Starting phenix.real_space_refine on Sun Aug 24 01:08:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz9_45057/08_2025/9bz9_45057_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz9_45057/08_2025/9bz9_45057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bz9_45057/08_2025/9bz9_45057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz9_45057/08_2025/9bz9_45057.map" model { file = "/net/cci-nas-00/data/ceres_data/9bz9_45057/08_2025/9bz9_45057_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz9_45057/08_2025/9bz9_45057_neut.cif" } resolution = 4.64 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 68 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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: 3.02, per 1000 atoms: 0.19 Number of scatterers: 16038 At special positions: 0 Unit cell: (93.288, 124.722, 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: 0.98 Conformation dependent library (CDL) restraints added in 487.1 milliseconds Enol-peptide restraints added in 238.4 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 64.1% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.515A 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: 3.568A 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: 3.665A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.694A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.627A 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: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.074A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.676A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.878A 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: 5.118A 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: 3.634A 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: 3.881A 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 181 removed outlier: 4.936A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix removed outlier: 3.576A pdb=" N GLN C 181 " --> pdb=" O TYR C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.567A 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: 3.643A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.359A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.478A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.393A 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: 7.500A 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 605 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: 6.382A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.048A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.806A 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 659 871 hydrogen bonds defined for protein. 2568 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: 2.17 Time building geometry restraints manager: 1.29 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: 4857 1.34 - 1.46: 3044 1.46 - 1.58: 8304 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.600 -0.060 1.25e-02 6.40e+03 2.33e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.577 -0.038 1.20e-02 6.94e+03 9.90e+00 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.032 1.08e-02 8.57e+03 8.90e+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 7.60e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.573 -0.033 1.25e-02 6.40e+03 7.09e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21564 2.09 - 4.19: 517 4.19 - 6.28: 44 6.28 - 8.38: 4 8.38 - 10.47: 5 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N SER A 609 " pdb=" CA SER A 609 " pdb=" C SER A 609 " ideal model delta sigma weight residual 110.41 119.07 -8.66 1.23e+00 6.61e-01 4.96e+01 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=" C ASN A 608 " pdb=" N SER A 609 " pdb=" CA SER A 609 " ideal model delta sigma weight residual 121.06 129.21 -8.15 1.88e+00 2.83e-01 1.88e+01 angle pdb=" N ASN C 288 " pdb=" CA ASN C 288 " pdb=" CB ASN C 288 " ideal model delta sigma weight residual 110.39 103.68 6.71 1.66e+00 3.63e-01 1.63e+01 angle pdb=" N SER A 609 " pdb=" CA SER A 609 " pdb=" CB SER A 609 " ideal model delta sigma weight residual 110.38 104.92 5.46 1.37e+00 5.33e-01 1.59e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 9470 35.80 - 71.60: 337 71.60 - 107.41: 37 107.41 - 143.21: 3 143.21 - 179.01: 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 -58.32 120.69 -179.01 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 301.68 151.20 150.49 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 31.88 148.09 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: 2150 0.094 - 0.187: 178 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 4.58e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 288 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.58e+00 pdb=" C ASN C 288 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN C 288 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY C 289 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 609 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.23e+00 pdb=" C SER A 609 " -0.040 2.00e-02 2.50e+03 pdb=" O SER A 609 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS A 610 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 608 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" CG ASN A 608 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN A 608 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 608 " 0.010 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 130 2.51 - 3.11: 11584 3.11 - 3.70: 27097 3.70 - 4.30: 41576 4.30 - 4.90: 65504 Nonbonded interactions: 145891 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 1.964 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.991 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.013 3.040 ... (remaining 145886 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: 1.030 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.910 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 16386 Z= 0.317 Angle : 0.754 10.473 22134 Z= 0.472 Chirality : 0.058 0.468 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.936 179.009 6154 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.40 % Allowed : 15.27 % Favored : 83.33 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.18), residues: 1932 helix: 0.59 (0.14), residues: 1151 sheet: 0.45 (0.41), residues: 128 loop : 0.21 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 196 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE C 168 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00556 (16386) covalent geometry : angle 0.75361 (22134) hydrogen bonds : bond 0.15437 ( 869) hydrogen bonds : angle 6.52098 ( 2568) *********************** 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 926 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 902 time to evaluate : 0.405 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: 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 33 VAL cc_start: 0.8856 (t) cc_final: 0.8413 (t) REVERT: A 51 LEU cc_start: 0.8122 (tp) cc_final: 0.7512 (tp) REVERT: A 81 PHE cc_start: 0.7597 (m-80) cc_final: 0.7374 (m-80) REVERT: A 125 VAL cc_start: 0.9045 (t) cc_final: 0.7560 (t) REVERT: A 143 LEU cc_start: 0.9043 (tp) cc_final: 0.8605 (tp) REVERT: A 166 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8068 (mm-30) REVERT: A 181 ASP cc_start: 0.8496 (m-30) cc_final: 0.8084 (m-30) REVERT: A 193 SER cc_start: 0.8717 (m) cc_final: 0.8516 (p) REVERT: A 213 ILE cc_start: 0.8120 (mt) cc_final: 0.7579 (mp) REVERT: A 224 VAL cc_start: 0.8883 (t) cc_final: 0.7943 (p) REVERT: A 283 VAL cc_start: 0.8505 (t) cc_final: 0.7262 (t) REVERT: A 288 PHE cc_start: 0.7249 (t80) cc_final: 0.6806 (t80) REVERT: A 300 VAL cc_start: 0.7424 (m) cc_final: 0.7063 (m) REVERT: A 322 MET cc_start: 0.7645 (mmp) cc_final: 0.6462 (mmm) REVERT: A 342 LEU cc_start: 0.9170 (tp) cc_final: 0.8674 (tp) REVERT: A 348 MET cc_start: 0.8437 (tmm) cc_final: 0.8148 (tmm) REVERT: A 360 PHE cc_start: 0.7566 (m-80) cc_final: 0.7291 (m-10) REVERT: A 362 ASP cc_start: 0.6186 (m-30) cc_final: 0.4947 (m-30) REVERT: A 367 VAL cc_start: 0.8092 (m) cc_final: 0.7839 (m) REVERT: A 370 ASN cc_start: 0.7524 (m-40) cc_final: 0.6771 (m-40) REVERT: A 416 ILE cc_start: 0.8779 (mt) cc_final: 0.8557 (mt) REVERT: A 431 LEU cc_start: 0.8996 (mt) cc_final: 0.8657 (mm) REVERT: A 436 LEU cc_start: 0.9252 (mt) cc_final: 0.8889 (mt) REVERT: A 500 ILE cc_start: 0.9201 (mt) cc_final: 0.8592 (mt) REVERT: A 550 MET cc_start: 0.6900 (mtm) cc_final: 0.6699 (mtp) REVERT: A 634 MET cc_start: 0.8337 (mmp) cc_final: 0.7983 (mpp) REVERT: A 641 ILE cc_start: 0.9277 (mm) cc_final: 0.9032 (mm) REVERT: A 652 ILE cc_start: 0.8789 (mt) cc_final: 0.8488 (mt) REVERT: A 653 SER cc_start: 0.9052 (OUTLIER) cc_final: 0.8696 (p) REVERT: A 682 ILE cc_start: 0.8321 (mt) cc_final: 0.8052 (mt) REVERT: B 41 ILE cc_start: 0.8853 (mm) cc_final: 0.8164 (mt) REVERT: B 51 LEU cc_start: 0.8561 (tp) cc_final: 0.8184 (tp) REVERT: B 95 MET cc_start: 0.7883 (tpp) cc_final: 0.7676 (tpp) REVERT: B 98 PHE cc_start: 0.7798 (t80) cc_final: 0.7462 (t80) REVERT: B 99 LYS cc_start: 0.9167 (mmtt) cc_final: 0.8345 (mmmm) REVERT: B 100 PHE cc_start: 0.7911 (t80) cc_final: 0.7618 (t80) REVERT: B 101 TYR cc_start: 0.7554 (m-80) cc_final: 0.7058 (m-80) REVERT: B 143 LEU cc_start: 0.9038 (tp) cc_final: 0.8824 (tp) REVERT: B 149 TYR cc_start: 0.8345 (t80) cc_final: 0.7635 (t80) REVERT: B 179 LEU cc_start: 0.8607 (tp) cc_final: 0.7581 (tp) REVERT: B 191 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8184 (mm-40) REVERT: B 213 ILE cc_start: 0.8783 (mt) cc_final: 0.8575 (tp) REVERT: B 232 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.8039 (m-40) REVERT: B 240 MET cc_start: 0.6884 (mpt) cc_final: 0.6323 (mpt) REVERT: B 288 PHE cc_start: 0.7313 (t80) cc_final: 0.6324 (t80) REVERT: B 322 MET cc_start: 0.7357 (mmm) cc_final: 0.5743 (tpp) REVERT: B 337 ILE cc_start: 0.8308 (pt) cc_final: 0.8011 (pt) REVERT: B 361 GLN cc_start: 0.6689 (tt0) cc_final: 0.6384 (tt0) REVERT: B 362 ASP cc_start: 0.6252 (m-30) cc_final: 0.5525 (m-30) REVERT: B 373 ILE cc_start: 0.9065 (mt) cc_final: 0.8323 (mt) REVERT: B 415 ASN cc_start: 0.8552 (t0) cc_final: 0.7838 (t0) REVERT: B 418 ASN cc_start: 0.7652 (m-40) cc_final: 0.6533 (m-40) REVERT: B 425 ILE cc_start: 0.9268 (mt) cc_final: 0.8740 (mt) REVERT: B 436 LEU cc_start: 0.9378 (mt) cc_final: 0.9098 (mt) REVERT: B 493 MET cc_start: 0.7437 (tmm) cc_final: 0.7146 (tmm) REVERT: B 494 MET cc_start: 0.7842 (mtp) cc_final: 0.7587 (mtp) REVERT: B 496 ASN cc_start: 0.7072 (t0) cc_final: 0.5335 (t0) REVERT: B 565 VAL cc_start: 0.9293 (t) cc_final: 0.9093 (p) REVERT: B 575 ARG cc_start: 0.7594 (mtm110) cc_final: 0.6952 (mtm180) REVERT: B 588 GLN cc_start: 0.7455 (mm-40) cc_final: 0.6997 (mm-40) REVERT: B 601 ILE cc_start: 0.7785 (mt) cc_final: 0.7235 (mt) REVERT: B 613 TYR cc_start: 0.7838 (t80) cc_final: 0.7529 (t80) REVERT: B 641 ILE cc_start: 0.9444 (mm) cc_final: 0.9122 (mm) REVERT: B 645 GLN cc_start: 0.8410 (tp-100) cc_final: 0.8210 (tp-100) REVERT: B 656 LEU cc_start: 0.8212 (mt) cc_final: 0.7882 (mt) REVERT: C 85 GLN cc_start: 0.5803 (mt0) cc_final: 0.4883 (tt0) REVERT: C 90 LEU cc_start: 0.5509 (mt) cc_final: 0.4979 (mt) REVERT: C 137 MET cc_start: 0.4147 (mtp) cc_final: 0.3341 (mtt) REVERT: C 194 ILE cc_start: 0.7431 (mt) cc_final: 0.7188 (mp) REVERT: C 205 VAL cc_start: 0.7608 (t) cc_final: 0.7334 (t) REVERT: C 275 PRO cc_start: 0.5456 (Cg_endo) cc_final: 0.4941 (Cg_exo) REVERT: D 31 LEU cc_start: 0.8392 (mt) cc_final: 0.8044 (mt) REVERT: D 100 VAL cc_start: 0.3534 (t) cc_final: 0.2881 (t) REVERT: D 205 VAL cc_start: 0.7168 (t) cc_final: 0.6775 (t) REVERT: D 317 ASP cc_start: 0.6461 (t0) cc_final: 0.5769 (t70) outliers start: 24 outliers final: 5 residues processed: 915 average time/residue: 0.1252 time to fit residues: 164.5545 Evaluate side-chains 632 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 625 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.0370 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 43 GLN A 147 GLN A 239 GLN A 320 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 232 ASN B 304 HIS ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN C 28 GLN C 84 HIS C 119 ASN C 132 GLN D 71 ASN D 80 HIS D 186 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.110337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.076555 restraints weight = 51451.