Starting phenix.real_space_refine on Thu Aug 6 15:08:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz5_45053/08_2026/9bz5_45053_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz5_45053/08_2026/9bz5_45053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bz5_45053/08_2026/9bz5_45053_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz5_45053/08_2026/9bz5_45053_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bz5_45053/08_2026/9bz5_45053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz5_45053/08_2026/9bz5_45053.map" } resolution = 3.93 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.67, per 1000 atoms: 0.23 Number of scatterers: 16038 At special positions: 0 Unit cell: (95.316, 134.862, 129.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 731.4 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: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.104A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.516A 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: 3.954A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.664A 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: 3.693A 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: 3.627A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.120A 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: 3.960A 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: 3.873A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.645A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.729A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.026A 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: 4.068A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.565A 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: 3.668A 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: 4.876A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.360A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.479A 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: 8.393A 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: 6.191A 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: 7.184A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.063A 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: 6.563A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.98 Time building geometry restraints manager: 1.75 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: 4788 1.34 - 1.46: 3077 1.46 - 1.58: 8340 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 4.82e+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 4.78e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.061 1.25e-02 6.40e+03 2.39e+01 bond pdb=" O3A TTP A 803 " pdb=" PB TTP A 803 " ideal model delta sigma weight residual 1.675 1.606 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.608 0.067 2.00e-02 2.50e+03 1.13e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21521 2.09 - 4.18: 532 4.18 - 6.27: 64 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 110.54 116.59 -6.05 1.36e+00 5.41e-01 1.98e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.10 -4.39 1.15e+00 7.56e-01 1.46e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.84 -4.34 1.23e+00 6.61e-01 1.24e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.69 -3.98 1.15e+00 7.56e-01 1.20e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.55 3.64 1.06e+00 8.90e-01 1.18e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.05: 9088 25.05 - 50.11: 655 50.11 - 75.16: 127 75.16 - 100.21: 26 100.21 - 125.26: 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 -98.24 125.26 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 -95.60 122.63 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 -134.26 12.26 0 2.50e+00 1.60e-01 2.40e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2136 0.094 - 0.187: 192 0.187 - 0.281: 28 0.281 - 0.374: 2 0.374 - 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 5.47e+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 4.62e+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 4.15e-02 2.76e+00 pdb=" N PRO D 75 " 0.072 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 1.12e-02 2.18e+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 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " 0.004 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=" CB TYR C 177 " 0.017 2.00e-02 2.50e+03 9.84e-03 1.94e+00 pdb=" CG TYR C 177 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR C 177 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR C 177 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C 177 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 177 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 177 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 177 " 0.010 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 129 2.51 - 3.11: 11556 3.11 - 3.70: 27042 3.70 - 4.30: 41544 4.30 - 4.90: 65416 Nonbonded interactions: 145687 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.012 3.040 ... (remaining 145682 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.910 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 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 10.451 22134 Z= 0.471 Chirality : 0.058 0.468 2360 Planarity : 0.003 0.042 2818 Dihedral : 17.681 125.263 6202 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.46 % Allowed : 15.21 % 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: 0.57 (0.18), residues: 1932 helix: 0.59 (0.14), residues: 1149 sheet: 0.47 (0.42), residues: 124 loop : 0.24 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 196 TYR 0.021 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 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 0.78757 / 0.47 (22134) hydrogen bonds : bond 0.15420 / 9.51 ( 871) hydrogen bonds : angle 6.51762 / 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 1013 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 988 time to evaluate : 0.605 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.8403 (mt) cc_final: 0.7793 (mp) REVERT: A 41 ILE cc_start: 0.8475 (mm) cc_final: 0.8014 (mm) REVERT: A 76 ASP cc_start: 0.8044 (m-30) cc_final: 0.7502 (m-30) REVERT: A 78 LYS cc_start: 0.8731 (tttt) cc_final: 0.8513 (ttmm) REVERT: A 121 ARG cc_start: 0.8688 (tpm-80) cc_final: 0.8411 (tpt170) REVERT: A 138 LYS cc_start: 0.8087 (mtpt) cc_final: 0.7869 (mtmm) REVERT: A 157 LEU cc_start: 0.9192 (tp) cc_final: 0.8621 (tp) REVERT: A 172 LEU cc_start: 0.9148 (mp) cc_final: 0.8753 (mp) REVERT: A 177 ASP cc_start: 0.8144 (t0) cc_final: 0.7587 (t0) REVERT: A 181 ASP cc_start: 0.7469 (m-30) cc_final: 0.7247 (m-30) REVERT: A 186 ILE cc_start: 0.9262 (mt) cc_final: 0.9061 (mt) REVERT: A 202 ASN cc_start: 0.8874 (t0) cc_final: 0.8311 (t0) REVERT: A 259 ASN cc_start: 0.7995 (m-40) cc_final: 0.7469 (m-40) REVERT: A 277 THR cc_start: 0.7734 (p) cc_final: 0.7416 (t) REVERT: A 300 VAL cc_start: 0.7802 (m) cc_final: 0.7530 (m) REVERT: A 319 MET cc_start: 0.7757 (tpp) cc_final: 0.7190 (tpp) REVERT: A 349 LEU cc_start: 0.8136 (mt) cc_final: 0.7884 (mt) REVERT: A 352 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6073 (mt-10) REVERT: A 362 ASP cc_start: 0.6228 (m-30) cc_final: 0.5855 (m-30) REVERT: A 367 VAL cc_start: 0.9081 (m) cc_final: 0.8571 (t) REVERT: A 378 PHE cc_start: 0.8932 (p90) cc_final: 0.8614 (p90) REVERT: A 435 SER cc_start: 0.9482 (p) cc_final: 0.8707 (t) REVERT: A 531 TYR cc_start: 0.7795 (m-80) cc_final: 0.7412 (m-10) REVERT: A 550 MET cc_start: 0.7109 (mtm) cc_final: 0.6004 (mtp) REVERT: A 573 SER cc_start: 0.9472 (p) cc_final: 0.9266 (t) REVERT: A 587 VAL cc_start: 0.8852 (t) cc_final: 0.8338 (t) REVERT: A 645 GLN cc_start: 0.7636 (tp40) cc_final: 0.7279 (tp40) REVERT: A 672 LEU cc_start: 0.8479 (mt) cc_final: 0.8207 (mt) REVERT: B 12 LEU cc_start: 0.8274 (mt) cc_final: 0.7834 (mt) REVERT: B 68 PHE cc_start: 0.8220 (p90) cc_final: 0.7738 (p90) REVERT: B 99 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8066 (mmtt) REVERT: B 121 ARG cc_start: 0.8725 (tpm170) cc_final: 0.8285 (tpp-160) REVERT: B 155 THR cc_start: 0.8585 (m) cc_final: 0.8307 (m) REVERT: B 177 ASP cc_start: 0.8204 (t0) cc_final: 0.7516 (t70) REVERT: B 202 ASN cc_start: 0.8759 (t0) cc_final: 0.8281 (t0) REVERT: B 204 SER cc_start: 0.8837 (m) cc_final: 0.8226 (t) REVERT: B 206 LEU cc_start: 0.8459 (mt) cc_final: 0.8229 (mt) REVERT: B 234 PHE cc_start: 0.8865 (m-80) cc_final: 0.8479 (m-10) REVERT: B 236 TYR cc_start: 0.7837 (t80) cc_final: 0.7610 (t80) REVERT: B 286 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6849 (m-30) REVERT: B 346 LEU cc_start: 0.8685 (mt) cc_final: 0.8466 (mt) REVERT: B 358 ILE cc_start: 0.9125 (mm) cc_final: 0.8892 (mm) REVERT: B 366 LYS cc_start: 0.8282 (ptpp) cc_final: 0.8070 (mtpt) REVERT: B 376 VAL cc_start: 0.9528 (t) cc_final: 0.9317 (m) REVERT: B 378 PHE cc_start: 0.8625 (p90) cc_final: 0.8390 (p90) REVERT: B 384 GLU cc_start: 0.9009 (pm20) cc_final: 0.8718 (pm20) REVERT: B 387 GLN cc_start: 0.7516 (mt0) cc_final: 0.7197 (mt0) REVERT: B 413 SER cc_start: 0.8525 (m) cc_final: 0.8268 (m) REVERT: B 442 THR cc_start: 0.8763 (p) cc_final: 0.8438 (m) REVERT: B 471 TYR cc_start: 0.8410 (t80) cc_final: 0.7492 (t80) REVERT: B 501 GLN cc_start: 0.7143 (tt0) cc_final: 0.6940 (tt0) REVERT: B 546 LEU cc_start: 0.8876 (mt) cc_final: 0.8346 (mt) REVERT: B 550 MET cc_start: 0.7858 (mtm) cc_final: 0.6478 (mtp) REVERT: B 576 LEU cc_start: 0.8646 (mt) cc_final: 0.8403 (mt) REVERT: B 612 TYR cc_start: 0.7481 (m-80) cc_final: 0.7171 (m-80) REVERT: C 56 MET cc_start: 0.1931 (mmm) cc_final: 0.1383 (ptm) REVERT: C 89 VAL cc_start: 0.5947 (t) cc_final: 0.4877 (t) REVERT: C 256 VAL cc_start: 0.5854 (t) cc_final: 0.5505 (p) REVERT: D 89 VAL cc_start: 0.7184 (t) cc_final: 0.6724 (t) outliers start: 25 outliers final: 5 residues processed: 998 average time/residue: 0.1391 time to fit residues: 203.4876 Evaluate side-chains 696 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 690 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 59 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.0030 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 ASN A 304 HIS A 312 GLN A 313 HIS A 370 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 61 ASN B 62 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 329 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN B 676 HIS C 127 GLN C 249 GLN C 263 ASN C 265 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.148803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.104984 restraints weight = 35714.