 172 LEU cc_start: 0.9356 (mp) cc_final: 0.9097 (mp) REVERT: A 232 ASN cc_start: 0.8907 (OUTLIER) cc_final: 0.8218 (m110) REVERT: A 346 LEU cc_start: 0.9452 (mt) cc_final: 0.9156 (mp) REVERT: A 357 TYR cc_start: 0.8984 (m-10) cc_final: 0.7984 (m-10) REVERT: A 361 GLN cc_start: 0.8588 (tp40) cc_final: 0.8367 (tp40) REVERT: A 384 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7185 (pm20) REVERT: A 402 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7387 (tm-30) REVERT: A 505 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8243 (mt-10) REVERT: A 515 ASP cc_start: 0.8835 (m-30) cc_final: 0.8606 (m-30) REVERT: A 571 TYR cc_start: 0.9217 (t80) cc_final: 0.8859 (t80) REVERT: A 640 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.8699 (tpp) REVERT: B 27 ASP cc_start: 0.8838 (p0) cc_final: 0.8418 (p0) REVERT: B 79 GLU cc_start: 0.8955 (tp30) cc_final: 0.8293 (tp30) REVERT: B 87 LYS cc_start: 0.8788 (mmmm) cc_final: 0.8541 (tttt) REVERT: B 116 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8636 (mt-10) REVERT: B 232 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8502 (m-40) REVERT: B 257 ASP cc_start: 0.8956 (m-30) cc_final: 0.8693 (m-30) REVERT: B 344 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8290 (mt-10) REVERT: B 384 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.7276 (pm20) REVERT: B 467 ASN cc_start: 0.9180 (t0) cc_final: 0.8905 (m-40) REVERT: B 526 GLU cc_start: 0.8620 (mp0) cc_final: 0.8336 (mm-30) REVERT: B 586 TYR cc_start: 0.8566 (m-80) cc_final: 0.8134 (m-80) REVERT: B 599 GLU cc_start: 0.8724 (pm20) cc_final: 0.8285 (pm20) REVERT: B 604 ARG cc_start: 0.9012 (mmt-90) cc_final: 0.8668 (mmt-90) REVERT: B 610 LYS cc_start: 0.9449 (ptpt) cc_final: 0.9121 (ptmm) REVERT: B 612 TYR cc_start: 0.8789 (m-80) cc_final: 0.7387 (m-80) REVERT: B 620 SER cc_start: 0.9497 (OUTLIER) cc_final: 0.9270 (p) REVERT: B 668 ASN cc_start: 0.8865 (m110) cc_final: 0.8590 (m110) REVERT: C 56 MET cc_start: 0.5538 (ptt) cc_final: 0.5012 (ppp) REVERT: C 74 MET cc_start: 0.7213 (ptt) cc_final: 0.6998 (ptt) REVERT: C 157 MET cc_start: 0.8716 (mtp) cc_final: 0.8248 (ttt) REVERT: C 178 PHE cc_start: 0.7881 (m-10) cc_final: 0.7507 (m-80) REVERT: C 238 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.7657 (m-40) REVERT: D 157 MET cc_start: 0.0248 (ppp) cc_final: -0.0202 (ppp) REVERT: D 174 TYR cc_start: 0.6178 (OUTLIER) cc_final: 0.5646 (t80) REVERT: D 185 MET cc_start: -0.1470 (mmm) cc_final: -0.1854 (mmm) REVERT: D 204 TYR cc_start: 0.7414 (OUTLIER) cc_final: 0.6983 (t80) REVERT: D 259 PHE cc_start: 0.5562 (OUTLIER) cc_final: 0.5131 (t80) outliers start: 53 outliers final: 37 residues processed: 475 average time/residue: 0.2728 time to fit residues: 198.4608 Evaluate side-chains 498 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 451 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 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 317 MET Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 620 SER 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 81 VAL Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain D residue 20 MET Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 259 PHE 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 81 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 chunk 190 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 180 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN D 24 GLN D 28 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.153732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.109845 restraints weight = 32313.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.113386 restraints weight = 15421.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.115645 restraints weight = 9223.473| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 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 = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.6356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 16386 Z= 0.154 Angle : 0.693 10.839 22134 Z= 0.353 Chirality : 0.045 0.276 2360 Planarity : 0.004 0.045 2818 Dihedral : 9.717 140.733 2245 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.09 % Allowed : 26.46 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.19), residues: 1932 helix: 1.03 (0.15), residues: 1147 sheet: -0.71 (0.49), residues: 110 loop : 0.27 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 44 HIS 0.021 0.001 HIS C 201 PHE 0.056 0.002 PHE C 92 TYR 0.038 0.001 TYR B 36 ARG 0.011 0.001 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 871) hydrogen bonds : angle 5.14894 ( 2571) covalent geometry : bond 0.00352 (16386) covalent geometry : angle 0.69279 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6114.77 seconds wall clock time: 107 minutes 55.34 seconds (6475.34 seconds total)