Starting phenix.real_space_refine on Sat Jun 14 07:50:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byv_45045/06_2025/9byv_45045_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byv_45045/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9byv_45045/06_2025/9byv_45045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byv_45045/06_2025/9byv_45045.map" model { file = "/net/cci-nas-00/data/ceres_data/9byv_45045/06_2025/9byv_45045_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byv_45045/06_2025/9byv_45045_neut.cif" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 9.48, per 1000 atoms: 0.59 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: 4.01 Conformation dependent library (CDL) restraints added in 2.0 seconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 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: 4.96 Time building geometry restraints manager: 4.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 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: 1.330 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: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 36.430 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.280 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.18), residues: 1932 helix: 0.58 (0.14), residues: 1151 sheet: 0.46 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 PHE 0.021 0.002 PHE C 168 TYR 0.020 0.002 TYR D 179 ARG 0.003 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.15422 ( 871) hydrogen bonds : angle 6.51813 ( 2571) covalent geometry : bond 0.00553 (16386) covalent geometry : angle 0.74038 (22134) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 864 time to evaluate : 1.821 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: A 38 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8482 (m) REVERT: A 116 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7110 (mt-10) REVERT: A 179 LEU cc_start: 0.9121 (tp) cc_final: 0.8787 (tp) REVERT: A 362 ASP cc_start: 0.6467 (m-30) cc_final: 0.6122 (m-30) REVERT: A 490 THR cc_start: 0.8604 (m) cc_final: 0.8298 (m) REVERT: A 576 LEU cc_start: 0.8938 (mt) cc_final: 0.8559 (mt) REVERT: A 606 TYR cc_start: 0.7504 (m-80) cc_final: 0.7292 (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: 0.8688 (tp) REVERT: B 186 ILE cc_start: 0.9326 (mt) cc_final: 0.8987 (mt) REVERT: B 190 MET cc_start: 0.8126 (mtm) cc_final: 0.7906 (mtm) REVERT: B 251 LEU cc_start: 0.7956 (tp) cc_final: 0.7748 (tp) REVERT: B 288 PHE cc_start: 0.8003 (t80) cc_final: 0.7674 (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: 0.8799 (mt) REVERT: B 420 MET cc_start: 0.7976 (mmm) cc_final: 0.7739 (mmm) REVERT: B 436 LEU cc_start: 0.9236 (mt) cc_final: 0.8920 (mt) REVERT: B 460 SER cc_start: 0.9036 (t) cc_final: 0.8774 (p) REVERT: B 471 TYR cc_start: 0.8197 (t80) cc_final: 0.7491 (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: 0.7699 (mtp) REVERT: B 584 ILE cc_start: 0.8945 (tp) cc_final: 0.8734 (tp) REVERT: B 612 TYR cc_start: 0.7224 (m-80) cc_final: 0.6876 (m-80) REVERT: C 286 VAL cc_start: 0.4799 (t) cc_final: 0.4055 (p) REVERT: D 89 VAL cc_start: 0.5044 (t) cc_final: 0.4265 (t) REVERT: D 126 LYS cc_start: 0.3277 (OUTLIER) cc_final: 0.2618 (tttt) REVERT: D 246 LEU cc_start: 0.5231 (mt) cc_final: 0.4755 (tp) REVERT: D 287 LEU cc_start: 0.4918 (mt) cc_final: 0.4440 (tp) outliers start: 24 outliers final: 9 residues processed: 877 average time/residue: 0.2953 time to fit residues: 373.5238 Evaluate side-chains 625 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 614 time to evaluate : 1.913 ------------------------------------------------------------------------------- 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 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 162 optimal weight: 0.3980 chunk 145 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 174 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 455 ASN A 501 GLN B 312 GLN B 313 HIS ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN B 338 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN C 28 GLN 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 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 = 0.3871 r_free = 0.3871 target = 0.149481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.106023 restraints weight = 30725.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.109832 restraints weight = 14143.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.112243 restraints weight = 8196.204| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3435 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= 0.157 Angle : 0.653 9.269 22134 Z= 0.338 Chirality : 0.044 0.300 2360 Planarity : 0.004 0.047 2818 Dihedral : 11.542 174.613 2261 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.55 % Allowed : 19.17 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.19), residues: 1932 helix: 1.44 (0.15), residues: 1130 sheet: 0.99 (0.55), residues: 68 loop : 0.33 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 44 HIS 0.019 0.001 HIS D 80 PHE 0.030 0.002 PHE D 172 TYR 0.025 0.002 TYR C 247 ARG 0.006 0.001 ARG B 686 Details of bonding type rmsd hydrogen bonds : bond 0.04707 ( 871) hydrogen bonds : angle 5.15654 ( 2571) covalent geometry : bond 0.00351 (16386) covalent geometry : angle 0.65341 (22134) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 648 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8799 (tptp) cc_final: 0.8396 (tppt) REVERT: A 76 ASP cc_start: 0.8422 (m-30) cc_final: 0.8051 (m-30) REVERT: A 119 GLU cc_start: 0.8358 (mp0) cc_final: 0.8098 (mp0) REVERT: A 250 TYR cc_start: 0.8703 (m-80) cc_final: 0.8174 (m-80) REVERT: A 290 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8026 (mt-10) REVERT: A 348 MET cc_start: 0.8133 (tmm) cc_final: 0.7676 (tmm) REVERT: A 384 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.6144 (pm20) REVERT: A 406 ASP cc_start: 0.8277 (m-30) cc_final: 0.7974 (t0) REVERT: A 446 ARG cc_start: 0.7285 (mmm160) cc_final: 0.6522 (mmm160) REVERT: A 452 ARG cc_start: 0.8933 (ttp80) cc_final: 0.8575 (ttt-90) REVERT: A 583 SER cc_start: 0.8961 (m) cc_final: 0.8446 (t) REVERT: A 590 SER cc_start: 0.9169 (t) cc_final: 0.8872 (t) REVERT: A 606 TYR cc_start: 0.8422 (m-80) cc_final: 0.8209 (m-10) REVERT: A 640 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.8679 (tpp) REVERT: A 653 SER cc_start: 0.8679 (m) cc_final: 0.8337 (m) REVERT: A 654 PHE cc_start: 0.9029 (t80) cc_final: 0.8813 (t80) REVERT: B 12 LEU cc_start: 0.9286 (mt) cc_final: 0.9052 (mp) REVERT: B 65 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7915 (mm-30) REVERT: B 95 MET cc_start: 0.9060 (mmm) cc_final: 0.8472 (tpp) REVERT: B 136 LYS cc_start: 0.9168 (mmmm) cc_final: 0.8777 (mmtt) REVERT: B 218 ASN cc_start: 0.8885 (OUTLIER) cc_final: 0.8483 (t0) REVERT: B 221 LYS cc_start: 0.9172 (mttm) cc_final: 0.8897 (mmtm) REVERT: B 232 ASN cc_start: 0.8815 (OUTLIER) cc_final: 0.8401 (t0) REVERT: B 274 ARG cc_start: 0.8066 (ttm-80) cc_final: 0.7768 (ttm-80) REVERT: B 308 LYS cc_start: 0.9074 (mtpt) cc_final: 0.8732 (mtmm) REVERT: B 312 GLN cc_start: 0.8660 (mt0) cc_final: 0.8375 (mt0) REVERT: B 322 MET cc_start: 0.9196 (tpp) cc_final: 0.8800 (tpp) REVERT: B 420 MET cc_start: 0.8827 (mmm) cc_final: 0.8573 (mmm) REVERT: B 446 ARG cc_start: 0.7575 (mmm160) cc_final: 0.7182 (mmm-85) REVERT: B 471 TYR cc_start: 0.8948 (t80) cc_final: 0.8184 (t80) REVERT: B 485 ARG cc_start: 0.9102 (mtm-85) cc_final: 0.8834 (mtm-85) REVERT: B 493 MET cc_start: 0.9621 (tmm) cc_final: 0.9262 (tmm) REVERT: B 546 LEU cc_start: 0.9524 (mt) cc_final: 0.9077 (mt) REVERT: B 627 LYS cc_start: 0.8927 (tttt) cc_final: 0.8539 (tttt) REVERT: