Starting phenix.real_space_refine on Thu Sep 18 10:06:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byv_45045/09_2025/9byv_45045_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byv_45045/09_2025/9byv_45045.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 { model { file = "/net/cci-nas-00/data/ceres_data/9byv_45045/09_2025/9byv_45045_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byv_45045/09_2025/9byv_45045_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9byv_45045/09_2025/9byv_45045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byv_45045/09_2025/9byv_45045.map" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 4.21, per 1000 atoms: 0.26 Number of scatterers: 16038 At special positions: 0 Unit cell: (100.683, 122.04, 132.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 771.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.516A 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: 3.985A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.953A 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: 4.851A 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: 3.628A 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: 4.074A 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: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.676A 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: 3.872A 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: 3.729A 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: 5.117A 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: 4.069A 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: 4.936A 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: 6.359A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.427A 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: 7.902A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.454A 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: 6.192A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.501A 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: 5.661A 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: 7.907A 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: 8.345A 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: 7.807A 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: 7.593A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.16 Time building geometry restraints manager: 2.07 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: 4719 1.34 - 1.46: 3125 1.46 - 1.58: 8361 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 1.600 -0.060 1.25e-02 6.40e+03 2.30e+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 9.02e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.569 -0.032 1.17e-02 7.31e+03 7.28e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.573 -0.032 1.25e-02 6.40e+03 6.73e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21572 2.09 - 4.18: 519 4.18 - 6.27: 38 6.27 - 8.36: 1 8.36 - 10.45: 4 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.64 -6.10 1.36e+00 5.41e-01 2.01e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.17 -4.46 1.15e+00 7.56e-01 1.51e+01 angle pdb=" N SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.26 -3.98 1.09e+00 8.42e-01 1.33e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.80 -4.30 1.23e+00 6.61e-01 1.22e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.51 3.68 1.06e+00 8.90e-01 1.20e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 9468 35.79 - 71.58: 339 71.58 - 107.37: 37 107.37 - 143.16: 3 143.16 - 178.95: 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 -58.32 120.63 -178.95 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 301.68 151.21 150.48 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 31.91 148.06 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 9847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2147 0.094 - 0.187: 180 0.187 - 0.281: 28 0.281 - 0.375: 3 0.375 - 0.468: 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 5.48e+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 4.58e+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 2.95e+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 4.12e-02 2.72e+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 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " -0.006 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 SER B 35 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.91e+00 pdb=" C SER B 35 " -0.024 2.00e-02 2.50e+03 pdb=" O SER B 35 " 0.009 2.00e-02 2.50e+03 pdb=" N TYR B 36 " 0.008 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 129 2.51 - 3.11: 11557 3.11 - 3.70: 27043 3.70 - 4.30: 41579 4.30 - 4.90: 65483 Nonbonded interactions: 145791 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.911 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 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 145786 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.240 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 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= 0.315 Angle : 0.740 10.454 22134 Z= 0.463 Chirality : 0.058 0.468 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.947 178.945 6154 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.40 % Allowed : 15.27 % Favored : 83.33 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.18), residues: 1932 helix: 0.58 (0.14), residues: 1151 sheet: 0.46 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 196 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE C 168 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00553 (16386) covalent geometry : angle 0.74038 (22134) hydrogen bonds : bond 0.15422 ( 871) hydrogen bonds : angle 6.51813 ( 2571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 864 time to evaluate : 0.652 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8484 (m) REVERT: A 116 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7111 (mt-10) REVERT: A 179 LEU cc_start: 0.9121 (tp) cc_final: 0.8784 (tp) REVERT: A 232 ASN cc_start: 0.8164 (OUTLIER) cc_final: 0.7964 (m-40) REVERT: A 362 ASP cc_start: 0.6467 (m-30) cc_final: 0.6136 (m-30) REVERT: A 490 THR cc_start: 0.8604 (m) cc_final: 0.8295 (m) REVERT: A 576 LEU cc_start: 0.8938 (mt) cc_final: 0.8556 (mt) REVERT: A 606 TYR cc_start: 0.7504 (m-80) cc_final: 0.7289 (m-10) REVERT: B 81 PHE cc_start: 0.7719 (m-80) cc_final: 0.7493 (m-80) REVERT: B 179 LEU cc_start: 0.8956 (tp) cc_final: 0.8687 (tp) REVERT: B 186 ILE cc_start: 0.9326 (mt) cc_final: 0.8995 (mt) REVERT: B 190 MET cc_start: 0.8126 (mtm) cc_final: 0.7906 (mtm) REVERT: B 288 PHE cc_start: 0.8003 (t80) cc_final: 0.7671 (t80) REVERT: B 362 ASP cc_start: 0.7308 (m-30) cc_final: 0.6983 (m-30) REVERT: B 373 ILE cc_start: 0.9064 (mt) cc_final: 0.8800 (mt) REVERT: B 420 MET cc_start: 0.7976 (mmm) cc_final: 0.7741 (mmm) REVERT: B 436 LEU cc_start: 0.9236 (mt) cc_final: 0.8922 (mt) REVERT: B 460 SER cc_start: 0.9036 (t) cc_final: 0.8771 (p) REVERT: B 471 TYR cc_start: 0.8197 (t80) cc_final: 0.7492 (t80) REVERT: B 546 LEU cc_start: 0.8958 (mt) cc_final: 0.8449 (mt) REVERT: B 550 MET cc_start: 0.8032 (mtm) cc_final: 0.7706 (mtp) REVERT: B 584 ILE cc_start: 0.8945 (tp) cc_final: 0.8730 (tp) REVERT: B 612 TYR cc_start: 0.7224 (m-80) cc_final: 0.6873 (m-80) REVERT: C 286 VAL cc_start: 0.4799 (t) cc_final: 0.4033 (p) REVERT: D 89 VAL cc_start: 0.5044 (t) cc_final: 0.4268 (t) REVERT: D 126 LYS cc_start: 0.3277 (OUTLIER) cc_final: 0.2610 (tttt) REVERT: D 246 LEU cc_start: 0.5231 (mt) cc_final: 0.4712 (tp) REVERT: D 287 LEU cc_start: 0.4918 (mt) cc_final: 0.4463 (tp) outliers start: 24 outliers final: 9 residues processed: 877 average time/residue: 0.1471 time to fit residues: 188.1110 Evaluate side-chains 624 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 612 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 126 LYS Chi-restraints excluded: chain D residue 127 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 312 GLN A 365 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN B 312 GLN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN B 338 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN C 107 ASN C 127 GLN D 71 ASN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN D 181 GLN D 186 GLN D 210 GLN D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.145736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.101458 restraints weight = 31721.