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.109024 restraints weight = 17931.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.111682 restraints weight = 10810.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.113360 restraints weight = 7446.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.114592 restraints weight = 5623.363| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16386 Z= 0.195 Angle : 0.699 9.486 22134 Z= 0.369 Chirality : 0.046 0.286 2360 Planarity : 0.004 0.034 2818 Dihedral : 10.015 128.026 2299 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.90 % Allowed : 22.14 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.19), residues: 1932 helix: 1.31 (0.15), residues: 1142 sheet: 0.03 (0.42), residues: 130 loop : 0.55 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 293 TYR 0.028 0.002 TYR C 162 PHE 0.029 0.002 PHE C 259 TRP 0.024 0.002 TRP B 558 HIS 0.010 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.20 (16386) covalent geometry : angle 0.69876 / 0.37 (22134) hydrogen bonds : bond 0.04830 / 3.05 ( 871) hydrogen bonds : angle 5.17873 / 3.69 ( 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 788 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 721 time to evaluate : 0.593 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 55 LEU cc_start: 0.9787 (mt) cc_final: 0.9455 (pp) REVERT: A 123 SER cc_start: 0.9640 (OUTLIER) cc_final: 0.9245 (p) REVERT: A 139 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8309 (mt-10) REVERT: A 157 LEU cc_start: 0.9607 (tp) cc_final: 0.9403 (tp) REVERT: A 191 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8658 (mm-40) REVERT: A 202 ASN cc_start: 0.9530 (t0) cc_final: 0.9141 (t0) REVERT: A 218 ASN cc_start: 0.8900 (t0) cc_final: 0.8668 (t0) REVERT: A 236 TYR cc_start: 0.9602 (t80) cc_final: 0.9383 (t80) REVERT: A 255 HIS cc_start: 0.8615 (t-90) cc_final: 0.8177 (t-90) REVERT: A 257 ASP cc_start: 0.9338 (m-30) cc_final: 0.8910 (m-30) REVERT: A 259 ASN cc_start: 0.8825 (m-40) cc_final: 0.8593 (m-40) REVERT: A 263 ASP cc_start: 0.8791 (m-30) cc_final: 0.8577 (m-30) REVERT: A 277 THR cc_start: 0.8856 (p) cc_final: 0.8507 (t) REVERT: A 279 SER cc_start: 0.8960 (m) cc_final: 0.8671 (p) REVERT: A 286 ASP cc_start: 0.8374 (m-30) cc_final: 0.8096 (m-30) REVERT: A 322 MET cc_start: 0.9019 (mmm) cc_final: 0.8243 (mmm) REVERT: A 335 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7873 (mm-30) REVERT: A 348 MET cc_start: 0.8768 (tmm) cc_final: 0.8315 (tmm) REVERT: A 362 ASP cc_start: 0.8279 (m-30) cc_final: 0.7278 (m-30) REVERT: A 379 SER cc_start: 0.9442 (t) cc_final: 0.9094 (t) REVERT: A 393 SER cc_start: 0.9396 (m) cc_final: 0.9094 (p) REVERT: A 402 GLU cc_start: 0.8006 (mp0) cc_final: 0.7677 (mp0) REVERT: A 505 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8386 (mt-10) REVERT: A 509 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8649 (mm-30) REVERT: A 515 ASP cc_start: 0.8995 (m-30) cc_final: 0.8313 (m-30) REVERT: A 602 GLU cc_start: 0.7557 (pt0) cc_final: 0.7093 (pt0) REVERT: A 606 TYR cc_start: 0.8154 (m-80) cc_final: 0.7238 (m-80) REVERT: A 615 MET cc_start: 0.9038 (mmp) cc_final: 0.8552 (mmm) REVERT: A 618 LEU cc_start: 0.9372 (tp) cc_final: 0.9148 (tt) REVERT: A 639 ASP cc_start: 0.9058 (m-30) cc_final: 0.8310 (m-30) REVERT: B 26 PHE cc_start: 0.9158 (m-80) cc_final: 0.8958 (m-10) REVERT: B 31 GLU cc_start: 0.8718 (mp0) cc_final: 0.8463 (mp0) REVERT: B 65 GLU cc_start: 0.8474 (mm-30) cc_final: 0.7749 (mm-30) REVERT: B 68 PHE cc_start: 0.9028 (p90) cc_final: 0.8756 (p90) REVERT: B 119 GLU cc_start: 0.9153 (mp0) cc_final: 0.8617 (mp0) REVERT: B 121 ARG cc_start: 0.9466 (tpm170) cc_final: 0.9099 (tpp-160) REVERT: B 139 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8911 (mm-30) REVERT: B 149 TYR cc_start: 0.9385 (t80) cc_final: 0.9073 (t80) REVERT: B 150 GLN cc_start: 0.9418 (tp40) cc_final: 0.8983 (tp-100) REVERT: B 174 GLU cc_start: 0.8557 (tp30) cc_final: 0.8137 (tp30) REVERT: B 202 ASN cc_start: 0.9372 (t0) cc_final: 0.9042 (t0) REVERT: B 234 PHE cc_start: 0.9553 (m-80) cc_final: 0.9352 (m-10) REVERT: B 236 TYR cc_start: 0.9100 (t80) cc_final: 0.8839 (t80) REVERT: B 251 LEU cc_start: 0.9205 (tp) cc_final: 0.9002 (tp) REVERT: B 257 ASP cc_start: 0.8706 (m-30) cc_final: 0.8160 (m-30) REVERT: B 279 SER cc_start: 0.8770 (m) cc_final: 0.8398 (t) REVERT: B 348 MET cc_start: 0.9155 (ptm) cc_final: 0.8515 (ptp) REVERT: B 386 LEU cc_start: 0.9564 (mt) cc_final: 0.9192 (mt) REVERT: B 393 SER cc_start: 0.9426 (m) cc_final: 0.8943 (p) REVERT: B 396 ASP cc_start: 0.8718 (p0) cc_final: 0.8422 (p0) REVERT: B 411 LEU cc_start: 0.9171 (mp) cc_final: 0.8966 (mp) REVERT: B 415 ASN cc_start: 0.9475 (t0) cc_final: 0.9040 (t0) REVERT: B 446 ARG cc_start: 0.7864 (mtp85) cc_final: 0.7525 (mtp85) REVERT: B 474 GLN cc_start: 0.8927 (mt0) cc_final: 0.8655 (mm-40) REVERT: B 475 ASN cc_start: 0.9231 (m-40) cc_final: 0.8793 (m110) REVERT: B 515 ASP cc_start: 0.9036 (m-30) cc_final: 0.8832 (m-30) REVERT: B 530 LYS cc_start: 0.9243 (pttt) cc_final: 0.9016 (pttm) REVERT: B 546 LEU cc_start: 0.9585 (mt) cc_final: 0.9368 (mt) REVERT: B 558 TRP cc_start: 0.9496 (m100) cc_final: 0.8660 (m100) REVERT: B 588 GLN cc_start: 0.9223 (mm-40) cc_final: 0.8563 (mm-40) REVERT: B 599 GLU cc_start: 0.8466 (pt0) cc_final: 0.8234 (pt0) REVERT: B 601 ILE cc_start: 0.9460 (mm) cc_final: 0.9098 (mm) REVERT: B 610 LYS cc_start: 0.8827 (ptmt) cc_final: 0.8589 (ptmm) REVERT: B 612 TYR cc_start: 0.9195 (m-80) cc_final: 0.8916 (m-80) REVERT: B 650 GLN cc_start: 0.8470 (mt0) cc_final: 0.8035 (mm-40) REVERT: B 680 LYS cc_start: 0.9047 (mttt) cc_final: 0.8725 (mttt) REVERT: B 683 TYR cc_start: 0.9151 (t80) cc_final: 0.8832 (t80) REVERT: C 149 ASP cc_start: 0.6827 (m-30) cc_final: 0.6569 (m-30) REVERT: C 154 PHE cc_start: 0.9073 (t80) cc_final: 0.8575 (t80) REVERT: C 157 MET cc_start: 0.9096 (mtt) cc_final: 0.8794 (mtt) REVERT: C 201 HIS cc_start: 0.9045 (m170) cc_final: 0.8840 (m170) REVERT: C 208 LEU cc_start: 0.7083 (mm) cc_final: 0.6789 (mm) REVERT: C 252 LEU cc_start: 0.7748 (mp) cc_final: 0.7389 (pp) REVERT: C 256 VAL cc_start: 0.8564 (t) cc_final: 0.8345 (t) REVERT: C 286 VAL cc_start: 0.7603 (OUTLIER) cc_final: 0.7303 (m) REVERT: C 288 ASN cc_start: 0.5164 (t0) cc_final: 0.4358 (m-40) REVERT: D 24 GLN cc_start: 0.9364 (tp-100) cc_final: 0.9145 (tp-100) REVERT: D 55 TYR cc_start: 0.6354 (t80) cc_final: 0.6023 (t80) REVERT: D 82 ASP cc_start: 0.8952 (m-30) cc_final: 0.8703 (t0) REVERT: D 154 PHE cc_start: 0.5774 (t80) cc_final: 0.5232 (t80) outliers start: 67 outliers final: 39 residues processed: 746 average time/residue: 0.1231 time to fit residues: 139.4809 Evaluate side-chains 691 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 650 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 164 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 182 optimal weight: 9.9990 chunk 159 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN ** 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 588 GLN A 668 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 28 GLN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN C 238 ASN ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** 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 = 0.3768 r_free = 0.3768 target = 0.138028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.097373 restraints weight = 36564.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.100914 restraints weight = 18248.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.103192 restraints weight = 11147.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.104772 restraints weight = 7757.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.105773 restraints weight = 5889.175| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 10 (20 function evaluations) r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.5608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 16386 Z= 0.291 Angle : 0.730 10.396 22134 Z= 0.384 Chirality : 0.047 0.228 2360 Planarity : 0.004 0.043 2818 Dihedral : 9.457 134.468 2293 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 5.65 % Allowed : 22.32 % Favored : 72.03 % 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: 1.24 (0.19), residues: 1932 helix: 1.27 (0.15), residues: 1132 sheet: -0.22 (0.40), residues: 144 loop : 0.49 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 293 TYR 0.023 0.002 TYR C 55 PHE 0.050 0.002 PHE C 109 TRP 0.028 0.003 TRP D 124 HIS 0.009 0.002 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.29 (16386) covalent geometry : angle 0.72999 / 0.38 (22134) hydrogen bonds : bond 0.04559 / 2.89 ( 871) hydrogen bonds : angle 5.23255 / 3.73 ( 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 756 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 659 time to evaluate : 0.615 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 31 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8554 (mp0) REVERT: A 95 MET cc_start: 0.9261 (mmm) cc_final: 0.8891 (tpp) REVERT: A 123 SER cc_start: 0.9691 (OUTLIER) cc_final: 0.9197 (p) REVERT: A 128 PHE cc_start: 0.9491 (t80) cc_final: 0.9254 (t80) REVERT: A 139 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8372 (mt-10) REVERT: A 157 LEU cc_start: 0.9633 (tp) cc_final: 0.9404 (tp) REVERT: A 161 ARG cc_start: 0.8267 (ttm110) cc_final: 0.7445 (mtp85) REVERT: A 190 MET cc_start: 0.9378 (mtp) cc_final: 0.9027 (mtp) REVERT: A 193 SER cc_start: 0.9561 (m) cc_final: 0.8998 (p) REVERT: A 202 ASN cc_start: 0.9521 (t0) cc_final: 0.9269 (t0) REVERT: A 246 SER cc_start: 0.7935 (m) cc_final: 0.7606 (p) REVERT: A 255 HIS cc_start: 0.8699 (t-90) cc_final: 0.8082 (t-90) REVERT: A 257 ASP cc_start: 0.9486 (m-30) cc_final: 0.8882 (m-30) REVERT: A 259 ASN cc_start: 0.8884 (m-40) cc_final: 0.8555 (m-40) REVERT: A 263 ASP cc_start: 0.8693 (m-30) cc_final: 0.8391 (m-30) REVERT: A 274 ARG cc_start: 0.8974 (ptm160) cc_final: 0.8626 (ptp-110) REVERT: A 277 THR cc_start: 0.8895 (p) cc_final: 0.8535 (t) REVERT: A 322 MET cc_start: 0.8830 (mmm) cc_final: 0.8451 (mmm) REVERT: A 335 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8169 (mm-30) REVERT: A 348 MET cc_start: 0.8877 (tmm) cc_final: 0.8298 (tmm) REVERT: A 349 LEU cc_start: 0.9655 (OUTLIER) cc_final: 0.9241 (mt) REVERT: A 350 ARG cc_start: 0.9333 (mtp180) cc_final: 0.9050 (mtp180) REVERT: A 379 SER cc_start: 0.9373 (t) cc_final: 0.9093 (t) REVERT: A 385 VAL cc_start: 0.9441 (t) cc_final: 0.9202 (p) REVERT: A 393 SER cc_start: 0.9331 (m) cc_final: 0.9037 (p) REVERT: A 402 GLU cc_start: 0.8169 (mp0) cc_final: 0.7827 (mp0) REVERT: A 426 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8220 (tm-30) REVERT: A 435 SER cc_start: 0.9629 (p) cc_final: 0.9421 (p) REVERT: A 501 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.8912 (tt0) REVERT: A 505 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8341 (mt-10) REVERT: A 515 ASP cc_start: 0.9127 (m-30) cc_final: 0.8571 (m-30) REVERT: A 548 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8292 (mm-30) REVERT: A 590 SER cc_start: 0.9442 (t) cc_final: 0.9016 (p) REVERT: A 603 GLU cc_start: 0.8616 (tt0) cc_final: 0.8339 (mm-30) REVERT: A 606 TYR cc_start: 0.8180 (m-80) cc_final: 0.7474 (m-80) REVERT: A 615 MET cc_start: 0.9262 (mmp) cc_final: 0.8828 (mmm) REVERT: B 8 LYS cc_start: 0.8867 (tppt) cc_final: 0.8597 (tppt) REVERT: B 16 ILE cc_start: 0.9572 (mm) cc_final: 0.9032 (tp) REVERT: B 31 GLU cc_start: 0.8684 (mp0) cc_final: 0.8458 (mp0) REVERT: B 65 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8094 (mm-30) REVERT: B 95 MET cc_start: 0.9217 (tpp) cc_final: 0.8967 (tpp) REVERT: B 99 LYS cc_start: 0.9401 (mmtt) cc_final: 0.9136 (mmtt) REVERT: B 104 TYR cc_start: 0.8943 (m-80) cc_final: 0.8522 (m-80) REVERT: B 117 ARG cc_start: 0.8836 (mtp85) cc_final: 0.8598 (mtp85) REVERT: B 119 GLU cc_start: 0.9191 (mp0) cc_final: 0.8609 (mp0) REVERT: B 135 GLU cc_start: 0.9017 (mp0) cc_final: 0.8722 (mp0) REVERT: B 139 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8905 (mm-30) REVERT: B 149 TYR cc_start: 0.9436 (t80) cc_final: 0.9085 (t80) REVERT: B 166 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8519 (mm-30) REVERT: B 172 LEU cc_start: 0.9414 (mp) cc_final: 0.9070 (mt) REVERT: B 221 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.9057 (mttm) REVERT: B 232 ASN cc_start: 0.9227 (m110) cc_final: 0.8745 (m110) REVERT: B 235 ARG cc_start: 0.9191 (ttm-80) cc_final: 0.8979 (ttm-80) REVERT: B 236 TYR cc_start: 0.9235 (t80) cc_final: 0.8879 (t80) REVERT: B 246 SER cc_start: 0.7911 (m) cc_final: 0.7477 (p) REVERT: B 250 TYR cc_start: 0.9195 (m-80) cc_final: 0.8788 (m-80) REVERT: B 257 ASP cc_start: 0.8668 (m-30) cc_final: 0.8227 (m-30) REVERT: B 279 SER cc_start: 0.9009 (m) cc_final: 0.8682 (t) REVERT: B 322 MET cc_start: 0.9340 (mmm) cc_final: 0.8653 (mmm) REVERT: B 393 SER cc_start: 0.9344 (m) cc_final: 0.8862 (p) REVERT: B 396 ASP cc_start: 0.8953 (p0) cc_final: 0.8635 (p0) REVERT: B 402 GLU cc_start: 0.8850 (tp30) cc_final: 0.8646 (tp30) REVERT: B 406 ASP cc_start: 0.8212 (m-30) cc_final: 0.8008 (m-30) REVERT: B 435 SER cc_start: 0.9844 (OUTLIER) cc_final: 0.9573 (t) REVERT: B 474 GLN cc_start: 0.8959 (mt0) cc_final: 0.8665 (mm-40) REVERT: B 475 ASN cc_start: 0.9368 (m-40) cc_final: 0.9005 (m110) REVERT: B 515 ASP cc_start: 0.9040 (m-30) cc_final: 0.8756 (m-30) REVERT: B 546 LEU cc_start: 0.9634 (mt) cc_final: 0.9395 (mt) REVERT: B 550 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7554 (mtp) REVERT: B 599 GLU cc_start: 0.8699 (pt0) cc_final: 0.8195 (pt0) REVERT: B 601 ILE cc_start: 0.9534 (mm) cc_final: 0.8900 (mm) REVERT: B 604 ARG cc_start: 0.8459 (mmt-90) cc_final: 0.8021 (mmt-90) REVERT: B 610 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8480 (ptmm) REVERT: B 612 TYR cc_start: 0.9238 (m-80) cc_final: 0.8862 (m-80) REVERT: B 615 MET cc_start: 0.9525 (mmp) cc_final: 0.9322 (mmp) REVERT: B 684 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.7539 (m-80) REVERT: C 21 PHE cc_start: 0.8270 (m-80) cc_final: 0.7937 (m-80) REVERT: C 66 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.6641 (t70) REVERT: C 69 GLN cc_start: 0.9199 (tp40) cc_final: 0.8987 (pt0) REVERT: C 154 PHE cc_start: 0.9204 (t80) cc_final: 0.8755 (t80) REVERT: C 157 MET cc_start: 0.9131 (mtt) cc_final: 0.8591 (mtt) REVERT: C 200 ILE cc_start: 0.9157 (mp) cc_final: 0.8952 (mp) REVERT: C 212 ILE cc_start: 0.7489 (mt) cc_final: 0.6570 (mt) REVERT: C 242 TYR cc_start: 0.9123 (t80) cc_final: 0.8867 (t80) REVERT: D 25 ASN cc_start: 0.8770 (t0) cc_final: 0.8503 (t0) REVERT: D 82 ASP cc_start: 0.8837 (m-30) cc_final: 0.8622 (m-30) REVERT: D 97 GLU cc_start: 0.6700 (OUTLIER) cc_final: 0.6434 (mp0) outliers start: 97 outliers final: 63 residues processed: 702 average time/residue: 0.1185 time to fit residues: 127.5817 Evaluate side-chains 670 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 596 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 240 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN A 469 HIS ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.136251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.095864 restraints weight = 37222.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.099387 restraints weight = 18625.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.101681 restraints weight = 11273.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.103264 restraints weight = 7772.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.104341 restraints weight = 5868.089| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.6150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16386 Z= 0.229 Angle : 0.692 9.248 22134 Z= 0.361 Chirality : 0.046 0.241 2360 Planarity : 0.004 0.047 2818 Dihedral : 9.230 134.634 2292 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 5.30 % Allowed : 24.88 % Favored : 69.81 % 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: 1.20 (0.15), residues: 1121 sheet: -0.59 (0.37), residues: 160 loop : 0.42 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 256 TYR 0.021 0.002 TYR B 683 PHE 0.052 0.002 PHE C 109 TRP 0.010 0.002 TRP B 558 HIS 0.006 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.23 (16386) covalent geometry : angle 0.69197 / 0.36 (22134) hydrogen bonds : bond 0.04223 / 2.68 ( 871) hydrogen bonds : angle 5.19769 / 3.68 ( 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 715 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 624 time to evaluate : 0.590 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 65 GLU cc_start: 0.8467 (mm-30) cc_final: 0.7658 (mp0) REVERT: A 123 SER cc_start: 0.9613 (OUTLIER) cc_final: 0.9124 (p) REVERT: A 128 PHE cc_start: 0.9488 (t80) cc_final: 0.9189 (t80) REVERT: A 139 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8384 (mt-10) REVERT: A 149 TYR cc_start: 0.9549 (t80) cc_final: 0.8760 (t80) REVERT: A 161 ARG cc_start: 0.8413 (ttm110) cc_final: 0.6955 (mtp85) REVERT: A 190 MET cc_start: 0.9375 (mtp) cc_final: 0.9130 (mtp) REVERT: A 202 ASN cc_start: 0.9485 (t0) cc_final: 0.9262 (t0) REVERT: A 228 LYS cc_start: 0.9364 (OUTLIER) cc_final: 0.9089 (mmtm) REVERT: A 255 HIS cc_start: 0.8620 (t-90) cc_final: 0.7983 (t-90) REVERT: A 257 ASP cc_start: 0.9441 (m-30) cc_final: 0.8897 (m-30) REVERT: A 259 ASN cc_start: 0.8913 (m-40) cc_final: 0.8581 (m-40) REVERT: A 263 ASP cc_start: 0.8668 (m-30) cc_final: 0.8387 (m-30) REVERT: A 274 ARG cc_start: 0.8907 (ptm160) cc_final: 0.8563 (ptp-110) REVERT: A 277 THR cc_start: 0.8883 (p) cc_final: 0.8443 (t) REVERT: A 286 ASP cc_start: 0.8654 (m-30) cc_final: 0.8294 (m-30) REVERT: A 335 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8177 (mm-30) REVERT: A 348 MET cc_start: 0.8907 (tmm) cc_final: 0.8384 (tmm) REVERT: A 349 LEU cc_start: 0.9648 (OUTLIER) cc_final: 0.9224 (mt) REVERT: A 350 ARG cc_start: 0.9339 (mtp180) cc_final: 0.9090 (mtp180) REVERT: A 362 ASP cc_start: 0.8337 (m-30) cc_final: 0.7770 (m-30) REVERT: A 384 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.7842 (pm20) REVERT: A 385 VAL cc_start: 0.9378 (t) cc_final: 0.9176 (t) REVERT: A 393 SER cc_start: 0.9306 (m) cc_final: 0.8996 (p) REVERT: A 402 GLU cc_start: 0.8300 (mp0) cc_final: 0.7925 (mp0) REVERT: A 426 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8264 (tm-30) REVERT: A 435 SER cc_start: 0.9654 (p) cc_final: 0.9415 (p) REVERT: A 501 GLN cc_start: 0.9244 (OUTLIER) cc_final: 0.8856 (tt0) REVERT: A 505 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8419 (mt-10) REVERT: A 515 ASP cc_start: 0.9098 (m-30) cc_final: 0.8585 (m-30) REVERT: A 548 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8236 (mm-30) REVERT: A 583 SER cc_start: 0.9229 (OUTLIER) cc_final: 0.8946 (t) REVERT: A 606 TYR cc_start: 0.7936 (m-80) cc_final: 0.7580 (m-80) REVERT: A 615 MET cc_start: 0.9275 (mmp) cc_final: 0.8734 (mmm) REVERT: B 8 LYS cc_start: 0.8880 (tppt) cc_final: 0.8592 (tppt) REVERT: B 31 GLU cc_start: 0.8653 (mp0) cc_final: 0.8361 (mp0) REVERT: B 65 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8212 (mm-30) REVERT: B 87 LYS cc_start: 0.9446 (mmmt) cc_final: 0.9177 (tptm) REVERT: B 99 LYS cc_start: 0.9391 (mmtt) cc_final: 0.9131 (mmtt) REVERT: B 104 TYR cc_start: 0.9001 (m-80) cc_final: 0.8541 (m-80) REVERT: B 119 GLU cc_start: 0.9125 (mp0) cc_final: 0.8450 (mp0) REVERT: B 127 LEU cc_start: 0.9721 (mm) cc_final: 0.9385 (mm) REVERT: B 135 GLU cc_start: 0.9019 (mp0) cc_final: 0.8735 (mp0) REVERT: B 139 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8813 (mm-30) REVERT: B 149 TYR