B 659 LYS cc_start: 0.8417 (mmmt) cc_final: 0.7972 (mmmt) REVERT: C 44 TRP cc_start: 0.8247 (t-100) cc_final: 0.7857 (t-100) REVERT: C 68 GLU cc_start: 0.8664 (mp0) cc_final: 0.7758 (tm-30) REVERT: C 72 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8788 (t) REVERT: C 112 LEU cc_start: 0.6422 (mt) cc_final: 0.6185 (mt) REVERT: C 124 TRP cc_start: 0.8461 (t60) cc_final: 0.8197 (t60) REVERT: C 269 MET cc_start: 0.8686 (tpt) cc_final: 0.8354 (tmm) REVERT: D 174 TYR cc_start: 0.7241 (t80) cc_final: 0.6618 (t80) REVERT: D 198 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8084 (mm-30) outliers start: 61 outliers final: 26 residues processed: 677 average time/residue: 0.2778 time to fit residues: 279.4495 Evaluate side-chains 589 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 558 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain B residue 141 VAL 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 314 MET Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 411 LEU 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 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 191 optimal weight: 20.0000 chunk 57 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 171 optimal weight: 10.0000 chunk 189 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 370 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 191 GLN B 320 ASN B 387 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN C 136 GLN C 181 GLN C 234 GLN C 249 GLN D 91 ASN D 146 GLN D 181 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.143307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.099615 restraints weight = 32001.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.103205 restraints weight = 15316.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.105466 restraints weight = 9070.259| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16386 Z= 0.240 Angle : 0.676 14.988 22134 Z= 0.351 Chirality : 0.046 0.370 2360 Planarity : 0.004 0.042 2818 Dihedral : 11.269 163.327 2248 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 5.36 % Allowed : 21.33 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.19), residues: 1932 helix: 1.38 (0.15), residues: 1139 sheet: -0.52 (0.45), residues: 114 loop : 0.51 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 623 HIS 0.007 0.001 HIS D 80 PHE 0.034 0.002 PHE D 172 TYR 0.028 0.002 TYR C 142 ARG 0.007 0.001 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.04366 ( 871) hydrogen bonds : angle 5.09872 ( 2571) covalent geometry : bond 0.00531 (16386) covalent geometry : angle 0.67643 (22134) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 581 time to evaluate : 1.960 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: A 8 LYS cc_start: 0.8776 (tptp) cc_final: 0.8354 (tppt) REVERT: A 40 TYR cc_start: 0.8946 (t80) cc_final: 0.8668 (t80) REVERT: A 76 ASP cc_start: 0.8509 (m-30) cc_final: 0.8222 (m-30) REVERT: A 119 GLU cc_start: 0.8537 (mp0) cc_final: 0.8259 (mp0) REVERT: A 179 LEU cc_start: 0.9268 (tp) cc_final: 0.8828 (tp) REVERT: A 214 LYS cc_start: 0.8031 (mmtt) cc_final: 0.7814 (mmtm) REVERT: A 250 TYR cc_start: 0.8780 (m-80) cc_final: 0.8573 (m-80) REVERT: A 263 ASP cc_start: 0.8116 (m-30) cc_final: 0.7841 (m-30) REVERT: A 290 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8176 (mt-10) REVERT: A 348 MET cc_start: 0.8203 (tmm) cc_final: 0.7869 (tmm) REVERT: A 359 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8055 (ttp) REVERT: A 361 GLN cc_start: 0.8762 (tp40) cc_final: 0.8420 (tp40) REVERT: A 362 ASP cc_start: 0.8249 (m-30) cc_final: 0.7771 (m-30) REVERT: A 384 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7554 (pm20) REVERT: A 394 TYR cc_start: 0.8814 (m-80) cc_final: 0.8526 (m-80) REVERT: A 406 ASP cc_start: 0.8346 (m-30) cc_final: 0.8132 (t0) REVERT: A 446 ARG cc_start: 0.7481 (mmm160) cc_final: 0.7107 (mmm160) REVERT: A 447 ASN cc_start: 0.8277 (m-40) cc_final: 0.8048 (m-40) REVERT: A 583 SER cc_start: 0.8954 (m) cc_final: 0.8725 (t) REVERT: A 598 MET cc_start: 0.8505 (mtm) cc_final: 0.8304 (mtm) REVERT: A 640 MET cc_start: 0.9305 (OUTLIER) cc_final: 0.8994 (tpp) REVERT: B 65 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8028 (mm-30) REVERT: B 95 MET cc_start: 0.9086 (mmm) cc_final: 0.8821 (tpp) REVERT: B 209 LYS cc_start: 0.8395 (ttmm) cc_final: 0.8152 (tptt) REVERT: B 218 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8557 (t0) REVERT: B 221 LYS cc_start: 0.9014 (mttm) cc_final: 0.8691 (mmtm) REVERT: B 236 TYR cc_start: 0.9145 (t80) cc_final: 0.8861 (t80) REVERT: B 257 ASP cc_start: 0.8583 (m-30) cc_final: 0.8260 (m-30) REVERT: B 274 ARG cc_start: 0.8254 (ttm-80) cc_final: 0.7918 (ttm-80) REVERT: B 276 LYS cc_start: 0.8854 (ptpp) cc_final: 0.8538 (mmmt) REVERT: B 349 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9107 (tp) REVERT: B 420 MET cc_start: 0.9022 (mmm) cc_final: 0.8781 (mmm) REVERT: B 434 ASP cc_start: 0.8512 (m-30) cc_final: 0.8102 (m-30) REVERT: B 471 TYR cc_start: 0.9056 (t80) cc_final: 0.8357 (t80) REVERT: B 493 MET cc_start: 0.9665 (tmm) cc_final: 0.9151 (tmm) REVERT: B 546 LEU cc_start: 0.9537 (mt) cc_final: 0.9131 (mt) REVERT: B 570 MET cc_start: 0.8165 (mtt) cc_final: 0.7954 (mtt) REVERT: B 586 TYR cc_start: 0.8895 (m-80) cc_final: 0.8441 (m-80) REVERT: B 602 GLU cc_start: 0.7940 (pp20) cc_final: 0.7104 (pp20) REVERT: B 627 LYS cc_start: 0.8832 (tttt) cc_final: 0.8603 (tttt) REVERT: C 43 THR cc_start: 0.6941 (OUTLIER) cc_final: 0.6499 (p) REVERT: C 55 TYR cc_start: 0.6127 (t80) cc_final: 0.5621 (t80) REVERT: C 68 GLU cc_start: 0.8844 (mp0) cc_final: 0.8119 (tm-30) REVERT: C 124 TRP cc_start: 0.8307 (t60) cc_final: 0.8056 (t60) REVERT: C 137 MET cc_start: 0.6967 (mpp) cc_final: 0.6684 (mpp) REVERT: C 269 MET cc_start: 0.8669 (tpt) cc_final: 0.8322 (tmm) REVERT: C 274 ASP cc_start: 0.8217 (p0) cc_final: 0.7868 (p0) REVERT: D 47 LEU cc_start: 0.5009 (mt) cc_final: 0.4795 (tp) REVERT: D 76 ILE cc_start: 0.7991 (tp) cc_final: 0.7694 (tp) REVERT: D 80 HIS cc_start: 0.7669 (m90) cc_final: 0.7272 (m90) REVERT: D 112 LEU cc_start: 0.3775 (tp) cc_final: 0.3511 (tt) REVERT: D 174 TYR cc_start: 0.7479 (t80) cc_final: 0.6702 (t80) REVERT: D 198 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7932 (mm-30) REVERT: D 219 GLU cc_start: 0.8338 (tp30) cc_final: 0.7570 (pm20) REVERT: D 266 LYS cc_start: 0.7358 (mtpt) cc_final: 0.7140 (mmmt) outliers start: 92 outliers final: 47 residues processed: 624 average time/residue: 0.2656 time to fit residues: 247.3462 Evaluate side-chains 571 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 518 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 270 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 349 LEU 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 421 GLU Chi-restraints excluded: chain A residue 425 ILE 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 526 GLU Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 ASN 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 289 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 367 VAL 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 583 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 200 ILE 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 C residue 234 GLN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 215 LYS 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 180 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 74 optimal weight: 0.3980 chunk 148 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 147 GLN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN B 320 ASN B 387 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.142448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.099246 restraints weight = 32525.