Starting phenix.real_space_refine on Fri Jul 3 19:53:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byv_45045/07_2026/9byv_45045_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byv_45045/07_2026/9byv_45045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9byv_45045/07_2026/9byv_45045_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byv_45045/07_2026/9byv_45045_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9byv_45045/07_2026/9byv_45045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byv_45045/07_2026/9byv_45045.map" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.01, per 1000 atoms: 0.19 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: 0.99 Conformation dependent library (CDL) restraints added in 682.6 milliseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 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: 2.60 Time building geometry restraints manager: 1.35 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=" O3B TTP B 801 " pdb=" PG TTP B 801 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" O3B TTP A 803 " pdb=" PG TTP A 803 " ideal model delta sigma weight residual 1.748 1.610 0.138 2.00e-02 2.50e+03 4.77e+01 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=" O3A TTP A 803 " pdb=" PB TTP A 803 " ideal model delta sigma weight residual 1.675 1.605 0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.15e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21523 2.09 - 4.18: 529 4.18 - 6.27: 65 6.27 - 8.36: 8 8.36 - 10.45: 9 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 - 25.06: 9090 25.06 - 50.11: 653 50.11 - 75.17: 127 75.17 - 100.22: 26 100.22 - 125.28: 2 Dihedral angle restraints: 9898 sinusoidal: 4140 harmonic: 5758 Sorted by residual: dihedral pdb=" O4' GDP A 802 " pdb=" C1' GDP A 802 " pdb=" N9 GDP A 802 " pdb=" C8 GDP A 802 " ideal model delta sinusoidal sigma weight residual 27.02 -98.26 125.28 1 2.00e+01 2.50e-03 3.79e+01 dihedral pdb=" O4' GDP B 804 " pdb=" C1' GDP B 804 " pdb=" N9 GDP B 804 " pdb=" C8 GDP B 804 " ideal model delta sinusoidal sigma weight residual 27.02 -95.57 122.59 1 2.00e+01 2.50e-03 3.69e+01 dihedral pdb=" C VAL C 125 " pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual -122.00 -134.31 12.31 0 2.50e+00 1.60e-01 2.43e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2142 0.094 - 0.187: 185 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 3.060 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 3.060 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 3.060 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.991 3.060 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: 1.060 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.350 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 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 0.139 16386 Z= 0.334 Angle : 0.788 10.454 22134 Z= 0.472 Chirality : 0.058 0.468 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.675 125.279 6202 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.40 % Allowed : 15.27 % Favored : 83.33 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.18), residues: 1932 helix: 0.58 (0.14), residues: 1151 sheet: 0.46 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 196 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE C 168 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.33 (16386) covalent geometry : angle 0.78779 / 0.47 (22134) hydrogen bonds : bond 0.15422 / 9.51 ( 871) hydrogen bonds : angle 6.51813 / 4.65 ( 2571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 864 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8484 (m) REVERT: A 116 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7111 (mt-10) REVERT: A 179 LEU cc_start: 0.9121 (tp) cc_final: 0.8784 (tp) REVERT: A 232 ASN cc_start: 0.8164 (OUTLIER) cc_final: 0.7964 (m-40) REVERT: A 362 ASP cc_start: 0.6467 (m-30) cc_final: 0.6136 (m-30) REVERT: A 490 THR cc_start: 0.8604 (m) cc_final: 0.8295 (m) REVERT: A 576 LEU cc_start: 0.8938 (mt) cc_final: 0.8557 (mt) REVERT: A 606 TYR cc_start: 0.7504 (m-80) cc_final: 0.7289 (m-10) REVERT: B 81 PHE cc_start: 0.7719 (m-80) cc_final: 0.7493 (m-80) REVERT: B 179 LEU cc_start: 0.8956 (tp) cc_final: 0.8687 (tp) REVERT: B 186 ILE cc_start: 0.9326 (mt) cc_final: 0.8995 (mt) REVERT: B 190 MET cc_start: 0.8126 (mtm) cc_final: 0.7906 (mtm) REVERT: B 288 PHE cc_start: 0.8003 (t80) cc_final: 0.7671 (t80) REVERT: B 362 ASP cc_start: 0.7308 (m-30) cc_final: 0.6983 (m-30) REVERT: B 373 ILE cc_start: 0.9064 (mt) cc_final: 0.8800 (mt) REVERT: B 420 MET cc_start: 0.7976 (mmm) cc_final: 0.7741 (mmm) REVERT: B 436 LEU cc_start: 0.9237 (mt) cc_final: 0.8922 (mt) REVERT: B 460 SER cc_start: 0.9036 (t) cc_final: 0.8771 (p) REVERT: B 471 TYR cc_start: 0.8196 (t80) cc_final: 0.7492 (t80) REVERT: B 546 LEU cc_start: 0.8958 (mt) cc_final: 0.8449 (mt) REVERT: B 550 MET cc_start: 0.8033 (mtm) cc_final: 0.7706 (mtp) REVERT: B 584 ILE cc_start: 0.8946 (tp) cc_final: 0.8731 (tp) REVERT: B 612 TYR cc_start: 0.7224 (m-80) cc_final: 0.6873 (m-80) REVERT: C 286 VAL cc_start: 0.4799 (t) cc_final: 0.4033 (p) REVERT: D 89 VAL cc_start: 0.5044 (t) cc_final: 0.4267 (t) REVERT: D 126 LYS cc_start: 0.3277 (OUTLIER) cc_final: 0.2611 (tttt) REVERT: D 246 LEU cc_start: 0.5231 (mt) cc_final: 0.4712 (tp) REVERT: D 287 LEU cc_start: 0.4919 (mt) cc_final: 0.4464 (tp) outliers start: 24 outliers final: 9 residues processed: 877 average time/residue: 0.1188 time to fit residues: 153.2866 Evaluate side-chains 624 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 612 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 126 LYS Chi-restraints excluded: chain D residue 127 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN A 312 GLN A 365 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN B 312 GLN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN B 338 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN C 101 HIS C 107 ASN C 127 GLN D 71 ASN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN D 181 GLN D 186 GLN D 201 HIS D 210 GLN D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.145266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.101621 restraints weight = 31689.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.105348 restraints weight = 14891.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.107707 restraints weight = 8685.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.109154 restraints weight = 6001.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.110030 restraints weight = 4679.953| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (14 function evaluations) r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 16386 Z= 0.225 Angle : 0.681 9.538 22134 Z= 0.355 Chirality : 0.046 0.293 2360 Planarity : 0.004 0.047 2818 Dihedral : 9.851 131.996 2311 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 4.43 % Allowed : 19.58 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.19), residues: 1932 helix: 1.42 (0.15), residues: 1132 sheet: -0.39 (0.46), residues: 114 loop : 0.53 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 686 TYR 0.020 0.002 TYR C 247 PHE 0.033 0.002 PHE D 168 TRP 0.015 0.002 TRP C 44 HIS 0.021 0.002 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.22 (16386) covalent geometry : angle 0.68058 / 0.36 (22134) hydrogen bonds : bond 0.04754 / 2.92 ( 871) hydrogen bonds : angle 5.15759 / 3.67 ( 2571) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 637 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8802 (tptp) cc_final: 0.8389 (tppt) REVERT: A 40 TYR cc_start: 0.8938 (t80) cc_final: 0.8684 (t80) REVERT: A 76 ASP cc_start: 0.8483 (m-30) cc_final: 0.8140 (m-30) REVERT: A 119 GLU cc_start: 0.8471 (mp0) cc_final: 0.8256 (mp0) REVERT: A 232 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8206 (m-40) REVERT: A 250 TYR cc_start: 