Starting phenix.real_space_refine on Thu Sep 18 10:02:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzo_45072/09_2025/9bzo_45072_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzo_45072/09_2025/9bzo_45072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bzo_45072/09_2025/9bzo_45072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzo_45072/09_2025/9bzo_45072.map" model { file = "/net/cci-nas-00/data/ceres_data/9bzo_45072/09_2025/9bzo_45072_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzo_45072/09_2025/9bzo_45072_neut.cif" } resolution = 4.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 4.01, per 1000 atoms: 0.25 Number of scatterers: 16038 At special positions: 0 Unit cell: (94.302, 130.806, 130.806, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 762.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.104A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.515A 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: 3.984A 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: 3.953A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.664A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.694A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.628A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.018A 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: 4.073A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.580A 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: 3.677A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.645A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.730A 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: 3.632A 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: 4.067A 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: 3.514A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.668A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A 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: 7.426A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.478A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.901A 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: 6.717A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.478A pdb=" N LEU A 656 " --> pdb=" O ARG A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.185A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.048A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.516A 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: 7.905A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.03 Time building geometry restraints manager: 2.41 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: 4874 1.34 - 1.46: 3050 1.46 - 1.58: 8280 1.58 - 1.70: 26 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.060 1.25e-02 6.40e+03 2.34e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.038 1.20e-02 6.94e+03 1.01e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.032 1.08e-02 8.57e+03 8.93e+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 7.37e+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: 21573 2.09 - 4.18: 519 4.18 - 6.27: 37 6.27 - 8.36: 1 8.36 - 10.45: 4 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.64 -6.10 1.36e+00 5.41e-01 2.01e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.16 -4.45 1.15e+00 7.56e-01 1.50e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.83 -4.33 1.23e+00 6.61e-01 1.24e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.71 -4.00 1.15e+00 7.56e-01 1.21e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.56 3.63 1.06e+00 8.90e-01 1.17e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 9468 35.80 - 71.60: 339 71.60 - 107.40: 37 107.40 - 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 301.68 151.14 150.54 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 31.89 148.08 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 9847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2143 0.093 - 0.185: 182 0.185 - 0.277: 30 0.277 - 0.370: 3 0.370 - 0.462: 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 2.05 0.46 2.00e-01 2.50e+01 5.35e+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 4.55e+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 2.96e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " -0.017 2.00e-02 2.50e+03 1.11e-02 2.17e+00 pdb=" CG PHE D 92 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 177 " -0.017 2.00e-02 2.50e+03 9.87e-03 1.95e+00 pdb=" CG TYR C 177 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR C 177 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR C 177 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C 177 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 177 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 177 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 177 " -0.010 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 129 2.51 - 3.11: 11552 3.11 - 3.70: 27036 3.70 - 4.30: 41525 4.30 - 4.90: 65391 Nonbonded interactions: 145633 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.991 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.013 3.040 ... (remaining 145628 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.970 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6206 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 16386 Z= 0.315 Angle : 0.740 10.446 22134 Z= 0.463 Chirality : 0.058 0.462 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.953 179.007 6154 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.34 % Allowed : 15.33 % 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: 0.56 (0.18), residues: 1932 helix: 0.59 (0.14), residues: 1151 sheet: 0.46 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 196 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.74021 (22134) hydrogen bonds : bond 0.15421 ( 871) hydrogen bonds : angle 6.51764 ( 2571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 974 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 951 time to evaluate : 0.632 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 51 LEU cc_start: 0.7829 (tp) cc_final: 0.7603 (tp) REVERT: A 71 LEU cc_start: 0.9357 (mt) cc_final: 0.9124 (mm) REVERT: A 95 MET cc_start: 0.8236 (tpp) cc_final: 0.7826 (mmm) REVERT: A 129 PHE cc_start: 0.7706 (m-10) cc_final: 0.7339 (m-10) REVERT: A 143 LEU cc_start: 0.8767 (tp) cc_final: 0.8530 (tp) REVERT: A 147 GLN cc_start: 0.8532 (mt0) cc_final: 0.8326 (mt0) REVERT: A 149 TYR cc_start: 0.7936 (t80) cc_final: 0.7589 (t80) REVERT: A 162 LYS cc_start: 0.7852 (ttpt) cc_final: 0.7282 (ttmm) REVERT: A 171 PHE cc_start: 0.8423 (m-80) cc_final: 0.8056 (m-80) REVERT: A 191 GLN cc_start: 0.8352 (mm-40) cc_final: 0.7552 (mt0) REVERT: A 199 VAL cc_start: 0.9238 (t) cc_final: 0.9018 (t) REVERT: A 226 VAL cc_start: 0.9057 (t) cc_final: 0.8748 (t) REVERT: A 267 ILE cc_start: 0.8851 (mp) cc_final: 0.8568 (tp) REVERT: A 278 LEU cc_start: 0.8842 (tp) cc_final: 0.8316 (tp) REVERT: A 287 LYS cc_start: 0.9090 (tptt) cc_final: 0.8764 (mmmm) REVERT: A 291 LEU cc_start: 0.8938 (mt) cc_final: 0.8687 (mt) REVERT: A 300 VAL cc_start: 0.7976 (m) cc_final: 0.7705 (m) REVERT: A 322 MET cc_start: 0.6879 (mmp) cc_final: 0.6193 (mmm) REVERT: A 349 LEU cc_start: 0.8582 (mt) cc_final: 0.8085 (mt) REVERT: A 373 ILE cc_start: 0.9336 (mt) cc_final: 0.9128 (mt) REVERT: A 377 LYS cc_start: 0.8334 (mttt) cc_final: 0.7416 (mtmm) REVERT: A 385 VAL cc_start: 0.8338 (t) cc_final: 0.8114 (t) REVERT: A 407 ILE cc_start: 0.8376 (mt) cc_final: 0.7958 (mt) REVERT: A 431 LEU cc_start: 0.9208 (mt) cc_final: 0.8872 (mt) REVERT: A 435 SER cc_start: 0.9237 (p) cc_final: 0.8138 (p) REVERT: A 436 LEU cc_start: 0.9338 (mt) cc_final: 0.8685 (mt) REVERT: A 493 MET cc_start: 0.8014 (tmm) cc_final: 0.7699 (tmm) REVERT: A 515 ASP cc_start: 0.7742 (m-30) cc_final: 0.7440 (m-30) REVERT: A 547 PHE cc_start: 0.7693 (m-80) cc_final: 0.7104 (m-10) REVERT: A 561 LEU cc_start: 0.9084 (tp) cc_final: 0.8797 (tp) REVERT: A 630 TYR cc_start: 0.7064 (m-80) cc_final: 0.6411 (m-10) REVERT: A 634 MET cc_start: 0.8595 (mmp) cc_final: 0.8293 (mmm) REVERT: A 641 ILE cc_start: 0.8969 (mm) cc_final: 0.8759 (mm) REVERT: A 648 ILE cc_start: 0.8283 (mm) cc_final: 0.8040 (mm) REVERT: A 650 GLN cc_start: 0.7405 (mt0) cc_final: 0.7093 (mt0) REVERT: A 653 SER cc_start: 0.9117 (OUTLIER) cc_final: 0.8897 (p) REVERT: A 664 THR cc_start: 0.8780 (p) cc_final: 0.8558 (p) REVERT: B 18 ILE cc_start: 0.8623 (mt) cc_final: 0.8413 (mp) REVERT: B 21 ASP cc_start: 0.7903 (m-30) cc_final: 0.7620 (m-30) REVERT: B 81 PHE cc_start: 0.7397 (m-80) cc_final: 0.7186 (m-80) REVERT: B 99 LYS cc_start: 0.9215 (mmtt) cc_final: 0.8767 (mmmt) REVERT: B 109 ASN cc_start: 0.8797 (m-40) cc_final: 0.8077 (m-40) REVERT: B 122 ILE cc_start: 0.9114 (mt) cc_final: 0.8772 (mt) REVERT: B 179 LEU cc_start: 0.8301 (tp) cc_final: 0.8045 (tp) REVERT: B 186 ILE cc_start: 0.9327 (mt) cc_final: 0.9079 (mt) REVERT: B 187 ASP cc_start: 0.7738 (t70) cc_final: 0.7221 (t0) REVERT: B 191 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8067 (mm-40) REVERT: B 192 LEU cc_start: 0.9001 (mt) cc_final: 0.8672 (mt) REVERT: B 204 SER cc_start: 0.8623 (m) cc_final: 0.8003 (m) REVERT: B 206 LEU cc_start: 0.9174 (mt) cc_final: 0.8667 (mt) REVERT: B 250 TYR cc_start: 0.7617 (m-80) cc_final: 0.7397 (m-80) REVERT: B 264 THR cc_start: 0.8002 (p) cc_final: 0.7345 (p) REVERT: B 265 LYS cc_start: 0.8508 (mmtt) cc_final: 0.8233 (mmmt) REVERT: B 286 ASP cc_start: 0.5893 (OUTLIER) cc_final: 0.5630 (m-30) REVERT: B 291 LEU cc_start: 0.9109 (mt) cc_final: 0.8877 (mt) REVERT: B 300 VAL cc_start: 0.8796 (m) cc_final: 0.8583 (m) REVERT: B 322 MET cc_start: 0.7844 (mmm) cc_final: 0.6034 (mmm) REVERT: B 337 ILE cc_start: 0.8650 (pt) cc_final: 0.8215 (mp) REVERT: B 343 LEU cc_start: 0.8274 (mt) cc_final: 0.7996 (mt) REVERT: B 359 MET cc_start: 0.8120 (ttt) cc_final: 0.7716 (ttt) REVERT: B 364 VAL cc_start: 0.8175 (t) cc_final: 0.7943 (t) REVERT: B 373 ILE cc_start: 0.9172 (mt) cc_final: 0.8142 (mt) REVERT: B 410 ASN cc_start: 0.8395 (m110) cc_final: 0.8154 (m110) REVERT: B 430 LYS cc_start: 0.8042 (mttt) cc_final: 0.7257 (mtpp) REVERT: B 431 LEU cc_start: 0.9080 (mt) cc_final: 0.8560 (mt) REVERT: B 508 LYS cc_start: 0.8646 (tttt) cc_final: 0.8367 (ttpt) REVERT: B 575 ARG cc_start: 0.8151 (mtm110) cc_final: 0.7804 (mtm-85) REVERT: B 586 TYR cc_start: 0.6731 (m-80) cc_final: 0.6393 (m-10) REVERT: B 612 TYR cc_start: 0.6928 (m-80) cc_final: 0.6575 (m-80) REVERT: B 656 LEU cc_start: 0.8166 (mt) cc_final: 0.7937 (mt) REVERT: B 683 TYR cc_start: 0.7618 (t80) cc_final: 0.7350 (t80) REVERT: C 17 PHE cc_start: 0.5346 (p90) cc_final: 0.4535 (p90) REVERT: C 67 THR cc_start: 0.6971 (m) cc_final: 0.6647 (m) REVERT: C 100 VAL cc_start: 0.3793 (t) cc_final: 0.2958 (t) REVERT: C 108 ILE cc_start: 0.7782 (mt) cc_final: 0.7083 (mm) REVERT: C 118 ILE cc_start: 0.6148 (mt) cc_final: 0.5522 (mp) REVERT: C 163 LEU cc_start: 0.7081 (tt) cc_final: 0.6225 (tt) REVERT: C 174 TYR cc_start: 0.3126 (OUTLIER) cc_final: 0.2879 (t80) REVERT: C 212 ILE cc_start: 0.8024 (mt) cc_final: 0.7135 (mt) REVERT: D 130 TYR cc_start: 0.4062 (m-80) cc_final: 0.3634 (m-80) outliers start: 23 outliers final: 6 residues processed: 967 average time/residue: 0.1547 time to fit residues: 211.0141 Evaluate side-chains 662 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 653 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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: 1.