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.079537 restraints weight = 31396.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.081419 restraints weight = 21965.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.082814 restraints weight = 16975.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.083840 restraints weight = 13801.607| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 16386 Z= 0.253 Angle : 0.704 7.971 22134 Z= 0.379 Chirality : 0.044 0.320 2360 Planarity : 0.004 0.039 2818 Dihedral : 11.589 179.915 2242 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.23 % Allowed : 3.09 % Favored : 96.68 % 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: 1.12 (0.18), residues: 1932 helix: 1.17 (0.15), residues: 1104 sheet: 0.01 (0.40), residues: 126 loop : 0.40 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 452 TYR 0.029 0.002 TYR C 247 PHE 0.042 0.003 PHE D 178 TRP 0.014 0.002 TRP A 558 HIS 0.007 0.002 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00520 (16386) covalent geometry : angle 0.70392 (22134) hydrogen bonds : bond 0.04737 ( 869) hydrogen bonds : angle 5.24424 ( 2568) *********************** 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 703 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 699 time to evaluate : 0.631 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 18 ILE cc_start: 0.9733 (mm) cc_final: 0.9257 (mt) REVERT: A 65 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8168 (mm-30) REVERT: A 87 LYS cc_start: 0.9221 (tptm) cc_final: 0.8955 (tptm) REVERT: A 107 LYS cc_start: 0.9390 (mttm) cc_final: 0.9153 (mmmt) REVERT: A 136 LYS cc_start: 0.9761 (mmpt) cc_final: 0.9495 (ttpp) REVERT: A 143 LEU cc_start: 0.9256 (tp) cc_final: 0.8997 (tp) REVERT: A 144 MET cc_start: 0.9315 (mtm) cc_final: 0.8837 (mtm) REVERT: A 145 ILE cc_start: 0.9424 (tp) cc_final: 0.9217 (tp) REVERT: A 194 LYS cc_start: 0.9452 (ttpt) cc_final: 0.9112 (ttpp) REVERT: A 195 LEU cc_start: 0.9558 (mt) cc_final: 0.9270 (mt) REVERT: A 252 ASN cc_start: 0.8574 (t0) cc_final: 0.8123 (t0) REVERT: A 279 SER cc_start: 0.7704 (m) cc_final: 0.7479 (p) REVERT: A 286 ASP cc_start: 0.9082 (m-30) cc_final: 0.8658 (m-30) REVERT: A 385 VAL cc_start: 0.9614 (t) cc_final: 0.9412 (t) REVERT: A 387 GLN cc_start: 0.8667 (mt0) cc_final: 0.8271 (mt0) REVERT: A 421 GLU cc_start: 0.9465 (tm-30) cc_final: 0.9261 (tm-30) REVERT: A 436 LEU cc_start: 0.9628 (mt) cc_final: 0.9402 (mt) REVERT: A 502 ARG cc_start: 0.9493 (tpt170) cc_final: 0.9233 (tpt90) REVERT: A 510 LYS cc_start: 0.9688 (mmmt) cc_final: 0.9017 (mmtm) REVERT: A 550 MET cc_start: 0.6545 (mtm) cc_final: 0.5412 (ptp) REVERT: A 571 TYR cc_start: 0.8911 (t80) cc_final: 0.8554 (t80) REVERT: A 572 HIS cc_start: 0.9505 (m90) cc_final: 0.9137 (m90) REVERT: A 599 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8523 (mt-10) REVERT: A 615 MET cc_start: 0.8911 (mmp) cc_final: 0.8517 (mmp) REVERT: A 626 TYR cc_start: 0.9147 (m-80) cc_final: 0.8750 (m-10) REVERT: A 634 MET cc_start: 0.9345 (mmp) cc_final: 0.9085 (mpp) REVERT: A 655 THR cc_start: 0.9448 (t) cc_final: 0.9105 (t) REVERT: A 667 LEU cc_start: 0.9449 (tt) cc_final: 0.9205 (tt) REVERT: A 683 TYR cc_start: 0.8498 (t80) cc_final: 0.7761 (t80) REVERT: B 19 GLN cc_start: 0.9354 (mt0) cc_final: 0.8886 (pp30) REVERT: B 51 LEU cc_start: 0.9468 (tp) cc_final: 0.9093 (tp) REVERT: B 77 ILE cc_start: 0.9756 (mt) cc_final: 0.9451 (mt) REVERT: B 87 LYS cc_start: 0.9297 (tptp) cc_final: 0.8979 (tptp) REVERT: B 89 PHE cc_start: 0.9273 (t80) cc_final: 0.9024 (t80) REVERT: B 95 MET cc_start: 0.9514 (tpp) cc_final: 0.8571 (tpp) REVERT: B 99 LYS cc_start: 0.9465 (mmmt) cc_final: 0.8759 (mmmt) REVERT: B 115 LEU cc_start: 0.9038 (mp) cc_final: 0.8803 (mp) REVERT: B 144 MET cc_start: 0.9635 (mtm) cc_final: 0.8991 (mtm) REVERT: B 149 TYR cc_start: 0.8978 (t80) cc_final: 0.8694 (t80) REVERT: B 150 GLN cc_start: 0.9053 (tp40) cc_final: 0.8745 (tp40) REVERT: B 161 ARG cc_start: 0.8839 (ttm110) cc_final: 0.8629 (mtt-85) REVERT: B 162 LYS cc_start: 0.9327 (tppt) cc_final: 0.8890 (mttm) REVERT: B 168 VAL cc_start: 0.9159 (t) cc_final: 0.8796 (p) REVERT: B 191 GLN cc_start: 0.9116 (mm-40) cc_final: 0.8849 (mm-40) REVERT: B 211 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8077 (mt-10) REVERT: B 220 THR cc_start: 0.8080 (p) cc_final: 0.7394 (p) REVERT: B 236 TYR cc_start: 0.8826 (t80) cc_final: 0.8589 (t80) REVERT: B 259 ASN cc_start: 0.8914 (m-40) cc_final: 0.8706 (m-40) REVERT: B 267 ILE cc_start: 0.8826 (pt) cc_final: 0.8523 (pt) REVERT: B 286 ASP cc_start: 0.9009 (m-30) cc_final: 0.8290 (m-30) REVERT: B 317 MET cc_start: 0.8628 (pmm) cc_final: 0.8283 (pmm) REVERT: B 319 MET cc_start: 0.9216 (tpp) cc_final: 0.8889 (tpp) REVERT: B 321 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8382 (tm-30) REVERT: B 322 MET cc_start: 0.8689 (mmm) cc_final: 0.7753 (mmm) REVERT: B 355 TYR cc_start: 0.9309 (m-10) cc_final: 0.8935 (m-10) REVERT: B 362 ASP cc_start: 0.8668 (m-30) cc_final: 0.7905 (m-30) REVERT: B 373 ILE cc_start: 0.9721 (mt) cc_final: 0.9509 (mt) REVERT: B 415 ASN cc_start: 0.9016 (t0) cc_final: 0.7723 (t0) REVERT: B 418 ASN cc_start: 0.9324 (m-40) cc_final: 0.8686 (m-40) REVERT: B 458 MET cc_start: 0.9445 (mmm) cc_final: 0.8999 (mmm) REVERT: B 467 ASN cc_start: 0.9233 (m-40) cc_final: 0.8890 (m110) REVERT: B 492 PHE cc_start: 0.9751 (m-80) cc_final: 0.9522 (m-80) REVERT: B 494 MET cc_start: 0.9437 (mtp) cc_final: 0.8642 (mtp) REVERT: B 496 ASN cc_start: 0.9721 (t0) cc_final: 0.9005 (t0) REVERT: B 499 SER cc_start: 0.9918 (t) cc_final: 0.9699 (p) REVERT: B 500 ILE cc_start: 0.9727 (mt) cc_final: 0.9468 (mt) REVERT: B 501 GLN cc_start: 0.9086 (tp-100) cc_final: 0.8562 (tp-100) REVERT: B 515 ASP cc_start: 0.9080 (m-30) cc_final: 0.8756 (m-30) REVERT: B 570 MET cc_start: 0.9234 (tpp) cc_final: 0.8690 (tpp) REVERT: B 574 TYR cc_start: 0.8325 (m-80) cc_final: 0.7983 (m-80) REVERT: B 575 ARG cc_start: 0.8831 (mtm110) cc_final: 0.8211 (mtm110) REVERT: B 588 GLN cc_start: 0.9376 (mm-40) cc_final: 0.8809 (mm-40) REVERT: B 601 ILE cc_start: 0.9269 (mt) cc_final: 0.8739 (mp) REVERT: B 613 TYR cc_start: 0.9350 (t80) cc_final: 0.8880 (t80) REVERT: B 615 MET cc_start: 0.9046 (mmp) cc_final: 0.8203 (mmp) REVERT: B 618 LEU cc_start: 0.8920 (mt) cc_final: 0.8646 (mt) REVERT: B 631 ASP cc_start: 0.9371 (t0) cc_final: 0.9165 (t0) REVERT: B 645 GLN cc_start: 0.9263 (tp-100) cc_final: 0.9012 (tp-100) REVERT: C 21 PHE cc_start: 0.8819 (m-80) cc_final: 0.8177 (m-80) REVERT: C 46 TYR cc_start: 0.7843 (m-80) cc_final: 0.7578 (m-80) REVERT: C 96 MET cc_start: 0.6629 (mmt) cc_final: 0.6007 (mmt) REVERT: C 139 VAL cc_start: 0.8842 (p) cc_final: 0.8544 (t) REVERT: C 204 TYR cc_start: 0.9565 (t80) cc_final: 0.9129 (t80) REVERT: C 315 LEU cc_start: 0.8395 (mt) cc_final: 0.7924 (mt) REVERT: D 33 GLU cc_start: 0.9370 (mp0) cc_final: 0.9135 (mp0) REVERT: D 46 TYR cc_start: 0.8832 (m-80) cc_final: 0.8407 (m-80) REVERT: D 96 MET cc_start: 0.8445 (mmt) cc_final: 0.7892 (mmm) REVERT: D 109 PHE cc_start: 0.7544 (OUTLIER) cc_final: 0.7038 (m-80) REVERT: D 185 MET cc_start: 0.6602 (mmm) cc_final: 0.5882 (mmp) REVERT: D 259 PHE cc_start: 0.7811 (t80) cc_final: 0.7297 (t80) REVERT: D 317 ASP cc_start: 0.9302 (t0) cc_final: 0.8185 (t0) outliers start: 4 outliers final: 2 residues processed: 702 average time/residue: 0.1380 time to fit residues: 140.6679 Evaluate side-chains 563 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 560 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 164 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 182 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 158 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 232 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 HIS ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN B 668 ASN B 676 HIS C 84 HIS D 25 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 238 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.112880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.078877 restraints weight = 49756.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.081975 restraints weight = 30076.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.084088 restraints weight = 21102.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.085456 restraints weight = 16361.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.086351 restraints weight = 13375.320| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16386 Z= 0.139 Angle : 0.603 8.977 22134 Z= 0.320 Chirality : 0.042 0.215 2360 Planarity : 0.004 0.050 2818 Dihedral : 11.118 178.342 2242 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.12 % Allowed : 2.21 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.19), residues: 1932 helix: 1.22 (0.15), residues: 1131 sheet: -0.28 (0.40), residues: 132 loop : 0.40 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 243 TYR 0.024 0.002 TYR A 606 PHE 0.031 0.002 PHE D 109 TRP 0.008 0.001 TRP C 30 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00302 (16386) covalent geometry : angle 0.60316 (22134) hydrogen bonds : bond 0.04137 ( 869) hydrogen bonds : angle 4.92207 ( 2568) *********************** 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 699 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 697 time to evaluate : 0.525 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 87 LYS cc_start: 0.9283 (tptm) cc_final: 0.8967 (tptm) REVERT: A 95 MET cc_start: 0.9744 (tpt) cc_final: 0.9530 (mmm) REVERT: A 107 LYS cc_start: 0.9397 (mttm) cc_final: 0.9133 (mmmt) REVERT: A 117 ARG cc_start: 0.9234 (mtp85) cc_final: 0.8818 (mmt180) REVERT: A 129 PHE cc_start: 0.9405 (m-80) cc_final: 0.9149 (m-80) REVERT: A 136 LYS cc_start: 0.9767 (mmpt) cc_final: 0.9463 (ttpt) REVERT: A 143 LEU cc_start: 0.9160 (tp) cc_final: 0.8909 (tp) REVERT: A 144 MET cc_start: 0.9111 (mtm) cc_final: 0.8663 (mtm) REVERT: A 150 GLN cc_start: 0.9252 (tp40) cc_final: 0.8742 (tm-30) REVERT: A 168 VAL cc_start: 0.9107 (m) cc_final: 0.8829 (p) REVERT: A 176 ASN cc_start: 0.8698 (t0) cc_final: 0.8429 (t0) REVERT: A 194 LYS cc_start: 0.9377 (ttpt) cc_final: 0.9144 (ttpp) REVERT: A 221 LYS cc_start: 0.7605 (mppt) cc_final: 0.7256 (mptt) REVERT: A 227 