0.8704 (m-80) cc_final: 0.7987 (m-80) REVERT: A 263 ASP cc_start: 0.7799 (m-30) cc_final: 0.7487 (m-30) REVERT: A 290 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8210 (mt-10) REVERT: A 317 MET cc_start: 0.8782 (ptp) cc_final: 0.8448 (ptp) REVERT: A 348 MET cc_start: 0.8208 (tmm) cc_final: 0.7830 (tmm) REVERT: A 384 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7611 (pm20) REVERT: A 394 TYR cc_start: 0.8827 (m-80) cc_final: 0.8619 (m-80) REVERT: A 406 ASP cc_start: 0.8277 (m-30) cc_final: 0.8026 (t0) REVERT: A 446 ARG cc_start: 0.7530 (mmm160) cc_final: 0.6860 (mmm160) REVERT: A 452 ARG cc_start: 0.9011 (ttp80) cc_final: 0.8718 (ttt-90) REVERT: A 583 SER cc_start: 0.8964 (m) cc_final: 0.8738 (t) REVERT: A 606 TYR cc_start: 0.8466 (m-80) cc_final: 0.8206 (m-10) REVERT: A 640 MET cc_start: 0.9346 (OUTLIER) cc_final: 0.8901 (tpp) REVERT: A 667 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8812 (tt) REVERT: B 136 LYS cc_start: 0.9162 (mmmm) cc_final: 0.8721 (mmtt) REVERT: B 182 ILE cc_start: 0.9513 (mt) cc_final: 0.9304 (mp) REVERT: B 218 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8512 (t0) REVERT: B 221 LYS cc_start: 0.9195 (mttm) cc_final: 0.8919 (mmtm) REVERT: B 236 TYR cc_start: 0.9104 (t80) cc_final: 0.8853 (t80) REVERT: B 274 ARG cc_start: 0.8233 (ttm-80) cc_final: 0.7655 (ttm-80) REVERT: B 308 LYS cc_start: 0.9071 (mtpt) cc_final: 0.8727 (mtmm) REVERT: B 322 MET cc_start: 0.9182 (tpp) cc_final: 0.8734 (tpp) REVERT: B 420 MET cc_start: 0.8935 (mmm) cc_final: 0.8684 (mmm) REVERT: B 471 TYR cc_start: 0.9050 (t80) cc_final: 0.8296 (t80) REVERT: B 546 LEU cc_start: 0.9533 (mt) cc_final: 0.9127 (mt) REVERT: B 627 LYS cc_start: 0.8955 (tttt) cc_final: 0.8533 (ttpt) REVERT: C 44 TRP cc_start: 0.8352 (t-100) cc_final: 0.8048 (t-100) REVERT: C 68 GLU cc_start: 0.8672 (mp0) cc_final: 0.7882 (tm-30) REVERT: C 72 THR cc_start: 0.9147 (OUTLIER) cc_final: 0.8868 (t) REVERT: C 76 ILE cc_start: 0.9119 (mt) cc_final: 0.8907 (pt) REVERT: C 112 LEU cc_start: 0.6439 (mt) cc_final: 0.6185 (mt) REVERT: C 124 TRP cc_start: 0.8379 (t60) cc_final: 0.8121 (t60) REVERT: C 154 PHE cc_start: 0.8796 (t80) cc_final: 0.8555 (t80) REVERT: C 269 MET cc_start: 0.8652 (tpt) cc_final: 0.8307 (tmm) REVERT: D 47 LEU cc_start: 0.4921 (mt) cc_final: 0.4358 (tp) REVERT: D 59 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7570 (tt) REVERT: D 174 TYR cc_start: 0.7543 (t80) cc_final: 0.6679 (t80) REVERT: D 198 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7264 (mm-30) REVERT: D 260 ILE cc_start: 0.7967 (mt) cc_final: 0.7716 (pt) outliers start: 76 outliers final: 31 residues processed: 670 average time/residue: 0.1070 time to fit residues: 108.3437 Evaluate side-chains 579 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 541 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 314 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 421 GLU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 240 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 164 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 182 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 147 GLN B 312 GLN B 320 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 192 ASN C 234 GLN C 249 GLN D 91 ASN D 181 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.145987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.102010 restraints weight = 32207.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.105684 restraints weight = 15130.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.107991 restraints weight = 8912.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109300 restraints weight = 6205.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.110216 restraints weight = 4923.163| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16386 Z= 0.176 Angle : 0.644 14.118 22134 Z= 0.335 Chirality : 0.045 0.363 2360 Planarity : 0.003 0.040 2818 Dihedral : 9.323 134.659 2300 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 4.55 % Allowed : 21.62 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.19), residues: 1932 helix: 1.39 (0.15), residues: 1134 sheet: -0.15 (0.41), residues: 146 loop : 0.57 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 274 TYR 0.029 0.002 TYR C 142 PHE 0.038 0.002 PHE D 172 TRP 0.007 0.001 TRP C 124 HIS 0.007 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (16386) covalent geometry : angle 0.64430 / 0.34 (22134) hydrogen bonds : bond 0.04261 / 2.64 ( 871) hydrogen bonds : angle 5.03320 / 3.57 ( 2571) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 589 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8768 (tptp) cc_final: 0.8328 (tppt) REVERT: A 40 TYR cc_start: 0.8905 (t80) cc_final: 0.8534 (t80) REVERT: A 76 ASP cc_start: 0.8398 (m-30) cc_final: 0.8110 (m-30) REVERT: A 119 GLU cc_start: 0.8475 (mp0) cc_final: 0.8185 (mp0) REVERT: A 232 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.8157 (m-40) REVERT: A 250 TYR cc_start: 0.8697 (m-80) cc_final: 0.8352 (m-80) REVERT: A 263 ASP cc_start: 0.8080 (m-30) cc_final: 0.7805 (m-30) REVERT: A 290 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8232 (mt-10) REVERT: A 348 MET cc_start: 0.8220 (tmm) cc_final: 0.7767 (tmm) REVERT: A 361 GLN cc_start: 0.8751 (tt0) cc_final: 0.8306 (tp40) REVERT: A 384 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7512 (pm20) REVERT: A 394 TYR cc_start: 0.8867 (m-80) cc_final: 0.8464 (m-80) REVERT: A 406 ASP cc_start: 0.8312 (m-30) cc_final: 0.8059 (t0) REVERT: A 446 ARG cc_start: 0.7488 (mmm160) cc_final: 0.6877 (mmm160) REVERT: A 452 ARG cc_start: 0.9018 (ttp80) cc_final: 0.8735 (ttt-90) REVERT: A 590 SER cc_start: 0.9084 (t) cc_final: 0.8147 (p) REVERT: A 598 MET cc_start: 0.8451 (mtm) cc_final: 0.8215 (mtm) REVERT: A 640 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8829 (tpp) REVERT: A 646 GLN cc_start: 0.8816 (pt0) cc_final: 0.8264 (pm20) REVERT: A 654 PHE cc_start: 0.9272 (t80) cc_final: 0.9050 (t80) REVERT: B 65 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8009 (mp0) REVERT: B 82 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8954 (mttp) REVERT: B 174 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7546 (tt0) REVERT: B 218 ASN cc_start: 0.8968 (m110) cc_final: 0.8520 (t0) REVERT: B 236 TYR cc_start: 0.9026 (t80) cc_final: 0.8817 (t80) REVERT: B 257 ASP cc_start: 0.8612 (m-30) cc_final: 0.8361 (m-30) REVERT: B 296 LYS cc_start: 0.8537 (mmmt) cc_final: 0.8284 (mmmt) REVERT: B 308 LYS cc_start: 0.9131 (mtpt) cc_final: 0.8734 (ptpt) REVERT: B 434 ASP cc_start: 0.8599 (m-30) cc_final: 0.8216 (m-30) REVERT: B 467 ASN cc_start: 0.9087 (t0) cc_final: 0.8747 (t0) REVERT: B 471 TYR cc_start: 0.9068 (t80) cc_final: 0.8439 (t80) REVERT: B 493 MET cc_start: 0.9626 (tmm) cc_final: 0.9318 (tmm) REVERT: B 546 LEU cc_start: 0.9524 (mt) cc_final: 0.9165 (mt) REVERT: B 550 MET cc_start: 0.8254 (mtm) cc_final: 0.8032 (mtp) REVERT: B 586 TYR cc_start: 0.9090 (m-80) cc_final: 0.8506 (m-80) REVERT: B 602 GLU cc_start: 0.7869 (pp20) cc_final: 0.7559 (pp20) REVERT: B 627 LYS cc_start: 0.8904 (tttt) cc_final: 0.8512 (ttpt) REVERT: B 628 GLU cc_start: 0.8466 (mt-10) cc_final: 0.7936 (mp0) REVERT: C 68 GLU cc_start: 0.8927 (mp0) cc_final: 0.8120 (tm-30) REVERT: C 124 TRP cc_start: 0.8212 (t60) cc_final: 0.7989 (t60) REVERT: C 137 MET cc_start: 0.6811 (mpp) cc_final: 0.6555 (mpp) REVERT: C 154 PHE cc_start: 0.8923 (t80) cc_final: 0.8607 (t80) REVERT: C 184 LEU cc_start: 0.7079 (mt) cc_final: 0.6426 (tt) REVERT: C 198 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8438 (mm-30) REVERT: C 240 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8776 (mm) REVERT: C 269 MET cc_start: 0.8690 (tpt) cc_final: 0.8337 (tmm) REVERT: C 285 ILE cc_start: 0.8886 (mp) cc_final: 0.8682 (tp) REVERT: D 47 LEU cc_start: 0.5160 (mt) cc_final: 0.4756 (tp) REVERT: D 59 LEU cc_start: 