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 HIS B 49 HIS ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN B 645 GLN B 676 HIS ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN C 233 ASN C 238 ASN ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN D 71 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.118132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.090475 restraints weight = 42737.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.092874 restraints weight = 28245.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.095089 restraints weight = 20882.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.096276 restraints weight = 16707.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.097042 restraints weight = 14117.724| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16386 Z= 0.213 Angle : 0.668 9.832 22134 Z= 0.359 Chirality : 0.044 0.213 2360 Planarity : 0.004 0.051 2818 Dihedral : 11.373 177.112 2242 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.41 % Allowed : 2.74 % Favored : 96.85 % 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: 1.19 (0.19), residues: 1932 helix: 1.14 (0.15), residues: 1146 sheet: 0.04 (0.41), residues: 138 loop : 0.57 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 164 TYR 0.020 0.002 TYR B 36 PHE 0.040 0.003 PHE C 166 TRP 0.012 0.002 TRP A 623 HIS 0.009 0.002 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00455 (16386) covalent geometry : angle 0.66765 (22134) hydrogen bonds : bond 0.04840 ( 871) hydrogen bonds : angle 5.26223 ( 2571) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 761 time to evaluate : 0.640 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: A 87 LYS cc_start: 0.9471 (tppt) cc_final: 0.9028 (tptm) REVERT: A 89 PHE cc_start: 0.8852 (t80) cc_final: 0.8566 (t80) REVERT: A 101 TYR cc_start: 0.9464 (m-80) cc_final: 0.9021 (m-10) REVERT: A 109 ASN cc_start: 0.9517 (p0) cc_final: 0.9264 (m-40) REVERT: A 115 LEU cc_start: 0.9456 (mt) cc_final: 0.9164 (mt) REVERT: A 119 GLU cc_start: 0.9176 (mp0) cc_final: 0.8041 (tm-30) REVERT: A 120 ASP cc_start: 0.9026 (m-30) cc_final: 0.8527 (m-30) REVERT: A 122 ILE cc_start: 0.9483 (mt) cc_final: 0.9276 (mt) REVERT: A 144 MET cc_start: 0.8955 (mtm) cc_final: 0.8504 (mtm) REVERT: A 147 GLN cc_start: 0.8930 (mt0) cc_final: 0.8466 (mt0) REVERT: A 149 TYR cc_start: 0.9472 (t80) cc_final: 0.9244 (t80) REVERT: A 168 VAL cc_start: 0.8783 (t) cc_final: 0.8522 (t) REVERT: A 173 LEU cc_start: 0.9466 (mt) cc_final: 0.9210 (mt) REVERT: A 199 VAL cc_start: 0.9212 (t) cc_final: 0.8942 (t) REVERT: A 236 TYR cc_start: 0.8708 (t80) cc_final: 0.8114 (t80) REVERT: A 278 LEU cc_start: 0.9527 (tp) cc_final: 0.9161 (tp) REVERT: A 280 ILE cc_start: 0.8617 (pt) cc_final: 0.8372 (pt) REVERT: A 300 VAL cc_start: 0.9607 (m) cc_final: 0.9173 (m) REVERT: A 326 PHE cc_start: 0.9545 (m-80) cc_final: 0.9255 (m-80) REVERT: A 349 LEU cc_start: 0.9546 (mt) cc_final: 0.9310 (mt) REVERT: A 359 MET cc_start: 0.8642 (ttp) cc_final: 0.8382 (ttp) REVERT: A 362 ASP cc_start: 0.9120 (m-30) cc_final: 0.8723 (m-30) REVERT: A 370 ASN cc_start: 0.9487 (m-40) cc_final: 0.9058 (m-40) REVERT: A 375 LYS cc_start: 0.8671 (mmmt) cc_final: 0.8229 (mmtm) REVERT: A 377 LYS cc_start: 0.8710 (mttt) cc_final: 0.8196 (mtmm) REVERT: A 386 LEU cc_start: 0.9322 (mt) cc_final: 0.9093 (mt) REVERT: A 407 ILE cc_start: 0.8868 (mt) cc_final: 0.8536 (mt) REVERT: A 408 SER cc_start: 0.9229 (p) cc_final: 0.9020 (t) REVERT: A 459 LYS cc_start: 0.9023 (mttp) cc_final: 0.8336 (mtpt) REVERT: A 468 LEU cc_start: 0.9766 (tp) cc_final: 0.9535 (tp) REVERT: A 469 HIS cc_start: 0.9122 (t-170) cc_final: 0.8909 (t-170) REVERT: A 474 GLN cc_start: 0.9313 (tm-30) cc_final: 0.9049 (tm-30) REVERT: A 493 MET cc_start: 0.9291 (tmm) cc_final: 0.8889 (tmm) REVERT: A 501 GLN cc_start: 0.9499 (mm-40) cc_final: 0.8822 (tp-100) REVERT: A 515 ASP cc_start: 0.9239 (m-30) cc_final: 0.8684 (m-30) REVERT: A 516 GLN cc_start: 0.9130 (mp10) cc_final: 0.8703 (mp10) REVERT: A 561 LEU cc_start: 0.9631 (tp) cc_final: 0.9319 (tp) REVERT: A 598 MET cc_start: 0.8524 (ttt) cc_final: 0.8186 (ttt) REVERT: A 615 MET cc_start: 0.8677 (mmp) cc_final: 0.8295 (mmp) REVERT: A 650 GLN cc_start: 0.8365 (mt0) cc_final: 0.8064 (mt0) REVERT: A 677 ARG cc_start: 0.9317 (mmm-85) cc_final: 0.8708 (mmm-85) REVERT: A 686 ARG cc_start: 0.7502 (mmm160) cc_final: 0.7190 (mmm160) REVERT: B 8 LYS cc_start: 0.9325 (tptp) cc_final: 0.8994 (tptp) REVERT: B 16 ILE cc_start: 0.9734 (pt) cc_final: 0.9483 (pt) REVERT: B 30 LYS cc_start: 0.9750 (tmtt) cc_final: 0.9392 (tptt) REVERT: B 41 ILE cc_start: 0.9620 (mm) cc_final: 0.9346 (mt) REVERT: B 51 LEU cc_start: 0.9085 (tp) cc_final: 0.8798 (tp) REVERT: B 54 LYS cc_start: 0.9715 (ttmm) cc_final: 0.9502 (ttmt) REVERT: B 95 MET cc_start: 0.9532 (mmp) cc_final: 0.9038 (mmp) REVERT: B 144 MET cc_start: 0.9481 (mtm) cc_final: 0.9242 (mtm) REVERT: B 195 LEU cc_start: 0.9403 (mt) cc_final: 0.9178 (mt) REVERT: B 211 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8212 (mm-30) REVERT: B 227 MET cc_start: 0.9179 (mtp) cc_final: 0.8813 (mtp) REVERT: B 250 TYR cc_start: 0.8178 (m-80) cc_final: 0.7032 (m-80) REVERT: B 286 ASP cc_start: 0.8559 (m-30) cc_final: 0.7827 (m-30) REVERT: B 291 LEU cc_start: 0.9578 (mt) cc_final: 0.9366 (mt) REVERT: B 322 MET cc_start: 0.8658 (mmm) cc_final: 0.8201 (mmm) REVERT: B 326 PHE cc_start: 0.9105 (m-80) cc_final: 0.8721 (m-80) REVERT: B 362 ASP cc_start: 0.8608 (m-30) cc_final: 0.7436 (m-30) REVERT: B 375 LYS cc_start: 0.9261 (mmmm) cc_final: 0.9053 (mmmm) REVERT: B 379 SER cc_start: 0.9023 (t) cc_final: 0.8591 (t) REVERT: B 390 GLN cc_start: 0.8717 (mm110) cc_final: 0.8408 (mm110) REVERT: B 410 ASN cc_start: 0.8818 (m110) cc_final: 0.8494 (m110) REVERT: B 420 MET cc_start: 0.9100 (mmm) cc_final: 0.8849 (mmm) REVERT: B 458 MET cc_start: 0.9606 (mmm) cc_final: 0.9313 (mmm) REVERT: B 468 LEU cc_start: 0.9654 (tp) cc_final: 0.9450 (tp) REVERT: B 500 ILE cc_start: 0.9658 (mt) cc_final: 0.9437 (mt) REVERT: B 570 MET cc_start: 0.8857 (mmm) cc_final: 0.8215 (mmm) REVERT: B 598 MET cc_start: 0.9218 (mtm) cc_final: 0.8927 (mtm) REVERT: B 612 TYR cc_start: 0.9179 (m-80) cc_final: 0.7891 (m-80) REVERT: B 613 TYR cc_start: 0.9128 (t80) cc_final: 0.8783 (t80) REVERT: B 648 ILE cc_start: 0.9368 (mm) cc_final: 0.9038 (mm) REVERT: B 656 LEU cc_start: 0.9604 (mt) cc_final: 0.9375 (mt) REVERT: B 673 TYR cc_start: 0.9121 (t80) cc_final: 0.8852 (t80) REVERT: C 17 PHE cc_start: 0.8691 (p90) cc_final: 0.7601 (p90) REVERT: C 21 PHE cc_start: 0.9236 (m-10) cc_final: 0.8600 (m-80) REVERT: C 92 PHE cc_start: 0.8138 (t80) cc_final: 0.7908 (t80) REVERT: C 96 MET cc_start: 0.8469 (tpt) cc_final: 0.8178 (tpt) REVERT: C 100 VAL cc_start: 0.6241 (t) cc_final: 0.5991 (t) REVERT: C 112 LEU cc_start: 0.7172 (mt) cc_final: 0.6972 (pp) REVERT: C 157 MET cc_start: 0.9575 (mtm) cc_final: 0.9289 (ptm) REVERT: C 163 LEU cc_start: 0.9609 (tt) cc_final: 0.9167 (tt) REVERT: C 178 PHE cc_start: 0.9212 (m-80) cc_final: 0.8971 (m-10) REVERT: C 214 ASN cc_start: 0.8517 (m-40) cc_final: 0.7963 (p0) REVERT: C 227 PHE cc_start: 0.7356 (m-80) cc_final: 0.7119 (m-80) REVERT: C 263 ASN cc_start: 0.6694 (m-40) cc_final: 0.6374 (m110) REVERT: C 285 ILE cc_start: 0.9010 (mm) cc_final: 0.8776 (mm) REVERT: D 17 PHE cc_start: 0.5381 (m-80) cc_final: 0.5128 (m-80) REVERT: D 21 PHE cc_start: 0.9157 (m-10) cc_final: 0.8894 (m-10) REVERT: D 74 MET cc_start: 0.8583 (mmp) cc_final: 0.8258 (mmt) REVERT: D 109 PHE cc_start: 0.8431 (m-80) cc_final: 0.7960 (m-10) REVERT: D 172 PHE cc_start: 0.9263 (m-80) cc_final: 0.8992 (m-80) REVERT: D 181 GLN cc_start: 0.7563 (pt0) cc_final: 0.7316 (pt0) REVERT: D 185 MET cc_start: 0.4381 (mmp) cc_final: 0.3544 (mmp) REVERT: D 189 GLU cc_start: 0.9177 (pt0) cc_final: 0.8478 (pt0) REVERT: D 214 ASN cc_start: 0.9151 (m-40) cc_final: 0.8739 (p0) REVERT: D 239 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8454 (pp20) outliers start: 7 outliers final: 1 residues processed: 767 average time/residue: 0.1381 time to fit residues: 154.7410 Evaluate side-chains 620 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 618 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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: 0.0370 chunk 131 optimal weight: 0.9980 chunk 164 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 182 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 overall best weight: 1.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 HIS B 320 ASN B 361 GLN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 216 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.112345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.082352 restraints weight = 49681.