cc_start: 0.9484 (t80) cc_final: 0.9121 (t80) REVERT: B 166 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8442 (mm-30) REVERT: B 172 LEU cc_start: 0.9446 (mp) cc_final: 0.9146 (mt) REVERT: B 202 ASN cc_start: 0.9504 (t0) cc_final: 0.8933 (t0) REVERT: B 221 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8963 (mttm) REVERT: B 232 ASN cc_start: 0.9190 (m110) cc_final: 0.8728 (m110) REVERT: B 246 SER cc_start: 0.7952 (m) cc_final: 0.7498 (p) REVERT: B 250 TYR cc_start: 0.9289 (m-80) cc_final: 0.8779 (m-80) REVERT: B 257 ASP cc_start: 0.8708 (m-30) cc_final: 0.8268 (m-30) REVERT: B 279 SER cc_start: 0.8994 (m) cc_final: 0.8532 (t) REVERT: B 317 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8318 (pmm) REVERT: B 375 LYS cc_start: 0.9549 (mttm) cc_final: 0.9331 (mttp) REVERT: B 393 SER cc_start: 0.9411 (m) cc_final: 0.8943 (p) REVERT: B 396 ASP cc_start: 0.8895 (p0) cc_final: 0.8613 (p0) REVERT: B 435 SER cc_start: 0.9820 (OUTLIER) cc_final: 0.9567 (t) REVERT: B 474 GLN cc_start: 0.8964 (mt0) cc_final: 0.8673 (mm-40) REVERT: B 475 ASN cc_start: 0.9357 (m-40) cc_final: 0.9021 (m110) REVERT: B 515 ASP cc_start: 0.9068 (m-30) cc_final: 0.8710 (m-30) REVERT: B 546 LEU cc_start: 0.9617 (mt) cc_final: 0.9372 (mt) REVERT: B 599 GLU cc_start: 0.8731 (pt0) cc_final: 0.8363 (pt0) REVERT: B 601 ILE cc_start: 0.9516 (mm) cc_final: 0.8790 (mm) REVERT: B 610 LYS cc_start: 0.8816 (ptmt) cc_final: 0.8516 (ptmm) REVERT: B 612 TYR cc_start: 0.9196 (m-80) cc_final: 0.8794 (m-80) REVERT: B 615 MET cc_start: 0.9480 (mmp) cc_final: 0.9233 (mmp) REVERT: B 650 GLN cc_start: 0.8650 (mt0) cc_final: 0.8053 (mm-40) REVERT: B 684 TYR cc_start: 0.8197 (OUTLIER) cc_final: 0.7462 (m-80) REVERT: C 20 MET cc_start: 0.9230 (tpp) cc_final: 0.9010 (tmm) REVERT: C 21 PHE cc_start: 0.8318 (m-80) cc_final: 0.8026 (m-80) REVERT: C 66 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7063 (t70) REVERT: C 69 GLN cc_start: 0.9235 (tp40) cc_final: 0.8914 (pt0) REVERT: C 74 MET cc_start: 0.9451 (tpp) cc_final: 0.8840 (tpp) REVERT: C 122 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7727 (m-80) REVERT: C 157 MET cc_start: 0.9207 (mtt) cc_final: 0.8920 (mtt) REVERT: C 162 TYR cc_start: 0.8818 (m-10) cc_final: 0.8008 (m-80) REVERT: C 212 ILE cc_start: 0.7465 (mt) cc_final: 0.7120 (mt) REVERT: C 242 TYR cc_start: 0.9232 (t80) cc_final: 0.8870 (t80) REVERT: D 21 PHE cc_start: 0.9206 (m-80) cc_final: 0.8566 (m-80) REVERT: D 24 GLN cc_start: 0.9311 (tp-100) cc_final: 0.9081 (tm-30) REVERT: D 204 TYR cc_start: 0.9355 (t80) cc_final: 0.9130 (t80) outliers start: 91 outliers final: 57 residues processed: 666 average time/residue: 0.1077 time to fit residues: 111.0132 Evaluate side-chains 662 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 592 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 123 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 129 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 168 optimal weight: 20.0000 chunk 157 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 387 GLN A 469 HIS ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN C 85 GLN D 24 GLN D 107 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.3779 r_free = 0.3779 target = 0.136899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.095224 restraints weight = 37624.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.098854 restraints weight = 18950.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.101189 restraints weight = 11595.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.102747 restraints weight = 8063.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.103680 restraints weight = 6131.968| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3249 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (22 function evaluations) r_final: 0.3249 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.6512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16386 Z= 0.205 Angle : 0.682 10.498 22134 Z= 0.354 Chirality : 0.046 0.220 2360 Planarity : 0.004 0.043 2818 Dihedral : 9.043 135.632 2292 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 5.71 % Allowed : 25.70 % Favored : 68.59 % 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: 0.98 (0.19), residues: 1932 helix: 1.09 (0.15), residues: 1135 sheet: -0.47 (0.39), residues: 148 loop : 0.37 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 117 TYR 0.022 0.002 TYR B 683 PHE 0.058 0.002 PHE C 109 TRP 0.010 0.002 TRP A 9 HIS 0.005 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 (16386) covalent geometry : angle 0.68238 / 0.35 (22134) hydrogen bonds : bond 0.04088 / 2.58 ( 871) hydrogen bonds : angle 5.16807 / 3.67 ( 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 722 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 624 time to evaluate : 0.603 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: 0.9015 (ttmm) cc_final: 0.8753 (ttpt) REVERT: A 12 LEU cc_start: 0.9507 (mp) cc_final: 0.9196 (mp) REVERT: A 15 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8247 (mt-10) REVERT: A 123 SER cc_start: 0.9506 (OUTLIER) cc_final: 0.9170 (p) REVERT: A 128 PHE cc_start: 0.9497 (t80) cc_final: 0.9100 (t80) REVERT: A 139 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8357 (mt-10) REVERT: A 149 TYR cc_start: 0.9542 (t80) cc_final: 0.8746 (t80) REVERT: A 150 GLN cc_start: 0.9418 (tp40) cc_final: 0.8958 (tm-30) REVERT: A 190 MET cc_start: 0.9379 (mtp) cc_final: 0.9148 (mtp) REVERT: A 202 ASN cc_start: 0.9410 (t0) cc_final: 0.9079 (t0) REVERT: A 221 LYS cc_start: 0.9223 (mmtp) cc_final: 0.9005 (mptt) REVERT: A 228 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9168 (mmtm) REVERT: A 255 HIS cc_start: 0.8716 (t-90) cc_final: 0.8470 (t-90) REVERT: A 263 ASP cc_start: 0.8773 (m-30) cc_final: 0.8488 (m-30) REVERT: A 277 THR cc_start: 0.8845 (p) cc_final: 0.8406 (t) REVERT: A 286 ASP cc_start: 0.8626 (m-30) cc_final: 0.8235 (m-30) REVERT: A 335 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8132 (mm-30) REVERT: A 348 MET cc_start: 0.8948 (tmm) cc_final: 0.8467 (tmm) REVERT: A 349 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9195 (mt) REVERT: A 350 ARG cc_start: 0.9313 (mtp180) cc_final: 0.9057 (mtp180) REVERT: A 362 ASP cc_start: 0.8282 (m-30) cc_final: 0.7508 (m-30) REVERT: A 384 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.7750 (pm20) REVERT: A 393 SER cc_start: 0.9331 (m) cc_final: 0.8899 (t) REVERT: A 402 GLU cc_start: 0.8340 (mp0) cc_final: 0.7534 (mp0) REVERT: A 420 MET cc_start: 0.9193 (mmm) cc_final: 0.8956 (tpt) REVERT: A 426 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8274 (tm-30) REVERT: A 435 SER cc_start: 0.9648 (p) cc_final: 0.9397 (p) REVERT: A 501 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.8818 (tt0) REVERT: A 505 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8398 (mt-10) REVERT: A 515 ASP cc_start: 0.9115 (m-30) cc_final: 0.8577 (m-30) REVERT: A 528 PHE cc_start: 0.9271 (m-80) cc_final: 0.8766 (m-80) REVERT: A 548 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8185 (mm-30) REVERT: A 606 TYR cc_start: 0.8000 (m-80) cc_final: 0.7350 (m-80) REVERT: A 615 MET cc_start: 0.9322 (mmp) cc_final: 0.8815 (mmp) REVERT: B 8 LYS cc_start: 0.8926 (tppt) cc_final: 0.8649 (tppt) REVERT: B 31 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: B 65 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8280 (mm-30) REVERT: B 87 LYS cc_start: 0.9457 (mmmt) cc_final: 0.9193 (tptm) REVERT: B 99 LYS cc_start: 0.9377 (mmtt) cc_final: 0.9135 (mmtt) REVERT: B 104 TYR cc_start: 0.8994 (m-80) cc_final: 0.8611 (m-80) REVERT: B 119 GLU cc_start: 0.9102 (mp0) cc_final: 0.8477 (mp0) REVERT: B 127 LEU cc_start: 0.9727 (mm) cc_final: 0.9381 (mm) REVERT: B 135 GLU cc_start: 0.9146 (mp0) cc_final: 0.8791 (mp0) REVERT: B 139 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8795 (mm-30) REVERT: B 149 TYR cc_start: 0.9476 (t80) cc_final: 0.9166 (t80) REVERT: B 166 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8339 (mm-30) REVERT: B 172 LEU cc_start: 0.9440 (mp) cc_final: 0.8521 (mt) REVERT: B 174 GLU cc_start: 0.8542 (tp30) cc_final: 0.8279 (tp30) REVERT: B 202 ASN cc_start: 0.9524 (t0) cc_final: 0.9163 (t0) REVERT: B 221 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8771 (mttm) REVERT: B 232 ASN cc_start: 0.9174 (m110) cc_final: 0.8752 (m110) REVERT: B 246 SER cc_start: 0.7986 (m) cc_final: 0.7547 (p) REVERT: B 250 TYR cc_start: 0.9314 (m-80) cc_final: 0.8733 (m-80) REVERT: B 257 ASP cc_start: 0.8832 (m-30) cc_final: 0.8329 (m-30) REVERT: B 263 ASP cc_start: 0.9260 (m-30) cc_final: 0.9040 (m-30) REVERT: B 274 ARG cc_start: 0.8621 (ptp-170) cc_final: 0.8180 (ttm110) REVERT: B 279 SER cc_start: 0.9017 (OUTLIER) cc_final: 0.8636 (t) REVERT: B 317 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8317 (pmm) REVERT: B 321 GLU cc_start: 0.8676 (pp20) cc_final: 0.8117 (pp20) REVERT: B 322 MET cc_start: 0.9325 (mmt) cc_final: 0.8737 (mmm) REVERT: B 375 LYS cc_start: 0.9545 (mttm) cc_final: 0.9336 (mttp) REVERT: B 393 SER cc_start: 0.9399 (m) cc_final: 0.8951 (p) REVERT: B 396 ASP cc_start: 0.8902 (p0) cc_final: 0.8554 (p0) REVERT: B 406 ASP cc_start: 0.8220 (m-30) cc_final: 0.7944 (t0) REVERT: B 435 SER cc_start: 0.9822 (OUTLIER) cc_final: 0.9554 (t) REVERT: B 474 GLN cc_start: 0.8958 (mt0) cc_final: 0.8692 (mt0) REVERT: B 475 ASN cc_start: 0.9367 (m-40) cc_final: 0.9027 (m110) REVERT: B 515 ASP cc_start: 0.9025 (m-30) cc_final: 0.8673 (m-30) REVERT: B 546 LEU cc_start: 0.9618 (mt) cc_final: 0.9381 (mt) REVERT: B 586 TYR cc_start: 0.9209 (m-80) cc_final: 0.8994 (m-80) REVERT: B 599 GLU cc_start: 0.8754 (pt0) cc_final: 0.8380 (pt0) REVERT: B 601 ILE cc_start: 0.9528 (mm) cc_final: 0.8759 (mm) REVERT: B 610 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8527 (ptmt) REVERT: B 612 TYR cc_start: 0.9188 (m-80) cc_final: 0.8934 (m-80) REVERT: B 615 MET cc_start: 0.9438 (mmp) cc_final: 0.9130 (mmp) REVERT: B 683 TYR cc_start: 0.9100 (t80) cc_final: 0.8430 (t80) REVERT: B 684 TYR cc_start: 0.8209 (OUTLIER) cc_final: 0.7191 (m-80) REVERT: C 74 MET cc_start: 0.9524 (tpp) cc_final: 0.9168 (tpp) REVERT: C 127 GLN cc_start: 0.8583 (mm110) cc_final: 0.7362 (pp30) REVERT: C 154 PHE cc_start: 0.9150 (t80) cc_final: 0.8571 (t80) REVERT: C 157 MET cc_start: 0.9315 (mtt) cc_final: 0.9018 (mtt) REVERT: C 208 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6690 (mm) REVERT: C 212 ILE cc_start: 0.7432 (mt) cc_final: 0.6377 (mt) REVERT: C 242 TYR cc_start: 0.9295 (t80) cc_final: 0.9061 (t80) REVERT: C 314 PRO cc_start: 0.9468 (Cg_exo) cc_final: 0.8876 (Cg_endo) REVERT: C 316 LYS cc_start: 0.8927 (mmtt) cc_final: 0.8649 (mmtt) REVERT: D 21 PHE cc_start: 0.9152 (m-80) cc_final: 0.8316 (m-80) REVERT: D 204 TYR cc_start: 0.9474 (t80) cc_final: 0.9017 (t80) REVERT: D 313 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8349 (tm-30) outliers start: 98 outliers final: 61 residues processed: 669 average time/residue: 0.1110 time to fit residues: 114.9935 Evaluate side-chains 670 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 595 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 55 TYR Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 0.8980 chunk 183 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 172 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.134328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.094118 restraints weight = 36700.