0.7017 (pp) cc_final: 0.6039 (tt) REVERT: D 80 HIS cc_start: 0.7563 (m90) cc_final: 0.7217 (m90) REVERT: D 112 LEU cc_start: 0.4558 (tp) cc_final: 0.4257 (tt) REVERT: D 174 TYR cc_start: 0.7397 (t80) cc_final: 0.6552 (t80) REVERT: D 198 GLU cc_start: 0.7710 (mm-30) cc_final: 0.6686 (tp30) REVERT: D 266 LYS cc_start: 0.7422 (mtpt) cc_final: 0.7196 (mmtt) outliers start: 78 outliers final: 46 residues processed: 628 average time/residue: 0.1136 time to fit residues: 108.7344 Evaluate side-chains 589 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 538 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 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 392 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 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 29 optimal weight: 0.5980 chunk 157 optimal weight: 0.9990 chunk 168 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 185 optimal weight: 8.9990 chunk 191 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 312 GLN B 320 ASN C 127 GLN C 192 ASN D 181 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.144420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.100813 restraints weight = 32280.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.104345 restraints weight = 15072.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.106726 restraints weight = 8840.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.108113 restraints weight = 6129.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109047 restraints weight = 4837.347| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4909 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= 0.171 Angle : 0.623 9.892 22134 Z= 0.324 Chirality : 0.044 0.368 2360 Planarity : 0.003 0.044 2818 Dihedral : 9.013 136.832 2300 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.31 % Allowed : 22.49 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.19), residues: 1932 helix: 1.39 (0.15), residues: 1136 sheet: -0.72 (0.45), residues: 118 loop : 0.42 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 686 TYR 0.018 0.001 TYR A 606 PHE 0.034 0.002 PHE D 168 TRP 0.008 0.001 TRP A 623 HIS 0.005 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (16386) covalent geometry : angle 0.62341 / 0.32 (22134) hydrogen bonds : bond 0.04072 / 2.54 ( 871) hydrogen bonds : angle 4.95170 / 3.53 ( 2571) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 576 time to evaluate : 0.606 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: 0.8787 (tptp) cc_final: 0.8418 (tppt) REVERT: A 40 TYR cc_start: 0.8923 (t80) cc_final: 0.8452 (t80) REVERT: A 76 ASP cc_start: 0.8394 (m-30) cc_final: 0.8181 (m-30) REVERT: A 119 GLU cc_start: 0.8481 (mp0) cc_final: 0.8202 (mp0) REVERT: A 144 MET cc_start: 0.8775 (mtm) cc_final: 0.8420 (mtm) REVERT: A 214 LYS cc_start: 0.8107 (mmtt) cc_final: 0.7885 (mmtt) REVERT: A 232 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8102 (m-40) REVERT: A 250 TYR cc_start: 0.8683 (m-80) cc_final: 0.8329 (m-80) REVERT: A 263 ASP cc_start: 0.8127 (m-30) cc_final: 0.7863 (m-30) REVERT: A 290 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8240 (mt-10) REVERT: A 348 MET cc_start: 0.8275 (tmm) cc_final: 0.7781 (tmm) REVERT: A 384 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.6613 (pm20) REVERT: A 394 TYR cc_start: 0.8922 (m-80) cc_final: 0.8424 (m-80) REVERT: A 427 LYS cc_start: 0.9085 (tppp) cc_final: 0.8666 (tppp) REVERT: A 446 ARG cc_start: 0.7501 (mmm160) cc_final: 0.7168 (mmm160) REVERT: A 505 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8458 (mt-10) REVERT: A 590 SER cc_start: 0.9061 (t) cc_final: 0.8559 (p) REVERT: A 640 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8826 (tpp) REVERT: A 654 PHE cc_start: 0.9299 (t80) cc_final: 0.9083 (t80) REVERT: A 684 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.7966 (m-80) REVERT: B 82 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8917 (mttp) REVERT: B 108 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8833 (p) REVERT: B 174 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7531 (tt0) REVERT: B 214 LYS cc_start: 0.8505 (mtmm) cc_final: 0.8282 (mttm) REVERT: B 218 ASN cc_start: 0.8993 (m110) cc_final: 0.8564 (t0) REVERT: B 236 TYR cc_start: 0.9051 (t80) cc_final: 0.8810 (t80) REVERT: B 257 ASP cc_start: 0.8674 (m-30) cc_final: 0.8461 (m-30) REVERT: B 308 LYS cc_start: 0.9181 (mtpt) cc_final: 0.8950 (ptpt) REVERT: B 374 SER cc_start: 0.9510 (t) cc_final: 0.9176 (t) REVERT: B 394 TYR cc_start: 0.9123 (m-80) cc_final: 0.8710 (m-80) REVERT: B 434 ASP cc_start: 0.8543 (m-30) cc_final: 0.8147 (m-30) REVERT: B 467 ASN cc_start: 0.9105 (t0) cc_final: 0.8749 (t0) REVERT: B 471 TYR cc_start: 0.9056 (t80) cc_final: 0.8453 (t80) REVERT: B 493 MET cc_start: 0.9610 (tmm) cc_final: 0.9244 (tmm) REVERT: B 546 LEU cc_start: 0.9524 (mt) cc_final: 0.9151 (mt) REVERT: B 586 TYR cc_start: 0.9129 (m-80) cc_final: 0.8578 (m-80) REVERT: B 602 GLU cc_start: 0.8012 (pp20) cc_final: 0.7268 (pp20) REVERT: B 627 LYS cc_start: 0.8866 (tttt) cc_final: 0.8371 (tttt) REVERT: B 628 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8055 (mp0) REVERT: C 21 PHE cc_start: 0.8538 (m-80) cc_final: 0.8245 (t80) REVERT: C 43 THR cc_start: 0.6457 (OUTLIER) cc_final: 0.6182 (p) REVERT: C 68 GLU cc_start: 0.8857 (mp0) cc_final: 0.8184 (tm-30) REVERT: C 103 LYS cc_start: 0.8232 (tppt) cc_final: 0.7919 (tppt) REVERT: C 107 ASN cc_start: 0.8975 (m110) cc_final: 0.8698 (m110) REVERT: C 124 TRP cc_start: 0.8253 (t60) cc_final: 0.8033 (t60) REVERT: C 154 PHE cc_start: 0.8993 (t80) cc_final: 0.8682 (t80) REVERT: C 174 TYR cc_start: 0.6944 (OUTLIER) cc_final: 0.6413 (t80) REVERT: C 186 GLN cc_start: 0.7256 (mp10) cc_final: 0.6738 (mp10) REVERT: C 198 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8448 (mm-30) REVERT: C 269 MET cc_start: 0.8671 (tpt) cc_final: 0.8343 (tmm) REVERT: C 274 ASP cc_start: 0.8108 (p0) cc_final: 0.7691 (p0) REVERT: D 59 LEU cc_start: 0.7023 (pp) cc_final: 0.6145 (tt) REVERT: D 116 GLU cc_start: 0.9141 (tp30) cc_final: 0.8790 (tp30) REVERT: D 174 TYR cc_start: 0.7615 (t80) cc_final: 0.6735 (t80) REVERT: D 198 GLU cc_start: 0.7665 (mm-30) cc_final: 0.6317 (tp30) REVERT: D 232 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6223 (mt) outliers start: 74 outliers final: 47 residues processed: 608 average time/residue: 0.1124 time to fit residues: 104.3072 Evaluate side-chains 556 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 500 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 108 THR 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 232 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 411 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain 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 174 TYR Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 240 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 115 optimal weight: 0.5980 chunk 168 optimal weight: 5.9990 chunk 157 optimal weight: 10.0000 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN B 147 GLN B 312 GLN B 320 ASN B 387 GLN B 410 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 107 ASN C 127 GLN C 132 GLN C 181 GLN D 25 ASN D 91 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.139087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.095305 restraints weight = 33289.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.098750 restraints weight = 15831.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.100958 restraints weight = 9463.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.102349 restraints weight = 6616.