Starting phenix.real_space_refine on Thu Sep 18 10:01:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz5_45053/09_2025/9bz5_45053_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz5_45053/09_2025/9bz5_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bz5_45053/09_2025/9bz5_45053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz5_45053/09_2025/9bz5_45053.map" model { file = "/net/cci-nas-00/data/ceres_data/9bz5_45053/09_2025/9bz5_45053_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz5_45053/09_2025/9bz5_45053_neut.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.48, per 1000 atoms: 0.22 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: 1.50 Conformation dependent library (CDL) restraints added in 835.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.104A 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: 2.81 Time building geometry restraints manager: 1.93 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=" 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=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.038 1.20e-02 6.94e+03 1.02e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.574 -0.031 1.08e-02 8.57e+03 8.45e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.569 -0.032 1.17e-02 7.31e+03 7.55e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.574 -0.034 1.25e-02 6.40e+03 7.21e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21571 2.09 - 4.18: 521 4.18 - 6.27: 37 6.27 - 8.36: 1 8.36 - 10.45: 4 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.59 -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 - 35.81: 9470 35.81 - 71.61: 337 71.61 - 107.42: 37 107.42 - 143.23: 3 143.23 - 179.04: 3 Dihedral angle restraints: 9850 sinusoidal: 4092 harmonic: 5758 Sorted by residual: dihedral pdb=" C2 TTP A 803 " pdb=" C1' TTP A 803 " pdb=" N1 TTP A 803 " pdb=" O4' TTP A 803 " ideal model delta sinusoidal sigma weight residual -58.32 120.72 -179.04 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 TTP B 801 " pdb=" C1' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " ideal model delta sinusoidal sigma weight residual 301.68 151.17 150.51 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" C5' TTP A 803 " pdb=" O5' TTP A 803 " pdb=" PA TTP A 803 " pdb=" O3A TTP A 803 " ideal model delta sinusoidal sigma weight residual 179.97 31.92 148.05 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 9847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2141 0.094 - 0.187: 187 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.870 Find NCS groups from input model: 0.220 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: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 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 0.061 16386 Z= 0.316 Angle : 0.740 10.451 22134 Z= 0.463 Chirality : 0.058 0.468 2360 Planarity : 0.003 0.042 2818 Dihedral : 17.953 179.036 6154 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 aren 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 covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.74017 (22134) hydrogen bonds : bond 0.15420 ( 871) hydrogen bonds : angle 6.51762 ( 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 : 0.610 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: 0.8013 (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: 0.7468 (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: 0.7411 (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: 0.8851 (t) cc_final: 0.8337 (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: 0.1352 time to fit residues: 195.8233 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 : 0.646 ------------------------------------------------------------------------------- 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: 2.9990 chunk 149 optimal weight: 0.0030 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 304 HIS A 312 GLN 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.149270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.106453 restraints weight = 35951.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.110339 restraints weight = 18078.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.112876 restraints weight = 10951.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.114614 restraints weight = 7523.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.115767 restraints weight = 5643.126| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16386 Z= 0.219 Angle : 0.720 9.779 22134 Z= 0.378 Chirality : 0.046 0.291 2360 Planarity : 0.004 0.035 2818 Dihedral : 11.488 167.785 2251 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 4.31 % Allowed : 21.85 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.19), residues: 1932 helix: 1.31 (0.15), residues: 1142 sheet: 0.05 (0.42), residues: 130 loop : 0.56 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 293 TYR 0.031 0.002 TYR C 162 PHE 0.030 0.002 PHE C 259 TRP 0.023 0.002 TRP B 558 HIS 0.010 0.002 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00482 (16386) covalent geometry : angle 0.72014 (22134) hydrogen bonds : bond 0.04836 ( 871) hydrogen bonds : angle 5.20472 ( 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 795 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 721 time to evaluate : 0.661 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: A 55 LEU cc_start: 0.9787 (mt) cc_final: 0.9468 (pp) REVERT: A 76 ASP cc_start: 0.9095 (m-30) cc_final: 0.8851 (m-30) REVERT: A 123 SER cc_start: 0.9655 (OUTLIER) cc_final: 0.9241 (p) REVERT: A 139 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8319 (mt-10) REVERT: A 202 ASN cc_start: 0.9537 (t0) cc_final: 0.9153 (t0) REVERT: A 221 LYS cc_start: 0.9229 (mmtp) cc_final: 0.8936 (mttt) REVERT: A 246 SER cc_start: 0.7824 (m) cc_final: 0.7483 (p) REVERT: A 255 HIS cc_start: 0.8624 (t-90) cc_final: 0.8197 (t-90) REVERT: A 257 ASP cc_start: 0.9353 (m-30) cc_final: 0.8915 (m-30) REVERT: A 259 ASN cc_start: 0.8826 (m-40) cc_final: 0.8595 (m-40) REVERT: A 261 PHE cc_start: 0.9432 (t80) cc_final: 0.9131 (t80) REVERT: A 277 THR cc_start: 0.8858 (p) cc_final: 0.8532 (t) REVERT: A 279 SER cc_start: 0.8987 (m) cc_final: 0.8679 (p) REVERT: A 322 MET cc_start: 0.8988 (mmm) cc_final: 0.8179 (mmm) REVERT: A 335 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7901 (mm-30) REVERT: A 348 MET cc_start: 0.8763 (tmm) cc_final: 0.8315 (tmm) REVERT: A 379 SER cc_start: 0.9439 (t) cc_final: 0.9152 (t) REVERT: A 393 SER cc_start: 0.9410 (m) cc_final: 0.9123 (p) REVERT: A 402 GLU cc_start: 0.7966 (mp0) cc_final: 0.7600 (mp0) REVERT: A 505 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8390 (mt-10) REVERT: A 509 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8642 (mm-30) REVERT: A 515 ASP cc_start: 0.9013 (m-30) cc_final: 0.8355 (m-30) REVERT: A 602 GLU cc_start: 0.7504 (pt0) cc_final: 0.7210 (pt0) REVERT: A 606 TYR cc_start: 0.8162 (m-80) cc_final: 0.7197 (m-80) REVERT: A 615 MET cc_start: 0.9079 (mmp) cc_final: 0.8615 (mmm) REVERT: A 618 LEU cc_start: 0.9379 (tp) cc_final: 0.9165 (tt) REVERT: A 639 ASP cc_start: 0.9026 (m-30) cc_final: 0.8293 (m-30) REVERT: A 640 MET cc_start: 0.9321 (tpp) cc_final: 0.8653 (tpp) REVERT: B 26 PHE cc_start: 0.9145 (m-80) cc_final: 0.8922 (m-10) REVERT: B 31 GLU cc_start: 0.8712 (mp0) cc_final: 0.8409 (mp0) REVERT: B 65 GLU cc_start: 0.8467 (mm-30) cc_final: 0.7815 (mm-30) REVERT: B 68 PHE cc_start: 0.9054 (p90) cc_final: 0.8789 (p90) REVERT: B 119 GLU cc_start: 0.9176 (mp0) cc_final: 0.8679 (mp0) REVERT: B 121 ARG cc_start: 0.9518 (tpm170) cc_final: 0.9113 (tpp-160) REVERT: B 128 PHE cc_start: 0.9588 (t80) cc_final: 0.9367 (t80) REVERT: B 139 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8888 (mm-30) REVERT: B 149 TYR cc_start: 0.9394 (t80) cc_final: 0.9076 (t80) REVERT: B 150 GLN cc_start: 0.9428 (tp40) cc_final: 0.9219 (tp-100) REVERT: B 174 GLU cc_start: 0.8543 (tp30) cc_final: 0.8103 (tp30) REVERT: B 202 ASN cc_start: 0.9389 (t0) cc_final: 0.8981 (t0) REVERT: B 236 TYR cc_start: 0.9102 (t80) cc_final: 0.8513 (t80) REVERT: B 246 SER cc_start: 0.7856 (m) cc_final: 0.7474 (p) REVERT: B 250 TYR cc_start: 0.9019 (m-80) cc_final: 0.8815 (m-80) REVERT: B 257 ASP cc_start: 0.8694 (m-30) cc_final: 0.8195 (m-30) REVERT: B 279 SER cc_start: 0.8806 (m) cc_final: 0.8361 (t) REVERT: B 348 MET cc_start: 0.9139 (ptm) cc_final: 0.8753 (ptm) REVERT: B 393 SER cc_start: 0.9425 (m) cc_final: 0.8943 (p) REVERT: B 396 ASP cc_start: 0.8774 (p0) cc_final: 0.8467 (p0) REVERT: B 411 LEU cc_start: 0.9180 (mp) cc_final: 0.8960 (mp) REVERT: B 415 ASN cc_start: 0.9458 (t0) cc_final: 0.9249 (t0) REVERT: B 446 ARG cc_start: 0.7857 (mtp85) cc_final: 0.7573 (mtp85) REVERT: B 471 TYR cc_start: 0.9400 (t80) cc_final: 0.8523 (t80) REVERT: B 474 GLN cc_start: 0.8925 (mt0) cc_final: 0.8603 (mm-40) REVERT: B 475 ASN cc_start: 0.9256 (m-40) cc_final: 0.8557 (m110) REVERT: B 515 ASP cc_start: 0.9035 (m-30) cc_final: 0.8831 (m-30) REVERT: B 546 LEU cc_start: 0.9578 (mt) cc_final: 0.9267 (mt) REVERT: B 601 ILE cc_start: 0.9472 (mm) cc_final: 0.9092 (mm) REVERT: B 610 LYS cc_start: 0.8768 (ptmt) cc_final: 0.8477 (ptmm) REVERT: B 612 TYR cc_start: 0.9172 (m-80) cc_final: 0.8887 (m-80) REVERT: B 680 LYS cc_start: 0.9045 (mttt) cc_final: 0.8612 (mtmt) REVERT: B 683 TYR cc_start: 0.9169 (t80) cc_final: 0.8834 (t80) REVERT: C 149 ASP cc_start: 0.6824 (m-30) cc_final: 0.6565 (m-30) REVERT: C 154 PHE cc_start: 0.9112 (t80) cc_final: 0.8590 (t80) REVERT: C 157 MET cc_start: 0.9106 (mtt) cc_final: 0.8800 (mtt) REVERT: C 208 LEU cc_start: 0.7013 (mm) cc_final: 0.6695 (mm) REVERT: C 242 TYR cc_start: 0.8853 (t80) cc_final: 0.8628 (t80) REVERT: C 252 LEU cc_start: 0.7734 (mp) cc_final: 0.7381 (pp) REVERT: C 256 VAL cc_start: 0.8576 (t) cc_final: 0.8361 (t) REVERT: C 286 VAL cc_start: 0.7543 (OUTLIER) cc_final: 0.7265 (m) REVERT: C 288 ASN cc_start: 0.5140 (t0) cc_final: 0.4291 (m-40) REVERT: D 24 GLN cc_start: 0.9351 (tp-100) cc_final: 0.9127 (tp-100) REVERT: D 55 TYR cc_start: 0.6266 (t80) cc_final: 0.5984 (t80) REVERT: D 82 ASP cc_start: 0.8954 (m-30) cc_final: 0.8714 (t0) REVERT: D 154 PHE cc_start: 0.5780 (t80) cc_final: 0.5220 (t80) REVERT: D 204 TYR cc_start: 0.9512 (t80) cc_final: 0.9285 (t80) outliers start: 74 outliers final: 44 residues processed: 752 average time/residue: 0.1168 time to fit residues: 132.7046 Evaluate side-chains 695 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 649 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 162 LYS 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 220 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 384 GLU 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 306 ILE 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: 10.0000 chunk 131 optimal weight: 0.6980 chunk 164 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 182 optimal weight: 0.8980 chunk 159 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 158 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 387 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN A 668 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN C 127 GLN ** 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 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.146832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.104780 restraints weight = 36686.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.108806 restraints weight = 18254.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.111418 restraints weight = 10916.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.113171 restraints weight = 7453.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.114267 restraints weight = 5588.824| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16386 Z= 0.150 Angle : 0.676 10.921 22134 Z= 0.347 Chirality : 0.045 0.274 2360 Planarity : 0.004 0.035 2818 Dihedral : 11.044 164.445 2245 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.02 % Allowed : 22.96 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.18), residues: 1932 helix: 1.36 (0.15), residues: 1138 sheet: 0.67 (0.45), residues: 100 loop : 0.36 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 293 TYR 0.019 0.002 TYR C 262 PHE 0.048 0.002 PHE C 109 TRP 0.026 0.002 TRP D 124 HIS 0.006 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00341 (16386) covalent geometry : angle 0.67586 (22134) hydrogen bonds : bond 0.04374 ( 871) hydrogen bonds : angle 5.03886 ( 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 749 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 680 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8898 (ttmm) cc_final: 0.8565 (ttpt) REVERT: A 55 LEU cc_start: 0.9796 (mt) cc_final: 0.9464 (pp) REVERT: A 76 ASP cc_start: 0.9101 (m-30) cc_final: 0.8852 (m-30) REVERT: A 99 LYS cc_start: 0.9290 (mmtm) cc_final: 0.8999 (mmtm) REVERT: A 123 SER cc_start: 0.9606 (OUTLIER) cc_final: 0.9255 (p) REVERT: A 139 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8275 (mt-10) REVERT: A 149 TYR cc_start: 0.9557 (t80) cc_final: 0.8695 (t80) REVERT: A 161 ARG cc_start: 0.8381 (ttm110) cc_final: 0.6778 (mtp85) REVERT: A 190 MET cc_start: 0.9332 (mtp) cc_final: 0.9039 (mtp) REVERT: A 202 ASN cc_start: 0.9503 (t0) cc_final: 0.9129 (t0) REVERT: A 209 LYS cc_start: 0.9408 (tttp) cc_final: 0.9076 (tptp) REVERT: A 255 HIS cc_start: 0.8543 (t-90) cc_final: 0.7901 (t-90) REVERT: A 257 ASP cc_start: 0.9433 (m-30) cc_final: 0.8818 (m-30) REVERT: A 259 ASN cc_start: 0.8917 (m-40) cc_final: 0.8707 (m-40) REVERT: A 274 ARG cc_start: 0.8704 (ptm160) cc_final: 0.8267 (ptm160) REVERT: A 277 THR cc_start: 0.8777 (p) cc_final: 0.8404 (t) REVERT: A 283 VAL cc_start: 0.9454 (t) cc_final: 0.9252 (t) REVERT: A 286 ASP cc_start: 0.8540 (m-30) cc_final: 0.8222 (m-30) REVERT: A 321 GLU cc_start: 0.8025 (pp20) cc_final: 0.7774 (pp20) REVERT: A 322 MET cc_start: 0.8773 (mmm) cc_final: 0.8273 (mmm) REVERT: A 335 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7988 (mm-30) REVERT: A 348 MET cc_start: 0.8816 (tmm) cc_final: 0.8249 (tmm) REVERT: A 350 ARG cc_start: 0.9232 (mtp180) cc_final: 0.9012 (mmm-85) REVERT: A 360 PHE cc_start: 0.9042 (m-80) cc_final: 0.8813 (m-80) REVERT: A 362 ASP cc_start: 0.8237 (m-30) cc_final: 0.7810 (m-30) REVERT: A 379 SER cc_start: 0.9334 (t) cc_final: 0.8912 (t) REVERT: A 393 SER cc_start: 0.9378 (m) cc_final: 0.9109 (p) REVERT: A 402 GLU cc_start: 0.8067 (mp0) cc_final: 0.7704 (mp0) REVERT: A 479 TYR cc_start: 0.9265 (t80) cc_final: 0.8977 (t80) REVERT: A 505 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8442 (mt-10) REVERT: A 515 ASP cc_start: 0.9013 (m-30) cc_final: 0.8451 (m-30) REVERT: A 590 SER cc_start: 0.9554 (t) cc_final: 0.9061 (p) REVERT: A 615 MET cc_start: 0.9166 (mmp) cc_final: 0.8753 (mmp) REVERT: A 639 ASP cc_start: 0.9002 (m-30) cc_final: 0.8199 (m-30) REVERT: A 640 MET cc_start: 0.9252 (tpp) cc_final: 0.8365 (tpp) REVERT: A 683 TYR cc_start: 0.8622 (t80) cc_final: 0.8400 (t80) REVERT: B 8 LYS cc_start: 0.8769 (tppt) cc_final: 0.8511 (tppt) REVERT: B 26 PHE cc_start: 0.9199 (m-80) cc_final: 0.8821 (m-10) REVERT: B 31 GLU cc_start: 0.8699 (mp0) cc_final: 0.8451 (mp0) REVERT: B 65 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7778 (mm-30) REVERT: B 68 PHE cc_start: 0.9085 (p90) cc_final: 0.8594 (p90) REVERT: B 95 MET cc_start: 0.9146 (tpp) cc_final: 0.8895 (tpp) REVERT: B 117 ARG cc_start: 0.8784 (mtp85) cc_final: 0.8582 (mtp85) REVERT: B 119 GLU cc_start: 0.9103 (mp0) cc_final: 0.8517 (mp0) REVERT: B 139 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8886 (mm-30) REVERT: B 149 TYR cc_start: 0.9369 (t80) cc_final: 0.9072 (t80) REVERT: B 236 TYR cc_start: 0.9073 (t80) cc_final: 0.8580 (t80) REVERT: B 246 SER cc_start: 0.7819 (m) cc_final: 0.7394 (p) REVERT: B 250 TYR cc_start: 0.8978 (m-80) cc_final: 0.8757 (m-80) REVERT: B 257 ASP cc_start: 0.8736 (m-30) cc_final: 0.8244 (m-30) REVERT: B 279 SER cc_start: 0.8810 (m) cc_final: 0.8463 (t) REVERT: B 317 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8398 (pmm) REVERT: B 393 SER cc_start: 0.9404 (m) cc_final: 0.8912 (p) REVERT: B 396 ASP cc_start: 0.8542 (p0) cc_final: 0.8262 (p0) REVERT: B 415 ASN cc_start: 0.9424 (t0) cc_final: 0.9011 (t0) REVERT: B 435 SER cc_start: 0.9761 (OUTLIER) cc_final: 0.9536 (t) REVERT: B 474 GLN cc_start: 0.8907 (mt0) cc_final: 0.8612 (mm-40) REVERT: B 475 ASN cc_start: 0.9278 (m-40) cc_final: 0.8851 (m110) REVERT: B 493 MET cc_start: 0.9641 (tmm) cc_final: 0.9384 (tmm) REVERT: B 515 ASP cc_start: 0.8987 (m-30) cc_final: 0.8699 (m-30) REVERT: B 546 LEU cc_start: 0.9616 (mt) cc_final: 0.9384 (mt) REVERT: B 550 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7499 (mtp) REVERT: B 588 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8860 (mm-40) REVERT: B 599 GLU cc_start: 0.8417 (pt0) cc_final: 0.8137 (pt0) REVERT: B 601 ILE cc_start: 0.9419 (mm) cc_final: 0.9015 (mm) REVERT: B 610 LYS cc_start: 0.8871 (ptmt) cc_final: 0.8588 (ptmm) REVERT: B 612 TYR cc_start: 0.9166 (m-80) cc_final: 0.8763 (m-80) REVERT: B 640 MET cc_start: 0.9249 (tpp) cc_final: 0.8973 (tpt) REVERT: B 658 LEU cc_start: 0.8864 (mm) cc_final: 0.8628 (mm) REVERT: B 680 LYS cc_start: 0.8977 (mttt) cc_final: 0.8645 (mttt) REVERT: B 683 TYR cc_start: 0.9109 (t80) cc_final: 0.8866 (t80) REVERT: C 66 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.6223 (t0) REVERT: C 68 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8926 (mm-30) REVERT: C 154 PHE cc_start: 0.9176 (t80) cc_final: 0.8632 (t80) REVERT: C 157 MET cc_start: 0.9132 (mtt) cc_final: 0.8805 (mtt) REVERT: C 212 ILE cc_start: 0.7216 (mt) cc_final: 0.6255 (mt) REVERT: C 242 TYR cc_start: 0.9078 (t80) cc_final: 0.8684 (t80) REVERT: C 288 ASN cc_start: 0.5274 (t0) cc_final: 0.4465 (m-40) REVERT: D 24 GLN cc_start: 0.9381 (tp-100) cc_final: 0.9141 (tp-100) REVERT: D 82 ASP cc_start: 0.8903 (m-30) cc_final: 0.7871 (m-30) REVERT: D 154 PHE cc_start: 0.6030 (t80) cc_final: 0.5445 (t80) REVERT: D 204 TYR cc_start: 0.9490 (t80) cc_final: 0.9202 (t80) outliers start: 69 outliers final: 35 residues processed: 710 average time/residue: 0.1280 time to fit residues: 137.2690 Evaluate side-chains 678 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 638 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 178 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 306 ILE 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 435 SER Chi-restraints excluded: chain A residue 443 THR 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 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 223 VAL 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 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 550 MET Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 287 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 168 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 185 optimal weight: 10.0000 chunk 191 optimal weight: 0.6980 chunk 159 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 50 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.141682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.100167 restraints weight = 36965.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.103933 restraints weight = 18647.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.106411 restraints weight = 11285.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.108071 restraints weight = 7778.