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.097629 restraints weight = 18299.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.099935 restraints weight = 11106.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.101422 restraints weight = 7687.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.102511 restraints weight = 5817.255| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (11 function evaluations) r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.6848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16386 Z= 0.242 Angle : 0.714 11.286 22134 Z= 0.371 Chirality : 0.047 0.221 2360 Planarity : 0.004 0.048 2818 Dihedral : 9.040 137.434 2292 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 5.65 % Allowed : 26.63 % 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: 0.77 (0.19), residues: 1932 helix: 0.97 (0.15), residues: 1152 sheet: -0.69 (0.38), residues: 160 loop : 0.22 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 117 TYR 0.022 0.002 TYR D 236 PHE 0.063 0.002 PHE C 92 TRP 0.017 0.002 TRP D 124 HIS 0.010 0.001 HIS A 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.24 (16386) covalent geometry : angle 0.71421 / 0.37 (22134) hydrogen bonds : bond 0.04160 / 2.64 ( 871) hydrogen bonds : angle 5.28081 / 3.74 ( 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 700 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 603 time to evaluate : 0.450 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: 0.9048 (ttmm) cc_final: 0.8809 (ptmt) REVERT: A 12 LEU cc_start: 0.9499 (mp) cc_final: 0.9201 (mp) REVERT: A 15 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8317 (mt-10) REVERT: A 31 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8630 (mp0) REVERT: A 65 GLU cc_start: 0.8519 (mm-30) cc_final: 0.7919 (mp0) REVERT: A 123 SER cc_start: 0.9515 (OUTLIER) cc_final: 0.9169 (p) REVERT: A 128 PHE cc_start: 0.9533 (t80) cc_final: 0.9234 (t80) REVERT: A 139 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8355 (mt-10) REVERT: A 149 TYR cc_start: 0.9563 (t80) cc_final: 0.8725 (t80) REVERT: A 150 GLN cc_start: 0.9434 (tp40) cc_final: 0.8933 (tm-30) REVERT: A 202 ASN cc_start: 0.9444 (t0) cc_final: 0.9137 (t0) REVERT: A 221 LYS cc_start: 0.9231 (mmtp) cc_final: 0.8972 (mptt) REVERT: A 228 LYS cc_start: 0.9447 (OUTLIER) cc_final: 0.9171 (mttm) REVERT: A 255 HIS cc_start: 0.8766 (t-90) cc_final: 0.8526 (t-90) REVERT: A 263 ASP cc_start: 0.8692 (m-30) cc_final: 0.8364 (m-30) REVERT: A 277 THR cc_start: 0.8818 (p) cc_final: 0.8373 (t) REVERT: A 286 ASP cc_start: 0.8698 (m-30) cc_final: 0.8352 (m-30) REVERT: A 348 MET cc_start: 0.8989 (tmm) cc_final: 0.8481 (tmm) REVERT: A 349 LEU cc_start: 0.9664 (OUTLIER) cc_final: 0.9211 (mt) REVERT: A 350 ARG cc_start: 0.9290 (mtp180) cc_final: 0.9015 (mtp180) REVERT: A 362 ASP cc_start: 0.8283 (m-30) cc_final: 0.7448 (m-30) REVERT: A 384 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.7810 (pm20) REVERT: A 393 SER cc_start: 0.9320 (m) cc_final: 0.8936 (t) REVERT: A 402 GLU cc_start: 0.8406 (mp0) cc_final: 0.7622 (mp0) REVERT: A 426 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8311 (tm-30) REVERT: A 453 ARG cc_start: 0.9325 (OUTLIER) cc_final: 0.8957 (ttt-90) REVERT: A 493 MET cc_start: 0.9127 (tmm) cc_final: 0.8737 (tmm) REVERT: A 501 GLN cc_start: 0.9272 (OUTLIER) cc_final: 0.8847 (tt0) REVERT: A 505 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8381 (mt-10) REVERT: A 515 ASP cc_start: 0.9120 (m-30) cc_final: 0.8649 (m-30) REVERT: A 528 PHE cc_start: 0.9340 (m-80) cc_final: 0.8836 (m-80) REVERT: A 548 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8167 (mm-30) REVERT: A 615 MET cc_start: 0.9316 (mmp) cc_final: 0.8778 (mmp) REVERT: A 686 ARG cc_start: 0.8509 (tpp80) cc_final: 0.8174 (tpp-160) REVERT: B 8 LYS cc_start: 0.8985 (tppt) cc_final: 0.8722 (tppt) REVERT: B 16 ILE cc_start: 0.9589 (mm) cc_final: 0.9385 (mm) REVERT: B 31 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8331 (mt-10) REVERT: B 65 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8338 (mm-30) REVERT: B 87 LYS cc_start: 0.9483 (mmmt) cc_final: 0.9237 (tptm) REVERT: B 95 MET cc_start: 0.9164 (tpp) cc_final: 0.8765 (tpp) REVERT: B 99 LYS cc_start: 0.9391 (mmtt) cc_final: 0.9070 (mmtt) REVERT: B 104 TYR cc_start: 0.9087 (m-80) cc_final: 0.8596 (m-80) REVERT: B 119 GLU cc_start: 0.9090 (mp0) cc_final: 0.8494 (mp0) REVERT: B 135 GLU cc_start: 0.9151 (mp0) cc_final: 0.8798 (mp0) REVERT: B 139 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8818 (mm-30) REVERT: B 149 TYR cc_start: 0.9514 (t80) cc_final: 0.9250 (t80) REVERT: B 172 LEU cc_start: 0.9410 (mp) cc_final: 0.8478 (mt) REVERT: B 174 GLU cc_start: 0.8548 (tp30) cc_final: 0.8296 (tp30) REVERT: B 202 ASN cc_start: 0.9451 (t0) cc_final: 0.8947 (t0) REVERT: B 232 ASN cc_start: 0.9181 (m110) cc_final: 0.8787 (m110) REVERT: B 246 SER cc_start: 0.7990 (m) cc_final: 0.7565 (p) REVERT: B 250 TYR cc_start: 0.9392 (m-80) cc_final: 0.8716 (m-80) REVERT: B 257 ASP cc_start: 0.8724 (m-30) cc_final: 0.8294 (m-30) REVERT: B 263 ASP cc_start: 0.9271 (m-30) cc_final: 0.9023 (m-30) REVERT: B 271 GLU cc_start: 0.9073 (mp0) cc_final: 0.8674 (mm-30) REVERT: B 274 ARG cc_start: 0.8433 (ptp-170) cc_final: 0.7995 (ptp-170) REVERT: B 279 SER cc_start: 0.9001 (OUTLIER) cc_final: 0.8575 (t) REVERT: B 317 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8359 (pmm) REVERT: B 375 LYS cc_start: 0.9511 (mttm) cc_final: 0.9168 (mttp) REVERT: B 393 SER cc_start: 0.9369 (m) cc_final: 0.8942 (p) REVERT: B 406 ASP cc_start: 0.8140 (m-30) cc_final: 0.7850 (t0) REVERT: B 413 SER cc_start: 0.9766 (OUTLIER) cc_final: 0.9478 (p) REVERT: B 435 SER cc_start: 0.9829 (OUTLIER) cc_final: 0.9551 (t) REVERT: B 441 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8464 (mt-10) REVERT: B 467 ASN cc_start: 0.9537 (OUTLIER) cc_final: 0.9254 (m-40) REVERT: B 474 GLN cc_start: 0.9000 (mt0) cc_final: 0.8726 (mm-40) REVERT: B 475 ASN cc_start: 0.9383 (m-40) cc_final: 0.9056 (m110) REVERT: B 515 ASP cc_start: 0.9077 (m-30) cc_final: 0.8706 (m-30) REVERT: B 546 LEU cc_start: 0.9633 (mt) cc_final: 0.9406 (mt) REVERT: B 599 GLU cc_start: 0.8776 (pt0) cc_final: 0.8394 (pt0) REVERT: B 601 ILE cc_start: 0.9565 (mm) cc_final: 0.8768 (mm) REVERT: B 610 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8545 (ptmt) REVERT: B 612 TYR cc_start: 0.9202 (m-80) cc_final: 0.8933 (m-80) REVERT: B 615 MET cc_start: 0.9417 (mmp) cc_final: 0.9140 (mmp) REVERT: B 683 TYR cc_start: 0.9188 (t80) cc_final: 0.8542 (t80) REVERT: B 684 TYR cc_start: 0.8206 (OUTLIER) cc_final: 0.7190 (m-80) REVERT: B 686 ARG cc_start: 0.8507 (mmt90) cc_final: 0.8258 (mmt180) REVERT: C 21 PHE cc_start: 0.8665 (m-80) cc_final: 0.8001 (m-80) REVERT: C 74 MET cc_start: 0.9457 (tpp) cc_final: 0.9250 (tpp) REVERT: C 127 GLN cc_start: 0.8565 (mm110) cc_final: 0.7366 (pp30) REVERT: C 208 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6823 (mm) REVERT: C 314 PRO cc_start: 0.9510 (Cg_exo) cc_final: 0.8902 (Cg_endo) REVERT: D 204 TYR cc_start: 0.9482 (t80) cc_final: 0.9062 (t80) REVERT: D 313 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8327 (tm-30) outliers start: 97 outliers final: 68 residues processed: 647 average time/residue: 0.1123 time to fit residues: 111.7762 Evaluate side-chains 669 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 585 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 55 TYR Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 186 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 156 optimal weight: 10.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 28 GLN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.136969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.098255 restraints weight = 36802.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.101709 restraints weight = 18066.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.104003 restraints weight = 10864.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.105439 restraints weight = 7460.