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.105154 restraints weight = 15029.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107472 restraints weight = 8856.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.108864 restraints weight = 6155.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109780 restraints weight = 4852.185| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 16386 Z= 0.243 Angle : 0.693 9.555 22134 Z= 0.360 Chirality : 0.046 0.306 2360 Planarity : 0.004 0.050 2818 Dihedral : 11.850 176.663 2263 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.84 % Allowed : 19.29 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.19), residues: 1932 helix: 1.36 (0.15), residues: 1132 sheet: -0.42 (0.46), residues: 114 loop : 0.52 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 686 TYR 0.020 0.002 TYR C 247 PHE 0.031 0.002 PHE D 168 TRP 0.015 0.002 TRP A 623 HIS 0.021 0.002 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00537 (16386) covalent geometry : angle 0.69296 (22134) hydrogen bonds : bond 0.04723 ( 871) hydrogen bonds : angle 5.15392 ( 2571) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 638 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8843 (tptp) cc_final: 0.8413 (tppt) REVERT: A 40 TYR cc_start: 0.8932 (t80) cc_final: 0.8610 (t80) REVERT: A 76 ASP cc_start: 0.8500 (m-30) cc_final: 0.8183 (m-30) REVERT: A 119 GLU cc_start: 0.8536 (mp0) cc_final: 0.8326 (mp0) REVERT: A 144 MET cc_start: 0.8849 (mtm) cc_final: 0.8533 (mtm) REVERT: A 214 LYS cc_start: 0.8006 (mmtt) cc_final: 0.7716 (mmtt) REVERT: A 250 TYR cc_start: 0.8644 (m-80) cc_final: 0.7943 (m-80) REVERT: A 263 ASP cc_start: 0.7828 (m-30) cc_final: 0.7499 (m-30) REVERT: A 290 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8232 (mt-10) REVERT: A 348 MET cc_start: 0.8170 (tmm) cc_final: 0.7779 (tmm) REVERT: A 359 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8376 (ttp) REVERT: A 384 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7630 (pm20) REVERT: A 394 TYR cc_start: 0.8864 (m-80) cc_final: 0.8573 (m-10) REVERT: A 406 ASP cc_start: 0.8318 (m-30) cc_final: 0.8077 (t0) REVERT: A 446 ARG cc_start: 0.7567 (mmm160) cc_final: 0.6891 (mmm160) REVERT: A 452 ARG cc_start: 0.9022 (ttp80) cc_final: 0.8742 (ttt-90) REVERT: A 583 SER cc_start: 0.8949 (m) cc_final: 0.8720 (t) REVERT: A 606 TYR cc_start: 0.8470 (m-80) cc_final: 0.8192 (m-10) REVERT: A 640 MET cc_start: 0.9324 (OUTLIER) cc_final: 0.8918 (tpp) REVERT: A 653 SER cc_start: 0.8796 (m) cc_final: 0.8593 (m) REVERT: A 667 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8924 (tt) REVERT: B 65 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7978 (mm-30) REVERT: B 136 LYS cc_start: 0.9176 (mmmm) cc_final: 0.8732 (mmtt) REVERT: B 182 ILE cc_start: 0.9498 (mt) cc_final: 0.9298 (mp) REVERT: B 218 ASN cc_start: 0.8936 (OUTLIER) cc_final: 0.8496 (t0) REVERT: B 221 LYS cc_start: 0.9185 (mttm) cc_final: 0.8886 (mmtm) REVERT: B 236 TYR cc_start: 0.9182 (t80) cc_final: 0.8979 (t80) REVERT: B 274 ARG cc_start: 0.8294 (ttm-80) cc_final: 0.7963 (ttm-80) REVERT: B 308 LYS cc_start: 0.9116 (mtpt) cc_final: 0.8761 (mtmm) REVERT: B 322 MET cc_start: 0.9145 (tpp) cc_final: 0.8740 (tpp) REVERT: B 348 MET cc_start: 0.7918 (tpp) cc_final: 0.7516 (tpp) REVERT: B 352 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7409 (mt-10) REVERT: B 396 ASP cc_start: 0.8589 (m-30) cc_final: 0.8339 (m-30) REVERT: B 420 MET cc_start: 0.8970 (mmm) cc_final: 0.8745 (mmm) REVERT: B 471 TYR cc_start: 0.9092 (t80) cc_final: 0.8351 (t80) REVERT: B 546 LEU cc_start: 0.9549 (mt) cc_final: 0.9141 (mt) REVERT: B 627 LYS cc_start: 0.8964 (tttt) cc_final: 0.8551 (ttpt) REVERT: C 44 TRP cc_start: 0.8381 (t-100) cc_final: 0.8099 (t-100) REVERT: C 68 GLU cc_start: 0.8672 (mp0) cc_final: 0.7823 (tm-30) REVERT: C 72 THR cc_start: 0.9134 (OUTLIER) cc_final: 0.8829 (t) REVERT: C 76 ILE cc_start: 0.9143 (mt) cc_final: 0.8928 (pt) REVERT: C 124 TRP cc_start: 0.8376 (t60) cc_final: 0.8090 (t60) REVERT: C 154 PHE cc_start: 0.8818 (t80) cc_final: 0.8567 (t80) REVERT: C 269 MET cc_start: 0.8715 (tpt) cc_final: 0.8373 (tmm) REVERT: D 47 LEU cc_start: 0.4919 (mt) cc_final: 0.4375 (tp) REVERT: D 59 LEU cc_start: 0.8045 (pp) cc_final: 0.7660 (tt) REVERT: D 76 ILE cc_start: 0.7426 (tp) cc_final: 0.7151 (tp) REVERT: D 80 HIS cc_start: 0.7529 (m-70) cc_final: 0.7285 (m-70) REVERT: D 168 PHE cc_start: 0.8861 (m-80) cc_final: 0.8444 (m-80) REVERT: D 174 TYR cc_start: 0.7598 (t80) cc_final: 0.6718 (t80) REVERT: D 198 GLU cc_start: 0.8504 (mm-30) cc_final: 0.6923 (tp30) outliers start: 83 outliers final: 37 residues processed: 675 average time/residue: 0.1346 time to fit residues: 136.9007 Evaluate side-chains 590 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 547 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 240 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 147 GLN B 312 GLN B 320 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 192 ASN C 249 GLN D 80 HIS D 91 ASN D 181 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.145094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.100714 restraints weight = 32012.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.104339 restraints weight = 15044.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.106641 restraints weight = 8891.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.108101 restraints weight = 6223.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.108871 restraints weight = 4876.963| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | 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: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16386 Z= 0.172 Angle : 0.646 13.102 22134 Z= 0.333 Chirality : 0.045 0.367 2360 Planarity : 0.004 0.039 2818 Dihedral : 11.140 168.937 2250 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 4.55 % Allowed : 21.79 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.19), residues: 1932 helix: 1.37 (0.15), residues: 1132 sheet: -0.34 (0.46), residues: 114 loop : 0.51 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 686 TYR 0.031 0.002 TYR C 142 PHE 0.042 0.002 PHE D 172 TRP 0.009 0.001 TRP C 124 HIS 0.017 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00389 (16386) covalent geometry : angle 0.64577 (22134) hydrogen bonds : bond 0.04226 ( 871) hydrogen bonds : angle 4.96985 ( 2571) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 598 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8785 (tptp) cc_final: 0.8367 (tppt) REVERT: A 40 TYR cc_start: 0.8890 (t80) cc_final: 0.8558 (t80) REVERT: A 76 ASP cc_start: 0.8406 (m-30) cc_final: 0.8121 (m-30) REVERT: A 119 GLU cc_start: 0.8514 (mp0) cc_final: 0.8223 (mp0) REVERT: A 144 MET cc_start: 0.8772 (mtm) cc_final: 0.8538 (mtm) REVERT: A 232 ASN cc_start: 0.8877 (OUTLIER) cc_final: 0.8608 (m-40) REVERT: A 250 TYR cc_start: 0.8709 (m-80) cc_final: 0.8371 (m-80) REVERT: A 263 ASP cc_start: 0.8067 (m-30) cc_final: 0.7840 (m-30) REVERT: A 290 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8251 (mt-10) REVERT: A 344 GLU cc_start: 0.8745 (mt-10) cc_final: 0.7900 (mp0) REVERT: A 348 MET cc_start: 0.8195 (tmm) cc_final: 0.7742 (tmm) REVERT: A 384 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7409 (pm20) REVERT: A 394 TYR cc_start: 0.8880 (m-80) cc_final: 0.8531 (m-80) REVERT: A 406 ASP cc_start: 0.8313 (m-30) cc_final: 0.8050 (t0) REVERT: A 446 ARG cc_start: 0.7528 (mmm160) cc_final: 0.6937 (mmm160) REVERT: A 452 ARG cc_start: 0.9015 (ttp80) cc_final: 0.8743 (ttt-90) REVERT: A 590 SER cc_start: 0.9152 (t) cc_final: 0.8259 (p) REVERT: A 598 MET cc_start: 0.8468 (mtm) cc_final: 0.8246 (mtm) REVERT: A 640 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8881 (tpp) REVERT: B 65 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7925 (mm-30) REVERT: B 82 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8927 (mttp) REVERT: B 95 MET cc_start: 0.9076 (mmm) cc_final: 0.8812 (tpp) REVERT: B 218 ASN cc_start: 0.8967 (m110) cc_final: 0.8509 (t0) REVERT: B 221 LYS cc_start: 0.9050 (mttm) cc_final: 0.8783 (mmtm) REVERT: B 236 TYR cc_start: 0.9084 (t80) cc_final: 0.8847 (t80) REVERT: B 257 ASP cc_start: 0.8560 (m-30) cc_final: 0.8340 (m-30) REVERT: B 274 ARG cc_start: 0.8238 (ttm-80) cc_final: 0.7659 (tpp80) REVERT: B 308 LYS cc_start: 0.9143 (mtpt) cc_final: 0.8925 (ptpt) REVERT: B 374 SER cc_start: 0.9452 (t) cc_final: 0.9131 (t) REVERT: B 434 ASP cc_start: 0.8561 (m-30) cc_final: 0.8167 (m-30) REVERT: B 471 TYR cc_start: 0.9074 (t80) cc_final: 0.8473 (t80) REVERT: B 493 MET cc_start: 0.9637 (tmm) cc_final: 0.9354 (tmm) REVERT: B 546 LEU cc_start: 0.9518 (mt) cc_final: 0.9140 (mt) REVERT: B 550 MET cc_start: 0.8236 (mtm) cc_final: 0.8019 (mtp) REVERT: B 586 TYR cc_start: 0.9100 (m-80) cc_final: 0.8688 (m-80) REVERT: B 595 MET cc_start: 0.8505 (mmm) cc_final: 0.7723 (mmm) REVERT: B 602 GLU cc_start: 0.7862 (pp20) cc_final: 0.7126 (pp20) REVERT: B 627 LYS cc_start: 0.8914 (tttt) cc_final: 0.8516 (ttpt) REVERT: B 628 GLU cc_start: 0.8493 (mt-10) cc_final: 0.7912 (mp0) REVERT: C 40 ASP cc_start: 0.4574 (m-30) cc_final: 0.4222 (m-30) REVERT: C 43 THR cc_start: 0.6754 (OUTLIER) cc_final: 0.6030 (p) REVERT: C 55 TYR cc_start: 0.6103 (t80) cc_final: 0.5680 (t80) REVERT: C 68 GLU cc_start: 0.8790 (mp0) cc_final: 0.8099 (tm-30) REVERT: C 124 TRP cc_start: 0.8254 (t60) cc_final: 0.8023 (t60) REVERT: C 154 PHE cc_start: 0.8931 (t80) cc_final: 0.8610 (t80) REVERT: C 178 PHE cc_start: 0.8512 (m-10) cc_final: 0.8159 (m-10) REVERT: C 240 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8749 (mm) REVERT: C 269 MET cc_start: 0.8610 (tpt) cc_final: 0.8300 (tmm) REVERT: D 47 LEU cc_start: 0.5350 (mt) cc_final: 0.4938 (tp) REVERT: D 59 LEU cc_start: 0.7225 (pp) cc_final: 0.6417 (tt) REVERT: D 76 ILE cc_start: 0.7630 (tp) cc_final: 0.7368 (tp) REVERT: D 80 HIS cc_start: 0.7540 (m90) cc_final: 0.7216 (m90) REVERT: D 112 LEU cc_start: 0.4664 (tp) cc_final: 0.4390 (tt) REVERT: D 150 GLU cc_start: 0.9210 (pm20) cc_final: 0.8930 (pm20) REVERT: D 168 PHE cc_start: 0.8804 (m-80) cc_final: 0.8462 (m-80) REVERT: D 174 TYR cc_start: 0.7473 (t80) cc_final: 0.6549 (t80) REVERT: D 198 GLU cc_start: 0.8419 (mm-30) cc_final: 0.6774 (tp30) REVERT: D 266 LYS cc_start: 0.7647 (mtpt) cc_final: 0.7371 (mmtt) outliers start: 78 outliers final: 42 residues processed: 635 average time/residue: 0.1334 time to fit residues: 127.9425 Evaluate side-chains 570 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 522 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 262 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 185 optimal weight: 8.9990 chunk 191 optimal weight: 20.0000 chunk 159 optimal weight: 30.0000 chunk 182 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 312 GLN B 320 ASN B 387 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 127 GLN C 192 ASN D 181 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.144007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.100465 restraints weight = 32641.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.103990 restraints weight = 15291.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.106230 restraints weight = 9014.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.107625 restraints weight = 6325.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.108550 restraints weight = 5001.563| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16386 Z= 0.224 Angle : 0.665 9.227 22134 Z= 0.343 Chirality : 0.046 0.372 2360 Planarity : 0.004 0.048 2818 Dihedral : 10.980 168.065 2248 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 5.07 % Allowed : 22.03 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.19), residues: 1932 helix: 1.34 (0.15), residues: 1132 sheet: -0.60 (0.45), residues: 114 loop : 0.48 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 686 TYR 0.018 0.002 TYR C 242 PHE 0.034 0.002 PHE C 109 TRP 0.010 0.001 TRP A 623 HIS 0.006 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00501 (16386) covalent geometry : angle 0.66500 (22134) hydrogen bonds : bond 0.04170 ( 871) hydrogen bonds : angle 4.96677 ( 2571) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 545 time to evaluate : 0.676 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: A 8 LYS cc_start: 0.8794 (tptp) cc_final: 0.8420 (tppt) REVERT: A 40 TYR cc_start: 0.8948 (t80) cc_final: 0.8540 (t80) REVERT: A 119 GLU cc_start: 0.8602 (mp0) cc_final: 0.8301 (mp0) REVERT: A 144 MET cc_start: 0.8704 (mtm) cc_final: 0.8497 (mtm) REVERT: A 232 ASN cc_start: 0.8964 (t0) cc_final: 0.8518 (m-40) REVERT: A 250 TYR cc_start: 0.8723 (m-80) cc_final: 0.8339 (m-80) REVERT: A 263 ASP cc_start: 0.8144 (m-30) cc_final: 0.7866 (m-30) REVERT: A 286 ASP cc_start: 0.7782 (m-30) cc_final: 0.7514 (m-30) REVERT: A 290 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8260 (mt-10) REVERT: A 348 MET cc_start: 0.8248 (tmm) cc_final: 0.7943 (tmm) REVERT: A 362 ASP cc_start: 0.8269 (m-30) cc_final: 0.7984 (m-30) REVERT: A 384 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.6855 (pm20) REVERT: A 427 LYS cc_start: 0.9074 (tppp) cc_final: 0.8663 (tppp) REVERT: A 446 ARG cc_start: 0.7656 (mmm160) cc_final: 0.7231 (mmm160) REVERT: A 640 MET cc_start: 0.9248 (OUTLIER) cc_final: 0.8949 (tpp) REVERT: A 684 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.7912 (m-80) REVERT: B 65 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7974 (mm-30) REVERT: B 82 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8939 (mttp) REVERT: B 95 MET cc_start: 0.9053 (mmm) cc_final: 0.8766 (tpp) REVERT: B 205 LYS cc_start: 0.8532 (mttm) cc_final: 0.8308 (mttp) REVERT: B 213 ILE cc_start: 0.9075 (mp) cc_final: 0.8869 (mt) REVERT: B 218 ASN cc_start: 0.9005 (m110) cc_final: 0.8509 (t0) REVERT: B 236 TYR cc_start: 0.9146 (t80) cc_final: 0.8911 (t80) REVERT: B 374 SER cc_start: 0.9514 (t) cc_final: 0.9201 (t) REVERT: B 394 TYR cc_start: 0.9189 (m-80) cc_final: 0.8814 (m-80) REVERT: B 434 ASP cc_start: 0.8543 (m-30) cc_final: 0.8176 (m-30) REVERT: B 467 ASN cc_start: 0.9002 (t0) cc_final: 0.8802 (t0) REVERT: B 471 TYR cc_start: 0.9151 (t80) cc_final: 0.8560 (t80) REVERT: B 493 MET cc_start: 0.9630 (tmm) cc_final: 0.9266 (tmm) REVERT: B 546 LEU cc_start: 0.9538 (mt) cc_final: 0.9164 (mt) REVERT: B 586 TYR cc_start: 0.9087 (m-80) cc_final: 0.8616 (m-80) REVERT: B 602 GLU cc_start: 0.7989 (pp20) cc_final: 0.7291 (pp20) REVERT: B 627 LYS cc_start: 0.8899 (tttt) cc_final: 0.8411 (tttt) REVERT: B 628 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8083 (mp0) REVERT: C 21 PHE cc_start: 0.8405 (m-80) cc_final: 0.8134 (t80) REVERT: C 43 THR cc_start: 0.6489 (OUTLIER) cc_final: 0.6191 (p) REVERT: C 103 LYS cc_start: 0.8168 (tppt) cc_final: 0.7774 (tppt) REVERT: C 124 TRP cc_start: 0.8268 (t60) cc_final: 0.8053 (t60) REVERT: C 137 MET cc_start: 0.7245 (mpt) cc_final: 0.7000 (mpp) REVERT: C 154 PHE cc_start: 0.9048 (t80) cc_final: 0.8710 (t80) REVERT: C 174 TYR cc_start: 0.7046 (OUTLIER) cc_final: 0.6478 (t80) REVERT: C 186 GLN cc_start: 0.7195 (mp10) cc_final: 0.6512 (mp10) REVERT: C 261 ARG cc_start: 0.7425 (mtm-85) cc_final: 0.7112 (mtm110) REVERT: C 269 MET cc_start: 0.8705 (tpt) cc_final: 0.8385 (tmm) REVERT: C 274 ASP cc_start: 0.8102 (p0) cc_final: 0.7719 (p0) REVERT: D 59 LEU cc_start: 0.7000 (pp) cc_final: 0.6127 (tt) REVERT: D 116 GLU cc_start: 0.9119 (tp30) cc_final: 0.8754 (tp30) REVERT: D 174 TYR cc_start: 0.7733 (t80) cc_final: 0.6951 (t80) REVERT: D 232 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6049 (mt) outliers start: 87 outliers final: 55 residues processed: 582 average time/residue: 0.1316 time to fit residues: 116.4095 Evaluate side-chains 543 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 481 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 240 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN B 147 GLN B 312 GLN B 320 ASN B 387 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 127 GLN C 132 GLN D 91 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.143452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.099750 restraints weight = 32472.