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.102694 restraints weight = 15421.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.104898 restraints weight = 9135.206| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16386 Z= 0.227 Angle : 0.661 10.542 22134 Z= 0.341 Chirality : 0.046 0.372 2360 Planarity : 0.004 0.049 2818 Dihedral : 10.966 163.567 2246 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.84 % Allowed : 22.09 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.19), residues: 1932 helix: 1.34 (0.15), residues: 1135 sheet: -0.80 (0.45), residues: 118 loop : 0.46 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 623 HIS 0.006 0.001 HIS A 255 PHE 0.036 0.002 PHE D 168 TYR 0.019 0.002 TYR A 606 ARG 0.006 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04183 ( 871) hydrogen bonds : angle 5.04074 ( 2571) covalent geometry : bond 0.00506 (16386) covalent geometry : angle 0.66094 (22134) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 554 time to evaluate : 1.833 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: 0.8816 (tptp) cc_final: 0.8447 (tppt) REVERT: A 40 TYR cc_start: 0.8905 (t80) cc_final: 0.8533 (t80) REVERT: A 76 ASP cc_start: 0.8483 (m-30) cc_final: 0.8203 (m-30) REVERT: A 119 GLU cc_start: 0.8582 (mp0) cc_final: 0.8289 (mp0) REVERT: A 164 ARG cc_start: 0.7282 (ptt90) cc_final: 0.6981 (ptt-90) REVERT: A 179 LEU cc_start: 0.9285 (tp) cc_final: 0.8883 (tp) REVERT: A 214 LYS cc_start: 0.8022 (mmtt) cc_final: 0.7774 (mmtt) REVERT: A 263 ASP cc_start: 0.8136 (m-30) cc_final: 0.7871 (m-30) REVERT: A 290 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8227 (mt-10) REVERT: A 348 MET cc_start: 0.8198 (tmm) cc_final: 0.7846 (tmm) REVERT: A 359 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.7926 (ttp) REVERT: A 361 GLN cc_start: 0.8825 (tp40) cc_final: 0.8514 (tp40) REVERT: A 384 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.6811 (pm20) REVERT: A 394 TYR cc_start: 0.8909 (m-80) cc_final: 0.8437 (m-80) REVERT: A 427 LYS cc_start: 0.9080 (tppp) cc_final: 0.8669 (tppp) REVERT: A 446 ARG cc_start: 0.7458 (mmm160) cc_final: 0.7063 (mmm160) REVERT: A 590 SER cc_start: 0.9131 (t) cc_final: 0.8715 (p) REVERT: A 632 MET cc_start: 0.8436 (mtm) cc_final: 0.8106 (mtp) REVERT: A 640 MET cc_start: 0.9286 (OUTLIER) cc_final: 0.9002 (tpp) REVERT: A 684 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.7926 (m-80) REVERT: B 65 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8049 (mm-30) REVERT: B 209 LYS cc_start: 0.8422 (ttmm) cc_final: 0.8180 (tptt) REVERT: B 218 ASN cc_start: 0.8987 (OUTLIER) cc_final: 0.8490 (t0) REVERT: B 236 TYR cc_start: 0.9153 (t80) cc_final: 0.8882 (t80) REVERT: B 274 ARG cc_start: 0.8221 (ttm-80) cc_final: 0.7945 (ttm-80) REVERT: B 349 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9177 (tp) REVERT: B 434 ASP cc_start: 0.8519 (m-30) cc_final: 0.8163 (m-30) REVERT: B 493 MET cc_start: 0.9614 (tmm) cc_final: 0.9207 (tmm) REVERT: B 546 LEU cc_start: 0.9545 (mt) cc_final: 0.9315 (mt) REVERT: B 550 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8282 (mtp) REVERT: B 586 TYR cc_start: 0.8963 (m-80) cc_final: 0.8435 (m-80) REVERT: B 602 GLU cc_start: 0.8018 (pp20) cc_final: 0.7114 (pp20) REVERT: B 627 LYS cc_start: 0.8890 (tttt) cc_final: 0.8445 (tttt) REVERT: B 628 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8138 (mp0) REVERT: C 21 PHE cc_start: 0.8403 (m-80) cc_final: 0.8144 (t80) REVERT: C 43 THR cc_start: 0.6824 (OUTLIER) cc_final: 0.6300 (p) REVERT: C 55 TYR cc_start: 0.6044 (t80) cc_final: 0.5424 (t80) REVERT: C 103 LYS cc_start: 0.8170 (tppt) cc_final: 0.7868 (tppt) REVERT: C 124 TRP cc_start: 0.8334 (t60) cc_final: 0.8095 (t60) REVERT: C 178 PHE cc_start: 0.8702 (m-80) cc_final: 0.8426 (m-80) REVERT: C 185 MET cc_start: 0.7889 (mpp) cc_final: 0.7525 (mmm) REVERT: C 269 MET cc_start: 0.8725 (tpt) cc_final: 0.8368 (tmm) REVERT: D 80 HIS cc_start: 0.7619 (m90) cc_final: 0.7374 (m90) REVERT: D 116 GLU cc_start: 0.9154 (tp30) cc_final: 0.8795 (tp30) REVERT: D 174 TYR cc_start: 0.7601 (t80) cc_final: 0.6715 (t80) REVERT: D 266 LYS cc_start: 0.7366 (mtpt) cc_final: 0.7132 (mmmt) REVERT: D 285 ILE cc_start: 0.7582 (mp) cc_final: 0.7320 (tp) outliers start: 83 outliers final: 51 residues processed: 584 average time/residue: 0.2714 time to fit residues: 236.5257 Evaluate side-chains 547 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 488 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 141 VAL 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 359 MET Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 384 GLU 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 442 THR Chi-restraints excluded: chain A residue 526 GLU 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 141 VAL 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 218 ASN 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 289 VAL 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 550 MET 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 137 MET 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 C residue 246 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 262 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 67 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 175 optimal weight: 8.9990 chunk 182 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 191 GLN B 312 GLN B 320 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN C 98 ASN C 127 GLN C 132 GLN C 136 GLN C 192 ASN C 234 GLN D 25 ASN D 91 ASN D 181 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.144409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.101311 restraints weight = 32672.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.104727 restraints weight = 15394.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.106963 restraints weight = 9090.320| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 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 = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16386 Z= 0.152 Angle : 0.635 9.429 22134 Z= 0.326 Chirality : 0.044 0.404 2360 Planarity : 0.004 0.098 2818 Dihedral : 10.409 158.540 2245 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.55 % Allowed : 22.84 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.19), residues: 1932 helix: 1.33 (0.15), residues: 1131 sheet: -0.76 (0.45), residues: 118 loop : 0.39 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 44 HIS 0.006 0.001 HIS C 201 PHE 0.033 0.002 PHE D 172 TYR 0.016 0.001 TYR C 247 ARG 0.006 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 871) hydrogen bonds : angle 4.97366 ( 2571) covalent geometry : bond 0.00350 (16386) covalent geometry : angle 0.63534 (22134) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 555 time to evaluate : 1.665 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: 0.8821 (tptp) cc_final: 0.8507 (tppt) REVERT: A 40 TYR cc_start: 0.8886 (t80) cc_final: 0.8512 (t80) REVERT: A 119 GLU cc_start: 0.8515 (mp0) cc_final: 0.8217 (mp0) REVERT: A 144 MET cc_start: 0.8682 (mtm) cc_final: 0.8338 (mtm) REVERT: A 172 LEU cc_start: 0.9311 (mp) cc_final: 0.8341 (mt) REVERT: A 173 LEU cc_start: 0.9350 (mt) cc_final: 0.9090 (mt) REVERT: A 179 LEU cc_start: 0.9249 (tp) cc_final: 0.8874 (tp) REVERT: A 214 LYS cc_start: 0.7918 (mmtt) cc_final: 0.7646 (mmtt) REVERT: A 250 TYR cc_start: 0.8685 (m-80) cc_final: 0.8392 (m-80) REVERT: A 263 ASP cc_start: 0.8168 (m-30) cc_final: 0.7905 (m-30) REVERT: A 286 ASP cc_start: 0.7655 (m-30) cc_final: 0.7447 (m-30) REVERT: A 290 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8189 (mt-10) REVERT: A 348 MET cc_start: 0.8240 (tmm) cc_final: 0.7090 (tmm) REVERT: A 352 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7126 (mt-10) REVERT: A 359 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.7963 (ttp) REVERT: A 361 GLN cc_start: 0.8804 (tp40) cc_final: 0.8463 (tp40) REVERT: A 384 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7597 (pm20) REVERT: A 406 ASP cc_start: 0.8320 (m-30) cc_final: 0.7939 (t0) REVERT: A 427 LYS cc_start: 0.9072 (tppp) cc_final: 0.8607 (tppp) REVERT: A 446 ARG cc_start: 0.7389 (mmm160) cc_final: 0.6957 (mmm160) REVERT: A 493 MET cc_start: 0.9106 (tmm) cc_final: 0.8898 (tmm) REVERT: A 590 SER cc_start: 0.9040 (t) cc_final: 0.8641 (p) REVERT: A 632 MET cc_start: 0.8376 (mtm) cc_final: 0.8038 (mtp) REVERT: A 640 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8947 (tpp) REVERT: A 684 TYR cc_start: 0.8411 (OUTLIER) cc_final: 0.8026 (m-80) REVERT: B 65 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8087 (mm-30) REVERT: B 218 ASN cc_start: 0.8965 (m110) cc_final: 0.8529 (t0) REVERT: B 236 TYR cc_start: 0.9121 (t80) cc_final: 0.8871 (t80) REVERT: B 257 ASP cc_start: 0.8579 (m-30) cc_final: 0.8190 (m-30) REVERT: B 274 ARG cc_start: 0.8157 (ttm-80) cc_final: 0.7853 (ttm-80) REVERT: B 322 MET cc_start: 0.9111 (tpp) cc_final: 0.8590 (tpp) REVERT: B 349 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9144 (tp) REVERT: B 373 ILE cc_start: 0.9565 (mt) cc_final: 0.9342 (mt) REVERT: B 374 SER cc_start: 0.9474 (t) cc_final: 0.9088 (m) REVERT: B 398 ASP cc_start: 0.8329 (t0) cc_final: 0.7963 (t0) REVERT: B 434 ASP cc_start: 0.8580 (m-30) cc_final: 0.8219 (m-30) REVERT: B 467 ASN cc_start: 0.8988 (t0) cc_final: 0.8704 (t0) REVERT: B 471 TYR cc_start: 0.9076 (t80) cc_final: 0.8443 (t80) REVERT: B 493 MET cc_start: 0.9542 (tmm) cc_final: 0.9158 (tmm) REVERT: B 546 LEU cc_start: 0.9524 (mt) cc_final: 0.9165 (mt) REVERT: B 586 TYR cc_start: 0.8908 (m-80) cc_final: 0.8272 (m-80) REVERT: B 595 MET cc_start: 0.8524 (mmm) cc_final: 0.8166 (mmm) REVERT: B 602 GLU cc_start: 0.8006 (pp20) cc_final: 0.6948 (pp20) REVERT: B 627 LYS cc_start: 0.8839 (tttt) cc_final: 0.8376 (tttt) REVERT: B 628 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8114 (mp0) REVERT: C 21 PHE cc_start: 0.8400 (m-80) cc_final: 0.8169 (t80) REVERT: C 44 TRP cc_start: 0.8196 (t-100) cc_final: 0.7869 (t-100) REVERT: C 68 GLU cc_start: 0.8453 (mm-30) cc_final: 0.7677 (tm-30) REVERT: C 103 LYS cc_start: 0.8414 (tppt) cc_final: 0.8068 (tppt) REVERT: C 122 PHE cc_start: 0.9371 (m-80) cc_final: 0.8875 (m-80) REVERT: C 124 TRP cc_start: 0.8291 (t60) cc_final: 0.8037 (t60) REVERT: C 185 MET cc_start: 0.7990 (mpp) cc_final: 0.7584 (mmm) REVERT: C 269 MET cc_start: 0.8782 (tpt) cc_final: 0.8405 (tmm) REVERT: D 116 GLU cc_start: 0.9154 (tp30) cc_final: 0.8803 (tp30) REVERT: D 174 TYR cc_start: 0.7600 (t80) cc_final: 0.7024 (t80) REVERT: D 219 GLU cc_start: 0.8467 (tp30) cc_final: 0.7898 (pm20) REVERT: D 232 LEU cc_start: 0.7388 (mt) cc_final: 0.6828 (mt) REVERT: D 285 ILE cc_start: 0.7583 (mp) cc_final: 0.7358 (tp) outliers start: 78 outliers final: 52 residues processed: 584 average time/residue: 0.2548 time to fit residues: 222.5244 Evaluate side-chains 565 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 508 time to evaluate : 1.638 ------------------------------------------------------------------------------- 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 384 GLU 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 584 ILE Chi-restraints excluded: chain A residue 589 SER 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 684 TYR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 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 276 LYS 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 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 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 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 217 THR Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 234 GLN Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 145 ILE 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 240 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 31 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 156 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 177 optimal weight: 0.0770 overall best weight: 3.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN C 234 GLN D 28 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.140134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.096938 restraints weight = 32977.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.100311 restraints weight = 15908.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.102423 restraints weight = 9482.468| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.5611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 16386 Z= 0.281 Angle : 0.717 12.224 22134 Z= 0.370 Chirality : 0.047 0.418 2360 Planarity : 0.004 0.045 2818 Dihedral : 10.607 164.658 2244 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 5.07 % Allowed : 23.83 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.19), residues: 1932 helix: 1.10 (0.15), residues: 1144 sheet: -0.97 (0.46), residues: 118 loop : 0.25 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 623 HIS 0.010 0.002 HIS D 80 PHE 0.037 0.002 PHE D 168 TYR 0.029 0.002 TYR D 262 ARG 0.007 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04226 ( 871) hydrogen bonds : angle 5.14893 ( 2571) covalent geometry : bond 0.00622 (16386) covalent geometry : angle 0.71746 (22134) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 512 time to evaluate : 1.864 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: 0.8838 (tptp) cc_final: 0.8481 (tppt) REVERT: A 40 TYR cc_start: 0.8973 (t80) cc_final: 0.8565 (t80) REVERT: A 65 GLU cc_start: 0.8486 (mm-30) cc_final: 0.7576 (mp0) REVERT: A 66 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8319 (tp30) REVERT: A 119 GLU cc_start: 0.8618 (mp0) cc_final: 0.8341 (mp0) REVERT: A 144 MET cc_start: 0.8659 (mtm) cc_final: 0.8389 (mtm) REVERT: A 164 ARG cc_start: 0.7568 (ptt180) cc_final: 0.7269 (ptt180) REVERT: A 214 LYS cc_start: 0.8110 (mmtt) cc_final: 0.7719 (mmtt) REVERT: A 250 TYR cc_start: 0.8720 (m-80) cc_final: 0.8474 (m-80) REVERT: A 263 ASP cc_start: 0.8151 (m-30) cc_final: 0.7884 (m-30) REVERT: A 290 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8196 (mt-10) REVERT: A 348 MET cc_start: 0.8253 (tmm) cc_final: 0.7031 (tmm) REVERT: A 352 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7100 (mt-10) REVERT: A 359 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8055 (ttp) REVERT: A 361 GLN cc_start: 0.8885 (tp40) cc_final: 0.8541 (tp40) REVERT: A 381 LEU cc_start: 0.9239 (tp) cc_final: 0.9002 (tp) REVERT: A 384 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7129 (pm20) REVERT: A 389 SER cc_start: 0.9308 (OUTLIER) cc_final: 0.8912 (p) REVERT: A 397 TYR cc_start: 0.8673 (t80) cc_final: 0.8388 (t80) REVERT: A 427 LYS cc_start: 0.9112 (tppp) cc_final: 0.8684 (tppp) REVERT: A 446 ARG cc_start: 0.7631 (mmm160) cc_final: 0.7246 (mmm160) REVERT: A 590 SER cc_start: 0.9150 (t) cc_final: 0.8868 (p) REVERT: A 640 MET cc_start: 0.9312 (OUTLIER) cc_final: 0.9015 (tpp) REVERT: A 684 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.8101 (m-80) REVERT: B 40 TYR cc_start: 0.9187 (t80) cc_final: 0.8635 (t80) REVERT: B 95 MET cc_start: 0.8958 (tpp) cc_final: 0.8449 (tmm) REVERT: B 211 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7385 (mt-10) REVERT: B 218 ASN cc_start: 0.9022 (m110) cc_final: 0.8548 (t0) REVERT: B 236 TYR cc_start: 0.9202 (t80) cc_final: 0.8917 (t80) REVERT: B 