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.106503 restraints weight = 5617.944| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.7099 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= 0.240 Angle : 0.722 11.642 22134 Z= 0.375 Chirality : 0.047 0.258 2360 Planarity : 0.004 0.048 2818 Dihedral : 8.938 137.872 2291 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 5.94 % Allowed : 27.51 % Favored : 66.55 % 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: 0.71 (0.19), residues: 1932 helix: 0.94 (0.15), residues: 1149 sheet: -0.59 (0.38), residues: 148 loop : 0.10 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 117 TYR 0.022 0.002 TYR D 236 PHE 0.063 0.002 PHE C 109 TRP 0.039 0.003 TRP D 44 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.24 (16386) covalent geometry : angle 0.72209 / 0.38 (22134) hydrogen bonds : bond 0.04151 / 2.65 ( 871) hydrogen bonds : angle 5.30303 / 3.77 ( 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 699 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 597 time to evaluate : 0.437 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 31 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8619 (mp0) REVERT: A 123 SER cc_start: 0.9494 (OUTLIER) cc_final: 0.9184 (p) REVERT: A 128 PHE cc_start: 0.9542 (t80) cc_final: 0.9218 (t80) REVERT: A 139 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8373 (mt-10) REVERT: A 149 TYR cc_start: 0.9538 (t80) cc_final: 0.8716 (t80) REVERT: A 202 ASN cc_start: 0.9393 (t0) cc_final: 0.9003 (t0) REVERT: A 221 LYS cc_start: 0.9246 (mmtp) cc_final: 0.8997 (mptt) REVERT: A 255 HIS cc_start: 0.8816 (t-90) cc_final: 0.8556 (t-90) REVERT: A 259 ASN cc_start: 0.8906 (m-40) cc_final: 0.8539 (m-40) REVERT: A 263 ASP cc_start: 0.8710 (m-30) cc_final: 0.8385 (m-30) REVERT: A 277 THR cc_start: 0.8793 (p) cc_final: 0.8340 (t) REVERT: A 286 ASP cc_start: 0.8717 (m-30) cc_final: 0.8423 (m-30) REVERT: A 348 MET cc_start: 0.8980 (tmm) cc_final: 0.8486 (tmm) REVERT: A 349 LEU cc_start: 0.9656 (OUTLIER) cc_final: 0.9191 (mt) REVERT: A 350 ARG cc_start: 0.9269 (mtp180) cc_final: 0.8995 (mtp180) REVERT: A 362 ASP cc_start: 0.8268 (m-30) cc_final: 0.7400 (m-30) REVERT: A 384 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7802 (pm20) REVERT: A 393 SER cc_start: 0.9329 (m) cc_final: 0.8971 (t) REVERT: A 402 GLU cc_start: 0.8437 (mp0) cc_final: 0.7689 (mp0) REVERT: A 410 ASN cc_start: 0.8301 (OUTLIER) cc_final: 0.8058 (t160) REVERT: A 420 MET cc_start: 0.9280 (mmm) cc_final: 0.9059 (tpt) REVERT: A 426 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8328 (tm-30) REVERT: A 453 ARG cc_start: 0.9323 (OUTLIER) cc_final: 0.8932 (ttt-90) REVERT: A 493 MET cc_start: 0.9011 (tmm) cc_final: 0.8624 (tmm) REVERT: A 501 GLN cc_start: 0.9298 (OUTLIER) cc_final: 0.8838 (tt0) REVERT: A 505 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8374 (mt-10) REVERT: A 515 ASP cc_start: 0.9152 (m-30) cc_final: 0.8651 (m-30) REVERT: A 615 MET cc_start: 0.9324 (mmp) cc_final: 0.8796 (mmp) REVERT: A 686 ARG cc_start: 0.8502 (tpp80) cc_final: 0.8203 (tpp-160) REVERT: B 8 LYS cc_start: 0.9037 (tppt) cc_final: 0.8774 (tppt) REVERT: B 31 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8338 (mt-10) REVERT: B 65 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8341 (mm-30) REVERT: B 82 LYS cc_start: 0.9657 (OUTLIER) cc_final: 0.9229 (mmtt) REVERT: B 87 LYS cc_start: 0.9478 (mmmt) cc_final: 0.9273 (tppt) REVERT: B 95 MET cc_start: 0.9177 (tpp) cc_final: 0.8783 (tpp) REVERT: B 99 LYS cc_start: 0.9403 (mmtt) cc_final: 0.9069 (mmtt) REVERT: B 104 TYR cc_start: 0.9131 (m-80) cc_final: 0.8500 (m-80) REVERT: B 111 LYS cc_start: 0.9605 (mmtp) cc_final: 0.9340 (mmtm) REVERT: B 119 GLU cc_start: 0.9068 (mp0) cc_final: 0.8395 (mp0) REVERT: B 135 GLU cc_start: 0.9144 (mp0) cc_final: 0.8781 (mp0) REVERT: B 139 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8795 (mm-30) REVERT: B 147 GLN cc_start: 0.9143 (mt0) cc_final: 0.8697 (mt0) REVERT: B 149 TYR cc_start: 0.9491 (t80) cc_final: 0.9143 (t80) REVERT: B 172 LEU cc_start: 0.9422 (mp) cc_final: 0.8490 (mt) REVERT: B 202 ASN cc_start: 0.9442 (t0) cc_final: 0.9080 (t0) REVERT: B 235 ARG cc_start: 0.9070 (ttm-80) cc_final: 0.8841 (tpp80) REVERT: B 246 SER cc_start: 0.7926 (m) cc_final: 0.7561 (p) REVERT: B 250 TYR cc_start: 0.9414 (m-80) cc_final: 0.8725 (m-80) REVERT: B 257 ASP cc_start: 0.8665 (m-30) cc_final: 0.8260 (m-30) REVERT: B 263 ASP cc_start: 0.9250 (m-30) cc_final: 0.8994 (m-30) REVERT: B 276 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8382 (pttm) REVERT: B 279 SER cc_start: 0.8983 (OUTLIER) cc_final: 0.8551 (t) REVERT: B 317 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8377 (pmm) REVERT: B 322 MET cc_start: 0.9350 (mmt) cc_final: 0.8764 (mmm) REVERT: B 375 LYS cc_start: 0.9514 (mttm) cc_final: 0.9177 (mttp) REVERT: B 393 SER cc_start: 0.9378 (m) cc_final: 0.8971 (p) REVERT: B 406 ASP cc_start: 0.8113 (m-30) cc_final: 0.7825 (t0) REVERT: B 413 SER cc_start: 0.9756 (OUTLIER) cc_final: 0.9546 (p) REVERT: B 467 ASN cc_start: 0.9523 (OUTLIER) cc_final: 0.9187 (m-40) REVERT: B 474 GLN cc_start: 0.9016 (mt0) cc_final: 0.8747 (mm-40) REVERT: B 475 ASN cc_start: 0.9393 (m-40) cc_final: 0.9064 (m110) REVERT: B 515 ASP cc_start: 0.9051 (m-30) cc_final: 0.8707 (m-30) REVERT: B 546 LEU cc_start: 0.9634 (mt) cc_final: 0.9419 (mt) REVERT: B 585 SER cc_start: 0.9505 (p) cc_final: 0.8918 (t) REVERT: B 599 GLU cc_start: 0.8753 (pt0) cc_final: 0.8518 (pt0) REVERT: B 601 ILE cc_start: 0.9563 (mm) cc_final: 0.8759 (mm) REVERT: B 610 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8522 (ptmt) REVERT: B 615 MET cc_start: 0.9422 (mmp) cc_final: 0.9150 (mmp) REVERT: B 636 LYS cc_start: 0.9524 (mmmt) cc_final: 0.9230 (mmmm) REVERT: B 683 TYR cc_start: 0.9173 (t80) cc_final: 0.8620 (t80) REVERT: B 684 TYR cc_start: 0.8159 (OUTLIER) cc_final: 0.7187 (m-80) REVERT: C 21 PHE cc_start: 0.8549 (m-80) cc_final: 0.7975 (m-80) REVERT: C 127 GLN cc_start: 0.8627 (mm110) cc_final: 0.7407 (pp30) REVERT: C 154 PHE cc_start: 0.9081 (t80) cc_final: 0.8401 (t80) REVERT: C 212 ILE cc_start: 0.6472 (mm) cc_final: 0.5531 (mm) REVERT: C 242 TYR cc_start: 0.9075 (t80) cc_final: 0.8871 (m-80) REVERT: C 318 ASP cc_start: 0.9186 (m-30) cc_final: 0.8843 (t0) REVERT: D 204 TYR cc_start: 0.9527 (t80) cc_final: 0.9144 (t80) REVERT: D 313 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8264 (tm-30) outliers start: 102 outliers final: 71 residues processed: 644 average time/residue: 0.1055 time to fit residues: 104.3277 Evaluate side-chains 658 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 572 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 55 TYR Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 134 optimal weight: 0.5980 chunk 153 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 97 optimal weight: 0.4980 chunk 151 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.138744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.098301 restraints weight = 37018.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.101708 restraints weight = 18217.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.104044 restraints weight = 11504.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.105741 restraints weight = 7889.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.106840 restraints weight = 5881.473| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.7274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16386 Z= 0.139 Angle : 0.721 11.586 22134 Z= 0.364 Chirality : 0.046 0.296 2360 Planarity : 0.004 0.038 2818 Dihedral : 8.502 137.203 2291 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.14 % Allowed : 30.24 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.78 (0.19), residues: 1932 helix: 0.98 (0.15), residues: 1129 sheet: -0.48 (0.40), residues: 140 loop : 0.16 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 117 TYR 0.023 0.001 TYR D 236 PHE 0.063 0.002 PHE C 109 TRP 0.031 0.002 TRP D 44 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (16386) covalent geometry : angle 0.72101 / 0.36 (22134) hydrogen bonds : bond 0.04035 / 2.59 ( 871) hydrogen bonds : angle 5.19062 / 3.68 ( 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 673 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 602 time to evaluate : 0.603 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 31 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8631 (mp0) REVERT: A 65 GLU cc_start: 0.8544 (mm-30) cc_final: 0.7878 (mp0) REVERT: A 128 PHE cc_start: 0.9466 (t80) cc_final: 0.9119 (t80) REVERT: A 139 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8368 (mt-10) REVERT: A 149 TYR cc_start: 0.9560 (t80) cc_final: 0.8518 (t80) REVERT: A 202 ASN cc_start: 0.9221 (t0) cc_final: 0.8850 (t0) REVERT: A 220 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8918 (t) REVERT: A 228 LYS cc_start: 0.9141 (mmtm) cc_final: 0.8874 (mttm) REVERT: A 255 HIS cc_start: 0.8733 (t-90) cc_final: 0.8533 (t-90) REVERT: A 263 ASP cc_start: 0.8698 (m-30) cc_final: 0.8361 (m-30) REVERT: A 277 THR cc_start: 0.8611 (p) cc_final: 0.8176 (t) REVERT: A 286 ASP cc_start: 0.8706 (m-30) cc_final: 0.8477 (m-30) REVERT: A 290 GLU cc_start: 0.9069 (tm-30) cc_final: 0.8582 (tm-30) REVERT: A 348 MET cc_start: 0.8896 (tmm) cc_final: 0.8400 (tmm) REVERT: A 362 ASP cc_start: 0.8220 (m-30) cc_final: 0.7335 (m-30) REVERT: A 377 LYS cc_start: 0.9047 (mttm) cc_final: 0.8486 (mttp) REVERT: A 384 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7706 (pm20) REVERT: A 393 SER cc_start: 0.9313 (m) cc_final: 0.8983 (t) REVERT: A 402 GLU cc_start: 0.8477 (mp0) cc_final: 0.7687 (mp0) REVERT: A 410 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.8065 (t160) REVERT: A 420 MET cc_start: 0.9264 (mmm) cc_final: 0.9049 (tpt) REVERT: A 426 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8233 (tm-30) REVERT: A 446 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7500 (mtp85) REVERT: A 493 MET cc_start: 0.8954 (tmm) cc_final: 0.8560 (tmm) REVERT: A 505 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8332 (mt-10) REVERT: A 515 ASP cc_start: 0.9076 (m-30) cc_final: 0.8638 (m-30) REVERT: A 615 MET cc_start: 0.9310 (mmp) cc_final: 0.8738 (mmp) REVERT: A 640 MET cc_start: 0.9501 (tpp) cc_final: 0.8139 (tpp) REVERT: A 686 ARG cc_start: 0.8508 (tpp80) cc_final: 0.8165 (tpp-160) REVERT: B 8 LYS cc_start: 0.9031 (tppt) cc_final: 0.8658 (tppt) REVERT: B 12 LEU cc_start: 0.9245 (mt) cc_final: 0.8963 (mt) REVERT: B 31 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8254 (mt-10) REVERT: B 65 