MET cc_start: 0.9364 (mtp) cc_final: 0.8879 (mtp) REVERT: A 252 ASN cc_start: 0.8508 (t0) cc_final: 0.7857 (t0) REVERT: A 254 PHE cc_start: 0.8213 (m-10) cc_final: 0.7816 (m-10) REVERT: A 286 ASP cc_start: 0.9105 (m-30) cc_final: 0.8411 (m-30) REVERT: A 362 ASP cc_start: 0.9169 (m-30) cc_final: 0.8733 (m-30) REVERT: A 366 LYS cc_start: 0.9386 (ptpp) cc_final: 0.8939 (ptpp) REVERT: A 370 ASN cc_start: 0.9349 (m-40) cc_final: 0.9097 (m110) REVERT: A 396 ASP cc_start: 0.8975 (p0) cc_final: 0.8752 (p0) REVERT: A 468 LEU cc_start: 0.9663 (tp) cc_final: 0.9446 (tp) REVERT: A 493 MET cc_start: 0.9385 (tmm) cc_final: 0.9171 (tmm) REVERT: A 574 TYR cc_start: 0.9080 (m-80) cc_final: 0.8330 (m-80) REVERT: A 584 ILE cc_start: 0.9552 (pt) cc_final: 0.9059 (pt) REVERT: A 601 ILE cc_start: 0.9007 (tt) cc_final: 0.8742 (tt) REVERT: A 615 MET cc_start: 0.8932 (mmp) cc_final: 0.8634 (mmp) REVERT: A 626 TYR cc_start: 0.9136 (m-80) cc_final: 0.8684 (m-10) REVERT: A 634 MET cc_start: 0.9309 (mmp) cc_final: 0.9103 (mpp) REVERT: A 637 VAL cc_start: 0.9766 (t) cc_final: 0.9392 (t) REVERT: A 645 GLN cc_start: 0.8352 (tp40) cc_final: 0.6996 (tp-100) REVERT: A 650 GLN cc_start: 0.7630 (mm110) cc_final: 0.7180 (tp40) REVERT: A 653 SER cc_start: 0.9084 (p) cc_final: 0.8874 (p) REVERT: A 667 LEU cc_start: 0.9433 (tt) cc_final: 0.9233 (tt) REVERT: A 680 LYS cc_start: 0.8392 (mttt) cc_final: 0.7835 (mttt) REVERT: B 41 ILE cc_start: 0.9673 (mm) cc_final: 0.9354 (mt) REVERT: B 51 LEU cc_start: 0.9459 (tp) cc_final: 0.9030 (tp) REVERT: B 77 ILE cc_start: 0.9704 (mt) cc_final: 0.9326 (mt) REVERT: B 87 LYS cc_start: 0.9328 (tptp) cc_final: 0.9037 (tptp) REVERT: B 89 PHE cc_start: 0.9142 (t80) cc_final: 0.8803 (t80) REVERT: B 95 MET cc_start: 0.9426 (tpp) cc_final: 0.8493 (tpp) REVERT: B 99 LYS cc_start: 0.9456 (mmmt) cc_final: 0.8732 (mmmt) REVERT: B 144 MET cc_start: 0.9523 (mtm) cc_final: 0.8866 (mtm) REVERT: B 149 TYR cc_start: 0.9045 (t80) cc_final: 0.8581 (t80) REVERT: B 161 ARG cc_start: 0.8750 (ttm110) cc_final: 0.8465 (mtt-85) REVERT: B 162 LYS cc_start: 0.9337 (tppt) cc_final: 0.8946 (mttp) REVERT: B 168 VAL cc_start: 0.9253 (t) cc_final: 0.8755 (p) REVERT: B 211 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8035 (mt-10) REVERT: B 236 TYR cc_start: 0.8655 (t80) cc_final: 0.8347 (t80) REVERT: B 257 ASP cc_start: 0.8368 (m-30) cc_final: 0.8097 (m-30) REVERT: B 263 ASP cc_start: 0.9449 (m-30) cc_final: 0.9231 (m-30) REVERT: B 286 ASP cc_start: 0.8968 (m-30) cc_final: 0.8287 (m-30) REVERT: B 317 MET cc_start: 0.8631 (pmm) cc_final: 0.7526 (pmm) REVERT: B 333 LYS cc_start: 0.9227 (tptm) cc_final: 0.8968 (tptp) REVERT: B 355 TYR cc_start: 0.9217 (m-10) cc_final: 0.8873 (m-10) REVERT: B 362 ASP cc_start: 0.8689 (m-30) cc_final: 0.7846 (m-30) REVERT: B 375 LYS cc_start: 0.9217 (mmmm) cc_final: 0.9006 (mmmm) REVERT: B 396 ASP cc_start: 0.8086 (p0) cc_final: 0.7321 (p0) REVERT: B 415 ASN cc_start: 0.9139 (t0) cc_final: 0.7896 (t0) REVERT: B 418 ASN cc_start: 0.9263 (m-40) cc_final: 0.8725 (m-40) REVERT: B 459 LYS cc_start: 0.8907 (mttm) cc_final: 0.8611 (mmmt) REVERT: B 467 ASN cc_start: 0.9320 (m-40) cc_final: 0.8973 (m110) REVERT: B 480 GLU cc_start: 0.9399 (pm20) cc_final: 0.8939 (mt-10) REVERT: B 493 MET cc_start: 0.9449 (tmm) cc_final: 0.9193 (tmm) REVERT: B 496 ASN cc_start: 0.9689 (t0) cc_final: 0.8496 (t0) REVERT: B 499 SER cc_start: 0.9922 (t) cc_final: 0.9532 (p) REVERT: B 500 ILE cc_start: 0.9735 (mt) cc_final: 0.9456 (mt) REVERT: B 501 GLN cc_start: 0.9002 (tp-100) cc_final: 0.8432 (tp-100) REVERT: B 515 ASP cc_start: 0.9102 (m-30) cc_final: 0.8751 (m-30) REVERT: B 543 ILE cc_start: 0.9320 (mp) cc_final: 0.9061 (mt) REVERT: B 575 ARG cc_start: 0.8773 (mtm110) cc_final: 0.7171 (mtm180) REVERT: B 588 GLN cc_start: 0.9402 (mm-40) cc_final: 0.8995 (mm-40) REVERT: B 601 ILE cc_start: 0.9115 (mt) cc_final: 0.8767 (mp) REVERT: B 618 LEU cc_start: 0.9101 (mt) cc_final: 0.8643 (mt) REVERT: B 650 GLN cc_start: 0.8377 (mm-40) cc_final: 0.8056 (mm-40) REVERT: B 667 LEU cc_start: 0.9469 (tt) cc_final: 0.9139 (tt) REVERT: B 668 ASN cc_start: 0.9707 (m110) cc_final: 0.9473 (m-40) REVERT: C 21 PHE cc_start: 0.9019 (m-80) cc_final: 0.8463 (m-80) REVERT: C 46 TYR cc_start: 0.7658 (m-80) cc_final: 0.7134 (m-80) REVERT: C 179 TYR cc_start: 0.9339 (t80) cc_final: 0.9099 (t80) REVERT: C 204 TYR cc_start: 0.9551 (t80) cc_final: 0.9202 (t80) REVERT: D 46 TYR cc_start: 0.8912 (m-80) cc_final: 0.8580 (m-80) REVERT: D 96 MET cc_start: 0.8093 (mmt) cc_final: 0.7612 (mmm) REVERT: D 185 MET cc_start: 0.7269 (mmm) cc_final: 0.6465 (mmm) REVERT: D 189 GLU cc_start: 0.9026 (tp30) cc_final: 0.8565 (mt-10) REVERT: D 239 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7208 (pm20) REVERT: D 259 PHE cc_start: 0.7568 (t80) cc_final: 0.7300 (t80) REVERT: D 317 ASP cc_start: 0.9280 (t0) cc_final: 0.8593 (t0) outliers start: 2 outliers final: 0 residues processed: 698 average time/residue: 0.1313 time to fit residues: 134.4298 Evaluate side-chains 569 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 568 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 8.9990 chunk 157 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 185 optimal weight: 10.0000 chunk 191 optimal weight: 20.0000 chunk 159 optimal weight: 6.9990 chunk 182 optimal weight: 20.0000 chunk 93 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN A 232 ASN ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN B 180 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN C 238 ASN D 23 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 249 GLN D 263 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.103947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.072506 restraints weight = 55379.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.075031 restraints weight = 32927.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.076899 restraints weight = 23229.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.078214 restraints weight = 17741.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.079121 restraints weight = 14306.629| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.6783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 16386 Z= 0.315 Angle : 0.756 8.811 22134 Z= 0.400 Chirality : 0.045 0.169 2360 Planarity : 0.005 0.053 2818 Dihedral : 11.484 177.170 2242 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 23.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % 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: 0.28 (0.18), residues: 1932 helix: 0.54 (0.15), residues: 1132 sheet: -0.26 (0.43), residues: 118 loop : -0.10 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 161 TYR 0.032 0.003 TYR D 174 PHE 0.029 0.003 PHE D 166 TRP 0.016 0.002 TRP A 558 HIS 0.011 0.002 HIS B 372 Details of bonding type rmsd covalent geometry : bond 0.00634 (16386) covalent geometry : angle 0.75570 (22134) hydrogen bonds : bond 0.04457 ( 869) hydrogen bonds : angle 5.29096 ( 2568) *********************** 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 636 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 636 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9509 (tptp) cc_final: 0.9220 (tptp) REVERT: A 95 MET cc_start: 0.9782 (tpt) cc_final: 0.9518 (tpp) REVERT: A 99 LYS cc_start: 0.9586 (mmtp) cc_final: 0.9340 (mmmm) REVERT: A 104 TYR cc_start: 0.8977 (m-80) cc_final: 0.8288 (m-80) REVERT: A 107 LYS cc_start: 0.9419 (mttm) cc_final: 0.8974 (tptt) REVERT: A 117 ARG cc_start: 0.9264 (mtp85) cc_final: 0.8992 (mmt180) REVERT: A 129 PHE cc_start: 0.9547 (m-80) cc_final: 0.9213 (m-80) REVERT: A 144 MET cc_start: 0.9087 (mtm) cc_final: 0.8699 (mtm) REVERT: A 150 GLN cc_start: 0.9088 (tp40) cc_final: 0.8849 (tp40) REVERT: A 151 PRO cc_start: 0.9678 (Cg_exo) cc_final: 0.9418 (Cg_endo) REVERT: A 163 ARG cc_start: 0.8965 (mmp80) cc_final: 0.8735 (mpt-90) REVERT: A 168 VAL cc_start: 0.9150 (m) cc_final: 0.8948 (p) REVERT: A 191 GLN cc_start: 0.8777 (mp10) cc_final: 0.8573 (mp10) REVERT: A 194 LYS cc_start: 0.9416 (ttpt) cc_final: 0.9149 (ttpp) REVERT: A 227 MET cc_start: 0.9339 (mtp) cc_final: 0.8931 (mtp) REVERT: A 252 ASN cc_start: 0.8743 (t0) cc_final: 0.8419 (t0) REVERT: A 286 ASP cc_start: 0.9153 (m-30) cc_final: 0.8640 (m-30) REVERT: A 312 GLN cc_start: 0.9056 (mp10) cc_final: 0.8781 (mp10) REVERT: A 335 GLU cc_start: 0.9323 (tp30) cc_final: 0.9115 (tm-30) REVERT: A 337 ILE cc_start: 0.9666 (pt) cc_final: 0.9057 (pt) REVERT: A 350 ARG cc_start: 0.8498 (mtp85) cc_final: 0.7762 (mtp85) REVERT: A 362 ASP cc_start: 0.9201 (m-30) cc_final: 0.8659 (m-30) REVERT: A 370 ASN cc_start: 0.9509 (m-40) cc_final: 0.9298 (m-40) REVERT: A 375 LYS cc_start: 0.9476 (mttt) cc_final: 0.9085 (mttt) REVERT: A 396 ASP cc_start: 0.9186 (p0) cc_final: 0.8907 (p0) REVERT: A 402 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8705 (tm-30) REVERT: A 468 LEU cc_start: 0.9562 (tp) cc_final: 0.9291 (tp) REVERT: A 493 MET cc_start: 0.9270 (tmm) cc_final: 0.8997 (tmm) REVERT: A 500 ILE cc_start: 0.9858 (mt) cc_final: 0.9488 (mt) REVERT: A 515 ASP cc_start: 0.9498 (m-30) cc_final: 0.9243 (m-30) REVERT: A 522 TYR cc_start: 0.9075 (m-80) cc_final: 0.8735 (m-80) REVERT: A 575 ARG cc_start: 0.8926 (ptp-110) cc_final: 0.8640 (mtm-85) REVERT: A 583 SER cc_start: 0.9480 (t) cc_final: 0.9239 (t) REVERT: A 601 ILE cc_start: 0.9022 (tt) cc_final: 0.8772 (tt) REVERT: A 602 GLU cc_start: 0.9093 (pt0) cc_final: 0.8110 (pt0) REVERT: A 615 MET cc_start: 0.8686 (mmp) cc_final: 0.8368 (mmp) REVERT: A 654 PHE cc_start: 0.9178 (t80) cc_final: 0.8898 (t80) REVERT: A 657 PHE cc_start: 0.8570 (m-80) cc_final: 0.8222 (m-80) REVERT: A 667 LEU cc_start: 0.9597 (tt) cc_final: 0.9378 (tt) REVERT: B 87 LYS cc_start: 0.9375 (tptp) cc_final: 0.9062 (tptp) REVERT: B 95 MET cc_start: 0.9615 (tpp) cc_final: 0.9205 (tpp) REVERT: B 99 LYS cc_start: 0.9573 (mmmt) cc_final: 0.9078 (mmmm) REVERT: B 144 MET cc_start: 0.9567 (mtm) cc_final: 0.9025 (mtm) REVERT: B 161 ARG cc_start: 0.8839 (ttm110) cc_final: 0.8418 (mtp85) REVERT: B 162 LYS cc_start: 0.9413 (tppt) cc_final: 0.9046 (mttm) REVERT: B 250 TYR cc_start: 0.8958 (m-80) cc_final: 0.8733 (m-80) REVERT: B 252 ASN cc_start: 0.8904 (t0) cc_final: 0.8682 (t0) REVERT: B 257 ASP cc_start: 0.8244 (m-30) cc_final: 0.7978 (m-30) REVERT: B 259 ASN cc_start: 0.9106 (m-40) cc_final: 0.8845 (m-40) REVERT: B 286 ASP cc_start: 0.9160 (m-30) cc_final: 0.8519 (m-30) REVERT: B 312 GLN cc_start: 0.9009 (pm20) cc_final: 0.8727 (pm20) REVERT: B 333 LYS cc_start: 0.9202 (tptm) cc_final: 0.8976 (tptp) REVERT: B 362 ASP cc_start: 0.8808 (m-30) cc_final: 0.7978 (m-30) REVERT: B 373 ILE cc_start: 0.9816 (mt) cc_final: 0.9082 (mt) REVERT: B 375 LYS cc_start: 0.9252 (mmmm) cc_final: 0.8987 (mmtt) REVERT: B 415 ASN cc_start: 0.8955 (t0) cc_final: 0.8049 (t0) REVERT: B 416 ILE cc_start: 0.9800 (mt) cc_final: 0.9503 (mt) REVERT: B 418 ASN cc_start: 0.9067 (m-40) cc_final: 0.8618 (m-40) REVERT: B 420 MET cc_start: 0.9121 (mmm) cc_final: 0.8720 (mmm) REVERT: B 426 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8781 (tm-30) REVERT: B 459 LYS cc_start: 0.9119 (mttm) cc_final: 0.8891 (mmmt) REVERT: B 467 ASN cc_start: 0.9296 (m-40) cc_final: 0.9072 (m-40) REVERT: B 472 LEU cc_start: 0.9785 (mt) cc_final: 0.9568 (mt) REVERT: B 496 ASN cc_start: 