257 ASP cc_start: 0.8658 (m-30) cc_final: 0.8327 (m-30) REVERT: B 374 SER cc_start: 0.9526 (t) cc_final: 0.9183 (t) REVERT: B 434 ASP cc_start: 0.8621 (m-30) cc_final: 0.8235 (m-30) REVERT: B 483 GLU cc_start: 0.9186 (mp0) cc_final: 0.8937 (mp0) REVERT: B 493 MET cc_start: 0.9612 (tmm) cc_final: 0.9251 (tmm) REVERT: B 546 LEU cc_start: 0.9487 (mt) cc_final: 0.9282 (mt) REVERT: B 586 TYR cc_start: 0.8962 (m-80) cc_final: 0.8231 (m-80) REVERT: B 595 MET cc_start: 0.8650 (mmm) cc_final: 0.8252 (mmm) REVERT: B 602 GLU cc_start: 0.7949 (pp20) cc_final: 0.7028 (pp20) REVERT: B 627 LYS cc_start: 0.8877 (tttt) cc_final: 0.8398 (tttt) REVERT: B 628 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8130 (mp0) REVERT: C 44 TRP cc_start: 0.8293 (t-100) cc_final: 0.8043 (t-100) REVERT: C 68 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7561 (tm-30) REVERT: C 82 ASP cc_start: 0.7797 (m-30) cc_final: 0.6970 (t70) REVERT: C 103 LYS cc_start: 0.8431 (tppt) cc_final: 0.8162 (tppt) REVERT: C 105 TYR cc_start: 0.8846 (m-80) cc_final: 0.8498 (m-80) REVERT: C 122 PHE cc_start: 0.9283 (m-80) cc_final: 0.8627 (m-80) REVERT: C 124 TRP cc_start: 0.8343 (t60) cc_final: 0.8089 (t60) REVERT: C 127 GLN cc_start: 0.9066 (tp40) cc_final: 0.8751 (mm110) REVERT: C 154 PHE cc_start: 0.8493 (m-10) cc_final: 0.8279 (m-80) REVERT: C 185 MET cc_start: 0.7993 (mpp) cc_final: 0.7293 (mmm) REVERT: D 80 HIS cc_start: 0.7801 (m90) cc_final: 0.7487 (m90) REVERT: D 87 LYS cc_start: 0.7749 (mttm) cc_final: 0.7267 (mttm) REVERT: D 109 PHE cc_start: 0.6847 (OUTLIER) cc_final: 0.6172 (m-10) REVERT: D 116 GLU cc_start: 0.9089 (tp30) cc_final: 0.8712 (tp30) REVERT: D 174 TYR cc_start: 0.7975 (t80) cc_final: 0.7360 (t80) REVERT: D 219 GLU cc_start: 0.8557 (tp30) cc_final: 0.7984 (pm20) REVERT: D 232 LEU cc_start: 0.7307 (mt) cc_final: 0.6782 (mt) REVERT: D 242 TYR cc_start: 0.6854 (t80) cc_final: 0.5836 (m-80) REVERT: D 285 ILE cc_start: 0.7599 (mp) cc_final: 0.7376 (tp) outliers start: 87 outliers final: 59 residues processed: 551 average time/residue: 0.2696 time to fit residues: 221.9998 Evaluate side-chains 537 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 472 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 77 ILE 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 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 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 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 437 THR Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 589 SER 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 141 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 194 LYS 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 267 ILE Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 277 THR 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 342 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 439 VAL 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 18 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 215 LYS 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 39 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 146 optimal weight: 5.9990 chunk 184 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 24 optimal weight: 0.0170 chunk 5 optimal weight: 4.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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 ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 312 GLN B 320 ASN B 387 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3805 r_free = 0.3805 target = 0.145591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.102929 restraints weight = 32382.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.106443 restraints weight = 15141.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.108672 restraints weight = 8880.454| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 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 = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.5866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16386 Z= 0.137 Angle : 0.665 9.817 22134 Z= 0.339 Chirality : 0.045 0.374 2360 Planarity : 0.004 0.057 2818 Dihedral : 9.815 154.283 2244 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.90 % Allowed : 25.76 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.19), residues: 1932 helix: 1.15 (0.15), residues: 1133 sheet: -0.58 (0.49), residues: 106 loop : 0.20 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 44 HIS 0.005 0.001 HIS A 255 PHE 0.035 0.002 PHE D 168 TYR 0.024 0.001 TYR D 276 ARG 0.007 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 871) hydrogen bonds : angle 4.97428 ( 2571) covalent geometry : bond 0.00311 (16386) covalent geometry : angle 0.66509 (22134) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 550 time to evaluate : 2.421 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: 0.8841 (tptp) cc_final: 0.8583 (tppt) REVERT: A 40 TYR cc_start: 0.8876 (t80) cc_final: 0.8504 (t80) REVERT: A 65 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7411 (mp0) REVERT: A 119 GLU cc_start: 0.8500 (mp0) cc_final: 0.8208 (mp0) REVERT: A 144 MET cc_start: 0.8649 (mtm) cc_final: 0.8355 (mtm) REVERT: A 164 ARG cc_start: 0.7468 (ptt180) cc_final: 0.7243 (ptt180) REVERT: A 172 LEU cc_start: 0.9344 (mp) cc_final: 0.8718 (mt) REVERT: A 214 LYS cc_start: 0.7972 (mmtt) cc_final: 0.7606 (mmtt) REVERT: A 232 ASN cc_start: 0.8828 (m-40) cc_final: 0.8283 (m-40) REVERT: A 263 ASP cc_start: 0.8154 (m-30) cc_final: 0.7906 (m-30) REVERT: A 290 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8196 (mt-10) REVERT: A 348 MET cc_start: 0.8217 (tmm) cc_final: 0.6922 (tmm) REVERT: A 352 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7010 (mt-10) REVERT: A 361 GLN cc_start: 0.8659 (tp40) cc_final: 0.8459 (tp40) REVERT: A 384 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7373 (pm20) REVERT: A 406 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8031 (t70) REVERT: A 410 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7786 (t160) REVERT: A 446 ARG cc_start: 0.7431 (mmm160) cc_final: 0.7107 (mmm160) REVERT: A 583 SER cc_start: 0.9159 (t) cc_final: 0.8756 (t) REVERT: A 590 SER cc_start: 0.9100 (t) cc_final: 0.8708 (p) REVERT: A 640 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8915 (tpp) REVERT: A 684 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.8157 (m-80) REVERT: B 95 MET cc_start: 0.8820 (tpp) cc_final: 0.8512 (mmm) REVERT: B 184 ARG cc_start: 0.8939 (tpp80) cc_final: 0.8568 (mmm-85) REVERT: B 191 GLN cc_start: 0.8329 (mm-40) cc_final: 0.8099 (mm-40) REVERT: B 218 ASN cc_start: 0.8984 (m110) cc_final: 0.8551 (t0) REVERT: B 257 ASP cc_start: 0.8615 (m-30) cc_final: 0.8213 (m-30) REVERT: B 374 SER cc_start: 0.9459 (t) cc_final: 0.9084 (m) REVERT: B 398 ASP cc_start: 0.8205 (t0) cc_final: 0.7957 (t0) REVERT: B 417 LEU cc_start: 0.9505 (tt) cc_final: 0.9291 (tp) REVERT: B 434 ASP cc_start: 0.8646 (m-30) cc_final: 0.8237 (m-30) REVERT: B 467 ASN cc_start: 0.8964 (t0) cc_final: 0.8684 (t0) REVERT: B 493 MET cc_start: 0.9499 (tmm) cc_final: 0.9087 (tmm) REVERT: B 571 TYR cc_start: 0.8637 (t80) cc_final: 0.8194 (t80) REVERT: B 586 TYR cc_start: 0.8871 (m-80) cc_final: 0.8575 (m-80) REVERT: B 602 GLU cc_start: 0.8024 (pp20) cc_final: 0.7064 (pp20) REVERT: B 603 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7913 (tm-30) REVERT: B 627 LYS cc_start: 0.8936 (tttt) cc_final: 0.8474 (tttt) REVERT: B 628 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8067 (mp0) REVERT: C 55 TYR cc_start: 0.5938 (t80) cc_final: 0.5216 (t80) REVERT: C 56 MET cc_start: 0.2665 (tpt) cc_final: 0.2378 (tpt) REVERT: C 82 ASP cc_start: 0.7946 (m-30) cc_final: 0.7284 (t70) REVERT: C 103 LYS cc_start: 0.8407 (tppt) cc_final: 0.8122 (tppt) REVERT: C 124 TRP cc_start: 0.8263 (t60) cc_final: 0.8034 (t60) REVERT: C 127 GLN cc_start: 0.9060 (tp40) cc_final: 0.8754 (mm-40) REVERT: C 154 PHE cc_start: 0.8499 (m-10) cc_final: 0.8212 (m-80) REVERT: D 109 PHE cc_start: 0.6653 (m-80) cc_final: 0.5936 (m-10) REVERT: D 116 GLU cc_start: 0.9099 (tp30) cc_final: 0.8736 (tp30) REVERT: D 149 ASP cc_start: 0.7807 (t0) cc_final: 0.7127 (p0) REVERT: D 174 TYR cc_start: 0.8016 (t80) cc_final: 0.7159 (t80) REVERT: D 177 TYR cc_start: 0.8369 (t80) cc_final: 0.7871 (t80) REVERT: D 210 GLN cc_start: 0.8421 (tp40) cc_final: 0.7840 (mm110) REVERT: D 219 GLU cc_start: 0.8517 (tp30) cc_final: 0.7984 (pm20) REVERT: D 232 LEU cc_start: 0.7283 (mt) cc_final: 0.6729 (mt) REVERT: D 285 ILE cc_start: 0.7595 (mp) cc_final: 0.7353 (tp) outliers start: 67 outliers final: 39 residues processed: 579 average time/residue: 0.2883 time to fit residues: 250.8993 Evaluate side-chains 533 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 489 time to evaluate : 1.688 ------------------------------------------------------------------------------- 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 124 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 410 ASN 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 684 TYR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 THR 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 289 VAL Chi-restraints excluded: chain B residue 317 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 599 GLU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 145 ILE 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 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 96 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 387 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** B 131 ASN B 147 GLN B 312 GLN B 320 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN D 52 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.143986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.101985 restraints weight = 32414.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.105383 restraints weight = 15320.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.107589 restraints weight = 9075.402| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 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 = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.6067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16386 Z= 0.166 Angle : 0.704 13.526 22134 Z= 0.358 Chirality : 0.046 0.357 2360 Planarity : 0.004 0.052 2818 Dihedral : 9.756 150.782 2242 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.90 % Allowed : 27.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.19), residues: 1932 helix: 1.08 (0.15), residues: 1131 sheet: -0.68 (0.50), residues: 106 loop : 0.18 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 44 HIS 0.006 0.001 HIS A 255 PHE 0.035 0.002 PHE D 168 TYR 0.034 0.001 TYR C 105 ARG 0.008 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 871) hydrogen bonds : angle 5.12804 ( 2571) covalent geometry : bond 0.00380 (16386) covalent geometry : angle 0.70400 (22134) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 500 time to evaluate : 1.941 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: 0.8798 (tptp) cc_final: 0.8481 (tppt) REVERT: A 40 TYR cc_start: 0.8881 (t80) cc_final: 0.8508 (t80) REVERT: A 65 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7457 (mp0) REVERT: A 119 GLU cc_start: 0.8524 (mp0) cc_final: 0.8241 (mp0) REVERT: A 144 MET cc_start: 0.8631 (mtm) cc_final: 0.8333 (mtm) REVERT: A 172 LEU cc_start: 0.9326 (mp) cc_final: 0.8691 (mt) REVERT: A 214 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7845 (mmtt) REVERT: A 221 LYS cc_start: 0.8108 (mttt) cc_final: 0.7893 (mttt) REVERT: A 232 ASN cc_start: 0.8814 (m-40) cc_final: 0.8260 (m110) REVERT: A 250 TYR cc_start: 0.8601 (m-80) cc_final: 0.8340 (m-80) REVERT: A 263 ASP cc_start: 0.8163 (m-30) cc_final: 0.7905 (m-30) REVERT: A 290 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8264 (mt-10) REVERT: A 348 MET cc_start: 0.8148 (tmm) cc_final: 0.7761 (tmm) REVERT: A 359 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8023 (ttp) REVERT: A 384 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7533 (pm20) REVERT: A 389 SER cc_start: 0.9256 (OUTLIER) cc_final: 0.8926 (p) REVERT: A 406 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8076 (t70) REVERT: A 410 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.7838 (t160) REVERT: A 427 LYS cc_start: 0.9026 (tppp) cc_final: 0.8576 (tppp) REVERT: A 446 ARG cc_start: 0.7479 (mmm160) cc_final: 0.7133 (mmm160) REVERT: A 493 MET cc_start: 0.8986 (tmm) cc_final: 0.8777 (tmm) REVERT: A 583 SER cc_start: 0.9163 (t) cc_final: 0.8755 (t) REVERT: A 590 SER cc_start: 0.9097 (t) cc_final: 0.8775 (p) REVERT: A 640 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8722 (tpp) REVERT: A 684 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.8092 (m-80) REVERT: B 65 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7645 (mp0) REVERT: B 184 ARG cc_start: 0.8977 (tpp80) cc_final: 0.8559 (mmm-85) REVERT: B 209 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8191 (tptt) REVERT: B 218 ASN cc_start: 0.9026 (m110) cc_final: 0.8479 (t0) REVERT: B 257 ASP cc_start: 0.8642 (m-30) cc_final: 0.8240 (m-30) REVERT: B 374 SER cc_start: 0.9473 (t) cc_final: 0.9067 (m) REVERT: B 394 TYR cc_start: 0.9090 (m-80) cc_final: 0.8676 (m-80) REVERT: B 398 ASP cc_start: 0.8276 (t0) cc_final: 0.8003 (t0) REVERT: B 434 ASP cc_start: 0.8660 (m-30) cc_final: 0.8262 (m-30) REVERT: B 467 ASN cc_start: 0.9028 (t0) cc_final: 0.8717 (t0) REVERT: B 483 GLU cc_start: 0.9369 (mp0) cc_final: 0.9167 (mp0) REVERT: B 493 MET cc_start: 0.9591 (tmm) cc_final: 0.9250 (tmm) REVERT: B 570 MET cc_start: 0.8207 (mtt) cc_final: 0.7832 (mtt) REVERT: B 571 TYR cc_start: 0.8713 (t80) cc_final: 0.8241 (t80) REVERT: B 602 GLU cc_start: 0.7997 (pp20) cc_final: 0.7422 (pp20) REVERT: B 627 LYS cc_start: 0.8930 (tttt) cc_final: 0.8448 (tttt) REVERT: B 628 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8038 (mp0) REVERT: C 55 TYR cc_start: 0.5406 (t80) cc_final: 0.5204 (t80) REVERT: C 56 MET cc_start: 0.2373 (tpt) cc_final: 0.2020 (tpt) REVERT: C 82 ASP cc_start: 0.8191 (m-30) cc_final: 0.7284 (t70) REVERT: C 103 LYS cc_start: 0.8405 (tppt) cc_final: 0.8080 (tppt) REVERT: C 124 TRP cc_start: 0.8271 (t60) cc_final: 0.8041 (t60) REVERT: C 154 PHE cc_start: 0.8500 (m-10) cc_final: 0.8121 (m-80) REVERT: C 282 ILE cc_start: 0.6886 (tp) cc_final: 0.5901 (pt) REVERT: D 47 LEU cc_start: 0.4172 (OUTLIER) cc_final: 0.3731 (tp) REVERT: D 116 GLU cc_start: 0.9114 (tp30) cc_final: 0.8744 (tp30) REVERT: D 157 MET cc_start: 0.8541 (ptm) cc_final: 0.7692 (ppp) REVERT: D 174 TYR cc_start: 0.8101 (t80) cc_final: 0.7225 (t80) REVERT: D 210 GLN cc_start: 0.8396 (tp40) cc_final: 0.7828 (mm110) REVERT: D 219 GLU cc_start: 0.8532 (tp30) cc_final: 0.7977 (pm20) REVERT: D 242 TYR cc_start: 0.6555 (t80) cc_final: 0.5367 (m-80) outliers start: 67 outliers final: 40 residues processed: 528 average time/residue: 0.2761 time to fit residues: 218.6450 Evaluate side-chains 530 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 481 time to evaluate : 1.743 ------------------------------------------------------------------------------- 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 124 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 168 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 410 ASN 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 684 TYR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 209 LYS 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 289 VAL Chi-restraints excluded: chain B residue 317 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 583 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 145 ILE 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 240 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 111 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 GLN A 410 ASN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 147 GLN B 312 GLN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN B 646 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.144341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.102273 restraints weight = 32469.