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.109218 restraints weight = 5851.438| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16386 Z= 0.218 Angle : 0.690 11.150 22134 Z= 0.360 Chirality : 0.045 0.241 2360 Planarity : 0.004 0.043 2818 Dihedral : 11.000 164.818 2244 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.66 % Allowed : 24.94 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.18), residues: 1932 helix: 1.33 (0.15), residues: 1115 sheet: 0.10 (0.43), residues: 114 loop : 0.22 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 293 TYR 0.020 0.002 TYR D 55 PHE 0.053 0.002 PHE C 109 TRP 0.011 0.002 TRP B 558 HIS 0.013 0.001 HIS A 647 Details of bonding type rmsd covalent geometry : bond 0.00482 (16386) covalent geometry : angle 0.69046 (22134) hydrogen bonds : bond 0.04234 ( 871) hydrogen bonds : angle 5.12880 ( 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 725 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 645 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8995 (ttmm) cc_final: 0.8620 (ttpp) REVERT: A 31 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8752 (pm20) REVERT: A 75 GLU cc_start: 0.8969 (mp0) cc_final: 0.8741 (pm20) REVERT: A 95 MET cc_start: 0.9273 (mmm) cc_final: 0.9015 (tpp) REVERT: A 123 SER cc_start: 0.9602 (OUTLIER) cc_final: 0.9197 (p) REVERT: A 139 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8314 (mt-10) REVERT: A 161 ARG cc_start: 0.8401 (ttm110) cc_final: 0.7806 (mtp85) REVERT: A 162 LYS cc_start: 0.9308 (ttpm) cc_final: 0.8922 (ttpp) REVERT: A 190 MET cc_start: 0.9349 (mtp) cc_final: 0.9096 (mtp) REVERT: A 202 ASN cc_start: 0.9510 (t0) cc_final: 0.9190 (t0) REVERT: A 252 ASN cc_start: 0.9343 (t0) cc_final: 0.9119 (t0) REVERT: A 255 HIS cc_start: 0.8724 (t-90) cc_final: 0.8111 (t-90) REVERT: A 257 ASP cc_start: 0.9499 (m-30) cc_final: 0.8909 (m-30) REVERT: A 261 PHE cc_start: 0.9542 (t80) cc_final: 0.9192 (t80) REVERT: A 274 ARG cc_start: 0.8808 (ptm160) cc_final: 0.8403 (ptm160) REVERT: A 277 THR cc_start: 0.8778 (p) cc_final: 0.8386 (t) REVERT: A 286 ASP cc_start: 0.8621 (m-30) cc_final: 0.8243 (m-30) REVERT: A 318 ASP cc_start: 0.9076 (t0) cc_final: 0.8795 (t0) REVERT: A 322 MET cc_start: 0.8837 (mmm) cc_final: 0.8381 (mmm) REVERT: A 335 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8084 (mm-30) REVERT: A 348 MET cc_start: 0.8868 (tmm) cc_final: 0.8344 (tmm) REVERT: A 349 LEU cc_start: 0.9663 (OUTLIER) cc_final: 0.9219 (mt) REVERT: A 350 ARG cc_start: 0.9322 (mtp180) cc_final: 0.9078 (mtp180) REVERT: A 362 ASP cc_start: 0.8235 (m-30) cc_final: 0.7552 (m-30) REVERT: A 393 SER cc_start: 0.9344 (m) cc_final: 0.9073 (p) REVERT: A 402 GLU cc_start: 0.8176 (mp0) cc_final: 0.7837 (mp0) REVERT: A 435 SER cc_start: 0.9681 (OUTLIER) cc_final: 0.9392 (p) REVERT: A 493 MET cc_start: 0.9134 (tmm) cc_final: 0.8777 (tmm) REVERT: A 501 GLN cc_start: 0.9234 (OUTLIER) cc_final: 0.8977 (tt0) REVERT: A 505 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8317 (mt-10) REVERT: A 515 ASP cc_start: 0.9121 (m-30) cc_final: 0.8528 (m-30) REVERT: A 550 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7311 (mtm) REVERT: A 615 MET cc_start: 0.9291 (mmp) cc_final: 0.8810 (mmp) REVERT: B 8 LYS cc_start: 0.8849 (tppt) cc_final: 0.8586 (tppt) REVERT: B 16 ILE cc_start: 0.9555 (mm) cc_final: 0.8919 (tp) REVERT: B 17 MET cc_start: 0.8733 (mmm) cc_final: 0.8053 (mmm) REVERT: B 31 GLU cc_start: 0.8628 (mp0) cc_final: 0.8302 (mp0) REVERT: B 65 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8179 (mm-30) REVERT: B 99 LYS cc_start: 0.9327 (mmtt) cc_final: 0.8823 (tmtt) REVERT: B 119 GLU cc_start: 0.9090 (mp0) cc_final: 0.8437 (mp0) REVERT: B 135 GLU cc_start: 0.9000 (mp0) cc_final: 0.8700 (mp0) REVERT: B 149 TYR cc_start: 0.9405 (t80) cc_final: 0.9058 (t80) REVERT: B 150 GLN cc_start: 0.9462 (tp40) cc_final: 0.9256 (tp-100) REVERT: B 235 ARG cc_start: 0.9188 (ttm-80) cc_final: 0.8871 (mtt90) REVERT: B 236 TYR cc_start: 0.9126 (t80) cc_final: 0.8668 (t80) REVERT: B 246 SER cc_start: 0.7830 (m) cc_final: 0.7491 (p) REVERT: B 250 TYR cc_start: 0.9200 (m-80) cc_final: 0.8727 (m-80) REVERT: B 257 ASP cc_start: 0.8844 (m-30) cc_final: 0.8349 (m-30) REVERT: B 279 SER cc_start: 0.8891 (m) cc_final: 0.8553 (t) REVERT: B 317 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8334 (pmm) REVERT: B 321 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8178 (tm-30) REVERT: B 322 MET cc_start: 0.9238 (mmt) cc_final: 0.8841 (mmm) REVERT: B 393 SER cc_start: 0.9404 (m) cc_final: 0.8955 (p) REVERT: B 396 ASP cc_start: 0.8690 (p0) cc_final: 0.8443 (p0) REVERT: B 415 ASN cc_start: 0.9411 (t0) cc_final: 0.9123 (t0) REVERT: B 435 SER cc_start: 0.9827 (OUTLIER) cc_final: 0.9519 (t) REVERT: B 474 GLN cc_start: 0.8944 (mt0) cc_final: 0.8643 (mm-40) REVERT: B 475 ASN cc_start: 0.9342 (m-40) cc_final: 0.8936 (m110) REVERT: B 493 MET cc_start: 0.9633 (tmm) cc_final: 0.9406 (tmm) REVERT: B 515 ASP cc_start: 0.9065 (m-30) cc_final: 0.8734 (m-30) REVERT: B 546 LEU cc_start: 0.9634 (mt) cc_final: 0.9407 (mt) REVERT: B 599 GLU cc_start: 0.8459 (pt0) cc_final: 0.8225 (pt0) REVERT: B 601 ILE cc_start: 0.9446 (mm) cc_final: 0.8966 (mm) REVERT: B 610 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8579 (ptmt) REVERT: B 612 TYR cc_start: 0.9201 (m-80) cc_final: 0.8925 (m-80) REVERT: B 640 MET cc_start: 0.9207 (tpp) cc_final: 0.8943 (tpp) REVERT: B 648 ILE cc_start: 0.9423 (mm) cc_final: 0.9212 (mm) REVERT: B 680 LYS cc_start: 0.8910 (mttt) cc_final: 0.8578 (mttt) REVERT: C 21 PHE cc_start: 0.8248 (m-80) cc_final: 0.7973 (m-80) REVERT: C 66 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.6719 (t0) REVERT: C 68 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8730 (mm-30) REVERT: C 74 MET cc_start: 0.9281 (mmm) cc_final: 0.9064 (tpp) REVERT: C 154 PHE cc_start: 0.9204 (t80) cc_final: 0.8690 (t80) REVERT: C 157 MET cc_start: 0.9226 (mtt) cc_final: 0.8941 (mtt) REVERT: C 208 LEU cc_start: 0.7165 (mm) cc_final: 0.6764 (mm) REVERT: C 212 ILE cc_start: 0.7564 (mt) cc_final: 0.6514 (mt) REVERT: C 242 TYR cc_start: 0.9182 (t80) cc_final: 0.8942 (t80) REVERT: C 252 LEU cc_start: 0.8400 (mp) cc_final: 0.8168 (pp) REVERT: C 269 MET cc_start: 0.8061 (ptt) cc_final: 0.7757 (ppp) REVERT: C 288 ASN cc_start: 0.5227 (t0) cc_final: 0.4348 (m-40) REVERT: D 25 ASN cc_start: 0.8613 (t0) cc_final: 0.8202 (t0) REVERT: D 82 ASP cc_start: 0.8799 (m-30) cc_final: 0.8514 (t0) REVERT: D 101 HIS cc_start: 0.7179 (m90) cc_final: 0.6915 (m90) REVERT: D 204 TYR cc_start: 0.9511 (t80) cc_final: 0.9254 (t80) REVERT: D 246 LEU cc_start: 0.6572 (tp) cc_final: 0.6366 (tt) outliers start: 80 outliers final: 50 residues processed: 676 average time/residue: 0.1229 time to fit residues: 126.7895 Evaluate side-chains 664 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 605 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 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 306 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 550 MET 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 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 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 346 LEU 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 439 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 495 VAL 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 687 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 97 GLU 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: 1.9990 chunk 120 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 129 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 489 ASN ** 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** C 24 GLN C 25 ASN C 28 GLN ** D 24 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.141044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.099663 restraints weight = 36762.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.103426 restraints weight = 18586.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.105782 restraints weight = 11317.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.107390 restraints weight = 7821.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.108587 restraints weight = 5913.017| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.6223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16386 Z= 0.159 Angle : 0.680 10.711 22134 Z= 0.345 Chirality : 0.045 0.227 2360 Planarity : 0.003 0.038 2818 Dihedral : 10.882 168.239 2243 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.37 % Allowed : 27.21 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.19), residues: 1932 helix: 1.23 (0.15), residues: 1113 sheet: -0.58 (0.38), residues: 148 loop : 0.33 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 293 TYR 0.019 0.002 TYR C 55 PHE 0.054 0.002 PHE C 109 TRP 0.016 0.002 TRP D 124 HIS 0.010 0.001 HIS A 647 Details of bonding type rmsd covalent geometry : bond 0.00361 (16386) covalent geometry : angle 0.67997 (22134) hydrogen bonds : bond 0.03988 ( 871) hydrogen bonds : angle 5.05973 ( 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 715 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 640 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9003 (ttmm) cc_final: 0.8735 (ttpt) REVERT: A 15 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8478 (mt-10) REVERT: A 31 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8821 (mp0) REVERT: A 75 GLU cc_start: 0.8989 (mp0) cc_final: 0.8786 (pm20) REVERT: A 95 MET cc_start: 0.9158 (mmm) cc_final: 0.8719 (tpp) REVERT: A 123 SER cc_start: 0.9497 (OUTLIER) cc_final: 0.9287 (p) REVERT: A 139 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8480 (mt-10) REVERT: A 161 ARG cc_start: 0.8412 (ttm110) cc_final: 0.7600 (mtp180) REVERT: A 190 MET cc_start: 0.9319 (mtp) cc_final: 0.9088 (mtp) REVERT: A 202 ASN cc_start: 0.9546 (t0) cc_final: 0.9237 (t0) REVERT: A 218 ASN cc_start: 0.8924 (t0) cc_final: 0.8626 (t0) REVERT: A 255 HIS cc_start: 0.8647 (t-90) cc_final: 0.8045 (t-90) REVERT: A 257 ASP cc_start: 0.9493 (m-30) cc_final: 0.8825 (m-30) REVERT: A 277 THR cc_start: 0.8746 (p) cc_final: 0.8393 (t) REVERT: A 286 ASP cc_start: 