0.9668 (t0) cc_final: 0.8217 (t0) REVERT: B 499 SER cc_start: 0.9868 (t) cc_final: 0.9585 (p) REVERT: B 500 ILE cc_start: 0.9778 (mt) cc_final: 0.9463 (mt) REVERT: B 501 GLN cc_start: 0.9007 (tp-100) cc_final: 0.8427 (tp-100) REVERT: B 515 ASP cc_start: 0.9176 (m-30) cc_final: 0.8794 (m-30) REVERT: B 531 TYR cc_start: 0.8606 (m-80) cc_final: 0.8390 (m-80) REVERT: B 570 MET cc_start: 0.9167 (tpp) cc_final: 0.8741 (tpp) REVERT: B 575 ARG cc_start: 0.8918 (mtm110) cc_final: 0.7349 (mtm180) REVERT: B 588 GLN cc_start: 0.9430 (mm-40) cc_final: 0.9118 (mm110) REVERT: B 615 MET cc_start: 0.9095 (mmp) cc_final: 0.8831 (mmp) REVERT: B 618 LEU cc_start: 0.9049 (mt) cc_final: 0.8741 (mt) REVERT: B 645 GLN cc_start: 0.8876 (tp-100) cc_final: 0.8671 (tp-100) REVERT: B 650 GLN cc_start: 0.8275 (mm-40) cc_final: 0.8016 (mm-40) REVERT: B 667 LEU cc_start: 0.9552 (tt) cc_final: 0.9301 (tt) REVERT: C 157 MET cc_start: 0.5180 (ptt) cc_final: 0.4871 (ptt) REVERT: C 183 LYS cc_start: 0.7605 (mttt) cc_final: 0.7382 (mtmt) REVERT: C 204 TYR cc_start: 0.9680 (t80) cc_final: 0.9349 (t80) REVERT: C 278 GLU cc_start: 0.9208 (pm20) cc_final: 0.8913 (pm20) REVERT: D 96 MET cc_start: 0.8472 (mmt) cc_final: 0.7935 (mmm) REVERT: D 179 TYR cc_start: 0.9250 (t80) cc_final: 0.9047 (t80) REVERT: D 185 MET cc_start: 0.7759 (mmm) cc_final: 0.7087 (mmm) REVERT: D 259 PHE cc_start: 0.7859 (t80) cc_final: 0.7428 (t80) outliers start: 0 outliers final: 0 residues processed: 636 average time/residue: 0.1337 time to fit residues: 124.9171 Evaluate side-chains 540 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 540 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 HIS ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN D 263 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.110841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.078738 restraints weight = 50959.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.081593 restraints weight = 30852.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.083548 restraints weight = 21309.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.084974 restraints weight = 16148.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.085953 restraints weight = 12992.072| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.6997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16386 Z= 0.131 Angle : 0.614 10.566 22134 Z= 0.323 Chirality : 0.043 0.192 2360 Planarity : 0.004 0.055 2818 Dihedral : 10.969 176.701 2242 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % 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: 0.61 (0.19), residues: 1932 helix: 0.79 (0.15), residues: 1147 sheet: -0.72 (0.43), residues: 142 loop : 0.23 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 161 TYR 0.029 0.002 TYR D 174 PHE 0.021 0.002 PHE A 129 TRP 0.008 0.001 TRP A 9 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00281 (16386) covalent geometry : angle 0.61403 (22134) hydrogen bonds : bond 0.03974 ( 869) hydrogen bonds : angle 4.97997 ( 2568) *********************** 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 660 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 660 time to evaluate : 0.785 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: A 8 LYS cc_start: 0.9521 (tptp) cc_final: 0.9255 (tppt) REVERT: A 65 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8324 (mm-30) REVERT: A 95 MET cc_start: 0.9560 (tpt) cc_final: 0.8879 (mmm) REVERT: A 99 LYS cc_start: 0.9569 (mmtp) cc_final: 0.9081 (mmtp) REVERT: A 104 TYR cc_start: 0.8766 (m-80) cc_final: 0.8045 (m-80) REVERT: A 117 ARG cc_start: 0.9211 (mtp85) cc_final: 0.8773 (mmt180) REVERT: A 119 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8559 (pm20) REVERT: A 120 ASP cc_start: 0.9307 (m-30) cc_final: 0.8542 (m-30) REVERT: A 129 PHE cc_start: 0.9513 (m-80) cc_final: 0.9144 (m-80) REVERT: A 136 LYS cc_start: 0.9791 (mmtt) cc_final: 0.9460 (ttpt) REVERT: A 144 MET cc_start: 0.8979 (mtm) cc_final: 0.8464 (mtm) REVERT: A 150 GLN cc_start: 0.9165 (tp40) cc_final: 0.8949 (tp40) REVERT: A 151 PRO cc_start: 0.9668 (Cg_exo) cc_final: 0.9282 (Cg_endo) REVERT: A 161 ARG cc_start: 0.9119 (ttm110) cc_final: 0.8901 (ttm110) REVERT: A 176 ASN cc_start: 0.8867 (t0) cc_final: 0.8644 (t0) REVERT: A 180 ASN cc_start: 0.8763 (m-40) cc_final: 0.8446 (m-40) REVERT: A 191 GLN cc_start: 0.9135 (mm-40) cc_final: 0.8834 (mp10) REVERT: A 194 LYS cc_start: 0.9370 (ttpt) cc_final: 0.9150 (ttpp) REVERT: A 221 LYS cc_start: 0.7401 (mppt) cc_final: 0.7179 (mptt) REVERT: A 227 MET cc_start: 0.9302 (mtp) cc_final: 0.8757 (mtp) REVERT: A 235 ARG cc_start: 0.8526 (ttp-110) cc_final: 0.8187 (ttp-110) REVERT: A 252 ASN cc_start: 0.8847 (t0) cc_final: 0.8500 (t0) REVERT: A 254 PHE cc_start: 0.8690 (m-10) cc_final: 0.8338 (m-10) REVERT: A 286 ASP cc_start: 0.9134 (m-30) cc_final: 0.8619 (m-30) REVERT: A 312 GLN cc_start: 0.8896 (mp10) cc_final: 0.8629 (mp10) REVERT: A 313 HIS cc_start: 0.8819 (m90) cc_final: 0.8368 (m170) REVERT: A 350 ARG cc_start: 0.8453 (mtp85) cc_final: 0.7832 (mtp85) REVERT: A 362 ASP cc_start: 0.9284 (m-30) cc_final: 0.8887 (m-30) REVERT: A 366 LYS cc_start: 0.9289 (ptpp) cc_final: 0.8973 (pttp) REVERT: A 370 ASN cc_start: 0.9480 (m-40) cc_final: 0.9080 (m110) REVERT: A 375 LYS cc_start: 0.9518 (mttt) cc_final: 0.9104 (mttt) REVERT: A 385 VAL cc_start: 0.9617 (t) cc_final: 0.9344 (m) REVERT: A 396 ASP cc_start: 0.9091 (p0) cc_final: 0.8814 (p0) REVERT: A 402 GLU cc_start: 0.9048 (tm-30) cc_final: 0.8816 (tm-30) REVERT: A 414 LEU cc_start: 0.9588 (mt) cc_final: 0.9319 (mt) REVERT: A 444 ASP cc_start: 0.8923 (t0) cc_final: 0.8473 (t0) REVERT: A 468 LEU cc_start: 0.9566 (tp) cc_final: 0.9286 (tp) REVERT: A 493 MET cc_start: 0.9315 (tmm) cc_final: 0.9017 (tmm) REVERT: A 500 ILE cc_start: 0.9853 (mt) cc_final: 0.9480 (mt) REVERT: A 506 ILE cc_start: 0.9764 (mm) cc_final: 0.9520 (mm) REVERT: A 515 ASP cc_start: 0.9484 (m-30) cc_final: 0.9204 (m-30) REVERT: A 571 TYR cc_start: 0.9126 (t80) cc_final: 0.8338 (t80) REVERT: A 575 ARG cc_start: 0.8845 (ptp-110) cc_final: 0.8410 (mtm-85) REVERT: A 583 SER cc_start: 0.9349 (t) cc_final: 0.9013 (t) REVERT: A 586 TYR cc_start: 0.9244 (m-80) cc_final: 0.9003 (m-10) REVERT: A 591 THR cc_start: 0.9125 (p) cc_final: 0.8866 (p) REVERT: A 595 MET cc_start: 0.9053 (tpp) cc_final: 0.8788 (tpp) REVERT: A 598 MET cc_start: 0.8442 (tmm) cc_final: 0.7884 (tmm) REVERT: A 599 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7946 (mt-10) REVERT: A 601 ILE cc_start: 0.9181 (tt) cc_final: 0.8707 (tt) REVERT: A 602 GLU cc_start: 0.8892 (pt0) cc_final: 0.8456 (mp0) REVERT: A 615 MET cc_start: 0.8660 (mmp) cc_final: 0.7768 (mmp) REVERT: A 626 TYR cc_start: 0.9257 (m-80) cc_final: 0.8994 (m-10) REVERT: A 653 SER cc_start: 0.9215 (p) cc_final: 0.8903 (p) REVERT: A 655 THR cc_start: 0.9045 (t) cc_final: 0.8803 (t) REVERT: A 686 ARG cc_start: 0.7252 (mmp-170) cc_final: 0.7023 (mmp-170) REVERT: B 27 ASP cc_start: 0.8985 (p0) cc_final: 0.8756 (p0) REVERT: B 41 ILE cc_start: 0.9784 (mm) cc_final: 0.9574 (mm) REVERT: B 51 LEU cc_start: 0.9468 (tp) cc_final: 0.9059 (tp) REVERT: B 77 ILE cc_start: 0.9717 (mt) cc_final: 0.9340 (mt) REVERT: B 81 PHE cc_start: 0.9493 (m-80) cc_final: 0.9229 (m-80) REVERT: B 87 LYS cc_start: 0.9358 (tptp) cc_final: 0.9036 (tptp) REVERT: B 95 MET cc_start: 0.9517 (tpp) cc_final: 0.8448 (tpp) REVERT: B 99 LYS cc_start: 0.9593 (mmmt) cc_final: 0.8759 (mmmt) REVERT: B 114 ILE cc_start: 0.9590 (mt) cc_final: 0.9291 (pt) REVERT: B 144 MET cc_start: 0.9402 (mtm) cc_final: 0.8965 (mtm) REVERT: B 149 TYR cc_start: 0.9407 (t80) cc_final: 0.8813 (t80) REVERT: B 162 LYS cc_start: 0.9377 (tppt) cc_final: 0.9123 (mttt) REVERT: B 191 GLN cc_start: 0.9137 (mm-40) cc_final: 0.8877 (mt0) REVERT: B 202 ASN cc_start: 0.5928 (p0) cc_final: 0.5609 (p0) REVERT: B 211 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8554 (mm-30) REVERT: B 236 TYR cc_start: 0.8945 (t80) cc_final: 0.8419 (t80) REVERT: B 259 ASN cc_start: 0.9086 (m-40) cc_final: 0.8863 (m-40) REVERT: B 286 ASP cc_start: 0.8976 (m-30) cc_final: 0.8343 (m-30) REVERT: B 287 LYS cc_start: 0.9494 (mmtt) cc_final: 0.9254 (mmmt) REVERT: B 317 MET cc_start: 0.8625 (pmm) cc_final: 0.8125 (pmm) REVERT: B 319 MET cc_start: 0.9081 (tpt) cc_final: 0.8875 (tpp) REVERT: B 322 MET cc_start: 0.8920 (ttt) cc_final: 0.8617 (ttt) REVERT: B 333 LYS cc_start: 0.9190 (tptm) cc_final: 0.8914 (tptp) REVERT: B 335 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8338 (mt-10) REVERT: B 350 ARG cc_start: 0.9180 (tpp80) cc_final: 0.8820 (tpp80) REVERT: B 359 MET cc_start: 0.7944 (ttp) cc_final: 0.7662 (ptp) REVERT: B 362 ASP cc_start: 0.8766 (m-30) cc_final: 0.8063 (m-30) REVERT: B 373 ILE cc_start: 0.9716 (mt) cc_final: 0.9117 (mt) REVERT: B 375 LYS cc_start: 0.9222 (mmmm) cc_final: 0.8939 (mmtt) REVERT: B 390 GLN cc_start: 0.8948 (mm-40) cc_final: 0.8734 (mm-40) REVERT: B 407 ILE cc_start: 0.8487 (mt) cc_final: 0.8137 (mt) REVERT: B 415 ASN cc_start: 0.9040 (t0) cc_final: 0.8235 (t0) REVERT: B 416 ILE cc_start: 0.9815 (mt) cc_final: 0.9515 (mt) REVERT: B 418 ASN cc_start: 0.9301 (m-40) cc_final: 0.8889 (m-40) REVERT: B 420 MET cc_start: 0.9092 (mmm) cc_final: 0.8845 (mmm) REVERT: B 427 LYS cc_start: 0.9721 (ptpp) cc_final: 0.9271 (ptpp) REVERT: B 459 LYS cc_start: 0.9182 (mttp) cc_final: 0.8650 (mtmt) REVERT: B 472 LEU cc_start: 0.9740 (mt) cc_final: 0.9482 (mt) REVERT: B 480 GLU cc_start: 0.9491 (pm20) cc_final: 0.9070 (mt-10) REVERT: B 496 ASN cc_start: 0.9666 (t0) cc_final: 0.8594 (t0) REVERT: B 499 SER cc_start: 0.9892 (t) cc_final: 0.9602 (p) REVERT: B 500 ILE cc_start: 0.9775 (mt) cc_final: 0.9533 (mt) REVERT: B 501 GLN cc_start: 0.8902 (tp-100) cc_final: 0.8350 (tp-100) REVERT: B 515 ASP cc_start: 0.9162 (m-30) cc_final: 0.8743 (m-30) REVERT: B 516 GLN cc_start: 0.9047 (tt0) cc_final: 0.8667 (tt0) REVERT: B 570 MET cc_start: 0.9165 (tpp) cc_final: 0.8517 (tpt) REVERT: B 575 ARG cc_start: 0.8730 (mtm110) cc_final: 0.7213 (mtm180) REVERT: B 601 ILE cc_start: 0.9450 (mp) cc_final: 0.9100 (mp) REVERT: B 602 GLU cc_start: 0.8513 (mp0) cc_final: 0.7567 (mp0) REVERT: B 618 LEU cc_start: 0.9120 (mt) cc_final: 0.8778 (mt) REVERT: B 650 GLN cc_start: 0.8315 (mm-40) cc_final: 0.7571 (mm-40) REVERT: B 667 LEU cc_start: 0.9581 (tt) cc_final: 0.9363 (tt) REVERT: C 46 TYR cc_start: 0.8686 (m-80) cc_final: 0.8441 (m-80) REVERT: C 179 TYR cc_start: 0.9449 (t80) cc_final: 0.9249 (t80) REVERT: C 185 MET cc_start: 0.8923 (mpp) cc_final: 0.8678 (mpp) REVERT: C 204 TYR cc_start: 0.9604 (t80) cc_final: 0.9389 (t80) REVERT: C 278 GLU cc_start: 0.9165 (pm20) cc_final: 0.8946 (pm20) REVERT: D 46 TYR cc_start: 0.8999 (m-80) cc_final: 0.8757 (m-10) REVERT: D 69 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8210 (tm-30) REVERT: D 179 TYR cc_start: 0.9162 (t80) cc_final: 0.8887 (t80) REVERT: D 185 MET cc_start: 0.7796 (mmm) cc_final: 0.6921 (mmm) REVERT: D 189 GLU cc_start: 0.8958 (tp30) cc_final: 0.8728 (pt0) REVERT: D 201 HIS cc_start: 0.8883 (m170) cc_final: 0.8610 (m170) REVERT: D 259 PHE cc_start: 0.7705 (t80) cc_final: 0.7319 (t80) outliers start: 0 outliers final: 0 residues processed: 660 average time/residue: 0.1310 time to fit residues: 126.6221 Evaluate side-chains 570 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 570 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 72 optimal weight: 6.9990 chunk 172 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** 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 = 0.3568 r_free = 0.3568 target = 0.110856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.079158 restraints weight = 51144.