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8302 (mm-30) REVERT: B 82 LYS cc_start: 0.9636 (OUTLIER) cc_final: 0.9222 (mmtt) REVERT: B 95 MET cc_start: 0.9126 (tpp) cc_final: 0.8733 (tpp) REVERT: B 99 LYS cc_start: 0.9383 (mmtt) cc_final: 0.9150 (mmtt) REVERT: B 111 LYS cc_start: 0.9566 (mmtp) cc_final: 0.9294 (mmtm) REVERT: B 119 GLU cc_start: 0.8969 (mp0) cc_final: 0.8279 (mp0) REVERT: B 127 LEU cc_start: 0.9701 (mm) cc_final: 0.9347 (mm) REVERT: B 135 GLU cc_start: 0.9089 (mp0) cc_final: 0.8714 (mp0) REVERT: B 139 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8763 (mm-30) REVERT: B 149 TYR cc_start: 0.9395 (t80) cc_final: 0.9067 (t80) REVERT: B 246 SER cc_start: 0.7847 (m) cc_final: 0.7504 (p) REVERT: B 250 TYR cc_start: 0.9377 (m-80) cc_final: 0.8592 (m-80) REVERT: B 257 ASP cc_start: 0.8601 (m-30) cc_final: 0.8128 (m-30) REVERT: B 263 ASP cc_start: 0.9218 (m-30) cc_final: 0.8976 (m-30) REVERT: B 279 SER cc_start: 0.8958 (OUTLIER) cc_final: 0.8605 (t) REVERT: B 317 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8215 (pmm) REVERT: B 322 MET cc_start: 0.9293 (mmt) cc_final: 0.8969 (mmm) REVERT: B 362 ASP cc_start: 0.8689 (m-30) cc_final: 0.8266 (m-30) REVERT: B 375 LYS cc_start: 0.9498 (mttm) cc_final: 0.9133 (mtmm) REVERT: B 387 GLN cc_start: 0.9163 (mt0) cc_final: 0.8845 (mt0) REVERT: B 393 SER cc_start: 0.9396 (m) cc_final: 0.9020 (p) REVERT: B 435 SER cc_start: 0.9817 (OUTLIER) cc_final: 0.9457 (t) REVERT: B 467 ASN cc_start: 0.9153 (OUTLIER) cc_final: 0.8795 (m-40) REVERT: B 474 GLN cc_start: 0.9059 (mt0) cc_final: 0.8848 (mm110) REVERT: B 475 ASN cc_start: 0.9343 (m-40) cc_final: 0.8983 (m110) REVERT: B 480 GLU cc_start: 0.8766 (mp0) cc_final: 0.8048 (mp0) REVERT: B 493 MET cc_start: 0.9544 (tmm) cc_final: 0.9206 (tmm) REVERT: B 494 MET cc_start: 0.9309 (mtt) cc_final: 0.8926 (mmt) REVERT: B 515 ASP cc_start: 0.9009 (m-30) cc_final: 0.8620 (m-30) REVERT: B 550 MET cc_start: 0.7896 (mtp) cc_final: 0.7596 (mtp) REVERT: B 585 SER cc_start: 0.9486 (p) cc_final: 0.8866 (t) REVERT: B 599 GLU cc_start: 0.8728 (pt0) cc_final: 0.8436 (pt0) REVERT: B 601 ILE cc_start: 0.9513 (mm) cc_final: 0.8628 (mm) REVERT: B 610 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8615 (ptmt) REVERT: B 630 TYR cc_start: 0.9222 (m-80) cc_final: 0.8935 (m-10) REVERT: B 632 MET cc_start: 0.8488 (mtp) cc_final: 0.7507 (mtp) REVERT: B 683 TYR cc_start: 0.9091 (t80) cc_final: 0.8618 (t80) REVERT: B 684 TYR cc_start: 0.8044 (OUTLIER) cc_final: 0.7424 (m-80) REVERT: C 21 PHE cc_start: 0.8409 (m-80) cc_final: 0.7873 (m-80) REVERT: C 137 MET cc_start: 0.8982 (mmp) cc_final: 0.8314 (mtt) REVERT: C 154 PHE cc_start: 0.9130 (t80) cc_final: 0.8467 (t80) REVERT: C 212 ILE cc_start: 0.6410 (mm) cc_final: 0.5603 (mm) REVERT: C 242 TYR cc_start: 0.9118 (t80) cc_final: 0.8761 (t80) REVERT: C 318 ASP cc_start: 0.9230 (m-30) cc_final: 0.8858 (t0) REVERT: D 137 MET cc_start: 0.1158 (mmt) cc_final: 0.0041 (mtm) REVERT: D 204 TYR cc_start: 0.9558 (t80) cc_final: 0.9220 (t80) outliers start: 71 outliers final: 40 residues processed: 636 average time/residue: 0.1135 time to fit residues: 110.7861 Evaluate side-chains 613 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 561 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 232 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 6.9990 chunk 133 optimal weight: 0.3980 chunk 149 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.138379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.099057 restraints weight = 36756.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.102667 restraints weight = 18225.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.105054 restraints weight = 11038.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.106607 restraints weight = 7588.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.107705 restraints weight = 5713.716| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.7515 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= 0.152 Angle : 0.756 12.665 22134 Z= 0.383 Chirality : 0.046 0.277 2360 Planarity : 0.004 0.035 2818 Dihedral : 8.406 139.120 2291 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.61 % Allowed : 31.41 % Favored : 64.98 % 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: 0.68 (0.19), residues: 1932 helix: 0.91 (0.15), residues: 1129 sheet: -0.44 (0.40), residues: 140 loop : 0.07 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 117 TYR 0.044 0.002 TYR D 105 PHE 0.065 0.002 PHE C 109 TRP 0.048 0.002 TRP D 44 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (16386) covalent geometry : angle 0.75635 / 0.38 (22134) hydrogen bonds : bond 0.04143 / 2.67 ( 871) hydrogen bonds : angle 5.25442 / 3.73 ( 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 646 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 584 time to evaluate : 0.667 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 31 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8574 (mp0) REVERT: A 128 PHE cc_start: 0.9499 (t80) cc_final: 0.9116 (t80) REVERT: A 135 GLU cc_start: 0.8940 (mp0) cc_final: 0.8701 (pm20) REVERT: A 139 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8363 (mt-10) REVERT: A 147 GLN cc_start: 0.9085 (mm-40) cc_final: 0.8693 (mm-40) REVERT: A 149 TYR cc_start: 0.9608 (t80) cc_final: 0.8677 (t80) REVERT: A 150 GLN cc_start: 0.9384 (tp40) cc_final: 0.8949 (tm-30) REVERT: A 161 ARG cc_start: 0.8427 (ttm110) cc_final: 0.7656 (mtp180) REVERT: A 202 ASN cc_start: 0.9278 (t0) cc_final: 0.8917 (t0) REVERT: A 220 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8950 (t) REVERT: A 228 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8789 (mttm) REVERT: A 255 HIS cc_start: 0.8677 (t-90) cc_final: 0.8400 (t-90) REVERT: A 263 ASP cc_start: 0.8703 (m-30) cc_final: 0.8347 (m-30) REVERT: A 277 THR cc_start: 0.8549 (p) cc_final: 0.8152 (t) REVERT: A 286 ASP cc_start: 0.8745 (m-30) cc_final: 0.8493 (m-30) REVERT: A 290 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8628 (tm-30) REVERT: A 348 MET cc_start: 0.8894 (tmm) cc_final: 0.8465 (tmm) REVERT: A 362 ASP cc_start: 0.8183 (m-30) cc_final: 0.7273 (m-30) REVERT: A 384 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.7619 (pm20) REVERT: A 393 SER cc_start: 0.9325 (m) cc_final: 0.8837 (p) REVERT: A 402 GLU cc_start: 0.8477 (mp0) cc_final: 0.7716 (mp0) REVERT: A 410 ASN cc_start: 0.8252 (OUTLIER) cc_final: 0.8049 (t160) REVERT: A 420 MET cc_start: 0.9288 (mmm) cc_final: 0.8983 (mmm) REVERT: A 426 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8276 (tm-30) REVERT: A 446 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7551 (mmm160) REVERT: A 467 ASN cc_start: 0.9103 (t0) cc_final: 0.8879 (m-40) REVERT: A 475 ASN cc_start: 0.9185 (m-40) cc_final: 0.8904 (m-40) REVERT: A 493 MET cc_start: 0.8916 (tmm) cc_final: 0.8513 (tmm) REVERT: A 505 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8414 (mt-10) REVERT: A 515 ASP cc_start: 0.9111 (m-30) cc_final: 0.8695 (m-30) REVERT: A 615 MET cc_start: 0.9321 (mmp) cc_final: 0.8714 (mmp) REVERT: A 640 MET cc_start: 0.9418 (tpp) cc_final: 0.8246 (tpp) REVERT: A 686 ARG cc_start: 0.8578 (tpp80) cc_final: 0.8224 (tpp-160) REVERT: B 8 LYS cc_start: 0.9040 (tppt) cc_final: 0.8673 (tppt) REVERT: B 12 LEU cc_start: 0.9254 (mt) cc_final: 0.8964 (mt) REVERT: B 31 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8229 (mt-10) REVERT: B 65 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8332 (mm-30) REVERT: B 75 GLU cc_start: 0.9126 (mp0) cc_final: 0.8873 (pm20) REVERT: B 82 LYS cc_start: 0.9633 (OUTLIER) cc_final: 0.9192 (mmtt) REVERT: B 87 LYS cc_start: 0.9190 (tppt) cc_final: 0.8910 (tptm) REVERT: B 95 MET cc_start: 0.9205 (tpp) cc_final: 0.8761 (tpp) REVERT: B 99 LYS cc_start: 0.9372 (mmtt) cc_final: 0.9111 (mmtt) REVERT: B 107 LYS cc_start: 0.9284 (mtpp) cc_final: 0.8769 (mtpp) REVERT: B 111 LYS cc_start: 0.9549 (mmtp) cc_final: 0.9347 (mmtm) REVERT: B 119 GLU cc_start: 0.8988 (mp0) cc_final: 0.8327 (mp0) REVERT: B 127 LEU cc_start: 0.9701 (mm) cc_final: 0.9305 (mm) REVERT: B 135 GLU cc_start: 0.9089 (mp0) cc_final: 0.8679 (mp0) REVERT: B 139 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8825 (mm-30) REVERT: B 147 GLN cc_start: 0.9419 (mt0) cc_final: 0.9133 (mt0) REVERT: B 149 TYR cc_start: 0.9311 (t80) cc_final: 0.8817 (t80) REVERT: B 235 ARG cc_start: 0.9277 (tpp80) cc_final: 0.8950 (ttm-80) REVERT: B 246 SER cc_start: 0.7786 (m) cc_final: 0.7507 (p) REVERT: B 250 TYR cc_start: 0.9363 (m-80) cc_final: 0.8523 (m-80) REVERT: B 257 ASP cc_start: 0.8643 (m-30) cc_final: 0.8159 (m-30) REVERT: B 263 ASP cc_start: 0.9237 (m-30) cc_final: 0.8971 (m-30) REVERT: B 279 SER cc_start: 0.8932 (m) cc_final: 0.8598 (t) REVERT: B 317 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8175 (pmm) REVERT: B 322 MET cc_start: 0.9304 (mmt) cc_final: 0.8997 (mmm) REVERT: B 362 ASP cc_start: 0.8699 (m-30) cc_final: 0.8440 (m-30) REVERT: B 375 LYS cc_start: 0.9506 (mttm) cc_final: 0.9127 (mtmm) REVERT: B 393 SER cc_start: 0.9347 (m) cc_final: 0.9019 (p) REVERT: B 467 ASN cc_start: 0.9284 (OUTLIER) cc_final: 0.9014 (m-40) REVERT: B 474 GLN cc_start: 0.9106 (mt0) cc_final: 0.8842 (mm-40) REVERT: B 475 ASN cc_start: 0.9296 (m-40) cc_final: 0.9011 (m110) REVERT: B 480 GLU cc_start: 0.8803 (mp0) cc_final: 0.8134 (mp0) REVERT: B 493 MET cc_start: 0.9542 (tmm) cc_final: 0.9310 (tmm) REVERT: B 515 ASP cc_start: 0.8994 (m-30) cc_final: 0.8625 (m-30) REVERT: B 599 GLU cc_start: 0.8807 (pt0) cc_final: 0.8458 (pt0) REVERT: B 601 ILE cc_start: 0.9564 (mm) cc_final: 0.8659 (mm) REVERT: B 610 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8682 (ptmt) REVERT: B 630 TYR cc_start: 0.9262 (m-80) cc_final: 0.9001 (m-10) REVERT: B 632 MET cc_start: 0.8439 (mtp) cc_final: 0.7587 (mtp) REVERT: B 640 MET cc_start: 0.9355 (tpp) cc_final: 0.8990 (tpp) REVERT: B 683 TYR cc_start: 0.9041 (t80) cc_final: 0.8691 (t80) REVERT: B 684 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.7458 (m-80) REVERT: B 686 ARG cc_start: 0.8656 (mmt180) cc_final: 0.8447 (mmt180) REVERT: C 19 GLN cc_start: 0.8955 (mp10) cc_final: 0.8483 (pm20) REVERT: C 21 PHE cc_start: 0.8485 (m-80) cc_final: 0.8243 (m-80) REVERT: C 154 PHE cc_start: 0.9116 (t80) cc_final: 0.8445 (t80) REVERT: C 204 TYR cc_start: 0.8693 (t80) cc_final: 0.8195 (t80) REVERT: C 212 ILE cc_start: 0.6431 (mm) cc_final: 0.5641 (mm) REVERT: C 318 ASP cc_start: 0.9236 (m-30) cc_final: 0.8867 (t0) REVERT: D 25 ASN cc_start: 0.9196 (t0) cc_final: 0.8945 (p0) REVERT: D 137 MET cc_start: 0.1356 (mmt) cc_final: 0.0470 (mtm) REVERT: D 204 TYR cc_start: 0.9597 (t80) cc_final: 0.9228 (t80) REVERT: D 313 GLU cc_start: 0.9123 (tt0) cc_final: 0.8694 (tm-30) REVERT: D 316 LYS cc_start: 0.9138 (ttmm) cc_final: 0.8865 (tmmt) outliers start: 62 outliers final: 41 residues processed: 612 average time/residue: 0.1187 time to fit residues: 111.9657 Evaluate side-chains 617 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 565 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 232 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 189 optimal weight: 0.9990 chunk 181 optimal weight: 4.9990 chunk 165 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 54 optimal weight: 0.0970 chunk 132 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.141510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.102301 restraints weight = 36616.