0.8572 (m-30) cc_final: 0.8299 (m-30) REVERT: A 321 GLU cc_start: 0.8316 (pp20) cc_final: 0.8067 (pp20) REVERT: A 322 MET cc_start: 0.8881 (mmm) cc_final: 0.8501 (mmm) REVERT: A 335 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8058 (mm-30) REVERT: A 348 MET cc_start: 0.8890 (tmm) cc_final: 0.8519 (tmm) REVERT: A 349 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9322 (mt) REVERT: A 350 ARG cc_start: 0.9286 (mtp180) cc_final: 0.9024 (mtp180) REVERT: A 362 ASP cc_start: 0.8227 (m-30) cc_final: 0.7444 (m-30) REVERT: A 384 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.7715 (pm20) REVERT: A 393 SER cc_start: 0.9321 (m) cc_final: 0.9044 (p) REVERT: A 402 GLU cc_start: 0.8288 (mp0) cc_final: 0.7909 (mp0) REVERT: A 420 MET cc_start: 0.9226 (mmm) cc_final: 0.8977 (tpt) REVERT: A 426 GLU cc_start: 0.8248 (tm-30) cc_final: 0.8039 (tm-30) REVERT: A 452 ARG cc_start: 0.9321 (OUTLIER) cc_final: 0.9097 (ttt-90) REVERT: A 493 MET cc_start: 0.9089 (tmm) cc_final: 0.8645 (tmm) REVERT: A 505 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8311 (mt-10) REVERT: A 515 ASP cc_start: 0.9078 (m-30) cc_final: 0.8502 (m-30) REVERT: A 528 PHE cc_start: 0.9147 (m-80) cc_final: 0.8662 (m-80) REVERT: A 550 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.7299 (mtm) REVERT: A 615 MET cc_start: 0.9318 (mmp) cc_final: 0.8806 (mmp) REVERT: A 640 MET cc_start: 0.9436 (tpp) cc_final: 0.8377 (tpp) REVERT: B 16 ILE cc_start: 0.9536 (mm) cc_final: 0.8886 (tp) REVERT: B 17 MET cc_start: 0.8735 (mmm) cc_final: 0.8133 (mmm) REVERT: B 31 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8097 (mp0) REVERT: B 65 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8253 (mm-30) REVERT: B 95 MET cc_start: 0.9177 (tpp) cc_final: 0.8768 (tpp) REVERT: B 117 ARG cc_start: 0.8921 (mtp85) cc_final: 0.8615 (mtp85) REVERT: B 119 GLU cc_start: 0.9030 (mp0) cc_final: 0.8265 (mp0) REVERT: B 127 LEU cc_start: 0.9720 (mm) cc_final: 0.9412 (mm) REVERT: B 149 TYR cc_start: 0.9449 (t80) cc_final: 0.9081 (t80) REVERT: B 232 ASN cc_start: 0.9186 (m110) cc_final: 0.8784 (m110) REVERT: B 235 ARG cc_start: 0.9169 (ttm-80) cc_final: 0.8967 (ttm-80) REVERT: B 236 TYR cc_start: 0.9140 (t80) cc_final: 0.8441 (t80) REVERT: B 246 SER cc_start: 0.7595 (m) cc_final: 0.7203 (p) REVERT: B 250 TYR cc_start: 0.9197 (m-80) cc_final: 0.8631 (m-80) REVERT: B 257 ASP cc_start: 0.8783 (m-30) cc_final: 0.8240 (m-30) REVERT: B 279 SER cc_start: 0.8801 (m) cc_final: 0.8507 (t) REVERT: B 317 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8307 (pmm) REVERT: B 344 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8542 (mt-10) REVERT: B 393 SER cc_start: 0.9349 (m) cc_final: 0.8958 (p) REVERT: B 396 ASP cc_start: 0.8616 (p0) cc_final: 0.8399 (p0) REVERT: B 415 ASN cc_start: 0.9281 (t0) cc_final: 0.8940 (t0) REVERT: B 435 SER cc_start: 0.9809 (OUTLIER) cc_final: 0.9488 (t) REVERT: B 437 THR cc_start: 0.9508 (m) cc_final: 0.9292 (m) REVERT: B 441 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8290 (mt-10) REVERT: B 467 ASN cc_start: 0.9331 (m-40) cc_final: 0.9073 (m-40) REVERT: B 474 GLN cc_start: 0.8924 (mt0) cc_final: 0.8552 (mm-40) REVERT: B 475 ASN cc_start: 0.9331 (m-40) cc_final: 0.8922 (m110) REVERT: B 493 MET cc_start: 0.9599 (tmm) cc_final: 0.9360 (tmm) REVERT: B 546 LEU cc_start: 0.9622 (mt) cc_final: 0.9407 (mt) REVERT: B 599 GLU cc_start: 0.8483 (pt0) cc_final: 0.8211 (pt0) REVERT: B 601 ILE cc_start: 0.9424 (mm) cc_final: 0.8936 (mm) REVERT: B 610 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8570 (ptmt) REVERT: B 612 TYR cc_start: 0.9200 (m-80) cc_final: 0.8903 (m-80) REVERT: B 683 TYR cc_start: 0.9091 (t80) cc_final: 0.8631 (t80) REVERT: B 684 TYR cc_start: 0.7897 (OUTLIER) cc_final: 0.7208 (m-80) REVERT: C 21 PHE cc_start: 0.8305 (m-80) cc_final: 0.7993 (m-80) REVERT: C 66 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.6642 (t0) REVERT: C 68 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8770 (mm-30) REVERT: C 74 MET cc_start: 0.9354 (mmm) cc_final: 0.9121 (tpp) REVERT: C 127 GLN cc_start: 0.8601 (mm110) cc_final: 0.7535 (pp30) REVERT: C 154 PHE cc_start: 0.9155 (t80) cc_final: 0.8671 (t80) REVERT: C 157 MET cc_start: 0.9263 (mtt) cc_final: 0.8990 (mtt) REVERT: C 208 LEU cc_start: 0.7190 (mm) cc_final: 0.6719 (mm) REVERT: C 212 ILE cc_start: 0.7568 (mt) cc_final: 0.6537 (mt) REVERT: C 242 TYR cc_start: 0.9205 (t80) cc_final: 0.8844 (t80) REVERT: C 252 LEU cc_start: 0.8520 (mp) cc_final: 0.8258 (pp) REVERT: C 269 MET cc_start: 0.8176 (ptt) cc_final: 0.7833 (ppp) REVERT: D 82 ASP cc_start: 0.8777 (m-30) cc_final: 0.8455 (t0) REVERT: D 120 GLU cc_start: 0.9418 (mt-10) cc_final: 0.8879 (tp30) REVERT: D 204 TYR cc_start: 0.9553 (t80) cc_final: 0.9270 (t80) REVERT: D 246 LEU cc_start: 0.6685 (tp) cc_final: 0.6413 (tt) outliers start: 75 outliers final: 47 residues processed: 671 average time/residue: 0.1188 time to fit residues: 121.6947 Evaluate side-chains 667 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 609 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 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 180 ASN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 306 ILE 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 414 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 550 MET 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 216 VAL Chi-restraints excluded: chain B residue 220 THR 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 346 LEU 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 472 LEU 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 660 ASP Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 55 TYR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 240 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: 0.8980 chunk 72 optimal weight: 1.9990 chunk 172 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 HIS ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 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 = 0.3871 r_free = 0.3871 target = 0.147212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.105469 restraints weight = 36650.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.109371 restraints weight = 18293.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.111813 restraints weight = 11078.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.113583 restraints weight = 7609.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.114626 restraints weight = 5698.723| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.6526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16386 Z= 0.140 Angle : 0.689 9.684 22134 Z= 0.349 Chirality : 0.045 0.231 2360 Planarity : 0.003 0.039 2818 Dihedral : 10.702 171.330 2243 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.31 % Allowed : 27.80 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.19), residues: 1932 helix: 1.20 (0.15), residues: 1112 sheet: -0.62 (0.38), residues: 148 loop : 0.22 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 665 TYR 0.021 0.001 TYR D 236 PHE 0.059 0.002 PHE C 109 TRP 0.013 0.001 TRP D 44 HIS 0.005 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00318 (16386) covalent geometry : angle 0.68944 (22134) hydrogen bonds : bond 0.03987 ( 871) hydrogen bonds : angle 5.02839 ( 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 712 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 638 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9015 (ttmm) cc_final: 0.8735 (ttpp) REVERT: A 15 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8446 (mt-10) REVERT: A 31 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8710 (mp0) REVERT: A 75 GLU cc_start: 0.8974 (mp0) cc_final: 0.8756 (pm20) REVERT: A 139 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8437 (mt-10) REVERT: A 161 ARG cc_start: 0.8366 (ttm110) cc_final: 0.7735 (mtp180) REVERT: A 190 MET cc_start: 0.9345 (mtp) cc_final: 0.9126 (mtp) REVERT: A 202 ASN cc_start: 0.9407 (t0) cc_final: 0.9022 (t0) REVERT: A 209 LYS cc_start: 0.9450 (tttp) cc_final: 0.9156 (ttmm) REVERT: A 218 ASN cc_start: 0.8902 (t0) cc_final: 0.8584 (t0) REVERT: A 255 HIS cc_start: 0.8629 (t-90) cc_final: 0.8013 (t-90) REVERT: A 257 ASP cc_start: 0.9491 (m-30) cc_final: 0.8807 (m-30) REVERT: A 277 THR cc_start: 0.8715 (p) cc_final: 0.8374 (t) REVERT: A 286 ASP cc_start: 0.8546 (m-30) cc_final: 0.8271 (m-30) REVERT: A 318 ASP cc_start: 0.9088 (t0) cc_final: 0.8734 (t70) REVERT: A 321 GLU cc_start: 0.8313 (pp20) cc_final: 0.8054 (pp20) REVERT: A 322 MET cc_start: 0.8890 (mmm) cc_final: 0.8531 (mmm) REVERT: A 335 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8074 (mm-30) REVERT: A 348 MET cc_start: 0.8917 (tmm) cc_final: 0.8299 (tmm) REVERT: A 349 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9184 (mt) REVERT: A 352 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8075 (mt-10) REVERT: A 362 ASP cc_start: 0.8147 (m-30) cc_final: 0.7299 (m-30) REVERT: A 393 SER cc_start: 0.9344 (m) cc_final: 0.9119 (p) REVERT: A 402 GLU cc_start: 0.8333 (mp0) cc_final: 0.7914 (mp0) REVERT: A 426 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8105 (tm-30) REVERT: A 435 SER cc_start: 0.9683 (OUTLIER) cc_final: 0.9406 (p) REVERT: A 505 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8242 (mt-10) REVERT: A 515 ASP cc_start: 0.9071 (m-30) cc_final: 0.8452 (m-30) REVERT: A 528 PHE cc_start: 0.9123 (m-80) cc_final: 0.8669 (m-80) REVERT: A 530 LYS cc_start: 0.9219 (ptpt) cc_final: 0.9017 (ptmt) REVERT: A 550 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7254 (mtm) REVERT: A 576 LEU cc_start: 0.9192 (mt) cc_final: 0.8889 (mt) REVERT: A 598 MET cc_start: 0.8721 (tpp) cc_final: 0.8420 (mmt) REVERT: A 615 MET cc_start: 0.9346 (mmp) cc_final: 0.8857 (mmp) REVERT: A 621 ASN cc_start: 0.9501 (OUTLIER) cc_final: 0.9290 (p0) REVERT: A 640 MET