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.103346 restraints weight = 15091.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.105622 restraints weight = 8890.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.107082 restraints weight = 6196.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.107722 restraints weight = 4860.968| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16386 Z= 0.173 Angle : 0.644 9.474 22134 Z= 0.330 Chirality : 0.044 0.374 2360 Planarity : 0.004 0.058 2818 Dihedral : 10.543 164.541 2248 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.43 % Allowed : 24.13 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.19), residues: 1932 helix: 1.32 (0.15), residues: 1147 sheet: -0.61 (0.46), residues: 114 loop : 0.37 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 686 TYR 0.015 0.001 TYR A 522 PHE 0.042 0.002 PHE D 168 TRP 0.006 0.001 TRP A 623 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00394 (16386) covalent geometry : angle 0.64435 (22134) hydrogen bonds : bond 0.03973 ( 871) hydrogen bonds : angle 4.87723 ( 2571) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 534 time to evaluate : 0.697 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: A 8 LYS cc_start: 0.8817 (tptp) cc_final: 0.8539 (tppt) REVERT: A 40 TYR cc_start: 0.8958 (t80) cc_final: 0.8447 (t80) REVERT: A 119 GLU cc_start: 0.8565 (mp0) cc_final: 0.8290 (mp0) REVERT: A 144 MET cc_start: 0.8643 (mtm) cc_final: 0.8393 (mtm) REVERT: A 214 LYS cc_start: 0.7908 (mmtt) cc_final: 0.7558 (mmtt) REVERT: A 221 LYS cc_start: 0.8321 (mttt) cc_final: 0.8104 (mttt) REVERT: A 232 ASN cc_start: 0.8715 (t0) cc_final: 0.8028 (m-40) REVERT: A 263 ASP cc_start: 0.8147 (m-30) cc_final: 0.7873 (m-30) REVERT: A 286 ASP cc_start: 0.7692 (m-30) cc_final: 0.7470 (m-30) REVERT: A 290 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8309 (mt-10) REVERT: A 348 MET cc_start: 0.8267 (tmm) cc_final: 0.7157 (tmm) REVERT: A 352 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7292 (mt-10) REVERT: A 362 ASP cc_start: 0.8394 (m-30) cc_final: 0.7931 (m-30) REVERT: A 384 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.6653 (pm20) REVERT: A 389 SER cc_start: 0.9361 (OUTLIER) cc_final: 0.9007 (p) REVERT: A 410 ASN cc_start: 0.8183 (OUTLIER) cc_final: 0.7713 (t160) REVERT: A 427 LYS cc_start: 0.9054 (tppp) cc_final: 0.8623 (tppp) REVERT: A 446 ARG cc_start: 0.7556 (mmm160) cc_final: 0.7119 (mmm160) REVERT: A 505 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8442 (mt-10) REVERT: A 590 SER cc_start: 0.9089 (t) cc_final: 0.8609 (p) REVERT: A 640 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8888 (tpp) REVERT: A 684 TYR cc_start: 0.8413 (OUTLIER) cc_final: 0.7994 (m-80) REVERT: B 65 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7910 (mm-30) REVERT: B 82 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8874 (mttp) REVERT: B 95 MET cc_start: 0.9047 (mmm) cc_final: 0.8758 (tpp) REVERT: B 108 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8919 (p) REVERT: B 218 ASN cc_start: 0.8975 (m110) cc_final: 0.8553 (t0) REVERT: B 236 TYR cc_start: 0.9095 (t80) cc_final: 0.8841 (t80) REVERT: B 257 ASP cc_start: 0.8517 (m-30) cc_final: 0.8119 (m-30) REVERT: B 278 LEU cc_start: 0.9136 (tp) cc_final: 0.8934 (mp) REVERT: B 349 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9200 (tp) REVERT: B 374 SER cc_start: 0.9514 (t) cc_final: 0.9197 (t) REVERT: B 394 TYR cc_start: 0.9157 (m-80) cc_final: 0.8771 (m-80) REVERT: B 398 ASP cc_start: 0.8221 (t0) cc_final: 0.7866 (t0) REVERT: B 434 ASP cc_start: 0.8596 (m-30) cc_final: 0.8230 (m-30) REVERT: B 493 MET cc_start: 0.9553 (tmm) cc_final: 0.9149 (tmm) REVERT: B 546 LEU cc_start: 0.9462 (mt) cc_final: 0.9179 (mt) REVERT: B 571 TYR cc_start: 0.8829 (t80) cc_final: 0.8509 (t80) REVERT: B 586 TYR cc_start: 0.9075 (m-80) cc_final: 0.8514 (m-80) REVERT: B 595 MET cc_start: 0.8603 (mmm) cc_final: 0.8143 (mmm) REVERT: B 602 GLU cc_start: 0.8053 (pp20) cc_final: 0.7206 (tm-30) REVERT: B 627 LYS cc_start: 0.8987 (tttt) cc_final: 0.8310 (ttpp) REVERT: B 628 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8026 (mp0) REVERT: C 21 PHE cc_start: 0.8408 (m-80) cc_final: 0.8107 (t80) REVERT: C 68 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7547 (tm-30) REVERT: C 103 LYS cc_start: 0.8362 (tppt) cc_final: 0.8032 (tppt) REVERT: C 107 ASN cc_start: 0.9028 (m-40) cc_final: 0.8641 (m-40) REVERT: C 124 TRP cc_start: 0.8281 (t60) cc_final: 0.8036 (t60) REVERT: C 154 PHE cc_start: 0.9166 (t80) cc_final: 0.8734 (t80) REVERT: C 174 TYR cc_start: 0.6928 (OUTLIER) cc_final: 0.6416 (t80) REVERT: C 186 GLN cc_start: 0.6699 (mp10) cc_final: 0.6445 (mp10) REVERT: C 259 PHE cc_start: 0.6936 (m-80) cc_final: 0.6717 (m-80) REVERT: C 261 ARG cc_start: 0.7452 (mtm-85) cc_final: 0.7162 (mtm110) REVERT: C 269 MET cc_start: 0.8709 (tpt) cc_final: 0.8342 (tmm) REVERT: D 59 LEU cc_start: 0.7022 (pp) cc_final: 0.6084 (tt) REVERT: D 80 HIS cc_start: 0.6998 (m-70) cc_final: 0.6768 (m-70) REVERT: D 109 PHE cc_start: 0.6916 (m-80) cc_final: 0.6398 (m-80) REVERT: D 116 GLU cc_start: 0.9128 (tp30) cc_final: 0.8791 (tp30) REVERT: D 178 PHE cc_start: 0.8711 (m-10) cc_final: 0.8399 (m-80) REVERT: D 219 GLU cc_start: 0.8437 (tp30) cc_final: 0.7839 (pm20) REVERT: D 232 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6290 (mt) outliers start: 76 outliers final: 46 residues processed: 567 average time/residue: 0.1329 time to fit residues: 114.7827 Evaluate side-chains 557 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 501 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 108 THR 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 216 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 262 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 172 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 147 GLN B 312 GLN B 320 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN C 136 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.143413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.100311 restraints weight = 32536.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.103820 restraints weight = 15210.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.106031 restraints weight = 9001.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.107363 restraints weight = 6317.