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.103148 restraints weight = 5241.691| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 16386 Z= 0.301 Angle : 0.716 8.989 22134 Z= 0.372 Chirality : 0.047 0.380 2360 Planarity : 0.004 0.049 2818 Dihedral : 8.917 141.895 2297 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 5.54 % Allowed : 22.32 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.19), residues: 1932 helix: 1.25 (0.15), residues: 1148 sheet: -0.86 (0.45), residues: 114 loop : 0.30 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 235 TYR 0.016 0.002 TYR A 626 PHE 0.035 0.002 PHE D 168 TRP 0.014 0.002 TRP A 623 HIS 0.009 0.002 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00665 / 0.30 (16386) covalent geometry : angle 0.71622 / 0.37 (22134) hydrogen bonds : bond 0.04269 / 2.66 ( 871) hydrogen bonds : angle 5.11533 / 3.64 ( 2571) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 507 time to evaluate : 0.465 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: 0.8856 (tptp) cc_final: 0.8500 (tppt) REVERT: A 40 TYR cc_start: 0.9007 (t80) cc_final: 0.8603 (t80) REVERT: A 119 GLU cc_start: 0.8622 (mp0) cc_final: 0.8347 (mp0) REVERT: A 214 LYS cc_start: 0.8318 (mmtt) cc_final: 0.8059 (mmtm) REVERT: A 250 TYR cc_start: 0.8663 (m-80) cc_final: 0.8314 (m-80) REVERT: A 263 ASP cc_start: 0.8097 (m-30) cc_final: 0.7858 (m-30) REVERT: A 290 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8268 (mt-10) REVERT: A 348 MET cc_start: 0.8269 (tmm) cc_final: 0.7158 (tmm) REVERT: A 352 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7256 (mt-10) REVERT: A 381 LEU cc_start: 0.9256 (tp) cc_final: 0.9049 (tp) REVERT: A 384 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7126 (pm20) REVERT: A 389 SER cc_start: 0.9388 (OUTLIER) cc_final: 0.8883 (p) REVERT: A 427 LYS cc_start: 0.9108 (tppp) cc_final: 0.8687 (tppp) REVERT: A 446 ARG cc_start: 0.7600 (mmm160) cc_final: 0.7220 (mmm160) REVERT: A 590 SER cc_start: 0.9141 (t) cc_final: 0.8730 (p) REVERT: A 603 GLU cc_start: 0.8539 (tt0) cc_final: 0.8304 (tt0) REVERT: A 640 MET cc_start: 0.9271 (OUTLIER) cc_final: 0.8959 (tpp) REVERT: A 684 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.7936 (m-80) REVERT: B 82 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8869 (mttm) REVERT: B 174 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7489 (tt0) REVERT: B 218 ASN cc_start: 0.8968 (OUTLIER) cc_final: 0.8500 (t0) REVERT: B 236 TYR cc_start: 0.9201 (t80) cc_final: 0.8884 (t80) REVERT: B 257 ASP cc_start: 0.8667 (m-30) cc_final: 0.8412 (m-30) REVERT: B 276 LYS cc_start: 0.8607 (mmmt) cc_final: 0.8357 (mmmt) REVERT: B 349 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9217 (tp) REVERT: B 394 TYR cc_start: 0.9221 (m-80) cc_final: 0.8805 (m-80) REVERT: B 434 ASP cc_start: 0.8610 (m-30) cc_final: 0.8244 (m-30) REVERT: B 467 ASN cc_start: 0.9242 (t0) cc_final: 0.8942 (t0) REVERT: B 493 MET cc_start: 0.9610 (tmm) cc_final: 0.9247 (tmm) REVERT: B 586 TYR cc_start: 0.9129 (m-80) cc_final: 0.8548 (m-80) REVERT: B 595 MET cc_start: 0.8654 (mmm) cc_final: 0.8126 (mmm) REVERT: B 602 GLU cc_start: 0.7994 (pp20) cc_final: 0.7347 (pp20) REVERT: B 627 LYS cc_start: 0.8956 (tttt) cc_final: 0.8312 (ttpp) REVERT: B 628 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8156 (mp0) REVERT: C 44 TRP cc_start: 0.8338 (t-100) cc_final: 0.8074 (t-100) REVERT: C 55 TYR cc_start: 0.6261 (t80) cc_final: 0.5531 (t80) REVERT: C 68 GLU cc_start: 0.8763 (mp0) cc_final: 0.8096 (tm-30) REVERT: C 103 LYS cc_start: 0.8405 (tppt) cc_final: 0.8108 (tppt) REVERT: C 105 TYR cc_start: 0.8745 (m-80) cc_final: 0.8395 (m-80) REVERT: C 107 ASN cc_start: 0.8968 (m-40) cc_final: 0.8648 (m-40) REVERT: C 118 ILE cc_start: 0.7526 (mm) cc_final: 0.6505 (mm) REVERT: C 122 PHE cc_start: 0.9348 (m-80) cc_final: 0.8797 (m-80) REVERT: C 124 TRP cc_start: 0.8333 (t60) cc_final: 0.8102 (t60) REVERT: C 154 PHE cc_start: 0.9091 (t80) cc_final: 0.8712 (t80) REVERT: C 269 MET cc_start: 0.8774 (tpt) cc_final: 0.8425 (tmm) REVERT: C 285 ILE cc_start: 0.8821 (mp) cc_final: 0.8597 (tp) REVERT: D 29 PHE cc_start: 0.7288 (t80) cc_final: 0.6384 (t80) REVERT: D 59 LEU cc_start: 0.6916 (pp) cc_final: 0.6060 (tt) REVERT: D 116 GLU cc_start: 0.9128 (tp30) cc_final: 0.8769 (tp30) REVERT: D 174 TYR cc_start: 0.7910 (t80) cc_final: 0.7120 (t80) REVERT: D 232 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6514 (mt) outliers start: 95 outliers final: 65 residues processed: 556 average time/residue: 0.1152 time to fit residues: 97.6436 Evaluate side-chains 538 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 465 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL 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 168 VAL Chi-restraints excluded: chain A residue 216 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 349 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE 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 392 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 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 46 TYR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 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 215 LYS Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 262 TYR Chi-restraints excluded: chain D residue 318 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 0.5980 chunk 183 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 136 optimal weight: 0.0070 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 GLN ** 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** ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN B 147 GLN B 312 GLN B 320 ASN B 387 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN D 28 GLN D 181 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.144388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.101922 restraints weight = 32589.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.105448 restraints weight = 15332.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.107712 restraints weight = 8984.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.109060 restraints weight = 6213.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.109997 restraints weight = 4894.096| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (13 function evaluations) r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.5690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16386 Z= 0.139 Angle : 0.651 11.036 22134 Z= 0.333 Chirality : 0.044 0.395 2360 Planarity : 0.003 0.052 2818 Dihedral : 8.265 138.914 2295 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.96 % Allowed : 25.00 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.19), residues: 1932 helix: 1.28 (0.15), residues: 1148 sheet: -0.91 (0.45), residues: 118 loop : 0.22 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 235 TYR 0.030 0.001 TYR C 173 PHE 0.037 0.002 PHE C 21 TRP 0.004 0.001 TRP C 30 HIS 0.006 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (16386) covalent geometry : angle 0.65099 / 0.33 (22134) hydrogen bonds : bond 0.03966 / 2.48 ( 871) hydrogen bonds : angle 4.93623 / 3.53 ( 2571) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 535 time to evaluate : 0.571 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: 0.8857 (tptp) cc_final: 0.8577 (tppt) REVERT: A 40 TYR cc_start: 0.8923 (t80) cc_final: 0.8458 (t80) REVERT: A 65 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7989 (mp0) REVERT: A 119 GLU cc_start: 0.8511 (mp0) cc_final: 0.8241 (mp0) REVERT: A 144 MET cc_start: 0.8610 (mtm) cc_final: 0.8258 (mtm) REVERT: A 214 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7719 (mmtt) REVERT: A 221 LYS cc_start: 0.8260 (mttt) cc_final: 0.7987 (mttt) REVERT: A 232 ASN cc_start: 0.8930 (m-40) cc_final: 0.8148 (m-40) REVERT: A 263 ASP cc_start: 0.8118 (m-30) cc_final: 0.7864 (m-30) REVERT: A 290 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8251 (mt-10) REVERT: A 348 MET cc_start: 0.8311 (tmm) cc_final: 0.7137 (tmm) REVERT: A 352 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7222 (mt-10) REVERT: A 384 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7416 (pm20) REVERT: A 406 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.7952 (t70) REVERT: A 410 ASN cc_start: 0.8149 (OUTLIER) cc_final: 0.7786 (t160) REVERT: A 446 ARG cc_start: 0.7429 (mmm160) cc_final: 0.7022 (mmm160) REVERT: A 505 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8341 (mt-10) REVERT: A 590 SER cc_start: 0.9101 (t) cc_final: 0.8361 (p) REVERT: A 640 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8889 (tpp) REVERT: A 684 TYR cc_start: 0.8286 (OUTLIER) cc_final: 0.7883 (m-80) REVERT: B 82 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8865 (mttp) REVERT: B 174 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7473 (tt0) REVERT: B 184 ARG cc_start: 0.8911 (tpp-160) cc_final: 0.8572 (mmm-85) REVERT: B 218 ASN cc_start: 0.8948 (m110) cc_final: 0.8498 (t0) REVERT: B 236 TYR cc_start: 0.9097 (t80) cc_final: 0.8860 (t80) REVERT: B 257 ASP cc_start: 0.8562 (m-30) cc_final: 0.8197 (m-30) REVERT: B 374 SER cc_start: 0.9511 (t) cc_final: 0.9122 (m) REVERT: B 398 ASP cc_start: 0.8143 (t0) cc_final: 0.7878 (t0) REVERT: B 421 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7905 (pt0) REVERT: B 434 ASP cc_start: 0.8651 (m-30) cc_final: 0.8246 (m-30) REVERT: B 467 ASN cc_start: 0.9101 (t0) cc_final: 0.8703 (t0) REVERT: B 493 MET cc_start: 0.9438 (tmm) cc_final: 0.9227 (tmm) REVERT: B 586 TYR cc_start: 0.9062 (m-80) cc_final: 0.8502 (m-80) REVERT: B 595 MET cc_start: 0.8551 (mmm) cc_final: 0.8153 (mmm) REVERT: B 602 GLU cc_start: 0.8035 (pp20) cc_final: 0.7329 (pp20) REVERT: B 613 TYR cc_start: 0.8923 (t80) cc_final: 0.8720 (t80) REVERT: B 627 LYS cc_start: 0.8938 (tttt) cc_final: 0.8413 (tttt) REVERT: B 628 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8124 (mp0) REVERT: C 56 MET cc_start: 0.3171 (tpt) cc_final: 0.2689 (tpt) REVERT: C 68 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8156 (tm-30) REVERT: C 103 LYS cc_start: 0.8389 (tppt) cc_final: 0.8101 (tppt) REVERT: C 107 ASN cc_start: 0.8977 (m-40) cc_final: 0.8551 (m-40) REVERT: C 118 ILE cc_start: 0.7615 (mm) cc_final: 0.7404 (mm) REVERT: C 124 TRP cc_start: 0.8231 (t60) cc_final: 0.7994 (t60) REVERT: C 127 GLN cc_start: 0.9082 (tp40) cc_final: 0.8769 (mm110) REVERT: C 154 PHE cc_start: 0.9168 (t80) cc_final: 0.8779 (t80) REVERT: C 174 TYR cc_start: 0.6988 (OUTLIER) cc_final: 0.6467 (t80) REVERT: C 269 MET cc_start: 0.8834 (tpt) cc_final: 0.8463 (tmm) REVERT: C 282 ILE cc_start: 0.6699 (tp) cc_final: 0.6051 (mm) REVERT: C 285 ILE cc_start: 0.8763 (mp) cc_final: 0.8491 (tp) REVERT: D 59 LEU cc_start: 0.6715 (pp) cc_final: 0.5802 (tt) REVERT: D 80 HIS cc_start: 0.7535 (m90) cc_final: 0.7319 (m90) REVERT: D 112 LEU cc_start: 0.3792 (tt) cc_final: 0.3395 (tt) REVERT: D 116 GLU cc_start: 0.9119 (tp30) cc_final: 0.8768 (tp30) REVERT: D 178 PHE cc_start: 0.8667 (m-10) cc_final: 0.8280 (m-80) REVERT: D 232 LEU cc_start: 0.6904 (OUTLIER) cc_final: 0.6325 (mt) outliers start: 68 outliers final: 39 residues processed: 568 average time/residue: 0.1049 time to fit residues: 91.9357 Evaluate side-chains 548 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 499 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 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 640 MET Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 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 46 TYR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 240 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 200 ILE Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 240 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 74 optimal weight: 0.1980 chunk 105 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 45 optimal weight: 0.5980 chunk 68 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 370 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN B 131 ASN B 147 GLN B 312 GLN B 320 ASN B 387 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.142218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.099416 restraints weight = 32898.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.102861 restraints weight = 15667.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.104988 restraints weight = 9345.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.106313 restraints weight = 6592.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.107336 restraints weight = 5241.516| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 16386 Z= 0.237 Angle : 0.700 11.773 22134 Z= 0.362 Chirality : 0.046 0.425 2360 Planarity : 0.004 0.049 2818 Dihedral : 8.218 142.580 2293 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.66 % Allowed : 25.87 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.19), residues: 1932 helix: 1.20 (0.15), residues: 1151 sheet: -0.90 (0.46), residues: 118 loop : 0.17 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 235 TYR 0.026 0.002 TYR C 105 PHE 0.036 0.002 PHE D 168 TRP 0.010 0.001 TRP A 623 HIS 0.007 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.24 (16386) covalent geometry : angle 0.69988 / 0.36 (22134) hydrogen bonds : bond 0.04044 / 2.50 ( 871) hydrogen bonds : angle 5.00229 / 3.56 ( 2571) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 495 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8853 (tptp) cc_final: 0.8578 (tppt) REVERT: A 40 TYR cc_start: 0.8973 (t80) cc_final: 0.8517 (t80) REVERT: A 119 GLU cc_start: 0.8579 (mp0) cc_final: 0.8311 (mp0) REVERT: A 144 MET cc_start: 0.8688 (mtm) cc_final: 0.8397 (mtm) REVERT: A 173 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9169 (mt) REVERT: A 214 LYS cc_start: 0.8346 (mmtt) cc_final: 0.7871 (mmtm) REVERT: A 232 ASN cc_start: 0.8918 (m-40) cc_final: 0.8508 (m-40) REVERT: A 250 TYR cc_start: 0.8665 (m-80) cc_final: 0.8282 (m-80) REVERT: A 263 ASP cc_start: 0.8096 (m-30) cc_final: 0.7864 (m-30) REVERT: A 290 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8346 (mt-10) REVERT: A 348 MET cc_start: 0.8205 (tmm) cc_final: 0.6981 (tmm) REVERT: A 352 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7177 (mt-10) REVERT: A 384 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7571 (pm20) REVERT: A 389 SER cc_start: 0.9376 (OUTLIER) cc_final: 0.8925 (p) REVERT: A 406 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.7671 (t70) REVERT: A 427 LYS cc_start: 0.9080 (tppp) cc_final: 0.8694 (tppp) REVERT: A 446 ARG cc_start: 0.7564 (mmm160) cc_final: 0.7227 (mmm160) REVERT: A 590 SER cc_start: 0.9198 (t) cc_final: 0.8810 (p) REVERT: A 640 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8966 (tpp) REVERT: A 684 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7935 (m-80) REVERT: B 40 TYR cc_start: 0.9194 (t80) cc_final: 0.8631 (t80) REVERT: B 82 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8927 (mttp) REVERT: B 95 MET cc_start: 0.8935 (tpp) cc_final: 0.8727 (mmm) REVERT: B 174 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7499 (tt0) REVERT: B 184 ARG cc_start: 0.8940 (tpp-160) cc_final: 0.8596 (mmm-85) REVERT: B 218 ASN cc_start: 0.9017 (m110) cc_final: 0.8496 (t0) REVERT: B 236 TYR cc_start: 0.9218 (t80) cc_final: 0.8899 (t80) REVERT: B 257 ASP cc_start: 0.8725 (m-30) cc_final: 0.8355 (m-30) REVERT: B 276 LYS cc_start: 0.8675 (mmmt) cc_final: 0.8388 (mppt) REVERT: B 374 SER cc_start: 0.9556 (t) cc_final: 0.9245 (t) REVERT: B 398 ASP cc_start: 0.8243 (t0) cc_final: 0.7982 (t0) REVERT: B 434 ASP cc_start: 0.8632 (m-30) cc_final: 0.8246 (m-30) REVERT: B 467 ASN cc_start: 0.9237 (t0) cc_final: 0.8853 (t0) REVERT: B 493 MET cc_start: 0.9584 (tmm) cc_final: 0.9248 (tmm) REVERT: B 550 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8301 (mtp) REVERT: B 571 TYR cc_start: 0.8739 (t80) cc_final: 0.8312 (t80) REVERT: B 586 TYR cc_start: 0.9087 (m-80) cc_final: 0.8502 (m-80) REVERT: B 595 MET cc_start: 0.8650 (mmm) cc_final: 0.8201 (mmm) REVERT: B 602 GLU