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.106023 restraints weight = 17993.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.108479 restraints weight = 10792.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.110033 restraints weight = 7362.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.111086 restraints weight = 5522.837| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.7767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16386 Z= 0.147 Angle : 0.794 13.258 22134 Z= 0.398 Chirality : 0.047 0.352 2360 Planarity : 0.004 0.035 2818 Dihedral : 8.160 140.084 2291 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.09 % Allowed : 33.04 % Favored : 63.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.19), residues: 1932 helix: 0.86 (0.15), residues: 1136 sheet: -0.40 (0.41), residues: 140 loop : -0.02 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 117 TYR 0.045 0.002 TYR D 105 PHE 0.065 0.002 PHE C 109 TRP 0.048 0.002 TRP D 44 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (16386) covalent geometry : angle 0.79394 / 0.40 (22134) hydrogen bonds : bond 0.04181 / 2.68 ( 871) hydrogen bonds : angle 5.24707 / 3.72 ( 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 650 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 597 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8557 (mp0) REVERT: A 65 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8017 (mp0) REVERT: A 139 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8358 (mt-10) REVERT: A 149 TYR cc_start: 0.9604 (t80) cc_final: 0.8658 (t80) REVERT: A 150 GLN cc_start: 0.9372 (tp40) cc_final: 0.8709 (tm-30) REVERT: A 161 ARG cc_start: 0.8428 (ttm110) cc_final: 0.7582 (mtp180) REVERT: A 202 ASN cc_start: 0.9182 (t0) cc_final: 0.8884 (t0) REVERT: A 209 LYS cc_start: 0.8832 (tptp) cc_final: 0.8558 (tppp) REVERT: A 228 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8709 (mttm) REVERT: A 255 HIS cc_start: 0.8621 (t-90) cc_final: 0.8341 (t-90) REVERT: A 263 ASP cc_start: 0.8612 (m-30) cc_final: 0.8263 (m-30) REVERT: A 277 THR cc_start: 0.8574 (p) cc_final: 0.8107 (t) REVERT: A 286 ASP cc_start: 0.8744 (m-30) cc_final: 0.8507 (m-30) REVERT: A 290 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8622 (tm-30) REVERT: A 348 MET cc_start: 0.8927 (tmm) cc_final: 0.8456 (tmm) REVERT: A 350 ARG cc_start: 0.9254 (mtp180) cc_final: 0.8907 (mtp180) REVERT: A 362 ASP cc_start: 0.8156 (m-30) cc_final: 0.7288 (m-30) REVERT: A 377 LYS cc_start: 0.9071 (mttm) cc_final: 0.8538 (mttp) REVERT: A 384 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7611 (pm20) REVERT: A 393 SER cc_start: 0.9314 (m) cc_final: 0.8849 (p) REVERT: A 402 GLU cc_start: 0.8436 (mp0) cc_final: 0.7683 (mp0) REVERT: A 426 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8240 (tm-30) REVERT: A 446 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7220 (mtp85) REVERT: A 458 MET cc_start: 0.9103 (mmm) cc_final: 0.8178 (tpp) REVERT: A 493 MET cc_start: 0.8912 (tmm) cc_final: 0.8417 (tmm) REVERT: A 505 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8325 (mt-10) REVERT: A 515 ASP cc_start: 0.9102 (m-30) cc_final: 0.8703 (m-30) REVERT: A 584 ILE cc_start: 0.9468 (pt) cc_final: 0.9086 (pt) REVERT: A 590 SER cc_start: 0.9411 (t) cc_final: 0.9002 (p) REVERT: A 615 MET cc_start: 0.9303 (mmp) cc_final: 0.8672 (mmp) REVERT: A 677 ARG cc_start: 0.9149 (tpp80) cc_final: 0.8720 (tpp80) REVERT: A 686 ARG cc_start: 0.8596 (tpp80) cc_final: 0.8281 (tpp-160) REVERT: B 31 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8230 (mt-10) REVERT: B 65 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8272 (mm-30) REVERT: B 82 LYS cc_start: 0.9625 (OUTLIER) cc_final: 0.9186 (mmtt) REVERT: B 95 MET cc_start: 0.9180 (tpp) cc_final: 0.8726 (tpp) REVERT: B 99 LYS cc_start: 0.9332 (mmtt) cc_final: 0.9128 (mmtt) REVERT: B 107 LYS cc_start: 0.9219 (mtpp) cc_final: 0.8726 (mtpp) REVERT: B 119 GLU cc_start: 0.8959 (mp0) cc_final: 0.8317 (mp0) REVERT: B 127 LEU cc_start: 0.9691 (mm) cc_final: 0.9300 (mm) REVERT: B 135 GLU cc_start: 0.9084 (mp0) cc_final: 0.8642 (mp0) REVERT: B 139 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8819 (mm-30) REVERT: B 191 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8143 (mt0) REVERT: B 235 ARG cc_start: 0.9246 (tpp80) cc_final: 0.8963 (ttm-80) REVERT: B 236 TYR cc_start: 0.9180 (t80) cc_final: 0.8722 (t80) REVERT: B 246 SER cc_start: 0.7747 (m) cc_final: 0.7428 (p) REVERT: B 250 TYR cc_start: 0.9329 (m-80) cc_final: 0.8433 (m-80) REVERT: B 257 ASP cc_start: 0.8636 (m-30) cc_final: 0.8171 (m-30) REVERT: B 263 ASP cc_start: 0.9223 (m-30) cc_final: 0.8948 (m-30) REVERT: B 279 SER cc_start: 0.8883 (m) cc_final: 0.8523 (t) REVERT: B 317 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8172 (pmm) REVERT: B 322 MET cc_start: 0.9319 (mmt) cc_final: 0.8991 (mmm) REVERT: B 375 LYS cc_start: 0.9460 (mttm) cc_final: 0.9080 (mtmm) REVERT: B 393 SER cc_start: 0.9326 (m) cc_final: 0.9010 (p) REVERT: B 396 ASP cc_start: 0.8590 (p0) cc_final: 0.8299 (p0) REVERT: B 467 ASN cc_start: 0.9121 (OUTLIER) cc_final: 0.8901 (m-40) REVERT: B 475 ASN cc_start: 0.9287 (m-40) cc_final: 0.8969 (m110) REVERT: B 480 GLU cc_start: 0.8789 (mp0) cc_final: 0.8268 (mp0) REVERT: B 493 MET cc_start: 0.9545 (tmm) cc_final: 0.9221 (tmm) REVERT: B 515 ASP cc_start: 0.8957 (m-30) cc_final: 0.8564 (m-30) REVERT: B 599 GLU cc_start: 0.8833 (pt0) cc_final: 0.8469 (pt0) REVERT: B 601 ILE cc_start: 0.9577 (mm) cc_final: 0.8669 (mm) REVERT: B 632 MET cc_start: 0.8389 (mtp) cc_final: 0.7527 (mtp) REVERT: B 640 MET cc_start: 0.9292 (tpp) cc_final: 0.8924 (tpp) REVERT: B 683 TYR cc_start: 0.9073 (t80) cc_final: 0.8652 (t80) REVERT: B 684 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.7447 (m-80) REVERT: B 686 ARG cc_start: 0.8683 (mmt180) cc_final: 0.8424 (mmt180) REVERT: C 21 PHE cc_start: 0.8468 (m-80) cc_final: 0.8210 (m-80) REVERT: C 154 PHE cc_start: 0.9116 (t80) cc_final: 0.8477 (t80) REVERT: C 204 TYR cc_start: 0.8567 (t80) cc_final: 0.8065 (t80) REVERT: C 212 ILE cc_start: 0.6402 (mm) cc_final: 0.5614 (mm) REVERT: C 242 TYR cc_start: 0.8996 (t80) cc_final: 0.8781 (m-80) REVERT: C 318 ASP cc_start: 0.9249 (m-30) cc_final: 0.8876 (t0) REVERT: D 25 ASN cc_start: 0.9056 (t0) cc_final: 0.8835 (p0) REVERT: D 46 TYR cc_start: 0.8276 (m-10) cc_final: 0.8040 (m-80) REVERT: D 55 TYR cc_start: 0.5965 (m-10) cc_final: 0.5609 (m-10) REVERT: D 137 MET cc_start: 0.1443 (mmt) cc_final: 0.0591 (mtm) REVERT: D 204 TYR cc_start: 0.9579 (t80) cc_final: 0.9257 (t80) REVERT: D 240 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7993 (mm) REVERT: D 313 GLU cc_start: 0.9048 (tt0) cc_final: 0.8754 (tm-30) outliers start: 53 outliers final: 37 residues processed: 619 average time/residue: 0.1127 time to fit residues: 107.7145 Evaluate side-chains 626 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 580 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR 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: 6.9990 chunk 1 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 39 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 148 optimal weight: 6.9990 chunk 125 optimal weight: 0.0670 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.141368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.101666 restraints weight = 36508.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.105334 restraints weight = 18057.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.107760 restraints weight = 10924.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.109312 restraints weight = 7508.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.110410 restraints weight = 5647.605| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.7947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16386 Z= 0.151 Angle : 0.821 13.755 22134 Z= 0.409 Chirality : 0.048 0.349 2360 Planarity : 0.004 0.042 2818 Dihedral : 8.058 140.920 2291 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.86 % Allowed : 33.92 % Favored : 63.23 % 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: 0.53 (0.18), residues: 1932 helix: 0.81 (0.15), residues: 1122 sheet: -0.16 (0.42), residues: 136 loop : -0.13 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 117 TYR 0.037 0.002 TYR B 571 PHE 0.072 0.002 PHE C 109 TRP 0.047 0.002 TRP D 44 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (16386) covalent geometry : angle 0.82097 / 0.41 (22134) hydrogen bonds : bond 0.04208 / 2.70 ( 871) hydrogen bonds : angle 5.30230 / 3.76 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3208.18 seconds wall clock time: 56 minutes 18.22 seconds (3378.22 seconds total)