cc_start: 0.9422 (OUTLIER) cc_final: 0.8450 (tpp) REVERT: A 646 GLN cc_start: 0.9475 (pt0) cc_final: 0.9239 (pt0) REVERT: A 657 PHE cc_start: 0.9017 (m-80) cc_final: 0.8768 (m-80) REVERT: A 686 ARG cc_start: 0.8461 (tpp80) cc_final: 0.7986 (tpp-160) REVERT: B 8 LYS cc_start: 0.8922 (tppt) cc_final: 0.8677 (tppt) REVERT: B 16 ILE cc_start: 0.9536 (mm) cc_final: 0.8895 (tp) REVERT: B 17 MET cc_start: 0.8713 (mmm) cc_final: 0.8097 (mmm) REVERT: B 65 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8237 (mm-30) REVERT: B 95 MET cc_start: 0.9118 (tpp) cc_final: 0.8689 (tpp) REVERT: B 99 LYS cc_start: 0.9351 (mmtt) cc_final: 0.8865 (tmtt) REVERT: B 111 LYS cc_start: 0.9541 (mmtp) cc_final: 0.9310 (mmtm) REVERT: B 117 ARG cc_start: 0.8821 (mtp85) cc_final: 0.8506 (mtp85) REVERT: B 119 GLU cc_start: 0.8973 (mp0) cc_final: 0.8248 (mp0) REVERT: B 127 LEU cc_start: 0.9740 (mm) cc_final: 0.9441 (mm) REVERT: B 149 TYR cc_start: 0.9389 (t80) cc_final: 0.8973 (t80) REVERT: B 232 ASN cc_start: 0.9173 (m110) cc_final: 0.8745 (m110) REVERT: B 236 TYR cc_start: 0.9097 (t80) cc_final: 0.8691 (t80) REVERT: B 246 SER cc_start: 0.7473 (m) cc_final: 0.7268 (p) REVERT: B 250 TYR cc_start: 0.9242 (m-80) cc_final: 0.8347 (m-80) REVERT: B 257 ASP cc_start: 0.8741 (m-30) cc_final: 0.8263 (m-30) REVERT: B 317 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8334 (pmm) REVERT: B 322 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.8731 (mmm) REVERT: B 393 SER cc_start: 0.9334 (m) cc_final: 0.9070 (p) REVERT: B 396 ASP cc_start: 0.8470 (p0) cc_final: 0.8263 (p0) REVERT: B 415 ASN cc_start: 0.9220 (t0) cc_final: 0.8998 (t0) REVERT: B 437 THR cc_start: 0.9491 (m) cc_final: 0.9187 (m) REVERT: B 441 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8207 (mt-10) REVERT: B 474 GLN cc_start: 0.8984 (mt0) cc_final: 0.8700 (mm-40) REVERT: B 475 ASN cc_start: 0.9172 (m-40) cc_final: 0.8837 (m110) REVERT: B 493 MET cc_start: 0.9573 (tmm) cc_final: 0.9321 (tmm) REVERT: B 586 TYR cc_start: 0.9112 (m-80) cc_final: 0.8881 (m-80) REVERT: B 599 GLU cc_start: 0.8453 (pt0) cc_final: 0.8189 (pt0) REVERT: B 601 ILE cc_start: 0.9414 (mm) cc_final: 0.8934 (mm) REVERT: B 610 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8559 (ptmt) REVERT: B 612 TYR cc_start: 0.9144 (m-80) cc_final: 0.8879 (m-80) REVERT: B 636 LYS cc_start: 0.9508 (mmmt) cc_final: 0.9245 (mmmm) REVERT: B 650 GLN cc_start: 0.8493 (mt0) cc_final: 0.8250 (mt0) REVERT: B 683 TYR cc_start: 0.9097 (t80) cc_final: 0.8661 (t80) REVERT: B 684 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.7303 (m-80) REVERT: C 19 GLN cc_start: 0.8896 (mp10) cc_final: 0.8604 (mp10) REVERT: C 21 PHE cc_start: 0.8344 (m-80) cc_final: 0.8088 (m-80) REVERT: C 66 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.6990 (t0) REVERT: C 68 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8748 (mm-30) REVERT: C 127 GLN cc_start: 0.8655 (mm110) cc_final: 0.7675 (pp30) REVERT: C 154 PHE cc_start: 0.9109 (t80) cc_final: 0.8671 (t80) REVERT: C 157 MET cc_start: 0.9256 (mtt) cc_final: 0.8957 (mtt) REVERT: C 185 MET cc_start: -0.2811 (mmm) cc_final: -0.3437 (mpp) REVERT: C 208 LEU cc_start: 0.7239 (mm) cc_final: 0.6771 (mm) REVERT: C 212 ILE cc_start: 0.7370 (mt) cc_final: 0.6198 (mt) REVERT: C 242 TYR cc_start: 0.9236 (t80) cc_final: 0.8980 (t80) REVERT: C 252 LEU cc_start: 0.8559 (mp) cc_final: 0.8209 (pp) REVERT: C 269 MET cc_start: 0.8196 (ptt) cc_final: 0.7792 (ptt) REVERT: D 82 ASP cc_start: 0.8655 (m-30) cc_final: 0.8279 (t0) REVERT: D 204 TYR cc_start: 0.9547 (t80) cc_final: 0.9271 (t80) REVERT: D 246 LEU cc_start: 0.6737 (tp) cc_final: 0.6495 (tt) outliers start: 74 outliers final: 47 residues processed: 667 average time/residue: 0.1243 time to fit residues: 126.2322 Evaluate side-chains 651 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 594 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 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 306 ILE 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 435 SER Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 550 MET 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 621 ASN Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 MET 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 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 346 LEU 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 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 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 66 ASP Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 246 LEU 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 97 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 240 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 GLN A 645 GLN ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN D 107 ASN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.138617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.097970 restraints weight = 36897.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.101519 restraints weight = 18571.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.103856 restraints weight = 11402.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.105375 restraints weight = 7895.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.106492 restraints weight = 6000.740| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 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 = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.6936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 16386 Z= 0.279 Angle : 0.772 12.232 22134 Z= 0.397 Chirality : 0.048 0.254 2360 Planarity : 0.004 0.054 2818 Dihedral : 11.055 168.474 2243 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.95 % Allowed : 27.97 % Favored : 67.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.19), residues: 1932 helix: 1.00 (0.15), residues: 1134 sheet: -0.67 (0.38), residues: 148 loop : 0.04 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 350 TYR 0.023 0.002 TYR D 236 PHE 0.066 0.003 PHE C 109 TRP 0.038 0.003 TRP D 44 HIS 0.012 0.002 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00608 (16386) covalent geometry : angle 0.77206 (22134) hydrogen bonds : bond 0.04260 ( 871) hydrogen bonds : angle 5.25164 ( 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 677 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 592 time to evaluate : 0.704 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: 0.9101 (ttmm) cc_final: 0.8882 (ttpt) REVERT: A 15 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8473 (mt-10) REVERT: A 31 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8793 (mp0) REVERT: A 65 GLU cc_start: 0.8577 (mm-30) cc_final: 0.7697 (mp0) REVERT: A 75 GLU cc_start: 0.8975 (mp0) cc_final: 0.8767 (pm20) REVERT: A 95 MET cc_start: 0.9237 (mmm) cc_final: 0.9020 (tpp) REVERT: A 139 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8507 (mt-10) REVERT: A 161 ARG cc_start: 0.8445 (ttm110) cc_final: 0.7649 (mtp85) REVERT: A 190 MET cc_start: 0.9392 (mtp) cc_final: 0.9059 (mtp) REVERT: A 193 SER cc_start: 0.9529 (m) cc_final: 0.9317 (p) REVERT: A 202 ASN cc_start: 0.9415 (t0) cc_final: 0.9027 (t0) REVERT: A 209 LYS cc_start: 0.9434 (tttp) cc_final: 0.9181 (ttmm) REVERT: A 255 HIS cc_start: 0.8730 (t-90) cc_final: 0.7990 (t-90) REVERT: A 257 ASP cc_start: 0.9437 (m-30) cc_final: 0.8788 (m-30) REVERT: A 266 LYS cc_start: 0.9487 (mtpp) cc_final: 0.9145 (ptpp) REVERT: A 277 THR cc_start: 0.8829 (p) cc_final: 0.8440 (t) REVERT: A 286 ASP cc_start: 0.8687 (m-30) cc_final: 0.8465 (m-30) REVERT: A 335 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8141 (mm-30) REVERT: A 348 MET cc_start: 0.8997 (tmm) cc_final: 0.8330 (tmm) REVERT: A 349 LEU cc_start: 0.9684 (OUTLIER) cc_final: 0.9191 (mt) REVERT: A 352 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8129 (mt-10) REVERT: A 362 ASP cc_start: 0.8285 (m-30) cc_final: 0.7362 (m-30) REVERT: A 384 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.7777 (pm20) REVERT: A 393 SER cc_start: 0.9326 (m) cc_final: 0.8954 (t) REVERT: A 402 GLU cc_start: 0.8390 (mp0) cc_final: 0.7607 (mp0) REVERT: A 444 ASP cc_start: 0.8470 (t0) cc_final: 0.8059 (t0) REVERT: A 446 ARG cc_start: 0.7922 (mtp85) cc_final: 0.7603 (mmm160) REVERT: A 493 MET cc_start: 0.8833 (tmm) cc_final: 0.8600 (tmm) REVERT: A 505 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8254 (mt-10) REVERT: A 515 ASP cc_start: 0.9134 (m-30) cc_final: 0.8694 (m-30) REVERT: A 615 MET cc_start: 0.9387 (mmp) cc_final: 0.8924 (mmp) REVERT: A 640 MET cc_start: 0.9521 (OUTLIER) cc_final: 0.8428 (tpp) REVERT: A 686 ARG cc_start: 0.8590 (tpp80) cc_final: 0.8271 (tpp-160) REVERT: B 8 LYS cc_start: 0.8915 (tppt) cc_final: 0.8681 (tppt) REVERT: B 16 ILE cc_start: 0.9602 (mm) cc_final: 0.8938 (tp) REVERT: B 17 MET cc_start: 0.8836 (mmm) cc_final: 0.8276 (mmm) REVERT: B 31 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8465 (pt0) REVERT: B 65 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8256 (mm-30) REVERT: B 95 MET cc_start: 0.9231 (tpp) cc_final: 0.8852 (tpp) REVERT: B 104 TYR cc_start: 0.8971 (m-80) cc_final: 0.8638 (m-80) REVERT: B 119 GLU cc_start: 0.9087 (mp0) cc_final: 0.8379 (mp0) REVERT: B 139 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8704 (mm-30) REVERT: B 149 TYR cc_start: 0.9476 (t80) cc_final: 0.9073 (t80) REVERT: B 232 ASN cc_start: 0.9135 (m110) cc_final: 0.8772 (m110) REVERT: B 235 ARG cc_start: 0.9179 (ttm-80) cc_final: 0.8795 (mmt90) REVERT: B 236 TYR cc_start: 0.9162 (t80) cc_final: 0.8507 (t80) REVERT: B 250 TYR cc_start: 0.9427 (m-80) cc_final: 0.8377 (m-80) REVERT: B 257 ASP cc_start: 0.8676 (m-30) cc_final: 0.8200 (m-30) REVERT: B 279 SER cc_start: 0.8848 (m) cc_final: 0.8610 (t) REVERT: B 322 MET cc_start: 0.9293 (OUTLIER) cc_final: 0.8829 (mmm) REVERT: B 384 GLU cc_start: 0.8826 (pm20) cc_final: 