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.105698 restraints weight = 15714.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.107893 restraints weight = 9324.208| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 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 = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.6258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16386 Z= 0.157 Angle : 0.723 13.513 22134 Z= 0.367 Chirality : 0.046 0.356 2360 Planarity : 0.004 0.051 2818 Dihedral : 9.577 146.496 2242 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.50 % Allowed : 28.67 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.19), residues: 1932 helix: 1.06 (0.15), residues: 1132 sheet: -0.73 (0.49), residues: 106 loop : 0.15 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP C 44 HIS 0.006 0.001 HIS A 255 PHE 0.035 0.002 PHE D 168 TYR 0.033 0.001 TYR C 105 ARG 0.011 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 871) hydrogen bonds : angle 5.15708 ( 2571) covalent geometry : bond 0.00357 (16386) covalent geometry : angle 0.72316 (22134) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 492 time to evaluate : 1.712 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: 0.8814 (tptp) cc_final: 0.8557 (tppt) REVERT: A 40 TYR cc_start: 0.8879 (t80) cc_final: 0.8523 (t80) REVERT: A 65 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7546 (mp0) REVERT: A 119 GLU cc_start: 0.8505 (mp0) cc_final: 0.8223 (mp0) REVERT: A 144 MET cc_start: 0.8610 (mtm) cc_final: 0.8300 (mtm) REVERT: A 214 LYS cc_start: 0.8145 (mmtt) cc_final: 0.7828 (mmtt) REVERT: A 221 LYS cc_start: 0.8151 (mttt) cc_final: 0.7903 (mttt) REVERT: A 232 ASN cc_start: 0.8751 (m-40) cc_final: 0.8224 (m110) REVERT: A 250 TYR cc_start: 0.8613 (m-80) cc_final: 0.8370 (m-80) REVERT: A 263 ASP cc_start: 0.8121 (m-30) cc_final: 0.7902 (m-30) REVERT: A 290 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8232 (mt-10) REVERT: A 348 MET cc_start: 0.8151 (tmm) cc_final: 0.6894 (tmm) REVERT: A 352 GLU cc_start: 0.7935 (mt-10) cc_final: 0.6979 (mt-10) REVERT: A 359 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.7939 (ttp) REVERT: A 361 GLN cc_start: 0.8612 (tp40) cc_final: 0.8283 (tp40) REVERT: A 384 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7560 (pm20) REVERT: A 389 SER cc_start: 0.9203 (OUTLIER) cc_final: 0.8877 (p) REVERT: A 406 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8085 (t70) REVERT: A 446 ARG cc_start: 0.7446 (mmm160) cc_final: 0.7143 (mmm160) REVERT: A 493 MET cc_start: 0.8998 (tmm) cc_final: 0.8748 (tmm) REVERT: A 583 SER cc_start: 0.9148 (t) cc_final: 0.8736 (t) REVERT: A 590 SER cc_start: 0.9082 (t) cc_final: 0.8746 (p) REVERT: A 615 MET cc_start: 0.9154 (mmp) cc_final: 0.8191 (mmp) REVERT: A 640 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8726 (tpp) REVERT: A 684 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.8188 (m-80) REVERT: A 686 ARG cc_start: 0.8552 (mtp85) cc_final: 0.8272 (mtp85) REVERT: B 65 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7892 (mp0) REVERT: B 119 GLU cc_start: 0.8882 (mp0) cc_final: 0.8566 (mp0) REVERT: B 136 LYS cc_start: 0.9216 (mmmm) cc_final: 0.8807 (mmmt) REVERT: B 184 ARG cc_start: 0.8968 (tpp80) cc_final: 0.8551 (mmm-85) REVERT: B 209 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8176 (tptt) REVERT: B 218 ASN cc_start: 0.9039 (m110) cc_final: 0.8459 (t0) REVERT: B 243 ARG cc_start: 0.6753 (OUTLIER) cc_final: 0.6509 (tmm-80) REVERT: B 257 ASP cc_start: 0.8600 (m-30) cc_final: 0.8182 (m-30) REVERT: B 287 LYS cc_start: 0.9165 (tptt) cc_final: 0.8738 (tppt) REVERT: B 290 GLU cc_start: 0.8259 (pp20) cc_final: 0.8028 (pp20) REVERT: B 374 SER cc_start: 0.9502 (t) cc_final: 0.9110 (m) REVERT: B 394 TYR cc_start: 0.9094 (m-80) cc_final: 0.8732 (m-80) REVERT: B 398 ASP cc_start: 0.8229 (t0) cc_final: 0.7954 (t0) REVERT: B 434 ASP cc_start: 0.8646 (m-30) cc_final: 0.8267 (m-30) REVERT: B 467 ASN cc_start: 0.8961 (t0) cc_final: 0.8638 (t0) REVERT: B 493 MET cc_start: 0.9565 (tmm) cc_final: 0.9225 (tmm) REVERT: B 546 LEU cc_start: 0.9449 (tp) cc_final: 0.9201 (tp) REVERT: B 570 MET cc_start: 0.8256 (mtt) cc_final: 0.7876 (mtt) REVERT: B 571 TYR cc_start: 0.8653 (t80) cc_final: 0.8195 (t80) REVERT: B 602 GLU cc_start: 0.8042 (pp20) cc_final: 0.6905 (pp20) REVERT: B 627 LYS cc_start: 0.8930 (tttt) cc_final: 0.8465 (tttt) REVERT: B 628 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8084 (mp0) REVERT: C 55 TYR cc_start: 0.5498 (t80) cc_final: 0.5278 (t80) REVERT: C 56 MET cc_start: 0.2394 (tpt) cc_final: 0.2046 (tpt) REVERT: C 82 ASP cc_start: 0.8214 (m-30) cc_final: 0.7407 (t70) REVERT: C 103 LYS cc_start: 0.8427 (tppt) cc_final: 0.8081 (tppt) REVERT: C 124 TRP cc_start: 0.8293 (t60) cc_final: 0.8004 (t60) REVERT: C 127 GLN cc_start: 0.9071 (tp40) cc_final: 0.8751 (mm110) REVERT: C 154 PHE cc_start: 0.8491 (m-10) cc_final: 0.8116 (m-80) REVERT: C 200 ILE cc_start: 0.8665 (pt) cc_final: 0.8423 (tp) REVERT: C 204 TYR cc_start: 0.7614 (t80) cc_final: 0.7154 (t80) REVERT: D 109 PHE cc_start: 0.6585 (m-80) cc_final: 0.5953 (m-10) REVERT: D 116 GLU cc_start: 0.9110 (tp30) cc_final: 0.8733 (tp30) REVERT: D 157 MET cc_start: 0.8438 (ptm) cc_final: 0.7556 (ppp) REVERT: D 174 TYR cc_start: 0.8087 (t80) cc_final: 0.7178 (t80) REVERT: D 210 GLN cc_start: 0.8388 (tp40) cc_final: 0.7807 (mm110) REVERT: D 219 GLU cc_start: 0.8457 (tp30) cc_final: 0.7914 (pm20) outliers start: 60 outliers final: 44 residues processed: 519 average time/residue: 0.2861 time to fit residues: 220.6218 Evaluate side-chains 528 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 476 time to evaluate : 1.846 ------------------------------------------------------------------------------- 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 124 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 168 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 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 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 684 TYR Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE 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 392 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 145 ILE 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 240 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 137 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 135 optimal weight: 0.4980 chunk 148 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 147 GLN B 312 GLN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.143423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.101795 restraints weight = 32725.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.105235 restraints weight = 15525.