cc_start: 0.8025 (pp20) cc_final: 0.7393 (pp20) REVERT: B 627 LYS cc_start: 0.8962 (tttt) cc_final: 0.8450 (ttpt) REVERT: B 628 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8247 (mp0) REVERT: C 68 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8063 (tm-30) REVERT: C 82 ASP cc_start: 0.8155 (m-30) cc_final: 0.7514 (t0) REVERT: C 103 LYS cc_start: 0.8392 (tppt) cc_final: 0.8053 (tppt) REVERT: C 107 ASN cc_start: 0.8967 (m-40) cc_final: 0.8532 (m-40) REVERT: C 127 GLN cc_start: 0.9098 (tp40) cc_final: 0.8790 (mm-40) REVERT: C 154 PHE cc_start: 0.9172 (t80) cc_final: 0.8689 (t80) REVERT: C 174 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.6761 (t80) REVERT: C 269 MET cc_start: 0.8821 (tpt) cc_final: 0.8449 (tmm) REVERT: C 282 ILE cc_start: 0.6875 (tp) cc_final: 0.6142 (mm) REVERT: D 59 LEU cc_start: 0.6548 (pp) cc_final: 0.5572 (tt) REVERT: D 80 HIS cc_start: 0.7603 (m90) cc_final: 0.7288 (m90) REVERT: D 116 GLU cc_start: 0.9032 (tp30) cc_final: 0.8635 (tp30) REVERT: D 149 ASP cc_start: 0.7750 (t0) cc_final: 0.7042 (p0) REVERT: D 174 TYR cc_start: 0.8048 (t80) cc_final: 0.7162 (t80) REVERT: D 210 GLN cc_start: 0.8319 (tp40) cc_final: 0.7956 (tp40) REVERT: D 219 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.6930 (pm20) REVERT: D 232 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6485 (mt) REVERT: D 242 TYR cc_start: 0.6730 (t80) cc_final: 0.5538 (m-80) outliers start: 80 outliers final: 50 residues processed: 530 average time/residue: 0.1056 time to fit residues: 85.4696 Evaluate side-chains 524 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 462 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 173 LEU Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 406 ASP 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 526 GLU 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 653 SER Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 194 LYS 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 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 421 GLU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 240 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 151 optimal weight: 20.0000 chunk 81 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN A 387 GLN A 410 ASN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 147 GLN B 312 GLN B 320 ASN B 387 GLN C 98 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.144324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.102132 restraints weight = 32735.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.105664 restraints weight = 15407.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.107820 restraints weight = 9108.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.109304 restraints weight = 6306.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.110154 restraints weight = 4939.524| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (17 function evaluations) r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.6129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16386 Z= 0.147 Angle : 0.693 10.088 22134 Z= 0.354 Chirality : 0.046 0.382 2360 Planarity : 0.004 0.052 2818 Dihedral : 7.908 140.689 2293 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.67 % Allowed : 27.21 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.19), residues: 1932 helix: 1.24 (0.15), residues: 1149 sheet: -0.44 (0.42), residues: 138 loop : 0.20 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 225 TYR 0.033 0.001 TYR B 613 PHE 0.035 0.002 PHE D 168 TRP 0.035 0.001 TRP C 44 HIS 0.006 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (16386) covalent geometry : angle 0.69282 / 0.35 (22134) hydrogen bonds : bond 0.03955 / 2.46 ( 871) hydrogen bonds : angle 4.97233 / 3.56 ( 2571) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 514 time to evaluate : 0.641 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: 0.8843 (tptp) cc_final: 0.8569 (tppt) REVERT: A 40 TYR cc_start: 0.8923 (t80) cc_final: 0.8442 (t80) REVERT: A 119 GLU cc_start: 0.8527 (mp0) cc_final: 0.8251 (mp0) REVERT: A 144 MET cc_start: 0.8613 (mtm) cc_final: 0.8307 (mtm) REVERT: A 173 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9117 (mt) REVERT: A 214 LYS cc_start: 0.8322 (mmtt) cc_final: 0.7904 (mmtt) REVERT: A 232 ASN cc_start: 0.8862 (m-40) cc_final: 0.8079 (m-40) REVERT: A 250 TYR cc_start: 0.8607 (m-80) cc_final: 0.8301 (m-80) REVERT: A 263 ASP cc_start: 0.8178 (m-30) cc_final: 0.7945 (m-30) REVERT: A 290 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8217 (mt-10) REVERT: A 348 MET cc_start: 0.8278 (tmm) cc_final: 0.7093 (tmm) REVERT: A 352 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7167 (mt-10) REVERT: A 384 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7388 (pm20) REVERT: A 406 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.7664 (t70) REVERT: A 410 ASN cc_start: 0.8056 (OUTLIER) cc_final: 0.7727 (t160) REVERT: A 446 ARG cc_start: 0.7458 (mmm160) cc_final: 0.7149 (mmm160) REVERT: A 505 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8383 (mt-10) REVERT: A 583 SER cc_start: 0.9091 (t) cc_final: 0.8697 (t) REVERT: A 590 SER cc_start: 0.9213 (t) cc_final: 0.8782 (p) REVERT: A 639 ASP cc_start: 0.9078 (m-30) cc_final: 0.8369 (m-30) REVERT: A 640 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8679 (tpp) REVERT: A 655 THR cc_start: 0.8956 (m) cc_final: 0.8532 (t) REVERT: A 684 TYR cc_start: 0.8310 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: B 65 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7793 (mp0) REVERT: B 82 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8881 (mttp) REVERT: B 174 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7458 (tt0) REVERT: B 184 ARG cc_start: 0.8906 (tpp-160) cc_final: 0.8611 (mmm-85) REVERT: B 218 ASN cc_start: 0.8996 (m110) cc_final: 0.8518 (t0) REVERT: B 236 TYR cc_start: 0.9197 (t80) cc_final: 0.8923 (t80) REVERT: B 257 ASP cc_start: 0.8473 (m-30) cc_final: 0.8143 (m-30) REVERT: B 374 SER cc_start: 0.9546 (t) cc_final: 0.9169 (m) REVERT: B 398 ASP cc_start: 0.8093 (t0) cc_final: 0.7850 (t0) REVERT: B 421 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7815 (pt0) REVERT: B 434 ASP cc_start: 0.8667 (m-30) cc_final: 0.8245 (m-30) REVERT: B 467 ASN cc_start: 0.9150 (t0) cc_final: 0.8745 (t0) REVERT: B 483 GLU cc_start: 0.9343 (mp0) cc_final: 0.9060 (pm20) REVERT: B 493 MET cc_start: 0.9533 (tmm) cc_final: 0.9230 (tmm) REVERT: B 586 TYR cc_start: 0.9021 (m-80) cc_final: 0.8762 (m-80) REVERT: B 595 MET cc_start: 0.8553 (mmm) cc_final: 0.8219 (mmm) REVERT: B 602 GLU cc_start: 0.8135 (pp20) cc_final: 0.7395 (pp20) REVERT: B 627 LYS cc_start: 0.8933 (tttt) cc_final: 0.8402 (tttt) REVERT: B 628 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8223 (mp0) REVERT: C 21 PHE cc_start: 0.8407 (t80) cc_final: 0.8167 (t80) REVERT: C 68 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8147 (tm-30) REVERT: C 82 ASP cc_start: 0.8173 (m-30) cc_final: 0.7483 (t70) REVERT: C 103 LYS cc_start: 0.8443 (tppt) cc_final: 0.8061 (tppt) REVERT: C 107 ASN cc_start: 0.8955 (m-40) cc_final: 0.8471 (m-40) REVERT: C 127 GLN cc_start: 0.9047 (tp40) cc_final: 0.8762 (mm-40) REVERT: C 154 PHE cc_start: 0.9168 (t80) cc_final: 0.8725 (t80) REVERT: C 174 TYR cc_start: 0.7086 (OUTLIER) cc_final: 0.6786 (t80) REVERT: C 200 ILE cc_start: 0.8524 (pt) cc_final: 0.8306 (tp) REVERT: D 59 LEU cc_start: 0.6496 (pp) cc_final: 0.5483 (tt) REVERT: D 80 HIS cc_start: 0.7618 (m90) cc_final: 0.7308 (m90) REVERT: D 116 GLU cc_start: 0.9073 (tp30) cc_final: 0.8715 (tp30) REVERT: D 146 GLN cc_start: 0.8373 (mm110) cc_final: 0.7881 (tt0) REVERT: D 157 MET cc_start: 0.8566 (ptm) cc_final: 0.7730 (ppp) REVERT: D 178 PHE cc_start: 0.8623 (m-10) cc_final: 0.8262 (m-80) REVERT: D 210 GLN cc_start: 0.8359 (tp40) cc_final: 0.7754 (mm110) REVERT: D 232 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6647 (mt) REVERT: D 259 PHE cc_start: 0.7511 (t80) cc_final: 0.6883 (t80) outliers start: 63 outliers final: 37 residues processed: 542 average time/residue: 0.1167 time to fit residues: 96.2617 Evaluate side-chains 545 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 497 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 115 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 173 LEU 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 599 GLU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 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 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 421 GLU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 68 GLU 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 231 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 240 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 ASN ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 147 GLN B 312 GLN B 320 ASN C 98 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.144440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.102991 restraints weight = 32461.