0.8508 (pm20) REVERT: B 393 SER cc_start: 0.9390 (m) cc_final: 0.9071 (p) REVERT: B 415 ASN cc_start: 0.9245 (t0) cc_final: 0.8978 (t0) REVERT: B 437 THR cc_start: 0.9550 (m) cc_final: 0.9208 (m) REVERT: B 441 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8261 (mt-10) REVERT: B 467 ASN cc_start: 0.9405 (m-40) cc_final: 0.9154 (m-40) REVERT: B 474 GLN cc_start: 0.8940 (mt0) cc_final: 0.8676 (mt0) REVERT: B 475 ASN cc_start: 0.9348 (m-40) cc_final: 0.9041 (m110) REVERT: B 493 MET cc_start: 0.9608 (tmm) cc_final: 0.9371 (tmm) REVERT: B 599 GLU cc_start: 0.8550 (pt0) cc_final: 0.8263 (pt0) REVERT: B 601 ILE cc_start: 0.9465 (mm) cc_final: 0.8941 (mm) REVERT: B 610 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8477 (ptmt) REVERT: B 612 TYR cc_start: 0.9196 (m-80) cc_final: 0.8895 (m-80) REVERT: B 636 LYS cc_start: 0.9511 (mmmt) cc_final: 0.9259 (mmmm) REVERT: B 640 MET cc_start: 0.9155 (tpp) cc_final: 0.8953 (tpp) REVERT: B 684 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.7328 (m-80) REVERT: C 21 PHE cc_start: 0.8441 (m-80) cc_final: 0.8185 (m-80) REVERT: C 68 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8666 (mm-30) REVERT: C 120 GLU cc_start: 0.9371 (OUTLIER) cc_final: 0.8622 (pt0) REVERT: C 127 GLN cc_start: 0.8601 (mm110) cc_final: 0.7529 (pp30) REVERT: C 154 PHE cc_start: 0.9125 (t80) cc_final: 0.8619 (t80) REVERT: C 157 MET cc_start: 0.9291 (mtt) cc_final: 0.8989 (mtt) REVERT: C 212 ILE cc_start: 0.7545 (mt) cc_final: 0.6496 (mt) REVERT: C 242 TYR cc_start: 0.9339 (t80) cc_final: 0.9035 (t80) REVERT: C 269 MET cc_start: 0.8272 (ptt) cc_final: 0.7841 (ptt) REVERT: D 24 GLN cc_start: 0.9396 (tp-100) cc_final: 0.9186 (tm-30) REVERT: D 82 ASP cc_start: 0.8692 (m-30) cc_final: 0.8364 (t0) REVERT: D 204 TYR cc_start: 0.9585 (t80) cc_final: 0.9190 (t80) outliers start: 85 outliers final: 65 residues processed: 623 average time/residue: 0.1160 time to fit residues: 110.4913 Evaluate side-chains 640 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 568 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE 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 127 LEU 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 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 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 550 MET 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 638 VAL Chi-restraints excluded: chain A residue 640 MET 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 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL 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 322 MET Chi-restraints excluded: chain B residue 346 LEU 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 495 VAL 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 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 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 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 97 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 242 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 153 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 GLN ** 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 191 GLN ** 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** ** D 238 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 = 0.141752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.100099 restraints weight = 36915.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.103849 restraints weight = 18625.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.106270 restraints weight = 11381.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.107873 restraints weight = 7886.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.109018 restraints weight = 6007.093| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.7154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16386 Z= 0.155 Angle : 0.752 10.732 22134 Z= 0.377 Chirality : 0.047 0.279 2360 Planarity : 0.004 0.040 2818 Dihedral : 10.687 163.645 2243 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.55 % Allowed : 30.36 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.19), residues: 1932 helix: 0.94 (0.15), residues: 1123 sheet: -0.47 (0.41), residues: 138 loop : -0.05 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 350 TYR 0.020 0.001 TYR D 236 PHE 0.079 0.002 PHE C 92 TRP 0.046 0.002 TRP D 44 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00353 (16386) covalent geometry : angle 0.75244 (22134) hydrogen bonds : bond 0.04132 ( 871) hydrogen bonds : angle 5.17951 ( 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 653 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 592 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9078 (ttmm) cc_final: 0.8775 (ttpp) REVERT: A 15 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8486 (mt-10) REVERT: A 31 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8713 (mp0) REVERT: A 65 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8294 (mm-30) REVERT: A 75 GLU cc_start: 0.9002 (mp0) cc_final: 0.8766 (pm20) REVERT: A 123 SER cc_start: 0.9446 (OUTLIER) cc_final: 0.9187 (p) REVERT: A 128 PHE cc_start: 0.9419 (t80) cc_final: 0.9093 (t80) REVERT: A 139 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8389 (mt-10) REVERT: A 161 ARG cc_start: 0.8447 (ttm110) cc_final: 0.7669 (mtp85) REVERT: A 190 MET cc_start: 0.9342 (mtp) cc_final: 0.9134 (mtp) REVERT: A 202 ASN cc_start: 0.9373 (t0) cc_final: 0.8962 (t0) REVERT: A 255 HIS cc_start: 0.8652 (t-90) cc_final: 0.8386 (t-90) REVERT: A 266 LYS cc_start: 0.9444 (mtpp) cc_final: 0.9098 (ptpp) REVERT: A 277 THR cc_start: 0.8753 (p) cc_final: 0.8355 (t) REVERT: A 290 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8733 (tm-30) REVERT: A 335 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8171 (mm-30) REVERT: A 348 MET cc_start: 0.8971 (tmm) cc_final: 0.8242 (tmm) REVERT: A 349 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9143 (mt) REVERT: A 352 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8184 (mt-10) REVERT: A 362 ASP cc_start: 0.8184 (m-30) cc_final: 0.7262 (m-30) REVERT: A 384 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7554 (pm20) REVERT: A 390 GLN cc_start: 0.8944 (mt0) cc_final: 0.8586 (mt0) REVERT: A 393 SER cc_start: 0.9313 (m) cc_final: 0.8979 (t) REVERT: A 402 GLU cc_start: 0.8418 (mp0) cc_final: 0.7620 (mp0) REVERT: A 426 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8176 (tm-30) REVERT: A 444 ASP cc_start: 0.8329 (t0) cc_final: 0.7830 (t0) REVERT: A 446 ARG cc_start: 0.7919 (mtp85) cc_final: 0.7530 (mmm160) REVERT: A 447 ASN cc_start: 0.8654 (m-40) cc_final: 0.8260 (t0) REVERT: A 493 MET cc_start: 0.8806 (tmm) cc_final: 0.8561 (tmm) REVERT: A 505 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8246 (mt-10) REVERT: A 515 ASP cc_start: 0.9095 (m-30) cc_final: 0.8531 (m-30) REVERT: A 528 PHE cc_start: 0.9187 (m-80) cc_final: 0.8792 (m-80) REVERT: A 550 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7387 (mtm) REVERT: A 615 MET cc_start: 0.9354 (mmp) cc_final: 0.8825 (mmp) REVERT: A 639 ASP cc_start: 0.9043 (t70) cc_final: 0.8772 (p0) REVERT: A 657 PHE cc_start: 0.9073 (m-80) cc_final: 0.8688 (m-80) REVERT: A 686 ARG cc_start: 0.8539 (tpp80) cc_final: 0.8262 (tpp-160) REVERT: B 8 LYS cc_start: 0.8953 (tppt) cc_final: 0.8711 (tppt) REVERT: B 16 ILE cc_start: 0.9583 (mm) cc_final: 0.8999 (tp) REVERT: B 17 MET cc_start: 0.8849 (mmm) cc_final: 0.8281 (mmm) REVERT: B 31 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8554 (mt-10) REVERT: B 65 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8270 (mm-30) REVERT: B 111 LYS cc_start: 0.9554 (mmtp) cc_final: 0.9307 (mmtm) REVERT: B 119 GLU cc_start: 0.8973 (mp0) cc_final: 0.8272 (mp0) REVERT: B 127 LEU cc_start: 0.9716 (mm) cc_final: 0.9381 (mm) REVERT: B 147 GLN cc_start: 0.9245 (mt0) cc_final: 0.8696 (tt0) REVERT: B 149 TYR cc_start: 0.9457 (t80) cc_final: 0.8972 (t80) REVERT: B 191 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8297 (mt0) REVERT: B 235 ARG cc_start: 0.9141 (ttm-80) cc_final: 0.8830 (mtt-85) REVERT: B 236 TYR cc_start: 0.9051 (t80) cc_final: 0.8646 (t80) REVERT: B 250 TYR cc_start: 0.9350 (m-80) cc_final: 0.8446 (m-80) REVERT: B 257 ASP cc_start: 0.8654 (m-30) cc_final: 0.8166 (m-30) REVERT: B 279 SER cc_start: 0.8736 (m) cc_final: 0.8464 (t) REVERT: B 317 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8261 (pmm) REVERT: B 322 MET cc_start: 0.9275 (OUTLIER) cc_final: 0.8814 (mmm) REVERT: B 359 MET cc_start: 0.8985 (ttm) cc_final: 0.8484 (tmm) REVERT: B 393 SER cc_start: 0.9417 (m) cc_final: 0.9096 (p) REVERT: B 415 ASN cc_start: 0.9196 (t0) cc_final: 0.8889 (t0) REVERT: B 437 THR cc_start: 0.9498 (m) cc_final: 0.9179 (m) REVERT: B 441 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8232 (mt-10) REVERT: B 474 GLN cc_start: 0.8935 (mt0) cc_final: 0.8621 (mt0) REVERT: B 475 ASN cc_start: 0.9296 (m-40) cc_final: 0.8971 (m110) REVERT: B 493 MET cc_start: 0.9607 (tmm) cc_final: 0.9389 (tmm) REVERT: B 494 MET cc_start: 0.9381 (ttm) cc_final: 0.9125 (mmt) REVERT: B 586 TYR cc_start: 0.9131 (m-80) cc_final: 0.8664 (m-80) REVERT: B 599 GLU cc_start: 0.8591 (pt0) cc_final: 0.8202 (pt0) REVERT: B 601 ILE cc_start: 0.9443 (mm) cc_final: 0.8923 (mm) REVERT: B 610 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8580 (ptmt) REVERT: B 612 TYR cc_start: 0.9167 (m-80) cc_final: 0.8878 (m-80) REVERT: B 615 MET cc_start: 0.9604 (mmp) cc_final: 0.9402 (mmp) REVERT: B 636 LYS cc_start: 0.9483 (mmmt) cc_final: 0.9235 (mmmm) REVERT: B 683 TYR cc_start: 0.9083 (t80) cc_final: 0.8686 (t80) REVERT: B 684 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.7407 (m-80) REVERT: B 686 ARG cc_start: 0.8592 (mmt180) cc_final: 0.8298 (mmt180) REVERT: C 21 PHE cc_start: 0.8379 (m-80) cc_final: 0.8132 (m-80) REVERT: C 68 