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.081829 restraints weight = 30250.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.083843 restraints weight = 21119.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.085137 restraints weight = 15936.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.086075 restraints weight = 12975.334| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.7291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16386 Z= 0.137 Angle : 0.604 8.012 22134 Z= 0.319 Chirality : 0.042 0.157 2360 Planarity : 0.004 0.067 2818 Dihedral : 10.828 176.106 2242 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.17 % Allowed : 1.11 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.19), residues: 1932 helix: 0.78 (0.15), residues: 1149 sheet: -0.81 (0.43), residues: 142 loop : 0.17 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 665 TYR 0.027 0.002 TYR A 522 PHE 0.042 0.002 PHE D 109 TRP 0.008 0.001 TRP A 9 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00297 (16386) covalent geometry : angle 0.60388 (22134) hydrogen bonds : bond 0.03835 ( 869) hydrogen bonds : angle 4.93075 ( 2568) *********************** 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 642 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 639 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9494 (tptp) cc_final: 0.9229 (tppt) REVERT: A 65 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8409 (mm-30) REVERT: A 95 MET cc_start: 0.9668 (tpt) cc_final: 0.8777 (mmm) REVERT: A 99 LYS cc_start: 0.9566 (mmtp) cc_final: 0.9173 (mmtp) REVERT: A 104 TYR cc_start: 0.8748 (m-80) cc_final: 0.8116 (m-80) REVERT: A 107 LYS cc_start: 0.9465 (mttm) cc_final: 0.9136 (mmmt) REVERT: A 120 ASP cc_start: 0.9342 (m-30) cc_final: 0.9128 (m-30) REVERT: A 129 PHE cc_start: 0.9576 (m-80) cc_final: 0.9177 (m-80) REVERT: A 136 LYS cc_start: 0.9781 (mmtt) cc_final: 0.9449 (ttpt) REVERT: A 144 MET cc_start: 0.8927 (mtm) cc_final: 0.8420 (mtm) REVERT: A 150 GLN cc_start: 0.9232 (tp40) cc_final: 0.9002 (tp40) REVERT: A 151 PRO cc_start: 0.9622 (Cg_exo) cc_final: 0.9384 (Cg_endo) REVERT: A 176 ASN cc_start: 0.8849 (t0) cc_final: 0.8592 (t0) REVERT: A 180 ASN cc_start: 0.8632 (m-40) cc_final: 0.8312 (m-40) REVERT: A 191 GLN cc_start: 0.9113 (mm-40) cc_final: 0.8611 (mp10) REVERT: A 194 LYS cc_start: 0.9320 (ttpt) cc_final: 0.9070 (ttpp) REVERT: A 195 LEU cc_start: 0.9643 (mt) cc_final: 0.9342 (mt) REVERT: A 205 LYS cc_start: 0.8566 (mmtt) cc_final: 0.8238 (mmmt) REVERT: A 227 MET cc_start: 0.9126 (mtp) cc_final: 0.8802 (mtp) REVERT: A 235 ARG cc_start: 0.8859 (ttp-110) cc_final: 0.8011 (mtm110) REVERT: A 252 ASN cc_start: 0.8785 (t0) cc_final: 0.8498 (t0) REVERT: A 286 ASP cc_start: 0.9097 (m-30) cc_final: 0.8532 (m-30) REVERT: A 313 HIS cc_start: 0.8580 (m90) cc_final: 0.8107 (m90) REVERT: A 320 ASN cc_start: 0.9429 (m-40) cc_final: 0.9162 (m110) REVERT: A 350 ARG cc_start: 0.8574 (mtp85) cc_final: 0.7961 (mtp85) REVERT: A 359 MET cc_start: 0.9148 (ttp) cc_final: 0.8910 (ttp) REVERT: A 362 ASP cc_start: 0.9252 (m-30) cc_final: 0.8777 (m-30) REVERT: A 366 LYS cc_start: 0.9273 (ptpp) cc_final: 0.9066 (pttp) REVERT: A 370 ASN cc_start: 0.9516 (m-40) cc_final: 0.9253 (m-40) REVERT: A 375 LYS cc_start: 0.9533 (mttt) cc_final: 0.9129 (mttt) REVERT: A 385 VAL cc_start: 0.9645 (t) cc_final: 0.9332 (m) REVERT: A 387 GLN cc_start: 0.8128 (mt0) cc_final: 0.7922 (mt0) REVERT: A 396 ASP cc_start: 0.9038 (p0) cc_final: 0.8785 (p0) REVERT: A 402 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8897 (tm-30) REVERT: A 405 LEU cc_start: 0.9103 (mt) cc_final: 0.8670 (mt) REVERT: A 414 LEU cc_start: 0.9621 (mt) cc_final: 0.9382 (mt) REVERT: A 468 LEU cc_start: 0.9600 (tp) cc_final: 0.9356 (tp) REVERT: A 493 MET cc_start: 0.9323 (tmm) cc_final: 0.9033 (tmm) REVERT: A 494 MET cc_start: 0.9477 (mtt) cc_final: 0.9233 (mtp) REVERT: A 500 ILE cc_start: 0.9859 (mt) cc_final: 0.9521 (mt) REVERT: A 515 ASP cc_start: 0.9496 (m-30) cc_final: 0.9227 (m-30) REVERT: A 571 TYR cc_start: 0.9085 (t80) cc_final: 0.8346 (t80) REVERT: A 575 ARG cc_start: 0.8847 (ptp-110) cc_final: 0.8595 (mtm-85) REVERT: A 583 SER cc_start: 0.9342 (t) cc_final: 0.9002 (t) REVERT: A 586 TYR cc_start: 0.9175 (m-80) cc_final: 0.8545 (m-80) REVERT: A 591 THR cc_start: 0.8999 (p) cc_final: 0.8784 (p) REVERT: A 595 MET cc_start: 0.9038 (tpp) cc_final: 0.8745 (tpp) REVERT: A 598 MET cc_start: 0.8438 (tmm) cc_final: 0.7819 (tmm) REVERT: A 599 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8098 (mt-10) REVERT: A 626 TYR cc_start: 0.9272 (m-80) cc_final: 0.9058 (m-10) REVERT: A 653 SER cc_start: 0.9281 (p) cc_final: 0.8995 (p) REVERT: A 667 LEU cc_start: 0.9614 (tt) cc_final: 0.9406 (tt) REVERT: B 51 LEU cc_start: 0.9488 (tp) cc_final: 0.9162 (tp) REVERT: B 77 ILE cc_start: 0.9722 (mt) cc_final: 0.9336 (mt) REVERT: B 87 LYS cc_start: 0.9388 (tptp) cc_final: 0.9059 (tptp) REVERT: B 95 MET cc_start: 0.9559 (tpp) cc_final: 0.8491 (tpp) REVERT: B 99 LYS cc_start: 0.9593 (mmmt) cc_final: 0.8770 (mmmt) REVERT: B 114 ILE cc_start: 0.9541 (mt) cc_final: 0.9245 (pt) REVERT: B 144 MET cc_start: 0.9402 (mtm) cc_final: 0.8959 (mtm) REVERT: B 149 TYR cc_start: 0.9419 (t80) cc_final: 0.8930 (t80) REVERT: B 202 ASN cc_start: 0.5954 (p0) cc_final: 0.5602 (p0) REVERT: B 211 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8521 (mm-30) REVERT: B 240 MET cc_start: 0.8286 (mpp) cc_final: 0.7830 (mpp) REVERT: B 257 ASP cc_start: 0.8350 (m-30) cc_final: 0.8107 (m-30) REVERT: B 259 ASN cc_start: 0.9126 (m-40) cc_final: 0.8901 (m110) REVERT: B 263 ASP cc_start: 0.9349 (m-30) cc_final: 0.9032 (m-30) REVERT: B 286 ASP cc_start: 0.9006 (m-30) cc_final: 0.8409 (m-30) REVERT: B 287 LYS cc_start: 0.9460 (mmtt) cc_final: 0.9171 (mmmm) REVERT: B 333 LYS cc_start: 0.9253 (tptm) cc_final: 0.9014 (tptp) REVERT: B 335 GLU cc_start: 0.8716 (mt-10) cc_final: 0.7945 (mt-10) REVERT: B 350 ARG cc_start: 0.9194 (tpp80) cc_final: 0.8894 (tpp80) REVERT: B 362 ASP cc_start: 0.8814 (m-30) cc_final: 0.8135 (m-30) REVERT: B 373 ILE cc_start: 0.9671 (mt) cc_final: 0.9117 (mt) REVERT: B 396 ASP cc_start: 0.7977 (p0) cc_final: 0.6575 (p0) REVERT: B 415 ASN cc_start: 0.9266 (t0) cc_final: 0.8317 (t0) REVERT: B 416 ILE cc_start: 0.9827 (mt) cc_final: 0.9527 (mt) REVERT: B 418 ASN cc_start: 0.9363 (m-40) cc_final: 0.9008 (m-40) REVERT: B 420 MET cc_start: 0.9185 (mmm) cc_final: 0.8806 (mmm) REVERT: B 426 GLU cc_start: 0.9234 (pm20) cc_final: 0.8867 (pm20) REVERT: B 427 LYS cc_start: 0.9689 (ptpp) cc_final: 0.9243 (ptpp) REVERT: B 459 LYS cc_start: 0.9189 (mttp) cc_final: 0.8703 (mtmt) REVERT: B 467 ASN cc_start: 0.9318 (m-40) cc_final: 0.9092 (m-40) REVERT: B 472 LEU cc_start: 0.9742 (mt) cc_final: 0.9527 (mt) REVERT: B 496 ASN cc_start: 0.9641 (t0) cc_final: 0.9203 (t0) REVERT: B 500 ILE cc_start: 0.9788 (mt) cc_final: 0.9248 (mt) REVERT: B 501 GLN cc_start: 0.8874 (tp-100) cc_final: 0.8372 (tp-100) REVERT: B 515 ASP cc_start: 0.9167 (m-30) cc_final: 0.8735 (m-30) REVERT: B 516 GLN cc_start: 0.9029 (tt0) cc_final: 0.8607 (tt0) REVERT: B 570 MET cc_start: 0.9189 (tpp) cc_final: 0.8289 (tpt) REVERT: B 575 ARG cc_start: 0.8578 (mtm110) cc_final: 0.8214 (mpp80) REVERT: B 588 GLN cc_start: 0.9514 (mm110) cc_final: 0.9134 (mm110) REVERT: B 595 MET cc_start: 0.9649 (mmt) cc_final: 0.9254 (mpp) REVERT: B 618 LEU cc_start: 0.9044 (mt) cc_final: 0.8766 (mt) REVERT: B 631 ASP cc_start: 0.9562 (m-30) cc_final: 0.9341 (m-30) REVERT: B 650 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7733 (mm-40) REVERT: B 656 LEU cc_start: 0.9452 (mt) cc_final: 0.9173 (mt) REVERT: B 667 LEU cc_start: 0.9578 (tt) cc_final: 0.9311 (tt) REVERT: C 46 TYR cc_start: 0.8786 (m-80) cc_final: 0.8560 (m-80) REVERT: C 108 ILE cc_start: 0.9277 (mt) cc_final: 0.9057 (mt) REVERT: C 157 MET cc_start: 0.4538 (ptt) cc_final: 0.4281 (ptt) REVERT: C 179 TYR cc_start: 0.9484 (t80) cc_final: 0.9257 (t80) REVERT: C 185 MET cc_start: 0.8837 (mpp) cc_final: 0.8585 (mpp) REVERT: C 204 TYR cc_start: 0.9615 (t80) cc_final: 0.9375 (t80) REVERT: C 278 GLU cc_start: 0.9114 (pm20) cc_final: 0.8887 (pm20) REVERT: D 46 TYR cc_start: 0.9001 (m-80) cc_final: 0.8746 (m-10) REVERT: D 179 TYR cc_start: 0.9150 (t80) cc_final: 0.8847 (t80) REVERT: D 185 MET cc_start: 0.7905 (mmm) cc_final: 0.6968 (mmm) REVERT: D 189 GLU cc_start: 0.8980 (tp30) cc_final: 0.8742 (pt0) REVERT: D 317 ASP cc_start: 0.9335 (t0) cc_final: 0.9062 (t0) outliers start: 3 outliers final: 2 residues processed: 641 average time/residue: 0.1234 time to fit residues: 116.6956 Evaluate side-chains 570 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 568 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.108022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.077055 restraints weight = 54088.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.079623 restraints weight = 32511.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.081512 restraints weight = 22887.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.082871 restraints weight = 17361.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.083539 restraints weight = 14036.882| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.7664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16386 Z= 0.231 Angle : 0.672 8.075 22134 Z= 0.360 Chirality : 0.043 0.168 2360 Planarity : 0.004 0.055 2818 Dihedral : 11.036 176.093 2242 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.19), residues: 1932 helix: 0.56 (0.15), residues: 1143 sheet: -0.83 (0.43), residues: 144 loop : 0.09 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 163 TYR 0.021 0.002 TYR D 174 PHE 0.028 0.002 PHE D 109 TRP 0.014 0.002 TRP A 623 HIS 0.008 0.002 HIS B 572 Details of bonding type rmsd covalent geometry : bond 0.00475 (16386) covalent geometry : angle 0.67246 (22134) hydrogen bonds : bond 0.04028 ( 869) hydrogen bonds : angle 5.15307 ( 2568) *********************** 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 623 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 623 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8284 (mp0) REVERT: A 87 LYS cc_start: 0.9624 (tptp) cc_final: 0.9364 (tptp) REVERT: A 95 MET cc_start: 0.9706 (tpt) cc_final: 0.8644 (mmm) REVERT: A 99 LYS cc_start: 0.9615 (mmtp) cc_final: 0.9153 (mmtp) REVERT: A 104 TYR cc_start: 0.8872 (m-80) cc_final: 0.8278 (m-80) REVERT: A 107 LYS cc_start: 0.9494 (mttm) cc_final: 0.9043 (tptt) REVERT: A 117 ARG cc_start: 0.9230 (mtp85) cc_final: 0.8728 (mmt180) REVERT: A 129 PHE cc_start: 0.9525 (m-80) cc_final: 0.9143 (m-80) REVERT: A 136 LYS cc_start: 0.9792 (mmtt) cc_final: 0.9466 (ttpt) REVERT: A 144 MET cc_start: 0.8924 (mtm) cc_final: 0.8559 (mtm) REVERT: A 150 GLN cc_start: 0.9256 (tp40) cc_final: 0.9004 (tp40) REVERT: A 151 PRO cc_start: 0.9725 (Cg_exo) cc_final: 0.9460 (Cg_endo) REVERT: A 176 ASN cc_start: 0.8707 (t0) cc_final: 0.8466 (t0) REVERT: A 180 ASN cc_start: 0.9004 (m-40) cc_final: 