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.108033 restraints weight = 5002.162| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.5584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16386 Z= 0.183 Angle : 0.655 11.243 22134 Z= 0.336 Chirality : 0.045 0.422 2360 Planarity : 0.004 0.053 2818 Dihedral : 10.364 164.783 2247 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.66 % Allowed : 24.48 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.19), residues: 1932 helix: 1.34 (0.15), residues: 1144 sheet: -0.80 (0.45), residues: 118 loop : 0.30 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 686 TYR 0.035 0.001 TYR C 105 PHE 0.044 0.002 PHE D 168 TRP 0.007 0.001 TRP A 623 HIS 0.007 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00414 (16386) covalent geometry : angle 0.65540 (22134) hydrogen bonds : bond 0.03927 ( 871) hydrogen bonds : angle 4.85515 ( 2571) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 513 time to evaluate : 0.664 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: A 8 LYS cc_start: 0.8827 (tptp) cc_final: 0.8550 (tppt) REVERT: A 40 TYR cc_start: 0.8947 (t80) cc_final: 0.8442 (t80) REVERT: A 119 GLU cc_start: 0.8575 (mp0) cc_final: 0.8306 (mp0) REVERT: A 144 MET cc_start: 0.8647 (mtm) cc_final: 0.8363 (mtm) REVERT: A 172 LEU cc_start: 0.9263 (mp) cc_final: 0.8564 (mt) REVERT: A 214 LYS cc_start: 0.7969 (mmtt) cc_final: 0.7598 (mmtt) REVERT: A 232 ASN cc_start: 0.8725 (t0) cc_final: 0.8054 (m-40) REVERT: A 250 TYR cc_start: 0.8679 (m-80) cc_final: 0.8390 (m-80) REVERT: A 263 ASP cc_start: 0.8156 (m-30) cc_final: 0.7898 (m-30) REVERT: A 290 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8362 (mt-10) REVERT: A 348 MET cc_start: 0.8284 (tmm) cc_final: 0.7077 (tmm) REVERT: A 352 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7250 (mt-10) REVERT: A 359 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8172 (ttp) REVERT: A 384 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.6671 (pm20) REVERT: A 389 SER cc_start: 0.9328 (OUTLIER) cc_final: 0.8966 (p) REVERT: A 406 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8060 (t70) REVERT: A 446 ARG cc_start: 0.7556 (mmm160) cc_final: 0.7136 (mmm160) REVERT: A 505 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8406 (mt-10) REVERT: A 590 SER cc_start: 0.9121 (t) cc_final: 0.8718 (p) REVERT: A 640 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8951 (tpp) REVERT: A 684 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.8145 (m-80) REVERT: B 82 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8898 (mttp) REVERT: B 95 MET cc_start: 0.8927 (mmm) cc_final: 0.8695 (tpp) REVERT: B 218 ASN cc_start: 0.8976 (OUTLIER) cc_final: 0.8541 (t0) REVERT: B 236 TYR cc_start: 0.9117 (t80) cc_final: 0.8884 (t80) REVERT: B 257 ASP cc_start: 0.8572 (m-30) cc_final: 0.8298 (m-30) REVERT: B 278 LEU cc_start: 0.9096 (tp) cc_final: 0.8871 (mp) REVERT: B 286 ASP cc_start: 0.8372 (m-30) cc_final: 0.8170 (m-30) REVERT: B 349 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9207 (tp) REVERT: B 374 SER cc_start: 0.9522 (t) cc_final: 0.9213 (t) REVERT: B 398 ASP cc_start: 0.8224 (t0) cc_final: 0.7939 (t0) REVERT: B 415 ASN cc_start: 0.9174 (t0) cc_final: 0.8840 (t0) REVERT: B 434 ASP cc_start: 0.8611 (m-30) cc_final: 0.8230 (m-30) REVERT: B 467 ASN cc_start: 0.8957 (t0) cc_final: 0.8549 (t0) REVERT: B 493 MET cc_start: 0.9595 (tmm) cc_final: 0.9151 (tmm) REVERT: B 571 TYR cc_start: 0.8807 (t80) cc_final: 0.8406 (t80) REVERT: B 586 TYR cc_start: 0.9044 (m-80) cc_final: 0.8575 (m-80) REVERT: B 595 MET cc_start: 0.8614 (mmm) cc_final: 0.8170 (mmm) REVERT: B 602 GLU cc_start: 0.8028 (pp20) cc_final: 0.7294 (pp20) REVERT: B 627 LYS cc_start: 0.8946 (tttt) cc_final: 0.8420 (tttt) REVERT: B 628 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8211 (mp0) REVERT: C 82 ASP cc_start: 0.7699 (m-30) cc_final: 0.7092 (t0) REVERT: C 103 LYS cc_start: 0.8372 (tppt) cc_final: 0.7973 (tppt) REVERT: C 107 ASN cc_start: 0.8990 (m-40) cc_final: 0.8501 (m-40) REVERT: C 124 TRP cc_start: 0.8312 (t60) cc_final: 0.8045 (t60) REVERT: C 127 GLN cc_start: 0.9084 (tp40) cc_final: 0.8796 (mm-40) REVERT: C 137 MET cc_start: 0.8597 (mpt) cc_final: 0.8357 (mtm) REVERT: C 154 PHE cc_start: 0.9158 (t80) cc_final: 0.8722 (t80) REVERT: C 174 TYR cc_start: 0.7104 (OUTLIER) cc_final: 0.6570 (t80) REVERT: C 186 GLN cc_start: 0.6657 (mp10) cc_final: 0.6424 (mp10) REVERT: C 269 MET cc_start: 0.8767 (tpt) cc_final: 0.8424 (tmm) REVERT: C 282 ILE cc_start: 0.6614 (tp) cc_final: 0.5856 (mm) REVERT: D 29 PHE cc_start: 0.7429 (t80) cc_final: 0.7027 (t80) REVERT: D 59 LEU cc_start: 0.6948 (pp) cc_final: 0.5982 (tt) REVERT: D 80 HIS cc_start: 0.6923 (m-70) cc_final: 0.6508 (m-70) REVERT: D 109 PHE cc_start: 0.6969 (m-80) cc_final: 0.6510 (m-80) REVERT: D 116 GLU cc_start: 0.9134 (tp30) cc_final: 0.8783 (tp30) REVERT: D 149 ASP cc_start: 0.7741 (t0) cc_final: 0.6976 (p0) REVERT: D 178 PHE cc_start: 0.8690 (m-10) cc_final: 0.8343 (m-80) REVERT: D 219 GLU cc_start: 0.8491 (tp30) cc_final: 0.7913 (pm20) REVERT: D 221 LYS cc_start: 0.8810 (mttt) cc_final: 0.8565 (mttm) REVERT: D 232 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6255 (mt) outliers start: 80 outliers final: 51 residues processed: 546 average time/residue: 0.1291 time to fit residues: 107.9273 Evaluate side-chains 541 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 479 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 82 LYS 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 216 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 262 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 186 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 115 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 147 GLN B 312 GLN B 320 ASN B 387 GLN B 410 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.137422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.094089 restraints weight = 32729.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.097411 restraints weight = 15878.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.099489 restraints weight = 9579.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.100668 restraints weight = 6847.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.101549 restraints weight = 5577.274| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 16386 Z= 0.302 Angle : 0.722 9.992 22134 Z= 0.374 Chirality : 0.048 0.425 2360 Planarity : 0.004 0.050 2818 Dihedral : 10.503 166.374 2247 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 5.30 % Allowed : 25.12 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.19), residues: 1932 helix: 1.18 (0.15), residues: 1154 sheet: -0.67 (0.40), residues: 148 loop : 0.36 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 686 TYR 0.033 0.002 TYR C 105 PHE 0.042 0.002 PHE D 168 TRP 0.013 0.002 TRP A 623 HIS 0.008 0.002 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00668 (16386) covalent geometry : angle 0.72169 (22134) hydrogen bonds : bond 0.04122 ( 871) hydrogen bonds : angle 4.99154 ( 2571) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 488 time to evaluate : 0.656 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: A 8 LYS cc_start: 0.8873 (tptp) cc_final: 0.8598 (tppt) REVERT: A 40 TYR cc_start: 0.9007 (t80) cc_final: 0.8535 (t80) REVERT: A 65 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7793 (mp0) REVERT: A 119 GLU cc_start: 0.8614 (mp0) cc_final: 0.8368 (mp0) REVERT: A 144 MET cc_start: 0.8704 (mtm) cc_final: 0.8495 (mtm) REVERT: A 173 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9101 (mt) REVERT: A 214 LYS cc_start: 0.8027 (mmtt) cc_final: 0.7681 (mmtm) REVERT: A 232 ASN cc_start: 0.8849 (t0) cc_final: 0.8286 (m-40) REVERT: A 250 TYR cc_start: 0.8701 (m-80) cc_final: 0.8380 (m-80) REVERT: A 263 ASP cc_start: 0.8182 (m-30) cc_final: 0.7930 (m-30) REVERT: A 290 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8380 (mt-10) REVERT: A 348 MET cc_start: 0.8226 (tmm) cc_final: 0.6981 (tmm) REVERT: A 352 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7248 (mt-10) REVERT: A 381 LEU cc_start: 0.9243 (tp) cc_final: 0.9018 (tp) REVERT: A 384 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7078 (pm20) REVERT: A 389 SER cc_start: 0.9289 (OUTLIER) cc_final: 0.8862 (p) REVERT: A 406 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.7583 (t70) REVERT: A 427 LYS cc_start: 0.9066 (tppp) cc_final: 0.8653 (tppp) REVERT: A 446 ARG cc_start: 0.7711 (mmm160) cc_final: 0.7262 (mmm160) REVERT: A 456 LYS cc_start: 0.9338 (mtpp) cc_final: 0.9085 (ttmm) REVERT: A 590 SER cc_start: 0.9160 (t) cc_final: 0.8840 (p) REVERT: A 640 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.8981 (tpp) REVERT: A 684 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.8138 (m-80) REVERT: B 40 TYR cc_start: 0.9186 (t80) cc_final: 0.8656 (t80) REVERT: B 82 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8938 (mttp) REVERT: B 95 MET cc_start: 0.9016 (mmm) cc_final: 0.8547 (tmm) REVERT: B 136 LYS cc_start: 0.9287 (mmmm) cc_final: 0.9048 (tppp) REVERT: B 184 ARG cc_start: 0.8946 (tpp-160) cc_final: 0.8712 (tpp-160) REVERT: B 218 ASN cc_start: 0.9016 (OUTLIER) cc_final: 0.8525 (t0) REVERT: B 236 TYR cc_start: 0.9163 (t80) cc_final: 0.8910 (t80) REVERT: B 257 ASP cc_start: 0.8695 (m-30) cc_final: 0.8344 (m-30) REVERT: B 349 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9231 (tp) REVERT: B 398 ASP cc_start: 0.8344 (t0) cc_final: 0.8041 (t0) REVERT: B 415 ASN cc_start: 0.9232 (t0) cc_final: 0.8833 (t0) REVERT: B 434 ASP cc_start: 0.8607 (m-30) cc_final: 0.8251 (m-30) REVERT: B 467 ASN cc_start: 0.9176 (t0) cc_final: 0.8780 (t0) REVERT: B 493 MET cc_start: 0.9621 (tmm) cc_final: 0.9245 (tmm) REVERT: B 571 TYR cc_start: 0.8901 (t80) cc_final: 0.8566 (t80) REVERT: B 586 TYR cc_start: 0.9086 (m-80) cc_final: 0.8482 (m-80) REVERT: B 595 MET cc_start: 0.8672 (mmm) cc_final: 0.8220 (mmm) REVERT: B 602 GLU cc_start: 0.7917 (pp20) cc_final: 0.7271 (pp20) REVERT: B 613 TYR cc_start: 0.8979 (t80) cc_final: 0.8762 (t80) REVERT: B 627 LYS cc_start: 0.9018 (tttt) cc_final: 0.8415 (tttt) REVERT: B 628 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8265 (mp0) REVERT: C 68 GLU cc_start: 0.8439 (mm-30) cc_final: 0.7575 (tm-30) REVERT: C 82 ASP cc_start: 0.8116 (m-30) cc_final: 0.7421 (t70) REVERT: C 103 LYS cc_start: 0.8351 (tppt) cc_final: 0.8055 (tppt) REVERT: C 127 GLN cc_start: 0.9083 (tp40) cc_final: 0.8776 (mm-40) REVERT: C 154 PHE cc_start: 0.9193 (t80) cc_final: 0.8827 (t80) REVERT: C 174 TYR cc_start: 0.7308 (OUTLIER) cc_final: 0.6894 (t80) REVERT: C 238 ASN cc_start: 0.7453 (t0) cc_final: 0.7194 (t0) REVERT: C 259 PHE cc_start: 0.7540 (m-80) cc_final: 0.7271 (m-80) REVERT: C 269 MET cc_start: 0.8743 (tpt) cc_final: 0.8350 (tmm) REVERT: D 59 LEU cc_start: 0.6967 (pp) cc_final: 0.6053 (tt) REVERT: D 80 HIS cc_start: 0.7233 (m-70) cc_final: 0.6806 (m-70) REVERT: D 87 LYS cc_start: 0.7699 (mttm) cc_final: 0.7259 (mttm) REVERT: D 109 PHE cc_start: 0.6989 (m-80) cc_final: 0.6536 (m-80) REVERT: D 112 LEU cc_start: 0.4616 (tp) cc_final: 0.4214 (tt) REVERT: D 116 GLU cc_start: 0.9115 (tp30) cc_final: 0.8753 (tp30) REVERT: D 149 ASP cc_start: 0.7838 (t0) cc_final: 0.7198 (p0) REVERT: D 178 PHE cc_start: 0.8806 (m-10) cc_final: 0.8443 (m-80) REVERT: D 210 GLN cc_start: 0.8399 (tp40) cc_final: 0.7778 (mm110) REVERT: D 219 GLU cc_start: 0.8529 (tp30) cc_final: 0.7922 (pm20) REVERT: D 232 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6609 (mt) REVERT: D 242 TYR cc_start: 0.6729 (t80) cc_final: 0.5501 (m-80) outliers start: 91 outliers final: 56 residues processed: 528 average time/residue: 0.1369 time to fit residues: 109.0017 Evaluate side-chains 542 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 475 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 262 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 153 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 158 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 151 optimal weight: 20.0000 chunk 81 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN A 370 ASN A 387 GLN A 410 ASN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 147 GLN B 202 ASN B 312 GLN B 320 ASN B 387 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.143620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.101251 restraints weight = 32738.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.104778 restraints weight = 15425.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107010 restraints weight = 9170.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108362 restraints weight = 6440.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.109099 restraints weight = 5079.781| |-----------------------------------------------------------------------------| 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) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.6062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16386 Z= 0.143 Angle : 0.677 10.979 22134 Z= 0.347 Chirality : 0.046 0.459 2360 Planarity : 0.004 0.054 2818 Dihedral : 9.909 158.621 2247 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 4.14 % Allowed : 26.69 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.19), residues: 1932 helix: 1.26 (0.16), residues: 1131 sheet: -0.38 (0.41), residues: 136 loop : 0.34 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 261 TYR 0.032 0.001 TYR D 276 PHE 0.041 0.002 PHE D 168 TRP 0.036 0.001 TRP C 44 HIS 0.006 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00326 (16386) covalent geometry : angle 0.67733 (22134) hydrogen bonds : bond 0.03907 ( 871) hydrogen bonds : angle 4.90233 ( 2571) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 539 time to evaluate : 0.653 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: A 8 LYS cc_start: 0.8852 (tptp) cc_final: 0.8586 (tppt) REVERT: A 40 TYR cc_start: 0.8897 (t80) cc_final: 0.8424 (t80) REVERT: A 65 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7989 (mp0) REVERT: A 119 GLU cc_start: 0.8543 (mp0) cc_final: 0.8283 (mp0) REVERT: A 144 MET cc_start: 0.8544 (mtm) cc_final: 0.8240 (mtm) REVERT: A 179 LEU cc_start: 0.9282 (tp) cc_final: 0.8939 (tp) REVERT: A 188 ILE cc_start: 0.9360 (mm) cc_final: 0.9126 (mm) REVERT: A 214 LYS cc_start: 0.7880 (mmtt) cc_final: 0.7511 (mmtt) REVERT: A 232 ASN cc_start: 0.8749 (t0) cc_final: 0.8335 (m-40) REVERT: A 250 TYR cc_start: 0.8657 (m-80) cc_final: 0.8443 (m-80) REVERT: A 263 ASP cc_start: 0.8171 (m-30) cc_final: 0.7935 (m-30) REVERT: A 290 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8258 (mt-10) REVERT: A 348 MET cc_start: 0.8258 (tmm) cc_final: 0.7078 (tmm) REVERT: A 352 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7239 (mt-10) REVERT: A 359 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8095 (ttp) REVERT: A 384 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7453 (pm20) REVERT: A 389 SER cc_start: 0.9296 (OUTLIER) cc_final: 0.8955 (p) REVERT: A 406 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.7712 (t70) REVERT: A 410 ASN cc_start: 0.8188 (OUTLIER) cc_final: 0.7834 (t160) REVERT: A 446 ARG cc_start: 0.7611 (mmm160) cc_final: 0.7239 (mmm160) REVERT: A 505 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8377 (mt-10) REVERT: A 590 SER cc_start: 0.9081 (t) cc_final: 0.8727 (p) REVERT: A 640 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8673 (tpp) REVERT: A 684 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.8123 (m-80) REVERT: B 65 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7843 (mp0) REVERT: B 82 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8857 (mttp) REVERT: B 95 MET cc_start: 0.8881 (mmm) cc_final: 0.8647 (tpp) REVERT: B 136 LYS cc_start: 0.9255 (mmmm) cc_final: 0.8898 (tptm) REVERT: B 174 GLU cc_start: 0.7478 (tt0) cc_final: 0.7142 (tt0) REVERT: B 184 ARG cc_start: 0.8906 (tpp-160) cc_final: 0.8608 (mmm-85) REVERT: B 218 ASN cc_start: 0.9003 (m110) cc_final: 0.8531 (t0) REVERT: B 257 ASP cc_start: 0.8589 (m-30) cc_final: 0.8333 (m-30) REVERT: B 276 LYS cc_start: 0.8742 (mppt) cc_final: 0.8460 (mmpt) REVERT: B 374 SER cc_start: 0.9523 (t) cc_final: 0.9226 (t) REVERT: B 398 ASP cc_start: 0.8149 (t0) cc_final: 0.7900 (t0) REVERT: B 415 ASN cc_start: 0.9038 (t0) cc_final: 0.8672 (t0) REVERT: B 434 ASP cc_start: 0.8654 (m-30) cc_final: 0.8210 (m-30) REVERT: B 467 ASN cc_start: 0.9045 (t0) cc_final: 0.8641 (t0) REVERT: B 493 MET cc_start: 0.9573 (tmm) cc_final: 0.9128 (tmm) REVERT: B 586 TYR cc_start: 0.9009 (m-80) cc_final: 0.8536 (m-80) REVERT: B 602 GLU cc_start: 0.8044 (pp20) cc_final: 0.7143 (tm-30) REVERT: B 627 LYS cc_start: 0.8892 (tttt) cc_final: 0.8441 (tttt) REVERT: B 628 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8017 (mp0) REVERT: C 65 LEU cc_start: 0.7773 (mm) cc_final: 0.7518 (mm) REVERT: C 67 THR cc_start: 0.7608 (p) cc_final: 0.7260 (p) REVERT: C 68 GLU cc_start: 0.8491 (mm-30) cc_final: 0.7713 (tm-30) REVERT: C 82 ASP cc_start: 0.8135 (m-30) cc_final: 0.7428 (t70) REVERT: C 103 LYS cc_start: 0.8436 (tppt) cc_final: 0.8095 (tppt) REVERT: C 120 GLU cc_start: 0.8062 (pp20) cc_final: 0.7838 (pp20) REVERT: C 124 TRP cc_start: 0.8315 (t60) cc_final: 0.8041 (t60) REVERT: C 154 PHE cc_start: 0.9106 (t80) cc_final: 0.8632 (t80) REVERT: C 210 GLN cc_start: 0.4704 (mm110) cc_final: 0.4344 (mm110) REVERT: C 238 ASN cc_start: 0.7167 (t0) cc_final: 0.6845 (t0) REVERT: C 259 PHE cc_start: 0.7556 (m-80) cc_final: 0.7338 (m-80) REVERT: C 269 MET cc_start: 0.8758 (tpt) cc_final: 0.8391 (tmm) REVERT: D 59 LEU cc_start: 0.6747 (pp) cc_final: 0.5877 (tt) REVERT: D 80 HIS cc_start: 0.7201 (m-70) cc_final: 0.6977 (m-70) REVERT: D 109 PHE cc_start: 0.6873 (m-80) cc_final: 0.6443 (m-80) REVERT: D 112 LEU cc_start: 0.4526 (tp) cc_final: 0.4172 (tt) REVERT: D 116 GLU cc_start: 0.9108 (tp30) cc_final: 0.8754 (tp30) REVERT: D 146 GLN cc_start: 0.8381 (mm110) cc_final: 0.8033 (tt0) REVERT: D 149 ASP cc_start: 0.7720 (t0) cc_final: 0.6907 (p0) REVERT: D 210 GLN cc_start: 0.8382 (tp40) cc_final: 0.7813 (mm110) REVERT: D 219 GLU cc_start: 0.8462 (tp30) cc_final: 0.7925 (pm20) REVERT: D 232 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6577 (mt) outliers start: 71 outliers final: 43 residues processed: 572 average time/residue: 0.1336 time to fit residues: 115.2597 Evaluate side-chains 537 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 485 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 262 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 147 GLN B 312 GLN B 313 HIS B 320 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.142156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.100548 restraints weight = 32689.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.103977 restraints weight = 15447.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106199 restraints weight = 9152.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.107581 restraints weight = 6410.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.108186 restraints weight = 5055.422| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.6249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16386 Z= 0.177 Angle : 0.716 17.196 22134 Z= 0.366 Chirality : 0.046 0.428 2360 Planarity : 0.004 0.058 2818 Dihedral : 9.880 157.770 2246 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.79 % Allowed : 27.51 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.19), residues: 1932 helix: 1.18 (0.15), residues: 1143 sheet: -0.42 (0.42), residues: 136 loop : 0.22 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 261 TYR 0.044 0.002 TYR C 174 PHE 0.040 0.002 PHE C 21 TRP 0.048 0.002 TRP C 44 HIS 0.007 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00407 (16386) covalent geometry : angle 0.71618 (22134) hydrogen bonds : bond 0.03947 ( 871) hydrogen bonds : angle 4.98278 ( 2571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 497 time to evaluate : 0.692 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: A 8 LYS cc_start: 0.8824 (tptp) cc_final: 0.8562 (tppt) REVERT: A 40 TYR cc_start: 0.8906 (t80) cc_final: 0.8417 (t80) REVERT: A 65 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7971 (mp0) REVERT: A 119 GLU cc_start: 0.8559 (mp0) cc_final: 0.8290 (mp0) REVERT: A 144 MET cc_start: 0.8641 (mtm) cc_final: 0.8320 (mtm) REVERT: A 179 LEU cc_start: 0.9265 (tp) cc_final: 0.8863 (tp) REVERT: A 214 LYS cc_start: 0.7984 (mmtt) cc_final: 0.7632 (mmtt) REVERT: A 221 LYS cc_start: 0.8096 (mttt) cc_final: 0.7873 (mttt) REVERT: A 232 ASN cc_start: 0.8778 (t0) cc_final: 0.8282 (m-40) REVERT: A 263 ASP cc_start: 0.8121 (m-30) cc_final: 0.7916 (m-30) REVERT: A 290 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8238 (mt-10) REVERT: A 348 MET cc_start: 0.8231 (tmm) cc_final: 0.7915 (tmm) REVERT: A 359 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8148 (ttp) REVERT: A 384 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7559 (pm20) REVERT: A 389 SER cc_start: 0.9251 (OUTLIER) cc_final: 0.8859 (p) REVERT: A 406 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8134 (t70) REVERT: A 410 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7928 (t160) REVERT: A 427 LYS cc_start: 0.9011 (tppp) cc_final: 0.8570 (tppp) REVERT: A 446 ARG cc_start: 0.7641 (mmm160) cc_final: 0.7261 (mmm160) REVERT: A 590 SER cc_start: 0.9123 (t) cc_final: 0.8785 (p) REVERT: A 640 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8693 (tpp) REVERT: A 684 TYR cc_start: 0.8482 (OUTLIER) cc_final: 0.8186 (m-80) REVERT: B 65 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8026 (mp0) REVERT: B 82 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8854 (mttp) REVERT: B 95 MET cc_start: 0.8883 (mmm) cc_final: 0.8479 (tmm) REVERT: B 136 LYS cc_start: 0.9251 (mmmm) cc_final: 0.8979 (tppp) REVERT: B 174 GLU cc_start: 0.7522 (tt0) cc_final: 0.7048 (tt0) REVERT: B 184 ARG cc_start: 0.8931 (tpp-160) cc_final: 0.8626 (mmm-85) REVERT: B 218 ASN cc_start: 0.8991 (m110) cc_final: 0.8505 (t0) REVERT: B 257 ASP cc_start: 0.8631 (m-30) cc_final: 0.8334 (m-30) REVERT: B 276 LYS cc_start: 0.8841 (mppt) cc_final: 0.8515 (mmpt) REVERT: B 374 SER cc_start: 0.9523 (t) cc_final: 0.9220 (t) REVERT: B 398 ASP cc_start: 0.8107 (t0) cc_final: 0.7861 (t0) REVERT: B 415 ASN cc_start: 0.9043 (t0) cc_final: 0.8674 (t0) REVERT: B 467 ASN cc_start: 0.9102 (t0) cc_final: 0.8716 (t0) REVERT: B 493 MET cc_start: 0.9589 (tmm) cc_final: 0.9118 (tmm) REVERT: B 586 TYR cc_start: 0.9020 (m-80) cc_final: 0.8473 (m-80) REVERT: B 602 GLU cc_start: 0.7851 (pp20) cc_final: 0.6863 (tm-30) REVERT: B 627 LYS cc_start: 0.8941 (tttt) cc_final: 0.8477 (tttt) REVERT: B 628 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8208 (mp0) REVERT: B 634 MET cc_start: 0.9114 (mmm) cc_final: 0.8900 (tpp) REVERT: C 55 TYR cc_start: 0.5922 (t80) cc_final: 0.5482 (t80) REVERT: C 82 ASP cc_start: 0.8304 (m-30) cc_final: 0.7426 (t70) REVERT: C 103 LYS cc_start: 0.8591 (tppt) cc_final: 0.8276 (tppt) REVERT: C 127 GLN cc_start: 0.9104 (tp40) cc_final: 0.8757 (mm110) REVERT: C 154 PHE cc_start: 0.9040 (t80) cc_final: 0.8567 (t80) REVERT: C 185 MET cc_start: 0.7398 (mmm) cc_final: 0.7117 (pmm) REVERT: C 210 GLN cc_start: 0.4686 (mm110) cc_final: 0.4355 (mm110) REVERT: D 59 LEU cc_start: 0.6755 (pp) cc_final: 0.5991 (tt) REVERT: D 80 HIS cc_start: 0.7228 (m-70) cc_final: 0.6985 (m-70) REVERT: D 109 PHE cc_start: 0.6827 (m-80) cc_final: 0.6392 (m-80) REVERT: D 112 LEU cc_start: 0.4681 (tp) cc_final: 0.4402 (tt) REVERT: D 116 GLU cc_start: 0.9108 (tp30) cc_final: 0.8742 (tp30) REVERT: D 146 GLN cc_start: 0.8357 (mm110) cc_final: 0.7856 (tt0) REVERT: D 157 MET cc_start: 0.8499 (ptm) cc_final: 0.7702 (ppp) REVERT: D 178 PHE cc_start: 0.8794 (m-80) cc_final: 0.8341 (m-80) REVERT: D 210 GLN cc_start: 0.8361 (tp40) cc_final: 0.7790 (mm110) REVERT: D 219 GLU cc_start: 0.8434 (tp30) cc_final: 0.7944 (pm20) REVERT: D 232 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.6584 (mt) REVERT: D 242 TYR cc_start: 0.6542 (t80) cc_final: 0.5279 (m-80) outliers start: 65 outliers final: 43 residues processed: 526 average time/residue: 0.1314 time to fit residues: 104.8262 Evaluate side-chains 535 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 483 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 262 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 189 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN B 131 ASN B 147 GLN B 202 ASN B 312 GLN B 320 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.140874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.098895 restraints weight = 32905.