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8650 (mm-30) REVERT: C 154 PHE cc_start: 0.9141 (t80) cc_final: 0.8691 (t80) REVERT: C 162 TYR cc_start: 0.8859 (m-80) cc_final: 0.8612 (m-80) REVERT: C 185 MET cc_start: -0.2747 (mmm) cc_final: -0.3146 (mpp) REVERT: C 212 ILE cc_start: 0.7448 (mt) cc_final: 0.6622 (mm) REVERT: C 269 MET cc_start: 0.8338 (ptt) cc_final: 0.8008 (ppp) REVERT: D 137 MET cc_start: 0.0938 (mmt) cc_final: -0.0187 (mtm) outliers start: 61 outliers final: 45 residues processed: 618 average time/residue: 0.1197 time to fit residues: 112.9374 Evaluate side-chains 616 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 562 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 123 SER Chi-restraints excluded: chain A residue 127 LEU 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 279 SER Chi-restraints excluded: chain A residue 306 ILE 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 414 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 644 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 191 GLN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 346 LEU 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 570 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 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 93 MET 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 312 VAL Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 55 TYR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 240 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 0.0980 chunk 133 optimal weight: 5.9990 chunk 149 optimal weight: 0.0030 chunk 16 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 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 = 0.3846 r_free = 0.3846 target = 0.145991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.105844 restraints weight = 36585.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.109668 restraints weight = 17985.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.112066 restraints weight = 10799.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.113818 restraints weight = 7375.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.114929 restraints weight = 5507.090| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.7437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16386 Z= 0.149 Angle : 0.793 13.616 22134 Z= 0.396 Chirality : 0.048 0.272 2360 Planarity : 0.004 0.039 2818 Dihedral : 10.482 161.853 2243 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.26 % Allowed : 31.53 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.19), residues: 1932 helix: 0.85 (0.15), residues: 1119 sheet: -0.37 (0.41), residues: 144 loop : -0.07 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 350 TYR 0.019 0.001 TYR C 105 PHE 0.066 0.002 PHE C 92 TRP 0.039 0.002 TRP D 44 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00334 (16386) covalent geometry : angle 0.79250 (22134) hydrogen bonds : bond 0.04180 ( 871) hydrogen bonds : angle 5.24255 ( 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 643 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 587 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9067 (ttmm) cc_final: 0.8827 (ttpt) REVERT: A 15 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8382 (mt-10) REVERT: A 31 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8648 (mp0) REVERT: A 75 GLU cc_start: 0.8994 (mp0) cc_final: 0.8784 (pm20) REVERT: A 123 SER cc_start: 0.9408 (OUTLIER) cc_final: 0.9141 (p) REVERT: A 128 PHE cc_start: 0.9389 (t80) cc_final: 0.9092 (t80) REVERT: A 139 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8523 (mt-10) REVERT: A 147 GLN cc_start: 0.8088 (mm-40) cc_final: 0.7862 (mm-40) REVERT: A 149 TYR cc_start: 0.9651 (t80) cc_final: 0.8642 (t80) REVERT: A 161 ARG cc_start: 0.8364 (ttm110) cc_final: 0.7389 (mtp85) REVERT: A 190 MET cc_start: 0.9307 (mtp) cc_final: 0.9090 (mtp) REVERT: A 202 ASN cc_start: 0.9348 (t0) cc_final: 0.9006 (t0) REVERT: A 209 LYS cc_start: 0.9389 (tttp) cc_final: 0.9079 (ttmm) REVERT: A 266 LYS cc_start: 0.9415 (mtpp) cc_final: 0.9149 (ptpp) REVERT: A 274 ARG cc_start: 0.8556 (ptm160) cc_final: 0.8100 (ttp-110) REVERT: A 277 THR cc_start: 0.8655 (p) cc_final: 0.8264 (t) REVERT: A 290 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8521 (tm-30) REVERT: A 295 ASP cc_start: 0.8731 (t0) cc_final: 0.8476 (t0) REVERT: A 345 LYS cc_start: 0.9610 (tttt) cc_final: 0.9369 (tttt) REVERT: A 348 MET cc_start: 0.8957 (tmm) cc_final: 0.8192 (tmm) REVERT: A 349 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9107 (mt) REVERT: A 352 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8208 (mt-10) REVERT: A 362 ASP cc_start: 0.8043 (m-30) cc_final: 0.7721 (m-30) REVERT: A 384 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7679 (pm20) REVERT: A 390 GLN cc_start: 0.8926 (mt0) cc_final: 0.8668 (mt0) REVERT: A 393 SER cc_start: 0.9299 (m) cc_final: 0.9011 (t) REVERT: A 402 GLU cc_start: 0.8414 (mp0) cc_final: 0.7640 (mp0) REVERT: A 426 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8177 (tm-30) REVERT: A 444 ASP cc_start: 0.8264 (t0) cc_final: 0.7804 (t0) REVERT: A 446 ARG cc_start: 0.7777 (mtp85) cc_final: 0.7567 (mmm160) REVERT: A 447 ASN cc_start: 0.8562 (m-40) cc_final: 0.8220 (t0) REVERT: A 493 MET cc_start: 0.8751 (tmm) cc_final: 0.8520 (tmm) REVERT: A 505 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8188 (mt-10) REVERT: A 515 ASP cc_start: 0.9066 (m-30) cc_final: 0.8531 (m-30) REVERT: A 526 GLU cc_start: 0.8519 (mp0) cc_final: 0.8266 (mp0) REVERT: A 528 PHE cc_start: 0.9091 (m-80) cc_final: 0.8879 (m-80) REVERT: A 588 GLN cc_start: 0.9388 (tp40) cc_final: 0.8914 (tp40) REVERT: A 598 MET cc_start: 0.8680 (mmm) cc_final: 0.8419 (mmt) REVERT: A 615 MET cc_start: 0.9344 (mmp) cc_final: 0.8825 (mmp) REVERT: A 639 ASP cc_start: 0.9039 (t70) cc_final: 0.8782 (p0) REVERT: A 657 PHE cc_start: 0.8902 (m-80) cc_final: 0.8557 (m-80) REVERT: A 686 ARG cc_start: 0.8552 (tpp80) cc_final: 0.8150 (tpp-160) REVERT: B 16 ILE cc_start: 0.9578 (mm) cc_final: 0.8978 (tp) REVERT: B 17 MET cc_start: 0.8853 (mmm) cc_final: 0.8385 (mmm) REVERT: B 31 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8513 (mt-10) REVERT: B 65 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8320 (mm-30) REVERT: B 95 MET cc_start: 0.9044 (tpp) cc_final: 0.8050 (tpp) REVERT: B 107 LYS cc_start: 0.9250 (mtpp) cc_final: 0.8834 (mtpp) REVERT: B 119 GLU cc_start: 0.8943 (mp0) cc_final: 0.8252 (mp0) REVERT: B 127 LEU cc_start: 0.9721 (mm) cc_final: 0.9390 (mm) REVERT: B 147 GLN cc_start: 0.9197 (mt0) cc_final: 0.8619 (tt0) REVERT: B 149 TYR cc_start: 0.9445 (t80) cc_final: 0.8935 (t80) REVERT: B 191 GLN cc_start: 0.8439 (mm-40) cc_final: 0.8184 (mt0) REVERT: B 232 ASN cc_start: 0.9137 (m110) cc_final: 0.8711 (m110) REVERT: B 235 ARG cc_start: 0.9173 (ttm-80) cc_final: 0.8848 (mtt-85) REVERT: B 236 TYR cc_start: 0.8959 (t80) cc_final: 0.8597 (t80) REVERT: B 257 ASP cc_start: 0.8657 (m-30) cc_final: 0.8230 (m-30) REVERT: B 279 SER cc_start: 0.8733 (m) cc_final: 0.8444 (t) REVERT: B 317 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8280 (pmm) REVERT: B 322 MET cc_start: 0.9278 (OUTLIER) cc_final: 0.8809 (mmm) REVERT: B 359 MET cc_start: 0.8920 (ttm) cc_final: 0.8462 (tmm) REVERT: B 393 SER cc_start: 0.9419 (m) cc_final: 0.9090 (p) REVERT: B 394 TYR cc_start: 0.9249 (m-80) cc_final: 0.8945 (m-80) REVERT: B 399 GLU cc_start: 0.8225 (tp30) cc_final: 0.8002 (tp30) REVERT: B 415 ASN cc_start: 0.8960 (t0) cc_final: 0.8742 (t0) REVERT: B 441 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8249 (mt-10) REVERT: B 475 ASN cc_start: 0.9252 (m-40) cc_final: 0.8978 (m110) REVERT: B 493 MET cc_start: 0.9593 (tmm) cc_final: 0.9392 (tmm) REVERT: B 494 MET cc_start: 0.9178 (ttm) cc_final: 0.8976 (mmt) REVERT: B 586 TYR cc_start: 0.9090 (m-80) cc_final: 0.8375 (m-80) REVERT: B 610 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8579 (ptmt) REVERT: B 612 TYR cc_start: 0.9124 (m-80) cc_final: 0.8852 (m-80) REVERT: B 633 ASP cc_start: 0.8544 (t0) cc_final: 0.8235 (t0) REVERT: B 634 MET cc_start: 0.8620 (mmm) cc_final: 0.8307 (tpt) REVERT: B 636 LYS cc_start: 0.9479 (mmmt) cc_final: 0.9176 (mmmm) REVERT: B 683 TYR cc_start: 0.9005 (t80) cc_final: 0.8563 (t80) REVERT: B 684 TYR cc_start: 0.7950 (OUTLIER) cc_final: 0.7409 (m-80) REVERT: B 686 ARG cc_start: 0.8589 (mmt180) cc_final: 0.8303 (mmt180) REVERT: C 21 PHE cc_start: 0.8360 (m-80) cc_final: 0.8118 (m-80) REVERT: C 68 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8564 (mm-30) REVERT: C 145 ILE cc_start: 0.7913 (mt) cc_final: 0.7670 (tp) REVERT: C 154 PHE cc_start: 0.9173 (t80) cc_final: 0.8749 (t80) REVERT: C 212 ILE cc_start: 0.7141 (mt) cc_final: 0.6930 (mm) REVERT: C 242 TYR cc_start: 0.9171 (t80) cc_final: 0.8920 (t80) REVERT: C 269 MET cc_start: 0.8383 (ptt) cc_final: 0.8092 (ppp) REVERT: D 82 ASP cc_start: 0.8291 (m-30) cc_final: 0.7623 (t0) REVERT: D 137 MET cc_start: 0.0997 (mmt) cc_final: 0.0071 (mtm) REVERT: D 240 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8695 (mm) outliers start: 56 outliers final: 37 residues processed: 608 average time/residue: 0.1157 time to fit residues: 108.0706 Evaluate side-chains 611 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 566 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 123 SER Chi-restraints excluded: chain A residue 127 LEU 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 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 414 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 644 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 220 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 346 LEU 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 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 177 TYR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 240 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 16 optimal weight: 0.2980 chunk 54 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** 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 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 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 = 0.3808 r_free = 0.3808 target = 0.144260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.103284 restraints weight = 36836.