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.107424 restraints weight = 9159.395| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 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 = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.6402 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= 0.178 Angle : 0.741 13.730 22134 Z= 0.379 Chirality : 0.046 0.351 2360 Planarity : 0.004 0.065 2818 Dihedral : 9.577 142.730 2242 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.26 % Allowed : 29.08 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.19), residues: 1932 helix: 1.03 (0.16), residues: 1130 sheet: -0.58 (0.43), residues: 136 loop : 0.18 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 44 HIS 0.006 0.001 HIS A 255 PHE 0.035 0.002 PHE D 168 TYR 0.033 0.002 TYR C 105 ARG 0.010 0.001 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.04177 ( 871) hydrogen bonds : angle 5.21085 ( 2571) covalent geometry : bond 0.00406 (16386) covalent geometry : angle 0.74146 (22134) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 477 time to evaluate : 1.925 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: 0.8785 (tptp) cc_final: 0.8525 (tppt) REVERT: A 40 TYR cc_start: 0.8876 (t80) cc_final: 0.8516 (t80) REVERT: A 65 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7635 (mp0) REVERT: A 119 GLU cc_start: 0.8538 (mp0) cc_final: 0.8251 (mp0) REVERT: A 144 MET cc_start: 0.8621 (mtm) cc_final: 0.8336 (mtm) REVERT: A 214 LYS cc_start: 0.8257 (mmtt) cc_final: 0.7980 (mmtt) REVERT: A 232 ASN cc_start: 0.8724 (m-40) cc_final: 0.8145 (m110) REVERT: A 250 TYR cc_start: 0.8637 (m-80) cc_final: 0.8395 (m-80) REVERT: A 290 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8238 (mt-10) REVERT: A 348 MET cc_start: 0.8090 (tmm) cc_final: 0.7650 (tmm) REVERT: A 359 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8077 (ttp) REVERT: A 361 GLN cc_start: 0.8621 (tp40) cc_final: 0.8260 (tp40) REVERT: A 384 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7594 (pm20) REVERT: A 389 SER cc_start: 0.9209 (OUTLIER) cc_final: 0.8892 (p) REVERT: A 406 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.8139 (t70) REVERT: A 446 ARG cc_start: 0.7568 (mmm160) cc_final: 0.7223 (mmm160) REVERT: A 493 MET cc_start: 0.8986 (tmm) cc_final: 0.8734 (tmm) REVERT: A 583 SER cc_start: 0.9161 (t) cc_final: 0.8752 (t) REVERT: A 590 SER cc_start: 0.9129 (t) cc_final: 0.8832 (p) REVERT: A 640 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8738 (tpp) REVERT: A 684 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.8232 (m-80) REVERT: A 686 ARG cc_start: 0.8607 (mtp85) cc_final: 0.8338 (mtp85) REVERT: B 119 GLU cc_start: 0.8952 (mp0) cc_final: 0.8604 (mp0) REVERT: B 136 LYS cc_start: 0.9224 (mmmm) cc_final: 0.8969 (mmmt) REVERT: B 184 ARG cc_start: 0.8969 (tpp80) cc_final: 0.8526 (mmm-85) REVERT: B 209 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8212 (tptt) REVERT: B 214 LYS cc_start: 0.8461 (mtmm) cc_final: 0.8257 (mtmm) REVERT: B 218 ASN cc_start: 0.9031 (OUTLIER) cc_final: 0.8441 (t0) REVERT: B 243 ARG cc_start: 0.6769 (OUTLIER) cc_final: 0.6543 (tmm-80) REVERT: B 257 ASP cc_start: 0.8643 (m-30) cc_final: 0.8236 (m-30) REVERT: B 374 SER cc_start: 0.9508 (t) cc_final: 0.9194 (t) REVERT: B 394 TYR cc_start: 0.9096 (m-80) cc_final: 0.8718 (m-80) REVERT: B 398 ASP cc_start: 0.8218 (t0) cc_final: 0.7933 (t0) REVERT: B 434 ASP cc_start: 0.8646 (m-30) cc_final: 0.8218 (m-30) REVERT: B 483 GLU cc_start: 0.9354 (mp0) cc_final: 0.8991 (pm20) REVERT: B 493 MET cc_start: 0.9601 (tmm) cc_final: 0.9243 (tmm) REVERT: B 570 MET cc_start: 0.8267 (mtt) cc_final: 0.7921 (mtt) REVERT: B 571 TYR cc_start: 0.8653 (t80) cc_final: 0.8253 (t80) REVERT: B 602 GLU cc_start: 0.7410 (pp20) cc_final: 0.6786 (pp20) REVERT: B 615 MET cc_start: 0.9129 (mmm) cc_final: 0.8824 (mmm) REVERT: B 627 LYS cc_start: 0.8942 (tttt) cc_final: 0.8463 (tttt) REVERT: B 628 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8098 (mp0) REVERT: C 27 LYS cc_start: 0.7928 (pttp) cc_final: 0.7714 (pttm) REVERT: C 45 LYS cc_start: 0.9290 (tptp) cc_final: 0.9067 (pttp) REVERT: C 55 TYR cc_start: 0.5600 (t80) cc_final: 0.5110 (t80) REVERT: C 56 MET cc_start: 0.2358 (tpt) cc_final: 0.1886 (tpt) REVERT: C 82 ASP cc_start: 0.8374 (m-30) cc_final: 0.7665 (t70) REVERT: C 103 LYS cc_start: 0.8417 (tppt) cc_final: 0.8055 (tppt) REVERT: C 124 TRP cc_start: 0.8305 (t60) cc_final: 0.8023 (t60) REVERT: C 127 GLN cc_start: 0.9126 (tp40) cc_final: 0.8817 (mm110) REVERT: C 154 PHE cc_start: 0.8473 (m-10) cc_final: 0.8077 (m-80) REVERT: C 178 PHE cc_start: 0.8775 (m-80) cc_final: 0.8506 (m-80) REVERT: C 186 GLN cc_start: 0.7195 (mp10) cc_final: 0.6902 (pm20) REVERT: C 200 ILE cc_start: 0.8689 (pt) cc_final: 0.8431 (tp) REVERT: C 204 TYR cc_start: 0.7654 (t80) cc_final: 0.7247 (t80) REVERT: C 269 MET cc_start: 0.8702 (tpt) cc_final: 0.8364 (tmm) REVERT: D 47 LEU cc_start: 0.4565 (OUTLIER) cc_final: 0.3820 (tp) REVERT: D 116 GLU cc_start: 0.9090 (tp30) cc_final: 0.8689 (tp30) REVERT: D 157 MET cc_start: 0.8430 (ptm) cc_final: 0.7539 (ppp) REVERT: D 174 TYR cc_start: 0.8117 (t80) cc_final: 0.7247 (t80) REVERT: D 210 GLN cc_start: 0.8406 (tp40) cc_final: 0.7839 (mm110) REVERT: D 219 GLU cc_start: 0.8420 (tp30) cc_final: 0.7922 (pm20) REVERT: D 242 TYR cc_start: 0.6626 (t80) cc_final: 0.5345 (m-80) outliers start: 56 outliers final: 42 residues processed: 502 average time/residue: 0.2789 time to fit residues: 208.8085 Evaluate side-chains 516 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 464 time to evaluate : 1.705 ------------------------------------------------------------------------------- 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 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 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 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 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 684 TYR Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE 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 392 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 151 ILE 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 240 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 81 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 179 optimal weight: 9.9990 chunk 190 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 180 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** 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 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN B 320 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.144955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.103472 restraints weight = 32374.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.106831 restraints weight = 15433.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.109008 restraints weight = 9213.978| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- 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: 0.7776 moved from start: 0.6529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16386 Z= 0.155 Angle : 0.737 13.453 22134 Z= 0.377 Chirality : 0.046 0.333 2360 Planarity : 0.004 0.058 2818 Dihedral : 9.361 142.141 2242 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.15 % Allowed : 29.08 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.19), residues: 1932 helix: 1.01 (0.16), residues: 1132 sheet: -0.74 (0.42), residues: 138 loop : 0.16 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP C 44 HIS 0.006 0.001 HIS A 255 PHE 0.035 0.002 PHE D 168 TYR 0.023 0.001 TYR B 471 ARG 0.016 0.001 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.04087 ( 871) hydrogen bonds : angle 5.19198 ( 2571) covalent geometry : bond 0.00356 (16386) covalent geometry : angle 0.73676 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6397.73 seconds wall clock time: 112 minutes 28.79 seconds (6748.79 seconds total)