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.106319 restraints weight = 15751.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.108472 restraints weight = 9494.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.109818 restraints weight = 6625.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.110592 restraints weight = 5245.674| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.6292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16386 Z= 0.150 Angle : 0.711 11.739 22134 Z= 0.363 Chirality : 0.046 0.384 2360 Planarity : 0.004 0.052 2818 Dihedral : 7.845 141.523 2293 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.38 % Allowed : 27.91 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.19), residues: 1932 helix: 1.22 (0.15), residues: 1147 sheet: -0.40 (0.43), residues: 138 loop : 0.19 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 235 TYR 0.033 0.001 TYR B 118 PHE 0.037 0.002 PHE D 168 TRP 0.032 0.001 TRP C 44 HIS 0.006 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (16386) covalent geometry : angle 0.71073 / 0.36 (22134) hydrogen bonds : bond 0.03891 / 2.41 ( 871) hydrogen bonds : angle 4.99630 / 3.57 ( 2571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 505 time to evaluate : 0.517 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: 0.8819 (tptp) cc_final: 0.8549 (tppt) REVERT: A 31 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8085 (mp0) REVERT: A 40 TYR cc_start: 0.8912 (t80) cc_final: 0.8445 (t80) REVERT: A 65 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8074 (mp0) REVERT: A 67 GLU cc_start: 0.8711 (mp0) cc_final: 0.8339 (pm20) REVERT: A 119 GLU cc_start: 0.8488 (mp0) cc_final: 0.8206 (mp0) REVERT: A 144 MET cc_start: 0.8634 (mtm) cc_final: 0.8339 (mtm) REVERT: A 148 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8577 (mp0) REVERT: A 173 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9152 (mt) REVERT: A 214 LYS cc_start: 0.8323 (mmtt) cc_final: 0.7909 (mmtt) REVERT: A 221 LYS cc_start: 0.8041 (mttt) cc_final: 0.7821 (mttt) REVERT: A 232 ASN cc_start: 0.8838 (m-40) cc_final: 0.8052 (m-40) REVERT: A 250 TYR cc_start: 0.8629 (m-80) cc_final: 0.8422 (m-80) REVERT: A 290 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8196 (mt-10) REVERT: A 348 MET cc_start: 0.8216 (tmm) cc_final: 0.7884 (tmm) REVERT: A 384 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7484 (pm20) REVERT: A 389 SER cc_start: 0.9295 (OUTLIER) cc_final: 0.8869 (p) REVERT: A 406 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.7620 (t70) REVERT: A 446 ARG cc_start: 0.7458 (mmm160) cc_final: 0.7154 (mmm160) REVERT: A 505 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8440 (mt-10) REVERT: A 590 SER cc_start: 0.9216 (t) cc_final: 0.8802 (p) REVERT: A 639 ASP cc_start: 0.9058 (m-30) cc_final: 0.8343 (m-30) REVERT: A 640 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8663 (tpp) REVERT: A 655 THR cc_start: 0.9000 (m) cc_final: 0.8540 (t) REVERT: B 82 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8829 (mttp) REVERT: B 174 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7450 (tt0) REVERT: B 184 ARG cc_start: 0.8899 (tpp-160) cc_final: 0.8601 (mmm-85) REVERT: B 218 ASN cc_start: 0.8968 (m110) cc_final: 0.8489 (t0) REVERT: B 236 TYR cc_start: 0.9192 (t80) cc_final: 0.8914 (t80) REVERT: B 257 ASP cc_start: 0.8462 (m-30) cc_final: 0.8162 (m-30) REVERT: B 276 LYS cc_start: 0.8847 (mmmt) cc_final: 0.8408 (mppt) REVERT: B 374 SER cc_start: 0.9545 (t) cc_final: 0.9219 (m) REVERT: B 396 ASP cc_start: 0.8210 (m-30) cc_final: 0.8008 (m-30) REVERT: B 398 ASP cc_start: 0.7992 (t0) cc_final: 0.7755 (t0) REVERT: B 421 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7762 (pt0) REVERT: B 467 ASN cc_start: 0.9106 (t0) cc_final: 0.8713 (t0) REVERT: B 493 MET cc_start: 0.9526 (tmm) cc_final: 0.9231 (tmm) REVERT: B 586 TYR cc_start: 0.8958 (m-80) cc_final: 0.8624 (m-80) REVERT: B 595 MET cc_start: 0.8537 (mmm) cc_final: 0.8175 (mmm) REVERT: B 602 GLU cc_start: 0.8114 (pp20) cc_final: 0.7174 (tm-30) REVERT: B 627 LYS cc_start: 0.8971 (tttt) cc_final: 0.8493 (tttt) REVERT: B 628 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8210 (mp0) REVERT: C 21 PHE cc_start: 0.8346 (t80) cc_final: 0.8006 (t80) REVERT: C 55 TYR cc_start: 0.5225 (t80) cc_final: 0.4704 (t80) REVERT: C 68 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8093 (tm-30) REVERT: C 82 ASP cc_start: 0.8242 (m-30) cc_final: 0.7416 (t70) REVERT: C 103 LYS cc_start: 0.8398 (tppt) cc_final: 0.7991 (tppt) REVERT: C 107 ASN cc_start: 0.8970 (m-40) cc_final: 0.8416 (m-40) REVERT: C 127 GLN cc_start: 0.8996 (tp40) cc_final: 0.8722 (mm-40) REVERT: C 154 PHE cc_start: 0.9112 (t80) cc_final: 0.8689 (t80) REVERT: C 174 TYR cc_start: 0.7303 (OUTLIER) cc_final: 0.6796 (t80) REVERT: C 200 ILE cc_start: 0.8541 (pt) cc_final: 0.8327 (tp) REVERT: D 59 LEU cc_start: 0.6422 (pp) cc_final: 0.5389 (tt) REVERT: D 80 HIS cc_start: 0.7727 (m90) cc_final: 0.7343 (m90) REVERT: D 116 GLU cc_start: 0.9046 (tp30) cc_final: 0.8669 (tp30) REVERT: D 146 GLN cc_start: 0.8402 (mm110) cc_final: 0.7873 (tt0) REVERT: D 157 MET cc_start: 0.8626 (ptm) cc_final: 0.8411 (ppp) REVERT: D 178 PHE cc_start: 0.8642 (m-10) cc_final: 0.8330 (m-80) REVERT: D 210 GLN cc_start: 0.8333 (tp40) cc_final: 0.7767 (mm110) REVERT: D 225 ARG cc_start: 0.8568 (mtm110) cc_final: 0.8304 (mtm180) REVERT: D 232 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6476 (mt) REVERT: D 242 TYR cc_start: 0.6477 (t80) cc_final: 0.5222 (m-80) REVERT: D 259 PHE cc_start: 0.7579 (t80) cc_final: 0.6938 (t80) outliers start: 58 outliers final: 37 residues processed: 528 average time/residue: 0.1145 time to fit residues: 92.5875 Evaluate side-chains 536 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 489 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 115 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 270 ASP 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 653 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE 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 421 GLU Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 77 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 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 240 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 189 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 147 GLN B 312 GLN B 320 ASN B 387 GLN B 410 ASN B 545 ASN C 98 ASN ** 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 = 0.3734 r_free = 0.3734 target = 0.139291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.096622 restraints weight = 33212.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.099956 restraints weight = 16122.