0.8645 (m-40) REVERT: A 194 LYS cc_start: 0.9368 (ttpt) cc_final: 0.9138 (ttpp) REVERT: A 205 LYS cc_start: 0.8592 (mmtt) cc_final: 0.8373 (mmmt) REVERT: A 227 MET cc_start: 0.9318 (mtp) cc_final: 0.8785 (mtp) REVERT: A 235 ARG cc_start: 0.8859 (ttp-110) cc_final: 0.8616 (ttp-110) REVERT: A 236 TYR cc_start: 0.8823 (t80) cc_final: 0.8563 (t80) REVERT: A 252 ASN cc_start: 0.8867 (t0) cc_final: 0.8540 (t0) REVERT: A 266 LYS cc_start: 0.9366 (ptmm) cc_final: 0.9049 (pptt) REVERT: A 286 ASP cc_start: 0.9131 (m-30) cc_final: 0.8560 (m-30) REVERT: A 312 GLN cc_start: 0.9015 (mp10) cc_final: 0.8788 (mp10) REVERT: A 320 ASN cc_start: 0.9420 (m-40) cc_final: 0.9163 (m110) REVERT: A 350 ARG cc_start: 0.8479 (mtp85) cc_final: 0.7809 (mtp85) REVERT: A 362 ASP cc_start: 0.9239 (m-30) cc_final: 0.8642 (m-30) REVERT: A 370 ASN cc_start: 0.9437 (m-40) cc_final: 0.9197 (m110) REVERT: A 375 LYS cc_start: 0.9501 (mttt) cc_final: 0.9085 (mttt) REVERT: A 385 VAL cc_start: 0.9617 (t) cc_final: 0.9349 (m) REVERT: A 414 LEU cc_start: 0.9574 (mt) cc_final: 0.9289 (mt) REVERT: A 446 ARG cc_start: 0.8842 (mtt-85) cc_final: 0.8221 (mtp-110) REVERT: A 468 LEU cc_start: 0.9617 (tp) cc_final: 0.9376 (tp) REVERT: A 493 MET cc_start: 0.9244 (tmm) cc_final: 0.8910 (tmm) REVERT: A 494 MET cc_start: 0.9475 (mtt) cc_final: 0.9163 (mtp) REVERT: A 515 ASP cc_start: 0.9461 (m-30) cc_final: 0.9178 (m-30) REVERT: A 562 LYS cc_start: 0.9762 (ttmt) cc_final: 0.9552 (tppt) REVERT: A 575 ARG cc_start: 0.8970 (ptp-110) cc_final: 0.8518 (ptp-110) REVERT: A 583 SER cc_start: 0.9459 (t) cc_final: 0.9157 (t) REVERT: A 586 TYR cc_start: 0.9135 (m-80) cc_final: 0.8931 (m-80) REVERT: A 591 THR cc_start: 0.9113 (p) cc_final: 0.8890 (p) REVERT: A 595 MET cc_start: 0.9119 (tpp) cc_final: 0.8916 (tpp) REVERT: A 598 MET cc_start: 0.8417 (tmm) cc_final: 0.7875 (tmm) REVERT: A 599 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8108 (mt-10) REVERT: A 602 GLU cc_start: 0.8932 (pt0) cc_final: 0.8541 (mp0) REVERT: A 615 MET cc_start: 0.8653 (mmp) cc_final: 0.8020 (mmp) REVERT: A 653 SER cc_start: 0.9343 (p) cc_final: 0.9118 (p) REVERT: A 657 PHE cc_start: 0.8056 (m-80) cc_final: 0.7765 (m-80) REVERT: A 682 ILE cc_start: 0.9163 (mt) cc_final: 0.8950 (mt) REVERT: B 51 LEU cc_start: 0.9531 (tp) cc_final: 0.9281 (tp) REVERT: B 77 ILE cc_start: 0.9600 (mt) cc_final: 0.9337 (mt) REVERT: B 87 LYS cc_start: 0.9381 (tptp) cc_final: 0.9041 (tptp) REVERT: B 95 MET cc_start: 0.9613 (tpp) cc_final: 0.8611 (tpp) REVERT: B 99 LYS cc_start: 0.9648 (mmmt) cc_final: 0.8836 (mmmt) REVERT: B 114 ILE cc_start: 0.9541 (mt) cc_final: 0.9241 (pt) REVERT: B 144 MET cc_start: 0.9397 (mtm) cc_final: 0.9054 (mtm) REVERT: B 149 TYR cc_start: 0.9436 (t80) cc_final: 0.9032 (t80) REVERT: B 211 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8544 (mm-30) REVERT: B 240 MET cc_start: 0.8241 (mpp) cc_final: 0.7809 (mpp) REVERT: B 252 ASN cc_start: 0.8928 (t0) cc_final: 0.8669 (t0) REVERT: B 257 ASP cc_start: 0.8439 (m-30) cc_final: 0.8070 (m-30) REVERT: B 259 ASN cc_start: 0.9072 (m-40) cc_final: 0.8765 (m110) REVERT: B 263 ASP cc_start: 0.9399 (m-30) cc_final: 0.9197 (m-30) REVERT: B 286 ASP cc_start: 0.9063 (m-30) cc_final: 0.8471 (m-30) REVERT: B 287 LYS cc_start: 0.9471 (mmtt) cc_final: 0.9237 (mmtp) REVERT: B 319 MET cc_start: 0.9148 (tpt) cc_final: 0.8808 (tpp) REVERT: B 322 MET cc_start: 0.8900 (tpt) cc_final: 0.8299 (tpp) REVERT: B 326 PHE cc_start: 0.9564 (m-80) cc_final: 0.8445 (m-80) REVERT: B 333 LYS cc_start: 0.9240 (tptm) cc_final: 0.8998 (tptp) REVERT: B 335 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8127 (mt-10) REVERT: B 350 ARG cc_start: 0.9129 (tpp80) cc_final: 0.8904 (tpp80) REVERT: B 362 ASP cc_start: 0.8821 (m-30) cc_final: 0.8168 (m-30) REVERT: B 373 ILE cc_start: 0.9724 (mt) cc_final: 0.9128 (mt) REVERT: B 396 ASP cc_start: 0.8417 (p0) cc_final: 0.7256 (p0) REVERT: B 415 ASN cc_start: 0.9185 (t0) cc_final: 0.8241 (t0) REVERT: B 416 ILE cc_start: 0.9810 (mt) cc_final: 0.9516 (mt) REVERT: B 418 ASN cc_start: 0.9212 (m-40) cc_final: 0.8902 (m-40) REVERT: B 420 MET cc_start: 0.9339 (mmm) cc_final: 0.8887 (mmm) REVERT: B 426 GLU cc_start: 0.9222 (pm20) cc_final: 0.8871 (pm20) REVERT: B 427 LYS cc_start: 0.9688 (ptpp) cc_final: 0.9255 (ptpp) REVERT: B 459 LYS cc_start: 0.9334 (mttp) cc_final: 0.8741 (mtmt) REVERT: B 496 ASN cc_start: 0.9487 (t0) cc_final: 0.9176 (t0) REVERT: B 500 ILE cc_start: 0.9779 (mt) cc_final: 0.9237 (mt) REVERT: B 501 GLN cc_start: 0.8902 (tp-100) cc_final: 0.8355 (tp-100) REVERT: B 515 ASP cc_start: 0.9140 (m-30) cc_final: 0.8682 (m-30) REVERT: B 516 GLN cc_start: 0.9156 (tt0) cc_final: 0.8809 (tt0) REVERT: B 570 MET cc_start: 0.9221 (tpp) cc_final: 0.8319 (tpt) REVERT: B 588 GLN cc_start: 0.9596 (mm110) cc_final: 0.9281 (mm110) REVERT: B 618 LEU cc_start: 0.9061 (mt) cc_final: 0.8791 (mt) REVERT: B 631 ASP cc_start: 0.9568 (m-30) cc_final: 0.9343 (m-30) REVERT: B 648 ILE cc_start: 0.9534 (mm) cc_final: 0.9313 (mt) REVERT: B 667 LEU cc_start: 0.9573 (tt) cc_final: 0.9347 (tt) REVERT: C 46 TYR cc_start: 0.8806 (m-80) cc_final: 0.8575 (m-80) REVERT: C 179 TYR cc_start: 0.9536 (t80) cc_final: 0.9295 (t80) REVERT: C 185 MET cc_start: 0.8814 (mpp) cc_final: 0.8509 (mpp) REVERT: C 196 ARG cc_start: 0.8854 (mtm110) cc_final: 0.8524 (mtm110) REVERT: C 204 TYR cc_start: 0.9642 (t80) cc_final: 0.9271 (t80) REVERT: C 278 GLU cc_start: 0.9180 (pm20) cc_final: 0.8971 (pm20) REVERT: D 46 TYR cc_start: 0.9052 (m-80) cc_final: 0.8814 (m-10) REVERT: D 65 LEU cc_start: 0.8112 (mt) cc_final: 0.7902 (mt) REVERT: D 179 TYR cc_start: 0.9079 (t80) cc_final: 0.8780 (t80) REVERT: D 185 MET cc_start: 0.7943 (mmm) cc_final: 0.6909 (mmm) REVERT: D 189 GLU cc_start: 0.9129 (tp30) cc_final: 0.8861 (pt0) REVERT: D 193 LEU cc_start: 0.8967 (mt) cc_final: 0.8674 (mt) REVERT: D 259 PHE cc_start: 0.7786 (t80) cc_final: 0.7189 (t80) outliers start: 0 outliers final: 0 residues processed: 623 average time/residue: 0.1135 time to fit residues: 104.2940 Evaluate side-chains 544 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 544 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 134 optimal weight: 0.1980 chunk 153 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 158 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 151 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** 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 = 0.3525 r_free = 0.3525 target = 0.108089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.077697 restraints weight = 54113.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.080258 restraints weight = 32535.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.082150 restraints weight = 22500.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.083441 restraints weight = 17187.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.084330 restraints weight = 13932.857| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.7908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16386 Z= 0.204 Angle : 0.661 7.424 22134 Z= 0.352 Chirality : 0.043 0.183 2360 Planarity : 0.004 0.073 2818 Dihedral : 11.120 174.691 2242 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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: 0.26 (0.19), residues: 1932 helix: 0.48 (0.15), residues: 1155 sheet: -0.99 (0.43), residues: 138 loop : 0.16 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 261 TYR 0.033 0.002 TYR D 142 PHE 0.037 0.002 PHE D 227 TRP 0.011 0.002 TRP A 558 HIS 0.007 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00425 (16386) covalent geometry : angle 0.66119 (22134) hydrogen bonds : bond 0.03936 ( 869) hydrogen bonds : angle 5.14144 ( 2568) *********************** 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 626 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 626 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 64 TYR cc_start: 0.9200 (m-80) cc_final: 0.8932 (m-80) REVERT: A 65 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8415 (mp0) REVERT: A 87 LYS cc_start: 0.9612 (tptp) cc_final: 0.9393 (tptp) REVERT: A 95 MET cc_start: 0.9690 (tpt) cc_final: 0.8726 (mmm) REVERT: A 99 LYS cc_start: 0.9602 (mmtp) cc_final: 0.9112 (mmtp) REVERT: A 104 TYR cc_start: 0.8863 (m-80) cc_final: 0.8315 (m-80) REVERT: A 107 LYS cc_start: 0.9471 (mttm) cc_final: 0.9009 (tptt) REVERT: A 117 ARG cc_start: 0.9162 (mtp85) cc_final: 0.8837 (mmt180) REVERT: A 129 PHE cc_start: 0.9525 (m-80) cc_final: 0.9123 (m-80) REVERT: A 136 LYS cc_start: 0.9796 (mmtt) cc_final: 0.9540 (ttpt) REVERT: A 144 MET cc_start: 0.8863 (mtm) cc_final: 0.8514 (mtm) REVERT: A 176 ASN cc_start: 0.8669 (t0) cc_final: 0.8464 (t0) REVERT: A 180 ASN cc_start: 0.8748 (m-40) cc_final: 0.8496 (m-40) REVERT: A 191 GLN cc_start: 0.9241 (mm-40) cc_final: 0.8836 (mt0) REVERT: A 194 LYS cc_start: 0.9379 (ttpt) cc_final: 0.9125 (ttpp) REVERT: A 205 LYS cc_start: 0.8550 (mmtt) cc_final: 0.8084 (mmtp) REVERT: A 227 MET cc_start: 0.9205 (mtp) cc_final: 0.8847 (mtp) REVERT: A 230 LEU cc_start: 0.9572 (mt) cc_final: 0.9365 (mt) REVERT: A 235 ARG cc_start: 0.8900 (ttp-110) cc_final: 0.8308 (mtm110) REVERT: A 252 ASN cc_start: 0.8922 (t0) cc_final: 0.8677 (t0) REVERT: A 286 ASP cc_start: 0.9105 (m-30) cc_final: 0.8577 (m-30) REVERT: A 313 HIS cc_start: 0.8618 (m90) cc_final: 0.8147 (m90) REVERT: A 349 LEU cc_start: 0.9471 (mt) cc_final: 0.8916 (mt) REVERT: A 350 ARG cc_start: 0.8516 (mtp85) cc_final: 0.7990 (mtp85) REVERT: A 362 ASP cc_start: 0.9262 (m-30) cc_final: 0.8629 (m-30) REVERT: A 370 ASN cc_start: 0.9483 (m-40) cc_final: 0.9267 (m-40) REVERT: A 375 LYS cc_start: 0.9496 (mttt) cc_final: 0.9146 (mttt) REVERT: A 385 VAL cc_start: 0.9602 (t) cc_final: 0.9309 (m) REVERT: A 387 GLN cc_start: 0.8316 (mt0) cc_final: 0.8018 (mt0) REVERT: A 390 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8935 (mm110) REVERT: A 414 LEU cc_start: 0.9586 (mt) cc_final: 0.9314 (mt) REVERT: A 426 GLU cc_start: 0.9167 (tm-30) cc_final: 0.8588 (tm-30) REVERT: A 431 LEU cc_start: 0.9089 (mm) cc_final: 0.8753 (tp) REVERT: A 446 ARG cc_start: 0.8875 (mtt-85) cc_final: 0.8625 (mmm-85) REVERT: A 468 LEU cc_start: 0.9588 (tp) cc_final: 0.9336 (tp) REVERT: A 493 MET cc_start: 0.9195 (tmm) cc_final: 0.8868 (tmm) REVERT: A 494 MET cc_start: 0.9358 (mtt) cc_final: 0.9133 (mtp) REVERT: A 500 ILE cc_start: 0.9870 (mt) cc_final: 0.9531 (mt) REVERT: A 501 GLN cc_start: 0.9587 (mm-40) cc_final: 0.8835 (tp-100) REVERT: A 515 ASP cc_start: 0.9452 (m-30) cc_final: 0.9196 (m-30) REVERT: A 562 LYS cc_start: 0.9758 (ttmt) cc_final: 0.9540 (tttp) REVERT: A 575 ARG cc_start: 0.8985 (ptp-110) cc_final: 0.8557 (mtm-85) REVERT: A 583 SER cc_start: 0.9464 (t) cc_final: 0.9176 (t) REVERT: A 598 MET cc_start: 0.8369 (tmm) cc_final: 0.7789 (tmm) REVERT: A 599 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8092 (mt-10) REVERT: A 602 GLU cc_start: 0.8918 (pt0) cc_final: 0.8523 (pt0) REVERT: A 632 MET cc_start: 0.8795 (mmp) cc_final: 0.8372 (mmm) REVERT: A 653 SER cc_start: 0.9255 (p) cc_final: 0.8997 (p) REVERT: A 654 PHE cc_start: 0.9315 (t80) cc_final: 0.8976 (t80) REVERT: B 51 LEU cc_start: 0.9554 (tp) cc_final: 0.9209 (tp) REVERT: B 77 ILE cc_start: 0.9555 (mt) cc_final: 0.9149 (mt) REVERT: B 81 PHE cc_start: 0.9525 (m-10) cc_final: 0.9211 (m-80) REVERT: B 87 LYS cc_start: 0.9403 (tptp) cc_final: 0.9098 (tptp) REVERT: B 95 MET cc_start: 0.9366 (tpp) cc_final: 0.8143 (tpp) REVERT: B 99 LYS cc_start: 0.9639 (mmmt) cc_final: 0.8759 (mmmt) REVERT: B 114 ILE cc_start: 0.9485 (mt) cc_final: 0.9208 (pt) REVERT: B 143 LEU cc_start: 0.9628 (tp) cc_final: 0.9400 (tp) REVERT: B 144 MET cc_start: 0.9357 (mtm) cc_final: 0.8982 (mtm) REVERT: B 148 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8727 (mm-30) REVERT: B 149 TYR cc_start: 0.9457 (t80) cc_final: 0.9026 (t80) REVERT: B 202 ASN cc_start: 0.6071 (p0) cc_final: 0.5707 (p0) REVERT: B 211 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8570 (mm-30) REVERT: B 236 TYR cc_start: 0.8995 (t80) cc_final: 0.8577 (t80) REVERT: B 240 MET cc_start: 0.8244 (mpp) cc_final: 0.7877 (mpp) REVERT: B 252 ASN cc_start: 0.9027 (t0) cc_final: 0.8825 (t0) REVERT: B 257 ASP cc_start: 0.8423 (m-30) cc_final: 0.8036 (m-30) REVERT: B 259 ASN cc_start: 0.9098 (m-40) cc_final: 0.8819 (m110) REVERT: B 286 ASP cc_start: 0.9061 (m-30) cc_final: 0.8467 (m-30) REVERT: B 287 LYS cc_start: 0.9441 (mmtt) cc_final: 0.9214 (mmtp) REVERT: B 319 MET cc_start: 0.9132 (tpt) cc_final: 0.8790 (tpp) REVERT: B 322 MET cc_start: 0.8838 (tpt) cc_final: 0.8192 (tpp) REVERT: B 326 PHE cc_start: 0.9554 (m-80) cc_final: 0.8636 (m-80) REVERT: B 357 TYR cc_start: 0.9060 (m-10) cc_final: 0.8715 (m-80) REVERT: B 359 MET cc_start: 0.8038 (ptp) cc_final: 0.7831 (ptp) REVERT: B 362 ASP cc_start: 0.8830 (m-30) cc_final: 0.8185 (m-30) REVERT: B 373 ILE cc_start: 0.9714 (mt) cc_final: 0.9141 (mt) REVERT: B 390 GLN cc_start: 0.8951 (mm-40) cc_final: 0.8750 (mm-40) REVERT: B 415 ASN cc_start: 0.9179 (t0) cc_final: 0.8321 (t0) REVERT: B 416 ILE cc_start: 0.9800 (mt) cc_final: 0.9466 (mt) REVERT: B 418 ASN cc_start: 0.9223 (m-40) cc_final: 0.8858 (m-40) REVERT: B 420 MET cc_start: 0.9317 (mmm) cc_final: 0.8780 (mmp) REVERT: B 426 GLU cc_start: 0.9208 (pm20) cc_final: 0.8776 (pm20) REVERT: B 427 LYS cc_start: 0.9696 (ptpp) cc_final: 0.9227 (ptpp) REVERT: B 459 LYS cc_start: 0.9355 (mttp) cc_final: 0.8794 (mtmt) REVERT: B 480 GLU cc_start: 0.9437 (pm20) cc_final: 0.9070 (mp0) REVERT: B 496 ASN cc_start: 0.9474 (t0) cc_final: 0.9050 (t0) REVERT: B 500 ILE cc_start: 0.9758 (mt) cc_final: 0.9369 (mt) REVERT: B 501 GLN cc_start: 0.8832 (tp-100) cc_final: 0.8294 (tp-100) REVERT: B 515 ASP cc_start: 0.9137 (m-30) cc_final: 0.8707 (m-30) REVERT: B 516 GLN cc_start: 0.9117 (tt0) cc_final: 0.8794 (tt0) REVERT: B 575 ARG cc_start: 0.8368 (mpp80) cc_final: 0.7975 (mpp80) REVERT: B 588 GLN cc_start: 0.9608 (mm110) cc_final: 0.9359 (mm110) REVERT: B 632 MET cc_start: 0.8899 (mmp) cc_final: 0.8560 (mmm) REVERT: B 650 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7647 (mm-40) REVERT: B 667 LEU cc_start: 0.9547 (tt) cc_final: 0.9226 (tt) REVERT: C 17 PHE cc_start: 0.8522 (p90) cc_final: 0.7485 (p90) REVERT: C 46 TYR cc_start: 0.8849 (m-80) cc_final: 0.8611 (m-80) REVERT: C 157 MET cc_start: 0.4516 (ptt) cc_final: 0.4245 (ptt) REVERT: C 179 TYR cc_start: 0.9553 (t80) cc_final: 0.9287 (t80) REVERT: C 185 MET cc_start: 0.8803 (mpp) cc_final: 0.8483 (mpp) REVERT: C 196 ARG cc_start: 0.8816 (mtm110) cc_final: 0.8609 (mtm110) REVERT: C 204 TYR cc_start: 0.9649 (t80) cc_final: 0.9186 (t80) REVERT: C 276 TYR cc_start: 0.9080 (t80) cc_final: 0.8868 (t80) REVERT: D 46 TYR cc_start: 0.9055 (m-80) cc_final: 0.8817 (m-10) REVERT: D 193 LEU cc_start: 0.8510 (mt) cc_final: 0.8299 (mt) outliers start: 0 outliers final: 0 residues processed: 626 average time/residue: 0.1206 time to fit residues: 110.9350 Evaluate side-chains 537 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 537 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 6.9990 chunk 133 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 88 optimal weight: 0.0040 chunk 77 optimal weight: 0.9980 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 HIS ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.112770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.081560 restraints weight = 51694.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.084219 restraints weight = 30845.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.086185 restraints weight = 21622.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.087556 restraints weight = 16346.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.088525 restraints weight = 13163.625| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.8075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16386 Z= 0.138 Angle : 0.646 8.638 22134 Z= 0.341 Chirality : 0.043 0.184 2360 Planarity : 0.004 0.052 2818 Dihedral : 11.098 173.595 2242 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.06 % Allowed : 0.23 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.19), residues: 1932 helix: 0.56 (0.15), residues: 1153 sheet: -0.42 (0.47), residues: 118 loop : -0.01 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 235 TYR 0.022 0.002 TYR B 613 PHE 0.036 0.002 PHE D 227 TRP 0.006 0.001 TRP A 623 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00304 (16386) covalent geometry : angle 0.64552 (22134) hydrogen bonds : bond 0.03814 ( 869) hydrogen bonds : angle 5.05827 ( 2568) *********************** 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 629 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 628 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.9412 (tptp) cc_final: 0.9115 (tptp) REVERT: A 65 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8484 (mm-30) REVERT: A 87 LYS cc_start: 0.9662 (tptp) cc_final: 0.9402 (tptp) REVERT: A 104 TYR cc_start: 0.8870 (m-80) cc_final: 0.8217 (m-80) REVERT: A 106 LEU cc_start: 0.9193 (tp) cc_final: 0.8876 (tp) REVERT: A 107 LYS cc_start: 0.9500 (mttm) cc_final: 0.9197 (mmmt) REVERT: A 114 ILE cc_start: 0.9472 (mp) cc_final: 0.8997 (mp) REVERT: A 129 PHE cc_start: 0.9545 (m-80) cc_final: 0.9129 (m-80) REVERT: A 136 LYS cc_start: 0.9831 (mmtt) cc_final: 0.9504 (ttpt) REVERT: A 144 MET cc_start: 0.8874 (mtm) cc_final: 0.8433 (mtm) REVERT: A 180 ASN cc_start: 0.8982 (m-40) cc_final: 0.8657 (m-40) REVERT: A 194 LYS cc_start: 0.9302 (ttpt) cc_final: 0.9052 (ttpp) REVERT: A 227 MET cc_start: 0.9210 (mtp) cc_final: 0.8663 (mtp) REVERT: A 235 ARG cc_start: 0.8869 (ttp-110) cc_final: 0.8545 (ttm110) REVERT: A 252 ASN cc_start: 0.8925 (t0) cc_final: 0.8622 (t0) REVERT: A 286 ASP cc_start: 0.9180 (m-30) cc_final: 0.8635 (m-30) REVERT: A 335 GLU cc_start: 0.9293 (tp30) cc_final: 0.9073 (tm-30) REVERT: A 349 LEU cc_start: 0.9462 (mt) cc_final: 0.8932 (mt) REVERT: A 350 ARG cc_start: 0.8536 (mtp85) cc_final: 0.8070 (mtp85) REVERT: A 362 ASP cc_start: 0.9244 (m-30) cc_final: 0.8704 (m-30) REVERT: A 370 ASN cc_start: 0.9441 (m-40) cc_final: 0.9210 (m-40) REVERT: A 375 LYS cc_start: 0.9511 (mttt) cc_final: 0.9144 (mttt) REVERT: A 390 GLN cc_start: 0.9278 (mm-40) cc_final: 0.8956 (mm-40) REVERT: A 414 LEU cc_start: 0.9635 (mt) cc_final: 0.9394 (mt) REVERT: A 426 GLU cc_start: 0.9204 (tm-30) cc_final: 0.8718 (tm-30) REVERT: A 431 LEU cc_start: 0.9016 (mm) cc_final: 0.8654 (tp) REVERT: A 446 ARG cc_start: 0.8894 (mtt-85) cc_final: 0.8186 (mtp-110) REVERT: A 456 LYS cc_start: 0.9655 (mmpt) cc_final: 0.9315 (mmmt) REVERT: A 468 LEU cc_start: 0.9564 (tp) cc_final: 0.9257 (tp) REVERT: A 479 TYR cc_start: 0.8765 (t80) cc_final: 0.8295 (t80) REVERT: A 493 MET cc_start: 0.9241 (tmm) cc_final: 0.8901 (tmm) REVERT: A 494 MET cc_start: 0.9543 (mtt) cc_final: 0.9119 (mtp) REVERT: A 500 ILE cc_start: 0.9874 (mt) cc_final: 0.9634 (mt) REVERT: A 515 ASP cc_start: 0.9465 (m-30) cc_final: 0.9199 (m-30) REVERT: A 575 ARG cc_start: 0.8930 (ptp-110) cc_final: 0.8270 (ptp-110) REVERT: A 583 SER cc_start: 0.9360 (t) cc_final: 0.9095 (t) REVERT: A 615 MET cc_start: 0.8751 (mmp) cc_final: 0.8240 (mmp) REVERT: A 618 LEU cc_start: 0.9349 (tt) cc_final: 0.9117 (tt) REVERT: A 632 MET cc_start: 0.8733 (mmp) cc_final: 0.8098 (mmm) REVERT: A 653 SER cc_start: 0.9208 (p) cc_final: 0.9007 (p) REVERT: A 654 PHE cc_start: 0.9167 (t80) cc_final: 0.8937 (t80) REVERT: A 677 ARG cc_start: 0.9440 (mmm-85) cc_final: 0.8246 (mmm-85) REVERT: A 682 ILE cc_start: 0.9155 (mt) cc_final: 0.8919 (mt) REVERT: B 51 LEU cc_start: 0.9564 (tp) cc_final: 0.9190 (tp) REVERT: B 77 ILE cc_start: 0.9521 (mt) cc_final: 0.9136 (mt) REVERT: B 81 PHE cc_start: 0.9511 (m-10) cc_final: 0.9120 (m-80) REVERT: B 87 LYS cc_start: 0.9382 (tptp) cc_final: 0.9063 (tptp) REVERT: B 95 MET cc_start: 0.9511 (tpp) cc_final: 0.8412 (tpp) REVERT: B 99 LYS cc_start: 0.9637 (mmmt) cc_final: 0.8771 (mmmt) REVERT: B 106 LEU cc_start: 0.9271 (tt) cc_final: 0.9018 (tt) REVERT: B 120 ASP cc_start: 0.9125 (m-30) cc_final: 0.8887 (m-30) REVERT: B 143 LEU cc_start: 0.9645 (tp) cc_final: 0.9425 (tp) REVERT: B 144 MET cc_start: 0.9422 (mtm) cc_final: 0.8829 (mtm) REVERT: B 145 ILE cc_start: 0.9716 (tp) cc_final: 0.9487 (tp) REVERT: B 147 GLN cc_start: 0.9389 (mm110) cc_final: 0.9072 (mm110) REVERT: B 148 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8662 (mm-30) REVERT: B 149 TYR cc_start: 0.9475 (t80) cc_final: 0.9037 (t80) REVERT: B 202 ASN cc_start: 0.5966 (p0) cc_final: 0.5584 (p0) REVERT: B 211 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8542 (mm-30) REVERT: B 240 MET cc_start: 0.8393 (mpp) cc_final: 0.7988 (mpp) REVERT: B 257 ASP cc_start: 0.8394 (m-30) cc_final: 0.8052 (m-30) REVERT: B 259 ASN cc_start: 0.9080 (m-40) cc_final: 0.8844 (m110) REVERT: B 286 ASP cc_start: 0.9085 (m-30) cc_final: 0.8516 (m-30) REVERT: B 319 MET cc_start: 0.9112 (tpt) cc_final: 0.8801 (tpp) REVERT: B 322 MET cc_start: 0.8891 (tpt) cc_final: 0.8177 (tpp) REVERT: B 326 PHE cc_start: 0.9511 (m-80) cc_final: 0.8555 (m-80) REVERT: B 335 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8256 (mt-10) REVERT: B 362 ASP cc_start: 0.8875 (m-30) cc_final: 0.8237 (m-30) REVERT: B 373 ILE cc_start: 0.9651 (mt) cc_final: 0.9112 (mt) REVERT: B 390 GLN cc_start: 0.8915 (mm-40) cc_final: 0.8707 (mm-40) REVERT: B 396 ASP cc_start: 0.8049 (p0) cc_final: 0.6674 (p0) REVERT: B 415 ASN cc_start: 0.9179 (t0) cc_final: 0.8183 (t0) REVERT: B 416 ILE cc_start: 0.9813 (mt) cc_final: 0.9510 (mt) REVERT: B 418 ASN cc_start: 0.9285 (m-40) cc_final: 0.8988 (m-40) REVERT: B 420 MET cc_start: 0.9282 (mmm) cc_final: 0.8795 (mmm) REVERT: B 426 GLU cc_start: 0.9241 (pm20) cc_final: 0.8840 (pm20) REVERT: B 427 LYS cc_start: 0.9715 (ptpp) cc_final: 0.9287 (ptpp) REVERT: B 459 LYS cc_start: 0.9313 (mttp) cc_final: 0.8839 (mtmt) REVERT: B 466 MET cc_start: 0.8607 (ptp) cc_final: 0.8292 (ptp) REVERT: B 467 ASN cc_start: 0.9143 (m-40) cc_final: 0.8408 (m-40) REVERT: B 480 GLU cc_start: 0.9444 (pm20) cc_final: 0.9104 (mp0) REVERT: B 496 ASN cc_start: 0.9461 (t0) cc_final: 0.8992 (t0) REVERT: B 500 ILE cc_start: 0.9773 (mt) cc_final: 0.9493 (mt) REVERT: B 501 GLN cc_start: 0.8826 (tp-100) cc_final: 0.8302 (tp-100) REVERT: B 515 ASP cc_start: 0.9101 (m-30) cc_final: 0.8675 (m-30) REVERT: B 516 GLN cc_start: 0.9040 (tt0) cc_final: 0.8694 (tt0) REVERT: B 585 SER cc_start: 0.9336 (p) cc_final: 0.8896 (t) REVERT: B 595 MET cc_start: 0.9526 (mmm) cc_final: 0.9124 (mpp) REVERT: B 602 GLU cc_start: 0.8597 (pp20) cc_final: 0.8178 (tm-30) REVERT: B 632 MET cc_start: 0.8758 (mmp) cc_final: 0.8349 (mmm) REVERT: B 650 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7613 (mm-40) REVERT: C 17 PHE cc_start: 0.8571 (p90) cc_final: 0.7617 (p90) REVERT: C 21 PHE cc_start: 0.9486 (m-80) cc_final: 0.8765 (m-80) REVERT: C 46 TYR cc_start: 0.8905 (m-80) cc_final: 0.8672 (m-80) REVERT: C 157 MET cc_start: 0.4241 (ptt) cc_final: 0.4041 (ptt) REVERT: C 179 TYR cc_start: 0.9508 (t80) cc_final: 0.9265 (t80) REVERT: C 185 MET cc_start: 0.8694 (mpp) cc_final: 0.8393 (mpp) REVERT: C 204 TYR cc_start: 0.9681 (t80) cc_final: 0.9001 (t80) REVERT: C 276 TYR cc_start: 0.9145 (t80) cc_final: 0.8905 (t80) REVERT: D 46 TYR cc_start: 0.9052 (m-80) cc_final: 0.8844 (m-10) REVERT: D 317 ASP cc_start: 0.9387 (t0) cc_final: 0.9152 (t0) outliers start: 1 outliers final: 0 residues processed: 629 average time/residue: 0.1164 time to fit residues: 108.1289 Evaluate side-chains 542 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 542 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 189 optimal weight: 0.9990 chunk 181 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** 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 = 0.3566 r_free = 0.3566 target = 0.109400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.078089 restraints weight = 53638.