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.102287 restraints weight = 15754.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.104428 restraints weight = 9425.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.105859 restraints weight = 6597.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.106625 restraints weight = 5219.015| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.6359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 16386 Z= 0.205 Angle : 0.743 16.468 22134 Z= 0.383 Chirality : 0.048 0.425 2360 Planarity : 0.004 0.051 2818 Dihedral : 9.888 157.600 2243 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.38 % Allowed : 28.38 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.19), residues: 1932 helix: 1.14 (0.15), residues: 1143 sheet: -0.49 (0.42), residues: 136 loop : 0.16 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 225 TYR 0.055 0.002 TYR C 204 PHE 0.040 0.002 PHE C 21 TRP 0.048 0.002 TRP C 44 HIS 0.006 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00465 (16386) covalent geometry : angle 0.74268 (22134) hydrogen bonds : bond 0.04016 ( 871) hydrogen bonds : angle 5.08341 ( 2571) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 483 time to evaluate : 0.526 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 8 LYS cc_start: 0.8832 (tptp) cc_final: 0.8569 (tppt) REVERT: A 31 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8158 (mp0) REVERT: A 40 TYR cc_start: 0.8919 (t80) cc_final: 0.8417 (t80) REVERT: A 65 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7968 (mp0) REVERT: A 119 GLU cc_start: 0.8588 (mp0) cc_final: 0.8326 (mp0) REVERT: A 144 MET cc_start: 0.8601 (mtm) cc_final: 0.8330 (mtm) REVERT: A 214 LYS cc_start: 0.8086 (mmtt) cc_final: 0.7752 (mmtt) REVERT: A 232 ASN cc_start: 0.8806 (t0) cc_final: 0.8306 (m-40) REVERT: A 250 TYR cc_start: 0.8683 (m-80) cc_final: 0.8250 (m-80) REVERT: A 263 ASP cc_start: 0.8153 (m-30) cc_final: 0.7922 (m-30) REVERT: A 290 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8233 (mt-10) REVERT: A 348 MET cc_start: 0.8162 (tmm) cc_final: 0.7796 (tmm) REVERT: A 359 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8164 (ttp) REVERT: A 384 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7545 (pm20) REVERT: A 389 SER cc_start: 0.9244 (OUTLIER) cc_final: 0.8813 (p) REVERT: A 406 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8143 (t70) REVERT: A 410 ASN cc_start: 0.8094 (OUTLIER) cc_final: 0.7821 (t160) REVERT: A 446 ARG cc_start: 0.7715 (mmm160) cc_final: 0.7313 (mmm160) REVERT: A 590 SER cc_start: 0.9196 (t) cc_final: 0.8838 (p) REVERT: A 640 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8710 (tpp) REVERT: A 684 TYR cc_start: 0.8472 (OUTLIER) cc_final: 0.8112 (m-80) REVERT: B 65 GLU cc_start: 0.8254 (mm-30) cc_final: 0.8014 (mp0) REVERT: B 82 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8865 (mttp) REVERT: B 95 MET cc_start: 0.8870 (mmm) cc_final: 0.8467 (tmm) REVERT: B 136 LYS cc_start: 0.9215 (mmmm) cc_final: 0.8852 (tptm) REVERT: B 184 ARG cc_start: 0.8930 (tpp-160) cc_final: 0.8626 (mmm-85) REVERT: B 218 ASN cc_start: 0.8996 (m110) cc_final: 0.8513 (t0) REVERT: B 257 ASP cc_start: 0.8640 (m-30) cc_final: 0.8294 (m-30) REVERT: B 374 SER cc_start: 0.9538 (t) cc_final: 0.9224 (t) REVERT: B 398 ASP cc_start: 0.8088 (t0) cc_final: 0.7854 (t0) REVERT: B 415 ASN cc_start: 0.9046 (t0) cc_final: 0.8668 (t0) REVERT: B 467 ASN cc_start: 0.9165 (t0) cc_final: 0.8795 (t0) REVERT: B 493 MET cc_start: 0.9599 (tmm) cc_final: 0.9218 (tmm) REVERT: B 571 TYR cc_start: 0.8637 (t80) cc_final: 0.8171 (t80) REVERT: B 586 TYR cc_start: 0.9019 (m-80) cc_final: 0.8475 (m-80) REVERT: B 602 GLU cc_start: 0.7789 (pp20) cc_final: 0.7084 (pp20) REVERT: B 615 MET cc_start: 0.9057 (mmm) cc_final: 0.8790 (mmm) REVERT: B 627 LYS cc_start: 0.8981 (tttt) cc_final: 0.8430 (tttt) REVERT: C 45 LYS cc_start: 0.9270 (tptp) cc_final: 0.9027 (pttp) REVERT: C 82 ASP cc_start: 0.8394 (m-30) cc_final: 0.7671 (t70) REVERT: C 103 LYS cc_start: 0.8653 (tppt) cc_final: 0.8370 (tppt) REVERT: C 154 PHE cc_start: 0.9031 (t80) cc_final: 0.8541 (t80) REVERT: C 210 GLN cc_start: 0.4744 (mm110) cc_final: 0.4444 (mm110) REVERT: C 250 VAL cc_start: 0.7589 (t) cc_final: 0.7268 (p) REVERT: D 52 GLN cc_start: 0.5379 (OUTLIER) cc_final: 0.4696 (pp30) REVERT: D 59 LEU cc_start: 0.6668 (pp) cc_final: 0.6012 (tt) REVERT: D 109 PHE cc_start: 0.6817 (m-80) cc_final: 0.6380 (m-80) REVERT: D 112 LEU cc_start: 0.4905 (tp) cc_final: 0.4582 (tt) REVERT: D 116 GLU cc_start: 0.9077 (tp30) cc_final: 0.8695 (tp30) REVERT: D 146 GLN cc_start: 0.8377 (mm110) cc_final: 0.8110 (tt0) REVERT: D 149 ASP cc_start: 0.7719 (t0) cc_final: 0.7010 (p0) REVERT: D 178 PHE cc_start: 0.8893 (m-80) cc_final: 0.8373 (m-80) REVERT: D 210 GLN cc_start: 0.8396 (tp40) cc_final: 0.7857 (mm110) REVERT: D 219 GLU cc_start: 0.8533 (tp30) cc_final: 0.7926 (pm20) REVERT: D 232 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6634 (mt) REVERT: D 242 TYR cc_start: 0.6548 (t80) cc_final: 0.5309 (m-80) outliers start: 58 outliers final: 44 residues processed: 507 average time/residue: 0.1289 time to fit residues: 99.9948 Evaluate side-chains 530 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 476 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 262 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 147 GLN B 202 ASN B 312 GLN B 320 ASN C 98 ASN C 127 GLN C 234 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.143931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.102152 restraints weight = 32438.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.105689 restraints weight = 15443.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.107885 restraints weight = 9113.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.109216 restraints weight = 6367.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.110129 restraints weight = 5032.229| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.6528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16386 Z= 0.151 Angle : 0.719 11.075 22134 Z= 0.373 Chirality : 0.046 0.413 2360 Planarity : 0.004 0.051 2818 Dihedral : 9.598 146.295 2243 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.09 % Allowed : 28.79 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.19), residues: 1932 helix: 1.10 (0.16), residues: 1143 sheet: -0.57 (0.42), residues: 136 loop : 0.07 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 225 TYR 0.054 0.002 TYR C 204 PHE 0.039 0.002 PHE C 21 TRP 0.066 0.002 TRP C 44 HIS 0.005 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00343 (16386) covalent geometry : angle 0.71937 (22134) hydrogen bonds : bond 0.04031 ( 871) hydrogen bonds : angle 5.05868 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3485.56 seconds wall clock time: 61 minutes 13.67 seconds (3673.67 seconds total)