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.085655 restraints weight = 30105.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.088005 restraints weight = 20634.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.089642 restraints weight = 15356.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.090980 restraints weight = 12199.966| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16386 Z= 0.154 Angle : 0.587 6.674 22134 Z= 0.315 Chirality : 0.042 0.170 2360 Planarity : 0.004 0.038 2818 Dihedral : 11.012 177.482 2242 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.17 % Allowed : 2.51 % Favored : 97.32 % 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: 1.07 (0.19), residues: 1932 helix: 1.16 (0.15), residues: 1129 sheet: -0.27 (0.39), residues: 144 loop : 0.36 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 235 TYR 0.031 0.002 TYR D 174 PHE 0.034 0.002 PHE B 81 TRP 0.007 0.001 TRP C 44 HIS 0.014 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00330 (16386) covalent geometry : angle 0.58725 (22134) hydrogen bonds : bond 0.04203 ( 871) hydrogen bonds : angle 5.00382 ( 2571) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 715 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 29 ASP cc_start: 0.9311 (t0) cc_final: 0.9020 (t70) REVERT: A 54 LYS cc_start: 0.9715 (ttmm) cc_final: 0.9497 (ttmm) REVERT: A 67 GLU cc_start: 0.9584 (mp0) cc_final: 0.9352 (pm20) REVERT: A 89 PHE cc_start: 0.8695 (t80) cc_final: 0.8435 (t80) REVERT: A 115 LEU cc_start: 0.9583 (mt) cc_final: 0.9199 (mt) REVERT: A 119 GLU cc_start: 0.9118 (mp0) cc_final: 0.8010 (tm-30) REVERT: A 120 ASP cc_start: 0.9217 (m-30) cc_final: 0.8752 (m-30) REVERT: A 136 LYS cc_start: 0.9559 (tttp) cc_final: 0.9248 (tttp) REVERT: A 144 MET cc_start: 0.8789 (mtm) cc_final: 0.8342 (mtm) REVERT: A 147 GLN cc_start: 0.8951 (mt0) cc_final: 0.8334 (mt0) REVERT: A 150 GLN cc_start: 0.9226 (tp40) cc_final: 0.9014 (tp40) REVERT: A 191 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8546 (mm-40) REVERT: A 199 VAL cc_start: 0.9499 (t) cc_final: 0.9246 (t) REVERT: A 236 TYR cc_start: 0.8808 (t80) cc_final: 0.8284 (t80) REVERT: A 279 SER cc_start: 0.8118 (m) cc_final: 0.7272 (p) REVERT: A 283 VAL cc_start: 0.9145 (t) cc_final: 0.8882 (t) REVERT: A 291 LEU cc_start: 0.9536 (mt) cc_final: 0.9136 (mp) REVERT: A 300 VAL cc_start: 0.9503 (m) cc_final: 0.8977 (m) REVERT: A 322 MET cc_start: 0.8908 (mmp) cc_final: 0.8289 (tmm) REVERT: A 326 PHE cc_start: 0.9665 (m-80) cc_final: 0.9053 (m-80) REVERT: A 335 GLU cc_start: 0.8115 (mp0) cc_final: 0.7708 (mp0) REVERT: A 359 MET cc_start: 0.8755 (ttp) cc_final: 0.8530 (ttp) REVERT: A 362 ASP cc_start: 0.9048 (m-30) cc_final: 0.8667 (m-30) REVERT: A 370 ASN cc_start: 0.9483 (m-40) cc_final: 0.8997 (m-40) REVERT: A 375 LYS cc_start: 0.8852 (mmmt) cc_final: 0.8506 (mmtm) REVERT: A 377 LYS cc_start: 0.8835 (mttt) cc_final: 0.8337 (mtmm) REVERT: A 407 ILE cc_start: 0.9010 (mt) cc_final: 0.8694 (mt) REVERT: A 458 MET cc_start: 0.8861 (mmp) cc_final: 0.8488 (mmp) REVERT: A 459 LYS cc_start: 0.9051 (mttp) cc_final: 0.8376 (mtmm) REVERT: A 493 MET cc_start: 0.9337 (tmm) cc_final: 0.8875 (tmm) REVERT: A 494 MET cc_start: 0.9662 (mpp) cc_final: 0.9224 (mmm) REVERT: A 501 GLN cc_start: 0.9383 (tp40) cc_final: 0.8635 (tp-100) REVERT: A 515 ASP cc_start: 0.9260 (m-30) cc_final: 0.8387 (m-30) REVERT: A 516 GLN cc_start: 0.9186 (mp10) cc_final: 0.8550 (mp10) REVERT: A 561 LEU cc_start: 0.9615 (tp) cc_final: 0.9395 (tp) REVERT: A 598 MET cc_start: 0.8653 (ttt) cc_final: 0.8388 (ttt) REVERT: A 615 MET cc_start: 0.9055 (mmp) cc_final: 0.8817 (mmp) REVERT: A 662 MET cc_start: 0.8657 (pmm) cc_final: 0.8158 (pmm) REVERT: A 664 THR cc_start: 0.9519 (p) cc_final: 0.9242 (p) REVERT: A 677 ARG cc_start: 0.9371 (mmm-85) cc_final: 0.8869 (mmm-85) REVERT: B 8 LYS cc_start: 0.9376 (tptp) cc_final: 0.9056 (tptp) REVERT: B 16 ILE cc_start: 0.9757 (pt) cc_final: 0.9490 (pt) REVERT: B 30 LYS cc_start: 0.9779 (tmtt) cc_final: 0.9429 (tptt) REVERT: B 95 MET cc_start: 0.9512 (mmp) cc_final: 0.9164 (mmm) REVERT: B 99 LYS cc_start: 0.9534 (mmmt) cc_final: 0.9186 (mttt) REVERT: B 119 GLU cc_start: 0.9143 (mp0) cc_final: 0.8713 (mp0) REVERT: B 191 GLN cc_start: 0.9008 (mm-40) cc_final: 0.8800 (mm-40) REVERT: B 195 LEU cc_start: 0.9562 (mt) cc_final: 0.9347 (mt) REVERT: B 211 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8315 (mm-30) REVERT: B 235 ARG cc_start: 0.8755 (ttm110) cc_final: 0.8251 (ttm110) REVERT: B 250 TYR cc_start: 0.8591 (m-80) cc_final: 0.7342 (m-80) REVERT: B 283 VAL cc_start: 0.9431 (t) cc_final: 0.9037 (t) REVERT: B 286 ASP cc_start: 0.8659 (m-30) cc_final: 0.7855 (m-30) REVERT: B 291 LEU cc_start: 0.9570 (mt) cc_final: 0.9329 (mt) REVERT: B 322 MET cc_start: 0.8822 (mmm) cc_final: 0.8497 (mmm) REVERT: B 349 LEU cc_start: 0.9397 (mm) cc_final: 0.9114 (mt) REVERT: B 359 MET cc_start: 0.8881 (ttt) cc_final: 0.8397 (tmm) REVERT: B 362 ASP cc_start: 0.8510 (m-30) cc_final: 0.7585 (m-30) REVERT: B 375 LYS cc_start: 0.9228 (mmmm) cc_final: 0.8991 (mmmm) REVERT: B 379 SER cc_start: 0.9216 (t) cc_final: 0.8439 (t) REVERT: B 390 GLN cc_start: 0.9029 (mm110) cc_final: 0.8626 (mm110) REVERT: B 402 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8246 (tm-30) REVERT: B 403 ILE cc_start: 0.9389 (mp) cc_final: 0.8981 (tp) REVERT: B 410 ASN cc_start: 0.8929 (m110) cc_final: 0.8545 (m110) REVERT: B 458 MET cc_start: 0.9571 (mmm) cc_final: 0.9263 (mmm) REVERT: B 468 LEU cc_start: 0.9660 (tp) cc_final: 0.9455 (tp) REVERT: B 570 MET cc_start: 0.8975 (mmm) cc_final: 0.8252 (mmm) REVERT: B 598 MET cc_start: 0.9300 (mtm) cc_final: 0.8942 (mtm) REVERT: B 612 TYR cc_start: 0.9032 (m-80) cc_final: 0.7962 (m-80) REVERT: B 613 TYR cc_start: 0.9058 (t80) cc_final: 0.8565 (t80) REVERT: B 615 MET cc_start: 0.8848 (mmp) cc_final: 0.8109 (mmt) REVERT: B 631 ASP cc_start: 0.9374 (t70) cc_final: 0.9109 (t0) REVERT: B 639 ASP cc_start: 0.9340 (m-30) cc_final: 0.9025 (m-30) REVERT: B 640 MET cc_start: 0.9502 (tpp) cc_final: 0.8938 (tpp) REVERT: B 648 ILE cc_start: 0.9322 (mm) cc_final: 0.8987 (mm) REVERT: B 656 LEU cc_start: 0.9657 (mt) cc_final: 0.9419 (mt) REVERT: B 673 TYR cc_start: 0.9140 (t80) cc_final: 0.8883 (t80) REVERT: B 679 ILE cc_start: 0.9636 (mm) cc_final: 0.9417 (mm) REVERT: B 687 THR cc_start: 0.8857 (t) cc_final: 0.7990 (t) REVERT: C 17 PHE cc_start: 0.8530 (p90) cc_final: 0.7432 (p90) REVERT: C 20 MET cc_start: 0.8862 (ptp) cc_final: 0.8524 (pmm) REVERT: C 21 PHE cc_start: 0.9174 (m-10) cc_final: 0.8196 (m-80) REVERT: C 49 LYS cc_start: 0.9090 (tptp) cc_final: 0.8845 (tptp) REVERT: C 96 MET cc_start: 0.8433 (tpt) cc_final: 0.7926 (tpt) REVERT: C 105 TYR cc_start: 0.8710 (m-80) cc_final: 0.8356 (m-80) REVERT: C 112 LEU cc_start: 0.7409 (mt) cc_final: 0.7130 (pp) REVERT: C 122 PHE cc_start: 0.8737 (m-80) cc_final: 0.8413 (m-80) REVERT: C 157 MET cc_start: 0.9652 (mtm) cc_final: 0.9282 (ptm) REVERT: C 178 PHE cc_start: 0.9236 (m-80) cc_final: 0.8880 (m-10) REVERT: C 204 TYR cc_start: 0.8832 (t80) cc_final: 0.8584 (t80) REVERT: C 205 VAL cc_start: 0.9053 (t) cc_final: 0.8841 (t) REVERT: C 207 LEU cc_start: 0.8925 (tt) cc_final: 0.8678 (pp) REVERT: C 239 GLU cc_start: 0.8689 (pt0) cc_final: 0.8487 (pt0) REVERT: C 263 ASN cc_start: 0.6762 (m110) cc_final: 0.6483 (p0) REVERT: D 66 ASP cc_start: 0.5725 (OUTLIER) cc_final: 0.5417 (p0) REVERT: D 109 PHE cc_start: 0.8911 (m-80) cc_final: 0.8149 (m-80) REVERT: D 169 TYR cc_start: 0.8718 (m-10) cc_final: 0.8463 (m-80) REVERT: D 172 PHE cc_start: 0.9431 (m-80) cc_final: 0.9114 (m-80) outliers start: 3 outliers final: 0 residues processed: 716 average time/residue: 0.1319 time to fit residues: 140.4222 Evaluate side-chains 603 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 602 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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: 9.9990 chunk 157 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 185 optimal weight: 1.9990 chunk 191 optimal weight: 0.0070 chunk 159 optimal weight: 10.0000 chunk 182 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN D 23 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.112422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.082507 restraints weight = 50316.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.085543 restraints weight = 30618.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.088135 restraints weight = 20950.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.089942 restraints weight = 15229.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.091084 restraints weight = 12016.698| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.5998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16386 Z= 0.145 Angle : 0.590 6.734 22134 Z= 0.314 Chirality : 0.043 0.193 2360 Planarity : 0.004 0.128 2818 Dihedral : 10.851 178.359 2242 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.12 % Allowed : 2.04 % Favored : 97.84 % 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: 0.91 (0.19), residues: 1932 helix: 1.11 (0.15), residues: 1123 sheet: -0.40 (0.40), residues: 144 loop : 0.17 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 225 TYR 0.025 0.001 TYR D 174 PHE 0.037 0.002 PHE C 172 TRP 0.009 0.001 TRP A 9 HIS 0.011 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00314 (16386) covalent geometry : angle 0.58995 (22134) hydrogen bonds : bond 0.03958 ( 871) hydrogen bonds : angle 5.01783 ( 2571) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 705 time to evaluate : 0.655 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 29 ASP cc_start: 0.9303 (t0) cc_final: 0.8958 (t0) REVERT: A 54 LYS cc_start: 0.9727 (ttmm) cc_final: 0.9512 (ttmm) REVERT: A 67 GLU cc_start: 0.9575 (mp0) cc_final: 0.9339 (pm20) REVERT: A 115 LEU cc_start: 0.9599 (mt) cc_final: 0.9252 (mt) REVERT: A 116 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7474 (tt0) REVERT: A 119 GLU cc_start: 0.9076 (mp0) cc_final: 0.8748 (mp0) REVERT: A 144 MET cc_start: 0.8683 (mtm) cc_final: 0.8282 (mtm) REVERT: A 147 GLN cc_start: 0.8842 (mt0) cc_final: 0.8219 (mt0) REVERT: A 172 LEU cc_start: 0.9447 (mp) cc_final: 0.9071 (mp) REVERT: A 173 LEU cc_start: 0.9464 (mt) cc_final: 0.9228 (mt) REVERT: A 190 MET cc_start: 0.9205 (mtp) cc_final: 0.8994 (mtp) REVERT: A 199 VAL cc_start: 0.9512 (t) cc_final: 0.9238 (t) REVERT: A 235 ARG cc_start: 0.8481 (mtm110) cc_final: 0.8007 (mtm110) REVERT: A 236 TYR cc_start: 0.8935 (t80) cc_final: 0.8522 (t80) REVERT: A 279 SER cc_start: 0.7887 (m) cc_final: 0.7468 (p) REVERT: A 283 VAL cc_start: 0.9202 (t) cc_final: 0.8958 (t) REVERT: A 286 ASP cc_start: 0.9218 (m-30) cc_final: 0.8877 (m-30) REVERT: A 291 LEU cc_start: 0.9329 (mt) cc_final: 0.9123 (mp) REVERT: A 359 MET cc_start: 0.8851 (ttp) cc_final: 0.8649 (ttp) REVERT: A 362 ASP cc_start: 0.8981 (m-30) cc_final: 0.8631 (m-30) REVERT: A 370 ASN cc_start: 0.9525 (m-40) cc_final: 0.9057 (m-40) REVERT: A 375 LYS cc_start: 0.8925 (mmmt) cc_final: 0.8543 (mmtm) REVERT: A 377 LYS cc_start: 0.8849 (mttt) cc_final: 0.8350 (mttp) REVERT: A 406 ASP cc_start: 0.8630 (m-30) cc_final: 0.8335 (m-30) REVERT: A 407 ILE cc_start: 0.9011 (mt) cc_final: 0.8668 (mt) REVERT: A 426 GLU cc_start: 0.9046 (tm-30) cc_final: 0.8724 (tm-30) REVERT: A 441 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8944 (mm-30) REVERT: A 459 LYS cc_start: 0.9140 (mttp) cc_final: 0.8419 (mtmm) REVERT: A 468 LEU cc_start: 0.9721 (tp) cc_final: 0.9422 (tp) REVERT: A 469 HIS cc_start: 0.8881 (t-170) cc_final: 0.8432 (t-170) REVERT: A 471 TYR cc_start: 0.9075 (t80) cc_final: 0.8821 (t80) REVERT: A 479 TYR cc_start: 0.9357 (t80) cc_final: 0.8701 (t80) REVERT: A 493 MET cc_start: 0.9396 (tmm) cc_final: 0.8903 (tmm) REVERT: A 501 GLN cc_start: 0.9346 (tp40) cc_final: 0.8656 (tp40) REVERT: A 515 ASP cc_start: 0.9265 (m-30) cc_final: 0.8687 (m-30) REVERT: A 516 GLN cc_start: 0.9175 (mp10) cc_final: 0.8810 (mp10) REVERT: A 558 TRP cc_start: 0.9434 (m100) cc_final: 0.9209 (m100) REVERT: A 561 LEU cc_start: 0.9622 (tp) cc_final: 0.9054 (tp) REVERT: A 598 MET cc_start: 0.8744 (ttt) cc_final: 0.8458 (ttt) REVERT: A 628 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8268 (mm-30) REVERT: A 675 HIS cc_start: 0.9434 (t-90) cc_final: 0.9126 (t-90) REVERT: B 8 LYS cc_start: 0.9359 (tptp) cc_final: 0.9056 (tptp) REVERT: B 16 ILE cc_start: 0.9763 (pt) cc_final: 0.9561 (pt) REVERT: B 30 LYS cc_start: 0.9770 (tmtt) cc_final: 0.9415 (tptt) REVERT: B 41 ILE cc_start: 0.9600 (mm) cc_final: 0.9380 (mt) REVERT: B 65 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8194 (tm-30) REVERT: B 99 LYS cc_start: 0.9541 (mmmt) cc_final: 0.9274 (mmmt) REVERT: B 149 TYR cc_start: 0.8943 (t80) cc_final: 0.8696 (t80) REVERT: B 211 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8184 (mm-30) REVERT: B 218 ASN cc_start: 0.9368 (m-40) cc_final: 0.8689 (m-40) REVERT: B 250 TYR cc_start: 0.8542 (m-80) cc_final: 0.7270 (m-80) REVERT: B 263 ASP cc_start: 0.9140 (m-30) cc_final: 0.8862 (m-30) REVERT: B 264 THR cc_start: 0.9045 (m) cc_final: 0.8814 (m) REVERT: B 283 VAL cc_start: 0.9421 (t) cc_final: 0.8940 (t) REVERT: B 291 LEU cc_start: 0.9579 (mt) cc_final: 0.9351 (mt) REVERT: B 322 MET cc_start: 0.8823 (mmm) cc_final: 0.8427 (mmm) REVERT: B 359 MET cc_start: 0.8944 (ttt) cc_final: 0.8399 (tmm) REVERT: B 362 ASP cc_start: 0.8763 (m-30) cc_final: 0.8032 (m-30) REVERT: B 375 LYS cc_start: 0.9226 (mmmm) cc_final: 0.8962 (mmmm) REVERT: B 379 SER cc_start: 0.9197 (t) cc_final: 0.8503 (t) REVERT: B 390 GLN cc_start: 0.9089 (mm110) cc_final: 0.8671 (mm110) REVERT: B 402 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8257 (tm-30) REVERT: B 403 ILE cc_start: 0.9373 (mp) cc_final: 0.8973 (tp) REVERT: B 410 ASN cc_start: 0.8994 (m110) cc_final: 0.8636 (m110) REVERT: B 415 ASN cc_start: 0.9410 (t0) cc_final: 0.8979 (t0) REVERT: B 416 ILE cc_start: 0.9573 (mt) cc_final: 0.9359 (mt) REVERT: B 419 VAL cc_start: 0.9508 (p) cc_final: 0.9157 (p) REVERT: B 420 MET cc_start: 0.9336 (mmm) cc_final: 0.8858 (mmp) REVERT: B 438 HIS cc_start: 0.9212 (t70) cc_final: 0.8959 (t-90) REVERT: B 458 MET cc_start: 0.9516 (mmm) cc_final: 0.9285 (mmm) REVERT: B 468 LEU cc_start: 0.9556 (tp) cc_final: 0.9314 (tp) REVERT: B 494 MET cc_start: 0.9574 (mtt) cc_final: 0.9109 (mtp) REVERT: B 598 MET cc_start: 0.9353 (mtm) cc_final: 0.8995 (mtm) REVERT: B 599 GLU cc_start: 0.8752 (pt0) cc_final: 0.8511 (pt0) REVERT: B 601 ILE cc_start: 0.9114 (mm) cc_final: 0.8778 (tp) REVERT: B 612 TYR cc_start: 0.8886 (m-80) cc_final: 0.7948 (m-80) REVERT: B 613 TYR cc_start: 0.9008 (t80) cc_final: 0.7966 (t80) REVERT: B 615 MET cc_start: 0.8783 (mmp) cc_final: 0.7226 (mmt) REVERT: B 631 ASP cc_start: 0.9366 (t70) cc_final: 0.9069 (t0) REVERT: B 639 ASP cc_start: 0.9313 (m-30) cc_final: 0.8903 (m-30) REVERT: B 640 MET cc_start: 0.9432 (tpp) cc_final: 0.8934 (tpp) REVERT: B 641 ILE cc_start: 0.9790 (mm) cc_final: 0.9577 (mm) REVERT: B 645 GLN cc_start: 0.8981 (tp-100) cc_final: 0.8725 (tp-100) REVERT: B 656 LEU cc_start: 0.9656 (mt) cc_final: 0.9404 (mt) REVERT: B 673 TYR cc_start: 0.9155 (t80) cc_final: 0.8836 (t80) REVERT: B 679 ILE cc_start: 0.9659 (mm) cc_final: 0.9419 (mm) REVERT: C 17 PHE cc_start: 0.8376 (p90) cc_final: 0.7318 (p90) REVERT: C 20 MET cc_start: 0.8831 (ptp) cc_final: 0.8579 (ptp) REVERT: C 21 PHE cc_start: 0.9129 (m-10) cc_final: 0.8528 (m-80) REVERT: C 49 LYS cc_start: 0.9095 (tptp) cc_final: 0.8843 (tptp) REVERT: C 97 GLU cc_start: 0.4898 (mm-30) cc_final: 0.4456 (mm-30) REVERT: C 105 TYR cc_start: 0.8852 (m-80) cc_final: 0.8438 (m-80) REVERT: C 112 LEU cc_start: 0.7490 (mt) cc_final: 0.7017 (pp) REVERT: C 157 MET cc_start: 0.9618 (mtm) cc_final: 0.9184 (ptm) REVERT: C 163 LEU cc_start: 0.9561 (tt) cc_final: 0.9025 (tt) REVERT: C 178 PHE cc_start: 0.9228 (m-80) cc_final: 0.8938 (m-10) REVERT: C 204 TYR cc_start: 0.8862 (t80) cc_final: 0.8586 (t80) REVERT: C 239 GLU cc_start: 0.8595 (pt0) cc_final: 0.7891 (pt0) REVERT: C 263 ASN cc_start: 0.6585 (m110) cc_final: 0.6326 (p0) REVERT: C 313 GLU cc_start: 0.9317 (mt-10) cc_final: 0.8889 (mp0) REVERT: D 109 PHE cc_start: 0.8872 (m-80) cc_final: 0.8205 (m-80) REVERT: D 112 LEU cc_start: 0.8615 (mm) cc_final: 0.7782 (pp) REVERT: D 169 TYR cc_start: 0.8780 (m-10) cc_final: 0.8504 (m-80) REVERT: D 172 PHE cc_start: 0.9295 (m-80) cc_final: 0.8989 (m-80) outliers start: 2 outliers final: 0 residues processed: 705 average time/residue: 0.1260 time to fit residues: 133.2879 Evaluate side-chains 602 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 602 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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: 3.9990 chunk 46 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 126 optimal weight: 0.8980 chunk 129 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 168 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN A 313 HIS ** 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 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN A 496 ASN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 410 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN D 288 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.109005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.079940 restraints weight = 51638.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.082987 restraints weight = 31032.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.085166 restraints weight = 21159.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.086832 restraints weight = 15816.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.088027 restraints weight = 12377.336| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.6691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16386 Z= 0.214 Angle : 0.647 7.214 22134 Z= 0.345 Chirality : 0.043 0.190 2360 Planarity : 0.005 0.112 2818 Dihedral : 10.949 179.178 2242 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.12 % Allowed : 2.51 % Favored : 97.38 % 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: 0.75 (0.19), residues: 1932 helix: 1.00 (0.15), residues: 1141 sheet: -0.46 (0.41), residues: 148 loop : 0.03 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 604 TYR 0.036 0.002 TYR C 276 PHE 0.035 0.003 PHE C 109 TRP 0.058 0.003 TRP D 124 HIS 0.019 0.002 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00450 (16386) covalent geometry : angle 0.64742 (22134) hydrogen bonds : bond 0.04094 ( 871) hydrogen bonds : angle 5.12416 ( 2571) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 675 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 29 ASP cc_start: 0.9351 (t0) cc_final: 0.9134 (t70) REVERT: A 116 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7806 (tt0) REVERT: A 144 MET cc_start: 0.8730 (mtm) cc_final: 0.8362 (mtm) REVERT: A 147 GLN cc_start: 0.8811 (mt0) cc_final: 0.8501 (mt0) REVERT: A 164 ARG cc_start: 0.7832 (ptm-80) cc_final: 0.6764 (ptm-80) REVERT: A 168 VAL cc_start: 0.8634 (t) cc_final: 0.8424 (m) REVERT: A 172 LEU cc_start: 0.9439 (mp) cc_final: 0.9070 (mp) REVERT: A 173 LEU cc_start: 0.9520 (mt) cc_final: 0.9299 (mt) REVERT: A 190 MET cc_start: 0.9187 (mtp) cc_final: 0.8884 (mtp) REVERT: A 199 VAL cc_start: 0.9501 (t) cc_final: 0.9194 (t) REVERT: A 221 LYS cc_start: 0.9007 (mmtm) cc_final: 0.8788 (mmtm) REVERT: A 235 ARG cc_start: 0.8495 (mtm110) cc_final: 0.8251 (mtm110) REVERT: A 236 TYR cc_start: 0.8976 (t80) cc_final: 0.8358 (t80) REVERT: A 254 PHE cc_start: 0.8166 (m-10) cc_final: 0.7401 (m-10) REVERT: A 286 ASP cc_start: 0.9223 (m-30) cc_final: 0.8897 (m-30) REVERT: A 322 MET cc_start: 0.9147 (mmp) cc_final: 0.8868 (mmm) REVERT: A 359 MET cc_start: 0.8915 (ttp) cc_final: 0.8300 (ttp) REVERT: A 362 ASP cc_start: 0.9018 (m-30) cc_final: 0.8645 (m-30) REVERT: A 370 ASN cc_start: 0.9620 (m-40) cc_final: 0.9200 (m110) REVERT: A 375 LYS cc_start: 0.8996 (mmmt) cc_final: 0.8489 (mmtm) REVERT: A 377 LYS cc_start: 0.8856 (mttt) cc_final: 0.8436 (mttp) REVERT: A 406 ASP cc_start: 0.8743 (m-30) cc_final: 0.8376 (m-30) REVERT: A 407 ILE cc_start: 0.9085 (mt) cc_final: 0.8703 (mt) REVERT: A 441 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8967 (mm-30) REVERT: A 469 HIS cc_start: 0.9140 (t-170) cc_final: 0.8811 (t-170) REVERT: A 490 THR cc_start: 0.9608 (m) cc_final: 0.8841 (m) REVERT: A 493 MET cc_start: 0.9092 (tmm) cc_final: 0.8800 (tmm) REVERT: A 494 MET cc_start: 0.9507 (mpp) cc_final: 0.9261 (mpp) REVERT: A 501 GLN cc_start: 0.9385 (tp40) cc_final: 0.8576 (tp40) REVERT: A 506 ILE cc_start: 0.9656 (mt) cc_final: 0.9416 (mt) REVERT: A 515 ASP cc_start: 0.9327 (m-30) cc_final: 0.8790 (m-30) REVERT: A 550 MET cc_start: 0.8659 (pmm) cc_final: 0.8145 (pmm) REVERT: A 561 LEU cc_start: 0.9650 (tp) cc_final: 0.9434 (tp) REVERT: A 570 MET cc_start: 0.9255 (mtp) cc_final: 0.8841 (mtp) REVERT: A 599 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8093 (tm-30) REVERT: A 628 GLU cc_start: 0.9247 (mt-10) cc_final: 0.9034 (mt-10) REVERT: A 640 MET cc_start: 0.9456 (tpp) cc_final: 0.9075 (tpp) REVERT: A 675 HIS cc_start: 0.9297 (t-90) cc_final: 0.8933 (t70) REVERT: B 8 LYS cc_start: 0.9345 (tptp) cc_final: 0.9067 (tptp) REVERT: B 30 LYS cc_start: 0.9777 (tmtt) cc_final: 0.9379 (tptt) REVERT: B 95 MET cc_start: 0.9336 (tpp) cc_final: 0.8982 (mmm) REVERT: B 99 LYS cc_start: 0.9548 (mmmt) cc_final: 0.9195 (mttp) REVERT: B 106 LEU cc_start: 0.9224 (tt) cc_final: 0.9003 (tt) REVERT: B 119 GLU cc_start: 0.9284 (mp0) cc_final: 0.8826 (mp0) REVERT: B 124 ILE cc_start: 0.9581 (mm) cc_final: 0.9323 (mm) REVERT: B 139 GLU cc_start: 0.9455 (mp0) cc_final: 0.9242 (mp0) REVERT: B 168 VAL cc_start: 0.9467 (t) cc_final: 0.9186 (m) REVERT: B 184 ARG cc_start: 0.9272 (mmm-85) cc_final: 0.9069 (mmm-85) REVERT: B 199 VAL cc_start: 0.9029 (t) cc_final: 0.8759 (p) REVERT: B 211 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8194 (mm-30) REVERT: B 235 ARG cc_start: 0.8748 (ttm110) cc_final: 0.8108 (ttm110) REVERT: B 250 TYR cc_start: 0.8746 (m-80) cc_final: 0.7566 (m-80) REVERT: B 263 ASP cc_start: 0.9228 (m-30) cc_final: 0.8834 (m-30) REVERT: B 266 LYS cc_start: 0.9083 (mtmm) cc_final: 0.8785 (ptpp) REVERT: B 283 VAL cc_start: 0.9529 (t) cc_final: 0.9221 (t) REVERT: B 291 LEU cc_start: 0.9557 (mt) cc_final: 0.9350 (mt) REVERT: B 322 MET cc_start: 0.8785 (mmm) cc_final: 0.8434 (mmm) REVERT: B 359 MET cc_start: 0.8946 (ttt) cc_final: 0.8456 (tmm) REVERT: B 375 LYS cc_start: 0.9291 (mmmm) cc_final: 0.9013 (mmmm) REVERT: B 379 SER cc_start: 0.9157 (t) cc_final: 0.8556 (t) REVERT: B 390 GLN cc_start: 0.9137 (mm110) cc_final: 0.8732 (mm-40) REVERT: B 410 ASN cc_start: 0.9062 (m-40) cc_final: 0.8747 (m-40) REVERT: B 415 ASN cc_start: 0.9285 (t0) cc_final: 0.8900 (t0) REVERT: B 420 MET cc_start: 0.9456 (mmm) cc_final: 0.9089 (mmm) REVERT: B 458 MET cc_start: 0.9531 (mmm) cc_final: 0.9286 (mmm) REVERT: B 493 MET cc_start: 0.9230 (ppp) cc_final: 0.8947 (ppp) REVERT: B 494 MET cc_start: 0.9513 (mtt) cc_final: 0.9184 (mtt) REVERT: B 574 TYR cc_start: 0.8918 (m-10) cc_final: 0.8660 (m-80) REVERT: B 598 MET cc_start: 0.9407 (mtm) cc_final: 0.9058 (mtm) REVERT: B 602 GLU cc_start: 0.8182 (mp0) cc_final: 0.7244 (mp0) REVERT: B 612 TYR cc_start: 0.8828 (m-80) cc_final: 0.7910 (m-80) REVERT: B 613 TYR cc_start: 0.9080 (t80) cc_final: 0.7858 (t80) REVERT: B 615 MET cc_start: 0.9015 (mmp) cc_final: 0.8169 (mmp) REVERT: B 631 ASP cc_start: 0.9361 (t70) cc_final: 0.9110 (t0) REVERT: B 636 LYS cc_start: 0.9636 (mptt) cc_final: 0.9311 (mmtt) REVERT: B 639 ASP cc_start: 0.9295 (m-30) cc_final: 0.8809 (m-30) REVERT: B 640 MET cc_start: 0.9385 (tpp) cc_final: 0.8859 (tpp) REVERT: B 667 LEU cc_start: 0.9597 (tp) cc_final: 0.9388 (tp) REVERT: B 673 TYR cc_start: 0.9107 (t80) cc_final: 0.8737 (t80) REVERT: B 679 ILE cc_start: 0.9565 (mm) cc_final: 0.9322 (mm) REVERT: C 17 PHE cc_start: 0.8400 (p90) cc_final: 0.7400 (p90) REVERT: C 20 MET cc_start: 0.8951 (ptp) cc_final: 0.8699 (ptp) REVERT: C 21 PHE cc_start: 0.9090 (m-10) cc_final: 0.8382 (m-80) REVERT: C 72 THR cc_start: 0.7701 (m) cc_final: 0.7454 (p) REVERT: C 105 TYR cc_start: 0.8854 (m-80) cc_final: 0.8401 (m-80) REVERT: C 112 LEU cc_start: 0.7242 (mt) cc_final: 0.6957 (pp) REVERT: C 122 PHE cc_start: 0.8697 (m-80) cc_final: 0.8342 (m-80) REVERT: C 157 MET cc_start: 0.9614 (mtm) cc_final: 0.9302 (ttp) REVERT: C 178 PHE cc_start: 0.9205 (m-80) cc_final: 0.8958 (m-10) REVERT: C 204 TYR cc_start: 0.9045 (t80) cc_final: 0.8542 (t80) REVERT: C 263 ASN cc_start: 0.6917 (m110) cc_final: 0.6663 (t0) REVERT: D 21 PHE cc_start: 0.8785 (m-10) cc_final: 0.8538 (m-10) REVERT: D 109 PHE cc_start: 0.8659 (m-80) cc_final: 0.7940 (m-80) REVERT: D 112 LEU cc_start: 0.8627 (mm) cc_final: 0.7810 (pp) REVERT: D 166 PHE cc_start: 0.8163 (t80) cc_final: 0.7826 (t80) REVERT: D 169 TYR cc_start: 0.9037 (m-10) cc_final: 0.8532 (m-80) REVERT: D 172 PHE cc_start: 0.9377 (m-80) cc_final: 0.9144 (m-80) REVERT: D 181 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.6483 (pt0) REVERT: D 185 MET cc_start: 0.4748 (mmm) cc_final: 0.4449 (mmp) REVERT: D 189 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8400 (pm20) REVERT: D 244 GLU cc_start: 0.9240 (mp0) cc_final: 0.9013 (mm-30) outliers start: 2 outliers final: 0 residues processed: 677 average time/residue: 0.1286 time to fit residues: 130.5467 Evaluate side-chains 582 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 580 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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: 3.9990 chunk 183 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 172 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 136 optimal weight: 0.0980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 255 HIS ** 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 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN A 675 HIS ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.111432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.081427 restraints weight = 50229.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.084632 restraints weight = 30584.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.086911 restraints weight = 21060.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.088517 restraints weight = 15705.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.089766 restraints weight = 12459.162| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.6999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16386 Z= 0.137 Angle : 0.602 9.180 22134 Z= 0.323 Chirality : 0.043 0.246 2360 Planarity : 0.004 0.076 2818 Dihedral : 10.582 178.210 2242 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.17 % Allowed : 1.22 % Favored : 98.60 % 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: 0.73 (0.18), residues: 1932 helix: 0.99 (0.15), residues: 1146 sheet: -0.23 (0.43), residues: 140 loop : -0.06 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 686 TYR 0.029 0.002 TYR D 174 PHE 0.043 0.002 PHE D 320 TRP 0.052 0.002 TRP D 124 HIS 0.013 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00301 (16386) covalent geometry : angle 0.60224 (22134) hydrogen bonds : bond 0.03959 ( 871) hydrogen bonds : angle 5.09519 ( 2571) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 696 time to evaluate : 0.522 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: A 8 LYS cc_start: 0.9197 (tptp) cc_final: 0.8765 (tppt) REVERT: A 15 GLU cc_start: 0.9219 (tp30) cc_final: 0.8690 (tp30) REVERT: A 29 ASP cc_start: 0.9326 (t0) cc_final: 0.9070 (t70) REVERT: A 116 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7756 (tt0) REVERT: A 119 GLU cc_start: 0.9051 (mp0) cc_final: 0.8737 (mp0) REVERT: A 144 MET cc_start: 0.8647 (mtm) cc_final: 0.8264 (mtm) REVERT: A 147 GLN cc_start: 0.8789 (mt0) cc_final: 0.8459 (mt0) REVERT: A 172 LEU cc_start: 0.9359 (mp) cc_final: 0.9042 (mp) REVERT: A 187 ASP cc_start: 0.9369 (t70) cc_final: 0.8906 (t70) REVERT: A 190 MET cc_start: 0.9149 (mtp) cc_final: 0.8905 (mtp) REVERT: A 191 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8461 (mp10) REVERT: A 199 VAL cc_start: 0.9581 (t) cc_final: 0.9053 (t) REVERT: A 235 ARG cc_start: 0.8495 (mtm110) cc_final: 0.8268 (mtm110) REVERT: A 236 TYR cc_start: 0.8919 (t80) cc_final: 0.8295 (t80) REVERT: A 279 SER cc_start: 0.7891 (m) cc_final: 0.7552 (p) REVERT: A 280 ILE cc_start: 0.8590 (pt) cc_final: 0.8082 (mp) REVERT: A 283 VAL cc_start: 0.9196 (t) cc_final: 0.8927 (t) REVERT: A 286 ASP cc_start: 0.9102 (m-30) cc_final: 0.8901 (m-30) REVERT: A 316 GLU cc_start: 0.9457 (tt0) cc_final: 0.9139 (tt0) REVERT: A 322 MET cc_start: 0.9203 (mmp) cc_final: 0.8895 (tpp) REVERT: A 359 MET cc_start: 0.8962 (ttp) cc_final: 0.8475 (ttp) REVERT: A 362 ASP cc_start: 0.8949 (m-30) cc_final: 0.8668 (m-30) REVERT: A 370 ASN cc_start: 0.9531 (m-40) cc_final: 0.9141 (m110) REVERT: A 375 LYS cc_start: 0.9048 (mmmt) cc_final: 0.8616 (mmtm) REVERT: A 377 LYS cc_start: 0.8852 (mttt) cc_final: 0.8279 (mttp) REVERT: A 381 LEU cc_start: 0.8974 (tp) cc_final: 0.8549 (pt) REVERT: A 398 ASP cc_start: 0.8567 (p0) cc_final: 0.8140 (p0) REVERT: A 403 ILE cc_start: 0.8887 (tp) cc_final: 0.8600 (tp) REVERT: A 406 ASP cc_start: 0.8726 (m-30) cc_final: 0.8411 (m-30) REVERT: A 407 ILE cc_start: 0.9088 (mt) cc_final: 0.8687 (mt) REVERT: A 426 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8762 (tm-30) REVERT: A 444 ASP cc_start: 0.9113 (t0) cc_final: 0.8614 (t0) REVERT: A 469 HIS cc_start: 0.8868 (t-170) cc_final: 0.8647 (t-170) REVERT: A 490 THR cc_start: 0.9574 (m) cc_final: 0.8688 (m) REVERT: A 493 MET cc_start: 0.9113 (tmm) cc_final: 0.8589 (tmm) REVERT: A 494 MET cc_start: 0.9566 (mpp) cc_final: 0.9004 (mmm) REVERT: A 501 GLN cc_start: 0.9395 (tp40) cc_final: 0.9123 (mm-40) REVERT: A 510 LYS cc_start: 0.9409 (mtpp) cc_final: 0.9198 (mtmm) REVERT: A 515 ASP cc_start: 0.9280 (m-30) cc_final: 0.8927 (m-30) REVERT: A 550 MET cc_start: 0.8725 (pmm) cc_final: 0.8397 (pmm) REVERT: A 598 MET cc_start: 0.8734 (ttt) cc_final: 0.8026 (ttt) REVERT: A 599 GLU cc_start: 0.8322 (tm-30) cc_final: 0.8082 (tm-30) REVERT: A 628 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8824 (mm-30) REVERT: A 632 MET cc_start: 0.8537 (mtp) cc_final: 0.8231 (mtp) REVERT: A 640 MET cc_start: 0.9418 (tpp) cc_final: 