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.107090 restraints weight = 18475.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.109462 restraints weight = 11296.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.111254 restraints weight = 7813.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.112334 restraints weight = 5886.958| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.7629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16386 Z= 0.160 Angle : 0.809 14.419 22134 Z= 0.406 Chirality : 0.048 0.279 2360 Planarity : 0.004 0.039 2818 Dihedral : 10.276 161.434 2242 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.91 % Allowed : 33.04 % Favored : 64.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.19), residues: 1932 helix: 0.78 (0.15), residues: 1120 sheet: -0.39 (0.40), residues: 156 loop : -0.08 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 274 TYR 0.026 0.001 TYR B 613 PHE 0.064 0.002 PHE C 109 TRP 0.050 0.002 TRP D 44 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00368 (16386) covalent geometry : angle 0.80888 (22134) hydrogen bonds : bond 0.04181 ( 871) hydrogen bonds : angle 5.26111 ( 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 631 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 581 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8432 (mt-10) REVERT: A 31 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8749 (mp0) REVERT: A 65 GLU cc_start: 0.8550 (mm-30) cc_final: 0.7955 (mp0) REVERT: A 75 GLU cc_start: 0.9034 (mp0) cc_final: 0.8810 (pm20) REVERT: A 123 SER cc_start: 0.9385 (OUTLIER) cc_final: 0.9121 (p) REVERT: A 128 PHE cc_start: 0.9422 (t80) cc_final: 0.9078 (t80) REVERT: A 139 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8529 (mt-10) REVERT: A 150 GLN cc_start: 0.9350 (tp40) cc_final: 0.8929 (tm-30) REVERT: A 161 ARG cc_start: 0.8463 (ttm110) cc_final: 0.7504 (mtp85) REVERT: A 190 MET cc_start: 0.9360 (mtp) cc_final: 0.9131 (mtp) REVERT: A 191 GLN cc_start: 0.8193 (mt0) cc_final: 0.7847 (mt0) REVERT: A 202 ASN cc_start: 0.9407 (t0) cc_final: 0.9051 (t0) REVERT: A 209 LYS cc_start: 0.9404 (tttp) cc_final: 0.9098 (ttmm) REVERT: A 228 LYS cc_start: 0.9453 (mttm) cc_final: 0.9145 (mmtt) REVERT: A 266 LYS cc_start: 0.9419 (mtpp) cc_final: 0.9155 (ptpp) REVERT: A 274 ARG cc_start: 0.8549 (ptm160) cc_final: 0.8126 (ttp-110) REVERT: A 290 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8554 (tm-30) REVERT: A 295 ASP cc_start: 0.8775 (t0) cc_final: 0.8524 (t0) REVERT: A 345 LYS cc_start: 0.9605 (tttt) cc_final: 0.9336 (tttt) REVERT: A 348 MET cc_start: 0.8942 (tmm) cc_final: 0.8213 (tmm) REVERT: A 352 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8279 (mt-10) REVERT: A 362 ASP cc_start: 0.8041 (m-30) cc_final: 0.7711 (m-30) REVERT: A 384 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7654 (pm20) REVERT: A 390 GLN cc_start: 0.8914 (mt0) cc_final: 0.8654 (mt0) REVERT: A 393 SER cc_start: 0.9278 (m) cc_final: 0.8833 (p) REVERT: A 402 GLU cc_start: 0.8461 (mp0) cc_final: 0.7710 (mp0) REVERT: A 416 ILE cc_start: 0.9321 (mt) cc_final: 0.9098 (mp) REVERT: A 426 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8228 (tm-30) REVERT: A 444 ASP cc_start: 0.8262 (t0) cc_final: 0.7832 (t0) REVERT: A 446 ARG cc_start: 0.7853 (mtp85) cc_final: 0.7629 (mmm160) REVERT: A 447 ASN cc_start: 0.8586 (m-40) cc_final: 0.7776 (t0) REVERT: A 493 MET cc_start: 0.8780 (tmm) cc_final: 0.8539 (tmm) REVERT: A 505 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8210 (mt-10) REVERT: A 515 ASP cc_start: 0.9083 (m-30) cc_final: 0.8549 (m-30) REVERT: A 528 PHE cc_start: 0.9099 (m-80) cc_final: 0.8894 (m-80) REVERT: A 598 MET cc_start: 0.8758 (mmm) cc_final: 0.8529 (mmm) REVERT: A 615 MET cc_start: 0.9371 (mmp) cc_final: 0.8842 (mmp) REVERT: A 639 ASP cc_start: 0.9064 (t70) cc_final: 0.8780 (p0) REVERT: A 657 PHE cc_start: 0.8929 (m-80) cc_final: 0.8579 (m-80) REVERT: A 686 ARG cc_start: 0.8582 (tpp80) cc_final: 0.8203 (tpp-160) REVERT: B 31 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8519 (mt-10) REVERT: B 65 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8362 (mm-30) REVERT: B 95 MET cc_start: 0.9108 (tpp) cc_final: 0.8715 (tpp) REVERT: B 107 LYS cc_start: 0.9249 (mtpp) cc_final: 0.8848 (mtpp) REVERT: B 119 GLU cc_start: 0.8963 (mp0) cc_final: 0.8276 (mp0) REVERT: B 127 LEU cc_start: 0.9727 (mm) cc_final: 0.9381 (mm) REVERT: B 147 GLN cc_start: 0.9252 (mt0) cc_final: 0.8712 (tt0) REVERT: B 149 TYR cc_start: 0.9432 (t80) cc_final: 0.8908 (t80) REVERT: B 181 ASP cc_start: 0.8808 (m-30) cc_final: 0.8599 (m-30) REVERT: B 232 ASN cc_start: 0.9131 (OUTLIER) cc_final: 0.8687 (m110) REVERT: B 235 ARG cc_start: 0.9173 (ttm-80) cc_final: 0.8830 (mtt-85) REVERT: B 236 TYR cc_start: 0.8967 (t80) cc_final: 0.8594 (t80) REVERT: B 257 ASP cc_start: 0.8704 (m-30) cc_final: 0.8236 (m-30) REVERT: B 274 ARG cc_start: 0.8384 (ptp-170) cc_final: 0.8111 (ptp-170) REVERT: B 279 SER cc_start: 0.8742 (m) cc_final: 0.8452 (t) REVERT: B 317 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8272 (pmm) REVERT: B 322 MET cc_start: 0.9286 (OUTLIER) cc_final: 0.9004 (mmm) REVERT: B 359 MET cc_start: 0.8937 (ttm) cc_final: 0.8442 (tmm) REVERT: B 393 SER cc_start: 0.9335 (m) cc_final: 0.8999 (p) REVERT: B 399 GLU cc_start: 0.8245 (tp30) cc_final: 0.7959 (tp30) REVERT: B 402 GLU cc_start: 0.8797 (tp30) cc_final: 0.8567 (tp30) REVERT: B 415 ASN cc_start: 0.9022 (t0) cc_final: 0.8779 (t0) REVERT: B 441 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8389 (mt-10) REVERT: B 475 ASN cc_start: 0.9279 (m-40) cc_final: 0.8996 (m110) REVERT: B 493 MET cc_start: 0.9610 (tmm) cc_final: 0.9385 (tmm) REVERT: B 494 MET cc_start: 0.9253 (ttm) cc_final: 0.8948 (mmt) REVERT: B 610 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8598 (ptmt) REVERT: B 612 TYR cc_start: 0.9174 (m-80) cc_final: 0.8926 (m-80) REVERT: B 633 ASP cc_start: 0.8497 (t0) cc_final: 0.8178 (t0) REVERT: B 636 LYS cc_start: 0.9444 (mmmt) cc_final: 0.9162 (mmmm) REVERT: B 683 TYR cc_start: 0.9023 (t80) cc_final: 0.8584 (t80) REVERT: B 684 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.7378 (m-80) REVERT: B 686 ARG cc_start: 0.8658 (mmt180) cc_final: 0.8344 (mmt180) REVERT: C 21 PHE cc_start: 0.8417 (m-80) cc_final: 0.8161 (m-80) REVERT: C 68 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8552 (mm-30) REVERT: C 154 PHE cc_start: 0.9207 (t80) cc_final: 0.8796 (t80) REVERT: C 162 TYR cc_start: 0.8842 (m-80) cc_final: 0.8563 (m-80) REVERT: C 185 MET cc_start: -0.2897 (mmm) cc_final: -0.3144 (mpp) REVERT: C 212 ILE cc_start: 0.7172 (mt) cc_final: 0.6880 (mm) REVERT: C 242 TYR cc_start: 0.9095 (t80) cc_final: 0.8831 (t80) REVERT: C 269 MET cc_start: 0.8384 (ptt) cc_final: 0.7922 (ptt) REVERT: D 16 ASP cc_start: 0.7072 (m-30) cc_final: 0.6828 (t0) REVERT: D 24 GLN cc_start: 0.9346 (tp-100) cc_final: 0.9039 (tm-30) REVERT: D 137 MET cc_start: 0.1283 (mmt) cc_final: 0.0508 (mtm) outliers start: 50 outliers final: 38 residues processed: 600 average time/residue: 0.1162 time to fit residues: 106.6729 Evaluate side-chains 613 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 568 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 123 SER Chi-restraints excluded: chain A residue 127 LEU 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 227 MET 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 414 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 644 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 220 THR Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 346 LEU 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 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 246 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 48 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 125 optimal weight: 0.0670 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** 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 = 0.3853 r_free = 0.3853 target = 0.146006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.106340 restraints weight = 36699.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.110058 restraints weight = 18016.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.112539 restraints weight = 10864.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.114137 restraints weight = 7402.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.115340 restraints weight = 5558.836| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.7815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16386 Z= 0.156 Angle : 0.822 14.100 22134 Z= 0.410 Chirality : 0.048 0.275 2360 Planarity : 0.004 0.038 2818 Dihedral : 10.033 162.412 2242 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.80 % Allowed : 33.39 % Favored : 63.81 % 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 aren not related in a simple way. whole: 0.44 (0.18), residues: 1932 helix: 0.75 (0.15), residues: 1118 sheet: -0.39 (0.40), residues: 154 loop : -0.13 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 350 TYR 0.042 0.001 TYR D 105 PHE 0.062 0.002 PHE C 109 TRP 0.049 0.002 TRP D 44 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00356 (16386) covalent geometry : angle 0.82238 (22134) hydrogen bonds : bond 0.04189 ( 871) hydrogen bonds : angle 5.27465 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3426.27 seconds wall clock time: 60 minutes 1.97 seconds (3601.97 seconds total)