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.080865 restraints weight = 32406.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.082513 restraints weight = 22867.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.083858 restraints weight = 17749.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.084746 restraints weight = 14520.396| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.8308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16386 Z= 0.165 Angle : 0.670 8.119 22134 Z= 0.356 Chirality : 0.043 0.165 2360 Planarity : 0.004 0.077 2818 Dihedral : 11.191 172.999 2242 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: 0.30 (0.19), residues: 1932 helix: 0.56 (0.15), residues: 1140 sheet: -0.60 (0.45), residues: 124 loop : -0.02 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 575 TYR 0.021 0.002 TYR A 118 PHE 0.035 0.002 PHE D 227 TRP 0.010 0.001 TRP A 623 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00360 (16386) covalent geometry : angle 0.67017 (22134) hydrogen bonds : bond 0.03858 ( 869) hydrogen bonds : angle 5.10487 ( 2568) ********************** 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 617 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 617 time to evaluate : 0.508 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: A 8 LYS cc_start: 0.9394 (tptp) cc_final: 0.9121 (tptp) REVERT: A 65 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8611 (mm-30) REVERT: A 87 LYS cc_start: 0.9629 (tptp) cc_final: 0.9394 (tptp) REVERT: A 95 MET cc_start: 0.9653 (tpt) cc_final: 0.8248 (tpp) REVERT: A 99 LYS cc_start: 0.9594 (mmtp) cc_final: 0.9244 (mmtp) REVERT: A 104 TYR cc_start: 0.8805 (m-80) cc_final: 0.8300 (m-80) REVERT: A 106 LEU cc_start: 0.9183 (tp) cc_final: 0.8888 (tp) REVERT: A 107 LYS cc_start: 0.9497 (mttm) cc_final: 0.9176 (mmmt) REVERT: A 114 ILE cc_start: 0.9499 (mp) cc_final: 0.8989 (mp) REVERT: A 129 PHE cc_start: 0.9539 (m-80) cc_final: 0.9109 (m-80) REVERT: A 136 LYS cc_start: 0.9833 (mmtt) cc_final: 0.9514 (ttpt) REVERT: A 144 MET cc_start: 0.8820 (mtm) cc_final: 0.8434 (mtm) REVERT: A 164 ARG cc_start: 0.8509 (ptm-80) cc_final: 0.8109 (ptm-80) REVERT: A 180 ASN cc_start: 0.8983 (m-40) cc_final: 0.8663 (m-40) REVERT: A 191 GLN cc_start: 0.9225 (mm-40) cc_final: 0.8854 (mt0) REVERT: A 194 LYS cc_start: 0.9325 (ttpt) cc_final: 0.9077 (ttpp) REVERT: A 227 MET cc_start: 0.9124 (mtp) cc_final: 0.8725 (mtp) REVERT: A 235 ARG cc_start: 0.8884 (ttp-110) cc_final: 0.8497 (ttp-110) REVERT: A 252 ASN cc_start: 0.8921 (t0) cc_final: 0.8664 (t0) REVERT: A 255 HIS cc_start: 0.7593 (t-90) cc_final: 0.7257 (t-90) REVERT: A 286 ASP cc_start: 0.9115 (m-30) cc_final: 0.8623 (m-30) REVERT: A 335 GLU cc_start: 0.9281 (tp30) cc_final: 0.9038 (tm-30) REVERT: A 349 LEU cc_start: 0.9475 (mt) cc_final: 0.8931 (mt) REVERT: A 350 ARG cc_start: 0.8549 (mtp85) cc_final: 0.8094 (mtp85) REVERT: A 362 ASP cc_start: 0.9233 (m-30) cc_final: 0.8669 (m-30) REVERT: A 370 ASN cc_start: 0.9469 (m-40) cc_final: 0.9213 (m-40) REVERT: A 375 LYS cc_start: 0.9493 (mttt) cc_final: 0.9082 (mttt) REVERT: A 414 LEU cc_start: 0.9618 (mt) cc_final: 0.9364 (mt) REVERT: A 426 GLU cc_start: 0.9238 (tm-30) cc_final: 0.8724 (tm-30) REVERT: A 431 LEU cc_start: 0.9088 (mm) cc_final: 0.8745 (tp) REVERT: A 446 ARG cc_start: 0.8929 (mtt-85) cc_final: 0.8155 (mtp-110) REVERT: A 447 ASN cc_start: 0.9178 (m-40) cc_final: 0.8291 (m-40) REVERT: A 456 LYS cc_start: 0.9694 (mmpt) cc_final: 0.9374 (mmmt) REVERT: A 468 LEU cc_start: 0.9557 (tp) cc_final: 0.9271 (tp) REVERT: A 479 TYR cc_start: 0.9010 (t80) cc_final: 0.8303 (t80) REVERT: A 493 MET cc_start: 0.9244 (tmm) cc_final: 0.8867 (tmm) REVERT: A 515 ASP cc_start: 0.9458 (m-30) cc_final: 0.9180 (m-30) REVERT: A 575 ARG cc_start: 0.8973 (ptp-110) cc_final: 0.8448 (ptp-110) REVERT: A 583 SER cc_start: 0.9372 (t) cc_final: 0.9049 (t) REVERT: A 586 TYR cc_start: 0.9150 (m-80) cc_final: 0.8944 (m-80) REVERT: A 598 MET cc_start: 0.8506 (tmm) cc_final: 0.7930 (tmm) REVERT: A 599 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8085 (mt-10) REVERT: A 615 MET cc_start: 0.8964 (mmp) cc_final: 0.8386 (mmp) REVERT: A 632 MET cc_start: 0.8678 (mmp) cc_final: 0.8264 (mmm) REVERT: A 677 ARG cc_start: 0.9426 (mmm-85) cc_final: 0.8244 (mmm-85) REVERT: A 686 ARG cc_start: 0.8205 (mmt-90) cc_final: 0.7824 (mmt180) REVERT: B 51 LEU cc_start: 0.9569 (tp) cc_final: 0.9240 (tp) REVERT: B 77 ILE cc_start: 0.9537 (mt) cc_final: 0.9156 (mt) REVERT: B 81 PHE cc_start: 0.9515 (m-10) cc_final: 0.9137 (m-80) REVERT: B 87 LYS cc_start: 0.9382 (tptp) cc_final: 0.9064 (tptp) REVERT: B 95 MET cc_start: 0.9556 (tpp) cc_final: 0.8587 (tpp) REVERT: B 99 LYS cc_start: 0.9645 (mmmt) cc_final: 0.8863 (mmmt) REVERT: B 120 ASP cc_start: 0.9100 (m-30) cc_final: 0.8844 (m-30) REVERT: B 144 MET cc_start: 0.9412 (mtm) cc_final: 0.8736 (mtm) REVERT: B 147 GLN cc_start: 0.9460 (mm110) cc_final: 0.8990 (mm110) REVERT: B 148 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8558 (mm-30) REVERT: B 149 TYR cc_start: 0.9451 (t80) cc_final: 0.9040 (t80) REVERT: B 184 ARG cc_start: 0.9363 (tpp80) cc_final: 0.9009 (tpp80) REVERT: B 202 ASN cc_start: 0.6036 (p0) cc_final: 0.5654 (p0) REVERT: B 211 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8537 (mm-30) REVERT: B 252 ASN cc_start: 0.8738 (t0) cc_final: 0.8165 (t0) REVERT: B 257 ASP cc_start: 0.8413 (m-30) cc_final: 0.8189 (m-30) REVERT: B 259 ASN cc_start: 0.9078 (m-40) cc_final: 0.8869 (m-40) REVERT: B 263 ASP cc_start: 0.9269 (m-30) cc_final: 0.8952 (m-30) REVERT: B 286 ASP cc_start: 0.8991 (m-30) cc_final: 0.8363 (m-30) REVERT: B 319 MET cc_start: 0.9122 (tpt) cc_final: 0.8825 (tpp) REVERT: B 322 MET cc_start: 0.8895 (tpt) cc_final: 0.8053 (tpp) REVERT: B 326 PHE cc_start: 0.9507 (m-80) cc_final: 0.8498 (m-80) REVERT: B 335 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8118 (mt-10) REVERT: B 359 MET cc_start: 0.8232 (ptp) cc_final: 0.7747 (ptm) REVERT: B 362 ASP cc_start: 0.8789 (m-30) cc_final: 0.8127 (m-30) REVERT: B 373 ILE cc_start: 0.9665 (mt) cc_final: 0.9072 (mt) REVERT: B 390 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8738 (mm-40) REVERT: B 396 ASP cc_start: 0.8083 (p0) cc_final: 0.6688 (p0) REVERT: B 413 SER cc_start: 0.9245 (m) cc_final: 0.8953 (t) REVERT: B 414 LEU cc_start: 0.9772 (mt) cc_final: 0.9494 (mt) REVERT: B 415 ASN cc_start: 0.8889 (t0) cc_final: 0.8238 (t0) REVERT: B 416 ILE cc_start: 0.9818 (mt) cc_final: 0.9484 (mt) REVERT: B 418 ASN cc_start: 0.9225 (m-40) cc_final: 0.8993 (m-40) REVERT: B 420 MET cc_start: 0.9273 (mmm) cc_final: 0.8799 (mmm) REVERT: B 426 GLU cc_start: 0.9221 (pm20) cc_final: 0.8876 (pm20) REVERT: B 427 LYS cc_start: 0.9717 (ptpp) cc_final: 0.9282 (ptpp) REVERT: B 459 LYS cc_start: 0.9310 (mttp) cc_final: 0.8818 (mtmt) REVERT: B 466 MET cc_start: 0.9265 (ptp) cc_final: 0.8848 (ptp) REVERT: B 501 GLN cc_start: 0.8752 (tp-100) cc_final: 0.8212 (tp-100) REVERT: B 515 ASP cc_start: 0.9087 (m-30) cc_final: 0.8640 (m-30) REVERT: B 516 GLN cc_start: 0.9110 (tt0) cc_final: 0.8795 (tt0) REVERT: B 602 GLU cc_start: 0.8542 (pp20) cc_final: 0.8076 (tm-30) REVERT: B 631 ASP cc_start: 0.9521 (m-30) cc_final: 0.9249 (m-30) REVERT: B 632 MET cc_start: 0.8917 (mmp) cc_final: 0.8622 (mmm) REVERT: B 657 PHE cc_start: 0.9341 (m-80) cc_final: 0.8965 (m-80) REVERT: C 17 PHE cc_start: 0.8517 (p90) cc_final: 0.7656 (p90) REVERT: C 21 PHE cc_start: 0.9461 (m-80) cc_final: 0.8765 (m-80) REVERT: C 46 TYR cc_start: 0.8900 (m-80) cc_final: 0.8694 (m-80) REVERT: C 137 MET cc_start: 0.6001 (mtp) cc_final: 0.5760 (mtt) REVERT: C 157 MET cc_start: 0.4351 (ptt) cc_final: 0.3961 (ptt) REVERT: C 179 TYR cc_start: 0.9470 (t80) cc_final: 0.9125 (t80) REVERT: C 185 MET cc_start: 0.8636 (mpp) cc_final: 0.8297 (mpp) REVERT: C 196 ARG cc_start: 0.8877 (mtm110) cc_final: 0.8602 (mtm110) REVERT: C 204 TYR cc_start: 0.9722 (t80) cc_final: 0.9037 (t80) REVERT: C 276 TYR cc_start: 0.9156 (t80) cc_final: 0.8916 (t80) REVERT: D 46 TYR cc_start: 0.9073 (m-80) cc_final: 0.8807 (m-10) REVERT: D 201 HIS cc_start: 0.8772 (m170) cc_final: 0.8544 (m170) outliers start: 0 outliers final: 0 residues processed: 617 average time/residue: 0.1102 time to fit residues: 100.6141 Evaluate side-chains 531 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 531 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 9.9990 chunk 1 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 25 optimal weight: 0.0060 chunk 148 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 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** C 25 ASN D 69 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.110039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.079011 restraints weight = 53117.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.082008 restraints weight = 31564.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.083854 restraints weight = 22125.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.085237 restraints weight = 16785.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.086160 restraints weight = 13625.622| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.8451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16386 Z= 0.135 Angle : 0.652 7.282 22134 Z= 0.346 Chirality : 0.043 0.159 2360 Planarity : 0.004 0.046 2818 Dihedral : 11.019 174.285 2242 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.06 % Allowed : 0.35 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.19), residues: 1932 helix: 0.61 (0.15), residues: 1138 sheet: -0.97 (0.45), residues: 132 loop : -0.08 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 575 TYR 0.019 0.001 TYR C 174 PHE 0.036 0.002 PHE D 227 TRP 0.020 0.001 TRP A 558 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00297 (16386) covalent geometry : angle 0.65230 (22134) hydrogen bonds : bond 0.03745 ( 869) hydrogen bonds : angle 5.05580 ( 2568) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3020.42 seconds wall clock time: 53 minutes 15.14 seconds (3195.14 seconds total)