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.101962 restraints weight = 9724.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.103360 restraints weight = 6947.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.104014 restraints weight = 5534.852| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 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 = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.6369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 16386 Z= 0.282 Angle : 0.798 13.279 22134 Z= 0.408 Chirality : 0.050 0.409 2360 Planarity : 0.004 0.052 2818 Dihedral : 8.074 144.604 2291 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.38 % Allowed : 28.32 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.19), residues: 1932 helix: 1.07 (0.15), residues: 1151 sheet: -0.72 (0.41), residues: 150 loop : 0.23 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 235 TYR 0.031 0.002 TYR B 118 PHE 0.033 0.002 PHE D 168 TRP 0.059 0.003 TRP C 44 HIS 0.007 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.28 (16386) covalent geometry : angle 0.79846 / 0.41 (22134) hydrogen bonds : bond 0.04182 / 2.61 ( 871) hydrogen bonds : angle 5.17080 / 3.70 ( 2571) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 488 time to evaluate : 0.546 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: 0.8863 (tptp) cc_final: 0.8586 (tppt) REVERT: A 40 TYR cc_start: 0.9001 (t80) cc_final: 0.8516 (t80) REVERT: A 65 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8275 (mp0) REVERT: A 119 GLU cc_start: 0.8582 (mp0) cc_final: 0.8328 (mp0) REVERT: A 144 MET cc_start: 0.8666 (mtm) cc_final: 0.8433 (mtm) REVERT: A 173 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9006 (mt) REVERT: A 214 LYS cc_start: 0.8438 (mmtt) cc_final: 0.8138 (mmtm) REVERT: A 232 ASN cc_start: 0.8905 (m-40) cc_final: 0.8528 (m-40) REVERT: A 250 TYR cc_start: 0.8671 (m-80) cc_final: 0.8412 (m-80) REVERT: A 290 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8223 (mt-10) REVERT: A 291 LEU cc_start: 0.9165 (mt) cc_final: 0.8955 (mp) REVERT: A 348 MET cc_start: 0.8170 (tmm) cc_final: 0.7791 (tmm) REVERT: A 384 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7104 (pm20) REVERT: A 389 SER cc_start: 0.9312 (OUTLIER) cc_final: 0.8840 (p) REVERT: A 406 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.7695 (t70) REVERT: A 427 LYS cc_start: 0.9054 (tppp) cc_final: 0.8633 (tppp) REVERT: A 446 ARG cc_start: 0.7739 (mmm160) cc_final: 0.7379 (mmm160) REVERT: A 590 SER cc_start: 0.9284 (t) cc_final: 0.8911 (p) REVERT: A 640 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8937 (tpp) REVERT: A 654 PHE cc_start: 0.9343 (t80) cc_final: 0.9134 (t80) REVERT: A 667 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8689 (tt) REVERT: B 65 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7772 (mp0) REVERT: B 82 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8895 (mttm) REVERT: B 174 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7482 (tt0) REVERT: B 184 ARG cc_start: 0.8945 (tpp-160) cc_final: 0.8570 (mmm-85) REVERT: B 218 ASN cc_start: 0.9038 (m110) cc_final: 0.8532 (t0) REVERT: B 236 TYR cc_start: 0.9220 (t80) cc_final: 0.8920 (t80) REVERT: B 257 ASP cc_start: 0.8536 (m-30) cc_final: 0.8270 (m-30) REVERT: B 276 LYS cc_start: 0.8909 (mmmt) cc_final: 0.8463 (mppt) REVERT: B 374 SER cc_start: 0.9605 (t) cc_final: 0.9220 (m) REVERT: B 398 ASP cc_start: 0.8182 (t0) cc_final: 0.7959 (t0) REVERT: B 467 ASN cc_start: 0.9216 (t0) cc_final: 0.8821 (t0) REVERT: B 483 GLU cc_start: 0.9351 (mp0) cc_final: 0.9005 (pm20) REVERT: B 493 MET cc_start: 0.9608 (tmm) cc_final: 0.9224 (tmm) REVERT: B 522 TYR cc_start: 0.8482 (m-10) cc_final: 0.8276 (m-10) REVERT: B 546 LEU cc_start: 0.9159 (mm) cc_final: 0.8939 (tp) REVERT: B 571 TYR cc_start: 0.8710 (t80) cc_final: 0.8273 (t80) REVERT: B 586 TYR cc_start: 0.9043 (m-80) cc_final: 0.8552 (m-80) REVERT: B 595 MET cc_start: 0.8647 (mmm) cc_final: 0.8219 (mmm) REVERT: B 602 GLU cc_start: 0.7922 (pp20) cc_final: 0.7219 (pp20) REVERT: B 627 LYS cc_start: 0.9012 (tttt) cc_final: 0.8561 (tttm) REVERT: B 628 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8256 (mp0) REVERT: C 21 PHE cc_start: 0.8352 (t80) cc_final: 0.7987 (t80) REVERT: C 45 LYS cc_start: 0.9246 (tptp) cc_final: 0.9013 (pttp) REVERT: C 55 TYR cc_start: 0.5779 (t80) cc_final: 0.5231 (t80) REVERT: C 82 ASP cc_start: 0.8614 (m-30) cc_final: 0.7998 (t70) REVERT: C 103 LYS cc_start: 0.8424 (tppt) cc_final: 0.8028 (tppt) REVERT: C 107 ASN cc_start: 0.8960 (m-40) cc_final: 0.8451 (m-40) REVERT: C 154 PHE cc_start: 0.9148 (t80) cc_final: 0.8679 (t80) REVERT: C 155 LYS cc_start: 0.8952 (mttt) cc_final: 0.8446 (pttt) REVERT: C 174 TYR cc_start: 0.7531 (OUTLIER) cc_final: 0.6945 (t80) REVERT: C 200 ILE cc_start: 0.8608 (pt) cc_final: 0.8392 (tp) REVERT: D 59 LEU cc_start: 0.6439 (pp) cc_final: 0.5449 (tt) REVERT: D 80 HIS cc_start: 0.7797 (m90) cc_final: 0.7356 (m90) REVERT: D 87 LYS cc_start: 0.7652 (mttm) cc_final: 0.7228 (mttm) REVERT: D 116 GLU cc_start: 0.9094 (tp30) cc_final: 0.8684 (tp30) REVERT: D 146 GLN cc_start: 0.8397 (mm110) cc_final: 0.7881 (tt0) REVERT: D 157 MET cc_start: 0.8840 (ptm) cc_final: 0.8262 (ppp) REVERT: D 174 TYR cc_start: 0.8296 (t80) cc_final: 0.7753 (t80) REVERT: D 210 GLN cc_start: 0.8490 (tp40) cc_final: 0.7993 (mm110) REVERT: D 232 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6863 (mt) REVERT: D 242 TYR cc_start: 0.6508 (t80) cc_final: 0.5235 (m-80) outliers start: 58 outliers final: 42 residues processed: 513 average time/residue: 0.1183 time to fit residues: 92.4793 Evaluate side-chains 528 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 477 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 173 LEU Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 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 653 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 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 421 GLU Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 232 LEU 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 93 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 0.0970 chunk 25 optimal weight: 4.9990 chunk 148 optimal weight: 0.0770 chunk 125 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 ASN ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 147 GLN B 312 GLN B 320 ASN B 387 GLN C 98 ASN 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 = 0.3803 r_free = 0.3803 target = 0.144146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.103275 restraints weight = 32171.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.106669 restraints weight = 15306.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.108856 restraints weight = 9307.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.110167 restraints weight = 6413.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.111236 restraints weight = 5044.518| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.6569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16386 Z= 0.148 Angle : 0.746 13.017 22134 Z= 0.381 Chirality : 0.047 0.393 2360 Planarity : 0.004 0.055 2818 Dihedral : 7.845 140.889 2291 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.91 % Allowed : 29.37 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.19), residues: 1932 helix: 1.03 (0.15), residues: 1148 sheet: -0.48 (0.42), residues: 136 loop : 0.14 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 235 TYR 0.036 0.001 TYR B 118 PHE 0.042 0.002 PHE D 92 TRP 0.057 0.002 TRP C 44 HIS 0.006 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (16386) covalent geometry : angle 0.74614 / 0.38 (22134) hydrogen bonds : bond 0.04064 / 2.54 ( 871) hydrogen bonds : angle 5.10843 / 3.65 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3020.61 seconds wall clock time: 53 minutes 13.90 seconds (3193.90 seconds total)