0.9133 (tpp) REVERT: A 653 SER cc_start: 0.8939 (p) cc_final: 0.8578 (p) REVERT: A 675 HIS cc_start: 0.9132 (t70) cc_final: 0.8869 (t70) REVERT: A 686 ARG cc_start: 0.7515 (mmm160) cc_final: 0.7252 (mmm160) REVERT: B 8 LYS cc_start: 0.9406 (tptp) cc_final: 0.9125 (tptp) REVERT: B 30 LYS cc_start: 0.9775 (tmtt) cc_final: 0.9374 (tptt) REVERT: B 41 ILE cc_start: 0.9603 (mm) cc_final: 0.9398 (mt) REVERT: B 82 LYS cc_start: 0.9545 (ptpp) cc_final: 0.9216 (ptpt) REVERT: B 95 MET cc_start: 0.9215 (tpp) cc_final: 0.8427 (tpp) REVERT: B 99 LYS cc_start: 0.9530 (mmmt) cc_final: 0.8985 (mmmt) REVERT: B 106 LEU cc_start: 0.9286 (tt) cc_final: 0.9075 (tt) REVERT: B 116 GLU cc_start: 0.8198 (tt0) cc_final: 0.7611 (tp30) REVERT: B 117 ARG cc_start: 0.8885 (mtp180) cc_final: 0.8594 (mmt180) REVERT: B 119 GLU cc_start: 0.9140 (mp0) cc_final: 0.8718 (mp0) REVERT: B 120 ASP cc_start: 0.9472 (m-30) cc_final: 0.9040 (m-30) REVERT: B 124 ILE cc_start: 0.9507 (mm) cc_final: 0.9286 (mm) REVERT: B 144 MET cc_start: 0.9381 (mtm) cc_final: 0.9160 (mtm) REVERT: B 184 ARG cc_start: 0.9314 (mmm-85) cc_final: 0.9064 (mmm-85) REVERT: B 187 ASP cc_start: 0.9430 (t70) cc_final: 0.9192 (t0) REVERT: B 211 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8376 (mm-30) REVERT: B 227 MET cc_start: 0.9319 (mtp) cc_final: 0.8956 (mtp) REVERT: B 235 ARG cc_start: 0.8760 (ttm110) cc_final: 0.8210 (ttm110) REVERT: B 250 TYR cc_start: 0.8592 (m-80) cc_final: 0.7375 (m-80) REVERT: B 263 ASP cc_start: 0.9275 (m-30) cc_final: 0.8949 (m-30) REVERT: B 283 VAL cc_start: 0.9535 (t) cc_final: 0.9131 (t) REVERT: B 286 ASP cc_start: 0.8941 (m-30) cc_final: 0.8430 (m-30) REVERT: B 291 LEU cc_start: 0.9538 (mt) cc_final: 0.9314 (mt) REVERT: B 322 MET cc_start: 0.8756 (mmm) cc_final: 0.8418 (mmm) REVERT: B 350 ARG cc_start: 0.8431 (mtp85) cc_final: 0.7728 (mtp85) REVERT: B 359 MET cc_start: 0.9006 (ttt) cc_final: 0.8568 (tmm) REVERT: B 375 LYS cc_start: 0.9251 (mmmm) cc_final: 0.8999 (mmmm) REVERT: B 379 SER cc_start: 0.9099 (t) cc_final: 0.8492 (t) REVERT: B 390 GLN cc_start: 0.9184 (mm110) cc_final: 0.8822 (mm-40) REVERT: B 410 ASN cc_start: 0.8976 (m-40) cc_final: 0.8694 (m-40) REVERT: B 415 ASN cc_start: 0.9423 (t0) cc_final: 0.9047 (t0) REVERT: B 419 VAL cc_start: 0.9598 (p) cc_final: 0.9308 (p) REVERT: B 420 MET cc_start: 0.9507 (mmm) cc_final: 0.9146 (mmm) REVERT: B 425 ILE cc_start: 0.9349 (mp) cc_final: 0.9075 (mp) REVERT: B 446 ARG cc_start: 0.9148 (mmm-85) cc_final: 0.8693 (mmm-85) REVERT: B 458 MET cc_start: 0.9460 (mmm) cc_final: 0.9126 (mmm) REVERT: B 460 SER cc_start: 0.9587 (m) cc_final: 0.9135 (m) REVERT: B 468 LEU cc_start: 0.9551 (tp) cc_final: 0.9265 (tp) REVERT: B 493 MET cc_start: 0.9199 (ppp) cc_final: 0.8975 (ppp) REVERT: B 494 MET cc_start: 0.9521 (mtt) cc_final: 0.9277 (mtt) REVERT: B 598 MET cc_start: 0.9432 (mtm) cc_final: 0.9084 (mtm) REVERT: B 612 TYR cc_start: 0.8893 (m-80) cc_final: 0.7771 (m-80) REVERT: B 613 TYR cc_start: 0.9072 (t80) cc_final: 0.7966 (t80) REVERT: B 615 MET cc_start: 0.9022 (mmp) cc_final: 0.8481 (mmp) REVERT: B 631 ASP cc_start: 0.9388 (t70) cc_final: 0.9110 (t0) REVERT: B 640 MET cc_start: 0.9377 (tpp) cc_final: 0.8878 (tpp) REVERT: B 645 GLN cc_start: 0.9107 (tp-100) cc_final: 0.8895 (tp-100) REVERT: B 648 ILE cc_start: 0.9272 (mm) cc_final: 0.8919 (mm) REVERT: B 675 HIS cc_start: 0.9343 (t-90) cc_final: 0.9138 (t-90) REVERT: B 679 ILE cc_start: 0.9590 (mm) cc_final: 0.9372 (mm) REVERT: C 17 PHE cc_start: 0.8195 (p90) cc_final: 0.7356 (p90) REVERT: C 20 MET cc_start: 0.8920 (ptp) cc_final: 0.8703 (ptp) REVERT: C 21 PHE cc_start: 0.9054 (m-10) cc_final: 0.8532 (m-80) REVERT: C 105 TYR cc_start: 0.8928 (m-80) cc_final: 0.8451 (m-80) REVERT: C 112 LEU cc_start: 0.7623 (mt) cc_final: 0.7344 (pp) REVERT: C 122 PHE cc_start: 0.8660 (m-80) cc_final: 0.8292 (m-10) REVERT: C 204 TYR cc_start: 0.9002 (t80) cc_final: 0.8501 (t80) REVERT: C 239 GLU cc_start: 0.8616 (pt0) cc_final: 0.8359 (pt0) REVERT: D 21 PHE cc_start: 0.8770 (m-10) cc_final: 0.8563 (m-10) REVERT: D 109 PHE cc_start: 0.8609 (m-80) cc_final: 0.7890 (m-80) REVERT: D 112 LEU cc_start: 0.8650 (mm) cc_final: 0.7826 (pp) REVERT: D 166 PHE cc_start: 0.7984 (t80) cc_final: 0.7761 (t80) REVERT: D 169 TYR cc_start: 0.9063 (m-10) cc_final: 0.8522 (m-80) REVERT: D 172 PHE cc_start: 0.9352 (m-80) cc_final: 0.9047 (m-80) REVERT: D 211 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8946 (mt-10) outliers start: 3 outliers final: 3 residues processed: 699 average time/residue: 0.1270 time to fit residues: 133.5195 Evaluate side-chains 606 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 603 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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: 8.9990 chunk 51 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 186 optimal weight: 0.9990 chunk 140 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 313 HIS ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 ASN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.108967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.080099 restraints weight = 51870.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.083208 restraints weight = 31048.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.085421 restraints weight = 21168.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.086693 restraints weight = 15668.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.087977 restraints weight = 12732.160| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.7368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16386 Z= 0.207 Angle : 0.670 12.874 22134 Z= 0.358 Chirality : 0.044 0.203 2360 Planarity : 0.004 0.071 2818 Dihedral : 10.708 177.653 2242 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: 0.70 (0.18), residues: 1932 helix: 0.98 (0.15), residues: 1141 sheet: -0.12 (0.45), residues: 128 loop : -0.16 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 163 TYR 0.044 0.002 TYR C 142 PHE 0.038 0.002 PHE C 168 TRP 0.055 0.003 TRP D 124 HIS 0.016 0.002 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00444 (16386) covalent geometry : angle 0.66952 (22134) hydrogen bonds : bond 0.04177 ( 871) hydrogen bonds : angle 5.24279 ( 2571) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 663 time to evaluate : 0.566 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: 0.9230 (tptp) cc_final: 0.8801 (tppt) REVERT: A 15 GLU cc_start: 0.9143 (tp30) cc_final: 0.8805 (tp30) REVERT: A 116 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7652 (tt0) REVERT: A 119 GLU cc_start: 0.9099 (mp0) cc_final: 0.8789 (mp0) REVERT: A 120 ASP cc_start: 0.9190 (m-30) cc_final: 0.8968 (m-30) REVERT: A 136 LYS cc_start: 0.9610 (ttmm) cc_final: 0.9273 (ttpt) REVERT: A 144 MET cc_start: 0.8686 (mtm) cc_final: 0.8295 (mtm) REVERT: A 147 GLN cc_start: 0.8761 (mt0) cc_final: 0.8488 (mt0) REVERT: A 173 LEU cc_start: 0.9478 (mt) cc_final: 0.9221 (mt) REVERT: A 190 MET cc_start: 0.9165 (mtp) cc_final: 0.8921 (mtp) REVERT: A 191 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8504 (mm-40) REVERT: A 235 ARG cc_start: 0.8474 (mtm110) cc_final: 0.8055 (mtm110) REVERT: A 236 TYR cc_start: 0.8953 (t80) cc_final: 0.8371 (t80) REVERT: A 261 PHE cc_start: 0.9089 (t80) cc_final: 0.8859 (t80) REVERT: A 280 ILE cc_start: 0.8553 (pt) cc_final: 0.8216 (mp) REVERT: A 286 ASP cc_start: 0.9175 (m-30) cc_final: 0.8953 (m-30) REVERT: A 359 MET cc_start: 0.9018 (ttp) cc_final: 0.8632 (ttp) REVERT: A 362 ASP cc_start: 0.8973 (m-30) cc_final: 0.8718 (m-30) REVERT: A 370 ASN cc_start: 0.9548 (m-40) cc_final: 0.9236 (m110) REVERT: A 375 LYS cc_start: 0.8998 (mmmt) cc_final: 0.8506 (mmtm) REVERT: A 377 LYS cc_start: 0.8804 (mttt) cc_final: 0.8254 (mttp) REVERT: A 381 LEU cc_start: 0.8992 (tp) cc_final: 0.8571 (pt) REVERT: A 407 ILE cc_start: 0.9099 (mt) cc_final: 0.8746 (mt) REVERT: A 469 HIS cc_start: 0.8957 (t-170) cc_final: 0.8645 (t-170) REVERT: A 479 TYR cc_start: 0.8981 (t80) cc_final: 0.8623 (t80) REVERT: A 490 THR cc_start: 0.9493 (m) cc_final: 0.9196 (m) REVERT: A 494 MET cc_start: 0.9432 (mpp) cc_final: 0.9183 (mpp) REVERT: A 501 GLN cc_start: 0.9409 (tp40) cc_final: 0.9140 (mm-40) REVERT: A 515 ASP cc_start: 0.9398 (m-30) cc_final: 0.8880 (m-30) REVERT: A 599 GLU cc_start: 0.8313 (tm-30) cc_final: 0.8097 (tm-30) REVERT: A 628 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8803 (mm-30) REVERT: A 632 MET cc_start: 0.8532 (mtp) cc_final: 0.8266 (mtp) REVERT: A 636 LYS cc_start: 0.9799 (mmtp) cc_final: 0.9575 (mmmm) REVERT: A 640 MET cc_start: 0.9397 (tpp) cc_final: 0.9025 (tpp) REVERT: A 646 GLN cc_start: 0.9193 (pm20) cc_final: 0.8958 (pm20) REVERT: A 647 HIS cc_start: 0.9265 (m-70) cc_final: 0.7939 (m170) REVERT: A 675 HIS cc_start: 0.9224 (t70) cc_final: 0.8902 (t70) REVERT: B 8 LYS cc_start: 0.9408 (tptp) cc_final: 0.9136 (tptp) REVERT: B 30 LYS cc_start: 0.9799 (tmtt) cc_final: 0.9403 (tptt) REVERT: B 67 GLU cc_start: 0.8947 (mp0) cc_final: 0.8687 (mp0) REVERT: B 95 MET cc_start: 0.9148 (tpp) cc_final: 0.8578 (tpp) REVERT: B 119 GLU cc_start: 0.9223 (mp0) cc_final: 0.8772 (mp0) REVERT: B 147 GLN cc_start: 0.9484 (mt0) cc_final: 0.9209 (mt0) REVERT: B 184 ARG cc_start: 0.9297 (mmm-85) cc_final: 0.9074 (mmm-85) REVERT: B 187 ASP cc_start: 0.9488 (t70) cc_final: 0.9254 (t0) REVERT: B 211 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8422 (mm-30) REVERT: B 235 ARG cc_start: 0.8602 (ttm110) cc_final: 0.8157 (ttm110) REVERT: B 250 TYR cc_start: 0.8678 (m-80) cc_final: 0.7449 (m-80) REVERT: B 263 ASP cc_start: 0.9291 (m-30) cc_final: 0.8918 (m-30) REVERT: B 283 VAL cc_start: 0.9531 (t) cc_final: 0.9220 (t) REVERT: B 286 ASP cc_start: 0.9076 (m-30) cc_final: 0.8201 (m-30) REVERT: B 291 LEU cc_start: 0.9524 (mt) cc_final: 0.9284 (mt) REVERT: B 322 MET cc_start: 0.8726 (mmm) cc_final: 0.8415 (mmm) REVERT: B 359 MET cc_start: 0.9069 (ttt) cc_final: 0.8503 (tmm) REVERT: B 362 ASP cc_start: 0.8875 (m-30) cc_final: 0.7659 (m-30) REVERT: B 375 LYS cc_start: 0.9280 (mmmm) cc_final: 0.9008 (mmmm) REVERT: B 379 SER cc_start: 0.9160 (t) cc_final: 0.8583 (t) REVERT: B 390 GLN cc_start: 0.9223 (mm110) cc_final: 0.8910 (mm-40) REVERT: B 410 ASN cc_start: 0.9083 (m-40) cc_final: 0.8877 (m-40) REVERT: B 415 ASN cc_start: 0.9282 (t0) cc_final: 0.8833 (t0) REVERT: B 416 ILE cc_start: 0.9641 (mt) cc_final: 0.9438 (mt) REVERT: B 418 ASN cc_start: 0.9151 (m110) cc_final: 0.8891 (m110) REVERT: B 420 MET cc_start: 0.9517 (mmm) cc_final: 0.9063 (mmm) REVERT: B 458 MET cc_start: 0.9451 (mmm) cc_final: 0.9190 (mmm) REVERT: B 468 LEU cc_start: 0.9513 (tp) cc_final: 0.9234 (tp) REVERT: B 472 LEU cc_start: 0.9601 (mm) cc_final: 0.9371 (mm) REVERT: B 493 MET cc_start: 0.9179 (ppp) cc_final: 0.8872 (ppp) REVERT: B 494 MET cc_start: 0.9506 (mtt) cc_final: 0.9168 (mtt) REVERT: B 530 LYS cc_start: 0.9029 (ptmm) cc_final: 0.8808 (ptmm) REVERT: B 586 TYR cc_start: 0.9344 (m-80) cc_final: 0.8992 (m-80) REVERT: B 602 GLU cc_start: 0.8036 (mp0) cc_final: 0.6314 (mp0) REVERT: B 606 TYR cc_start: 0.8545 (m-80) cc_final: 0.7955 (m-80) REVERT: B 613 TYR cc_start: 0.9110 (t80) cc_final: 0.6985 (t80) REVERT: B 615 MET cc_start: 0.9009 (mmp) cc_final: 0.8224 (mmp) REVERT: B 631 ASP cc_start: 0.9395 (t70) cc_final: 0.9090 (t0) REVERT: B 636 LYS cc_start: 0.9624 (mptt) cc_final: 0.9311 (mmtt) REVERT: B 639 ASP cc_start: 0.9371 (m-30) cc_final: 0.8957 (m-30) REVERT: B 640 MET cc_start: 0.9353 (tpp) cc_final: 0.8812 (tpp) REVERT: B 641 ILE cc_start: 0.9725 (mm) cc_final: 0.9472 (mm) REVERT: B 673 TYR cc_start: 0.9139 (t80) cc_final: 0.8813 (t80) REVERT: B 675 HIS cc_start: 0.9294 (t-90) cc_final: 0.8983 (t-90) REVERT: B 679 ILE cc_start: 0.9597 (mm) cc_final: 0.9367 (mm) REVERT: C 17 PHE cc_start: 0.8404 (p90) cc_final: 0.7425 (p90) REVERT: C 20 MET cc_start: 0.8946 (ptp) cc_final: 0.8737 (ptp) REVERT: C 21 PHE cc_start: 0.8997 (m-10) cc_final: 0.8299 (m-80) REVERT: C 105 TYR cc_start: 0.8955 (m-80) cc_final: 0.8529 (m-80) REVERT: C 112 LEU cc_start: 0.7669 (mt) cc_final: 0.7377 (pp) REVERT: C 122 PHE cc_start: 0.8686 (m-80) cc_final: 0.8376 (m-80) REVERT: C 157 MET cc_start: 0.9619 (ptm) cc_final: 0.9106 (ppp) REVERT: C 204 TYR cc_start: 0.9038 (t80) cc_final: 0.8452 (t80) REVERT: C 208 LEU cc_start: 0.9419 (mt) cc_final: 0.9185 (mt) REVERT: C 239 GLU cc_start: 0.8438 (pt0) cc_final: 0.7932 (pt0) REVERT: D 21 PHE cc_start: 0.8818 (m-10) cc_final: 0.8553 (m-10) REVERT: D 109 PHE cc_start: 0.8561 (m-80) cc_final: 0.7863 (m-80) REVERT: D 112 LEU cc_start: 0.8708 (mm) cc_final: 0.7952 (pp) REVERT: D 157 MET cc_start: 0.9573 (ptm) cc_final: 0.8827 (ppp) REVERT: D 166 PHE cc_start: 0.7917 (t80) cc_final: 0.7585 (t80) REVERT: D 169 TYR cc_start: 0.9035 (m-10) cc_final: 0.8820 (m-80) REVERT: D 172 PHE cc_start: 0.9456 (m-80) cc_final: 0.9148 (m-80) REVERT: D 179 TYR cc_start: 0.8289 (t80) cc_final: 0.7950 (t80) REVERT: D 205 VAL cc_start: 0.9671 (t) cc_final: 0.9425 (t) REVERT: D 211 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8852 (mt-10) REVERT: D 244 GLU cc_start: 0.9152 (mp0) cc_final: 0.8909 (mm-30) outliers start: 0 outliers final: 0 residues processed: 663 average time/residue: 0.1258 time to fit residues: 125.1156 Evaluate side-chains 580 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 580 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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: 10.0000 chunk 99 optimal weight: 7.9990 chunk 61 optimal weight: 0.0270 chunk 19 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 158 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 overall best weight: 1.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 HIS C 25 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.111174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.081915 restraints weight = 51544.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.085116 restraints weight = 30829.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.087344 restraints weight = 21040.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.089013 restraints weight = 15647.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.090188 restraints weight = 12276.066| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.7612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16386 Z= 0.169 Angle : 0.656 11.286 22134 Z= 0.349 Chirality : 0.044 0.227 2360 Planarity : 0.004 0.055 2818 Dihedral : 10.575 177.221 2242 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.18), residues: 1932 helix: 0.93 (0.15), residues: 1141 sheet: -0.33 (0.45), residues: 128 loop : -0.20 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 604 TYR 0.034 0.002 TYR C 142 PHE 0.044 0.002 PHE D 227 TRP 0.061 0.003 TRP D 124 HIS 0.012 0.002 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00369 (16386) covalent geometry : angle 0.65565 (22134) hydrogen bonds : bond 0.04089 ( 871) hydrogen bonds : angle 5.20037 ( 2571) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 665 time to evaluate : 0.651 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: 0.9239 (tptp) cc_final: 0.8782 (tppt) REVERT: A 15 GLU cc_start: 0.9214 (tp30) cc_final: 0.8755 (tp30) REVERT: A 116 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7648 (tt0) REVERT: A 119 GLU cc_start: 0.9086 (mp0) cc_final: 0.8811 (mp0) REVERT: A 136 LYS cc_start: 0.9605 (ttmm) cc_final: 0.9293 (ttpt) REVERT: A 144 MET cc_start: 0.8615 (mtm) cc_final: 0.8353 (mtm) REVERT: A 147 GLN cc_start: 0.8816 (mt0) cc_final: 0.8545 (mt0) REVERT: A 164 ARG cc_start: 0.7957 (ptm-80) cc_final: 0.6542 (ptm-80) REVERT: A 173 LEU cc_start: 0.9506 (mt) cc_final: 0.9286 (mt) REVERT: A 190 MET cc_start: 0.9147 (mtp) cc_final: 0.8944 (mtp) REVERT: A 191 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8572 (mm-40) REVERT: A 235 ARG cc_start: 0.8476 (mtm110) cc_final: 0.8054 (mtm110) REVERT: A 236 TYR cc_start: 0.8919 (t80) cc_final: 0.8348 (t80) REVERT: A 261 PHE cc_start: 0.9131 (t80) cc_final: 0.8914 (t80) REVERT: A 280 ILE cc_start: 0.8583 (pt) cc_final: 0.8196 (mp) REVERT: A 286 ASP cc_start: 0.9259 (m-30) cc_final: 0.8895 (m-30) REVERT: A 322 MET cc_start: 0.9239 (mmm) cc_final: 0.8855 (tpp) REVERT: A 352 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8618 (tm-30) REVERT: A 359 MET cc_start: 0.9024 (ttp) cc_final: 0.8578 (ttp) REVERT: A 362 ASP cc_start: 0.8944 (m-30) cc_final: 0.8711 (m-30) REVERT: A 370 ASN cc_start: 0.9421 (m-40) cc_final: 0.9150 (m110) REVERT: A 375 LYS cc_start: 0.8978 (mmmt) cc_final: 0.8636 (mmtm) REVERT: A 377 LYS cc_start: 0.8696 (mttt) cc_final: 0.8109 (mttp) REVERT: A 381 LEU cc_start: 0.8992 (tp) cc_final: 0.8573 (pt) REVERT: A 407 ILE cc_start: 0.9087 (mt) cc_final: 0.8777 (mt) REVERT: A 469 HIS cc_start: 0.8923 (t-170) cc_final: 0.8633 (t-170) REVERT: A 479 TYR cc_start: 0.8831 (t80) cc_final: 0.8594 (t80) REVERT: A 490 THR cc_start: 0.9395 (m) cc_final: 0.8866 (m) REVERT: A 494 MET cc_start: 0.9337 (mpp) cc_final: 0.9051 (mpp) REVERT: A 501 GLN cc_start: 0.9413 (tp40) cc_final: 0.9129 (mm-40) REVERT: A 515 ASP cc_start: 0.9544 (m-30) cc_final: 0.9200 (m-30) REVERT: A 562 LYS cc_start: 0.9739 (ttmm) cc_final: 0.9342 (tttt) REVERT: A 598 MET cc_start: 0.8869 (ttt) cc_final: 0.8193 (ttt) REVERT: A 628 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8887 (mm-30) REVERT: A 632 MET cc_start: 0.8484 (mtp) cc_final: 0.8270 (mtp) REVERT: A 636 LYS cc_start: 0.9792 (mmtp) cc_final: 0.9561 (mmmm) REVERT: A 640 MET cc_start: 0.9437 (tpp) cc_final: 0.9080 (tpp) REVERT: A 645 GLN cc_start: 0.8859 (tp-100) cc_final: 0.8591 (tp-100) REVERT: A 646 GLN cc_start: 0.9162 (pm20) cc_final: 0.8885 (pm20) REVERT: A 647 HIS cc_start: 0.9290 (m-70) cc_final: 0.7795 (m170) REVERT: A 653 SER cc_start: 0.8711 (p) cc_final: 0.8462 (p) REVERT: A 655 THR cc_start: 0.9098 (m) cc_final: 0.8778 (t) REVERT: A 675 HIS cc_start: 0.9205 (t70) cc_final: 0.8884 (t70) REVERT: B 30 LYS cc_start: 0.9808 (tmtt) cc_final: 0.9413 (tptt) REVERT: B 67 GLU cc_start: 0.9186 (mp0) cc_final: 0.8953 (mp0) REVERT: B 82 LYS cc_start: 0.9514 (ptpp) cc_final: 0.9176 (ptpt) REVERT: B 95 MET cc_start: 0.9282 (tpp) cc_final: 0.8639 (tpp) REVERT: B 119 GLU cc_start: 0.9217 (mp0) cc_final: 0.8801 (mp0) REVERT: B 120 ASP cc_start: 0.9435 (m-30) cc_final: 0.9219 (m-30) REVERT: B 144 MET cc_start: 0.9315 (mtm) cc_final: 0.9078 (mtm) REVERT: B 147 GLN cc_start: 0.9503 (mt0) cc_final: 0.9232 (mt0) REVERT: B 184 ARG cc_start: 0.9288 (mmm-85) cc_final: 0.9059 (mmm-85) REVERT: B 187 ASP cc_start: 0.9467 (t70) cc_final: 0.9211 (t0) REVERT: B 211 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8416 (mm-30) REVERT: B 235 ARG cc_start: 0.8629 (ttm110) cc_final: 0.8194 (ttm110) REVERT: B 250 TYR cc_start: 0.8635 (m-80) cc_final: 0.7397 (m-80) REVERT: B 263 ASP cc_start: 0.9139 (m-30) cc_final: 0.8773 (m-30) REVERT: B 283 VAL cc_start: 0.9547 (t) cc_final: 0.9229 (t) REVERT: B 286 ASP cc_start: 0.8768 (m-30) cc_final: 0.7874 (m-30) REVERT: B 291 LEU cc_start: 0.9524 (mt) cc_final: 0.9285 (mt) REVERT: B 322 MET cc_start: 0.8686 (mmm) cc_final: 0.8342 (mmm) REVERT: B 348 MET cc_start: 0.9059 (tpt) cc_final: 0.8661 (tpp) REVERT: B 359 MET cc_start: 0.9063 (ttt) cc_final: 0.8520 (tmm) REVERT: B 362 ASP cc_start: 0.8684 (m-30) cc_final: 0.7550 (m-30) REVERT: B 375 LYS cc_start: 0.9271 (mmmm) cc_final: 0.8979 (mmmm) REVERT: B 379 SER cc_start: 0.9138 (t) cc_final: 0.8521 (t) REVERT: B 390 GLN cc_start: 0.9238 (mm110) cc_final: 0.8887 (mm-40) REVERT: B 410 ASN cc_start: 0.9133 (m-40) cc_final: 0.8871 (m-40) REVERT: B 415 ASN cc_start: 0.9452 (t0) cc_final: 0.8829 (t0) REVERT: B 418 ASN cc_start: 0.9171 (m110) cc_final: 0.8886 (m110) REVERT: B 420 MET cc_start: 0.9512 (mmm) cc_final: 0.9138 (mmm) REVERT: B 425 ILE cc_start: 0.9317 (mp) cc_final: 0.9055 (mp) REVERT: B 458 MET cc_start: 0.9554 (mmm) cc_final: 0.9181 (mmm) REVERT: B 469 HIS cc_start: 0.8889 (t-170) cc_final: 0.8639 (t70) REVERT: B 493 MET cc_start: 0.9145 (ppp) cc_final: 0.8853 (ppp) REVERT: B 494 MET cc_start: 0.9528 (mtt) cc_final: 0.9208 (mtt) REVERT: B 586 TYR cc_start: 0.9355 (m-80) cc_final: 0.9111 (m-10) REVERT: B 602 GLU cc_start: 0.7887 (mp0) cc_final: 0.6692 (mp0) REVERT: B 606 TYR cc_start: 0.8507 (m-80) cc_final: 0.7904 (m-80) REVERT: B 615 MET cc_start: 0.9047 (mmp) cc_final: 0.8406 (mmp) REVERT: B 631 ASP cc_start: 0.9358 (t70) cc_final: 0.9050 (t0) REVERT: B 639 ASP cc_start: 0.9392 (m-30) cc_final: 0.8863 (m-30) REVERT: B 640 MET cc_start: 0.9343 (tpp) cc_final: 0.8814 (tpp) REVERT: B 641 ILE cc_start: 0.9699 (mm) cc_final: 0.9454 (mm) REVERT: B 673 TYR cc_start: 0.9105 (t80) cc_final: 0.8702 (t80) REVERT: B 679 ILE cc_start: 0.9613 (mm) cc_final: 0.9324 (mm) REVERT: C 17 PHE cc_start: 0.8385 (p90) cc_final: 0.7685 (p90) REVERT: C 21 PHE cc_start: 0.8971 (m-10) cc_final: 0.8566 (m-80) REVERT: C 96 MET cc_start: 0.8423 (tpt) cc_final: 0.8189 (tpt) REVERT: C 105 TYR cc_start: 0.8974 (m-80) cc_final: 0.8496 (m-80) REVERT: C 112 LEU cc_start: 0.7586 (mt) cc_final: 0.7353 (pp) REVERT: C 122 PHE cc_start: 0.8667 (m-80) cc_final: 0.8325 (m-10) REVERT: C 157 MET cc_start: 0.9572 (ptm) cc_final: 0.9006 (ppp) REVERT: C 204 TYR cc_start: 0.9025 (t80) cc_final: 0.8632 (t80) REVERT: C 311 THR cc_start: 0.8201 (t) cc_final: 0.7585 (t) REVERT: C 313 GLU cc_start: 0.9355 (mt-10) cc_final: 0.8529 (mm-30) REVERT: D 21 PHE cc_start: 0.8638 (m-10) cc_final: 0.8420 (m-10) REVERT: D 96 MET cc_start: 0.8496 (mmp) cc_final: 0.8010 (mmp) REVERT: D 109 PHE cc_start: 0.8515 (m-80) cc_final: 0.7775 (m-80) REVERT: D 112 LEU cc_start: 0.8743 (mm) cc_final: 0.7973 (pp) REVERT: D 166 PHE cc_start: 0.7874 (t80) cc_final: 0.7573 (t80) REVERT: D 169 TYR cc_start: 0.9077 (m-10) cc_final: 0.8741 (m-80) REVERT: D 172 PHE cc_start: 0.9477 (m-80) cc_final: 0.9144 (m-80) REVERT: D 179 TYR cc_start: 0.8347 (t80) cc_final: 0.8014 (t80) REVERT: D 193 LEU cc_start: 0.9003 (mt) cc_final: 0.8689 (pp) REVERT: D 211 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8889 (mt-10) REVERT: D 244 GLU cc_start: 0.9117 (mp0) cc_final: 0.8874 (mm-30) outliers start: 0 outliers final: 0 residues processed: 665 average time/residue: 0.1258 time to fit residues: 125.4918 Evaluate side-chains 573 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 573 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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: 3.9990 chunk 133 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 114 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 100 optimal weight: 0.0470 chunk 88 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.112903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.084155 restraints weight = 51321.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.087307 restraints weight = 30250.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.089509 restraints weight = 20522.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.091104 restraints weight = 15172.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.092330 restraints weight = 11856.712| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.7861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16386 Z= 0.164 Angle : 0.674 10.548 22134 Z= 0.357 Chirality : 0.045 0.346 2360 Planarity : 0.004 0.049 2818 Dihedral : 10.526 176.834 2242 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 0.50 (0.19), residues: 1932 helix: 0.86 (0.15), residues: 1141 sheet: -0.65 (0.42), residues: 148 loop : -0.18 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 604 TYR 0.034 0.002 TYR D 174 PHE 0.032 0.002 PHE C 109 TRP 0.061 0.002 TRP D 124 HIS 0.013 0.002 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00359 (16386) covalent geometry : angle 0.67428 (22134) hydrogen bonds : bond 0.04078 ( 871) hydrogen bonds : angle 5.26287 ( 2571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 664 time to evaluate : 0.711 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: A 8 LYS cc_start: 0.9244 (tptp) cc_final: 0.8790 (tppt) REVERT: A 15 GLU cc_start: 0.9200 (tp30) cc_final: 0.8744 (tp30) REVERT: A 116 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7522 (tt0) REVERT: A 119 GLU cc_start: 0.9077 (mp0) cc_final: 0.8746 (mp0) REVERT: A 136 LYS cc_start: 0.9580 (ttmm) cc_final: 0.9276 (ttpt) REVERT: A 144 MET cc_start: 0.8564 (mtm) cc_final: 0.8297 (mtm) REVERT: A 147 GLN cc_start: 0.8794 (mt0) cc_final: 0.8513 (mt0) REVERT: A 164 ARG cc_start: 0.8003 (ptm-80) cc_final: 0.6538 (ptm-80) REVERT: A 173 LEU cc_start: 0.9490 (mt) cc_final: 0.9222 (mt) REVERT: A 190 MET cc_start: 0.9140 (mtp) cc_final: 0.8935 (mtp) REVERT: A 191 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8453 (mm-40) REVERT: A 221 LYS cc_start: 0.8941 (mmtm) cc_final: 0.8737 (mmtm) REVERT: A 236 TYR cc_start: 0.8951 (t80) cc_final: 0.8411 (t80) REVERT: A 261 PHE cc_start: 0.9126 (t80) cc_final: 0.8840 (t80) REVERT: A 280 ILE cc_start: 0.8587 (pt) cc_final: 0.8205 (mp) REVERT: A 286 ASP cc_start: 0.9191 (m-30) cc_final: 0.8816 (m-30) REVERT: A 307 TYR cc_start: 0.9549 (t80) cc_final: 0.9196 (t80) REVERT: A 322 MET cc_start: 0.9267 (mmm) cc_final: 0.8753 (tpp) REVERT: A 352 GLU cc_start: 0.9004 (tm-30) cc_final: 0.8707 (tm-30) REVERT: A 359 MET cc_start: 0.9007 (ttp) cc_final: 0.8387 (ttp) REVERT: A 362 ASP cc_start: 0.8918 (m-30) cc_final: 0.8692 (m-30) REVERT: A 370 ASN cc_start: 0.9399 (m-40) cc_final: 0.9120 (m110) REVERT: A 377 LYS cc_start: 0.8740 (mttt) cc_final: 0.8272 (mtmt) REVERT: A 381 LEU cc_start: 0.9035 (tp) cc_final: 0.8560 (pt) REVERT: A 469 HIS cc_start: 0.8851 (t-170) cc_final: 0.8592 (t-170) REVERT: A 479 TYR cc_start: 0.8732 (t80) cc_final: 0.8408 (t80) REVERT: A 515 ASP cc_start: 0.9454 (m-30) cc_final: 0.9168 (m-30) REVERT: A 562 LYS cc_start: 0.9745 (ttmm) cc_final: 0.9374 (tttt) REVERT: A 570 MET cc_start: 0.9195 (mtp) cc_final: 0.8788 (mtp) REVERT: A 598 MET cc_start: 0.8957 (ttt) cc_final: 0.8686 (ttt) REVERT: A 599 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8066 (tm-30) REVERT: A 636 LYS cc_start: 0.9788 (mmtp) cc_final: 0.9560 (mmmm) REVERT: A 640 MET cc_start: 0.9403 (tpp) cc_final: 0.8949 (tpp) REVERT: A 646 GLN cc_start: 0.9157 (pm20) cc_final: 0.8871 (pm20) REVERT: A 647 HIS cc_start: 0.9259 (m-70) cc_final: 0.7701 (m170) REVERT: A 655 THR cc_start: 0.9059 (m) cc_final: 0.8760 (t) REVERT: A 675 HIS cc_start: 0.9188 (t70) cc_final: 0.8832 (t70) REVERT: B 30 LYS cc_start: 0.9779 (tmtt) cc_final: 0.9360 (tptt) REVERT: B 67 GLU cc_start: 0.9174 (mp0) cc_final: 0.8908 (mp0) REVERT: B 82 LYS cc_start: 0.9518 (ptpp) cc_final: 0.9169 (ptpt) REVERT: B 95 MET cc_start: 0.9252 (tpp) cc_final: 0.8077 (tpp) REVERT: B 98 PHE cc_start: 0.9546 (t80) cc_final: 0.9219 (t80) REVERT: B 99 LYS cc_start: 0.9563 (mmmt) cc_final: 0.8896 (mmmt) REVERT: B 117 ARG cc_start: 0.8901 (mtp180) cc_final: 0.8578 (mmm160) REVERT: B 119 GLU cc_start: 0.9202 (mp0) cc_final: 0.8840 (mp0) REVERT: B 184 ARG cc_start: 0.9290 (mmm-85) cc_final: 0.9045 (mmm-85) REVERT: B 187 ASP cc_start: 0.9433 (t70) cc_final: 0.9200 (t0) REVERT: B 211 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8415 (mm-30) REVERT: B 227 MET cc_start: 0.9193 (ttp) cc_final: 0.8922 (ttp) REVERT: B 235 ARG cc_start: 0.8680 (ttm110) cc_final: 0.8201 (ttm110) REVERT: B 250 TYR cc_start: 0.8738 (m-80) cc_final: 0.7556 (m-80) REVERT: B 263 ASP cc_start: 0.9147 (m-30) cc_final: 0.8771 (m-30) REVERT: B 283 VAL cc_start: 0.9536 (t) cc_final: 0.9208 (t) REVERT: B 286 ASP cc_start: 0.8766 (m-30) cc_final: 0.8269 (m-30) REVERT: B 322 MET cc_start: 0.8653 (mmm) cc_final: 0.8279 (mmm) REVERT: B 359 MET cc_start: 0.9049 (ttt) cc_final: 0.8518 (tmm) REVERT: B 375 LYS cc_start: 0.9237 (mmmm) cc_final: 0.8952 (mmmm) REVERT: B 379 SER cc_start: 0.9124 (t) cc_final: 0.8574 (t) REVERT: B 390 GLN cc_start: 0.9223 (mm110) cc_final: 0.8848 (mm-40) REVERT: B 410 ASN cc_start: 0.9109 (m-40) cc_final: 0.8904 (m-40) REVERT: B 415 ASN cc_start: 0.9446 (t0) cc_final: 0.9063 (t0) REVERT: B 420 MET cc_start: 0.9490 (mmm) cc_final: 0.9125 (mmm) REVERT: B 425 ILE cc_start: 0.9321 (mp) cc_final: 0.9065 (mp) REVERT: B 458 MET cc_start: 0.9544 (mmm) cc_final: 0.9192 (mmm) REVERT: B 469 HIS cc_start: 0.8834 (t-170) cc_final: 0.8569 (t70) REVERT: B 472 LEU cc_start: 0.9527 (mm) cc_final: 0.9317 (mm) REVERT: B 493 MET cc_start: 0.9135 (ppp) cc_final: 0.8833 (ppp) REVERT: B 494 MET cc_start: 0.9510 (mtt) cc_final: 0.9178 (mtt) REVERT: B 585 SER cc_start: 0.9270 (p) cc_final: 0.9061 (p) REVERT: B 586 TYR cc_start: 0.9338 (m-80) cc_final: 0.9059 (m-10) REVERT: B 606 TYR cc_start: 0.8498 (m-80) cc_final: 0.7597 (m-80) REVERT: B 613 TYR cc_start: 0.9088 (t80) cc_final: 0.8082 (t80) REVERT: B 615 MET cc_start: 0.9050 (mmp) cc_final: 0.8563 (mmp) REVERT: B 631 ASP cc_start: 0.9357 (t70) cc_final: 0.9008 (t0) REVERT: B 640 MET cc_start: 0.9330 (tpp) cc_final: 0.8793 (tpp) REVERT: B 641 ILE cc_start: 0.9717 (mm) cc_final: 0.9486 (mm) REVERT: B 679 ILE cc_start: 0.9626 (mm) cc_final: 0.9398 (mm) REVERT: C 17 PHE cc_start: 0.8361 (p90) cc_final: 0.7737 (p90) REVERT: C 20 MET cc_start: 0.8901 (ptp) cc_final: 0.8692 (pmm) REVERT: C 21 PHE cc_start: 0.9014 (m-10) cc_final: 0.8419 (m-80) REVERT: C 96 MET cc_start: 0.8448 (tpt) cc_final: 0.8066 (tpt) REVERT: C 105 TYR cc_start: 0.8927 (m-80) cc_final: 0.8473 (m-80) REVERT: C 112 LEU cc_start: 0.7607 (mt) cc_final: 0.7389 (pp) REVERT: C 122 PHE cc_start: 0.8614 (m-80) cc_final: 0.8307 (m-80) REVERT: C 157 MET cc_start: 0.9564 (ptm) cc_final: 0.8966 (ppp) REVERT: C 172 PHE cc_start: 0.9273 (m-80) cc_final: 0.8955 (m-80) REVERT: C 204 TYR cc_start: 0.8979 (t80) cc_final: 0.8598 (t80) REVERT: C 311 THR cc_start: 0.8182 (t) cc_final: 0.7519 (t) REVERT: C 313 GLU cc_start: 0.9375 (mt-10) cc_final: 0.8576 (mm-30) REVERT: D 21 PHE cc_start: 0.8618 (m-10) cc_final: 0.8358 (m-10) REVERT: D 109 PHE cc_start: 0.8465 (m-80) cc_final: 0.7740 (m-80) REVERT: D 112 LEU cc_start: 0.8768 (mm) cc_final: 0.8004 (pp) REVERT: D 157 MET cc_start: 0.9542 (ptm) cc_final: 0.9323 (ppp) REVERT: D 166 PHE cc_start: 0.7846 (t80) cc_final: 0.7469 (t80) REVERT: D 169 TYR cc_start: 0.9047 (m-10) cc_final: 0.8717 (m-80) REVERT: D 172 PHE cc_start: 0.9418 (m-80) cc_final: 0.9086 (m-80) REVERT: D 179 TYR cc_start: 0.8368 (t80) cc_final: 0.7977 (t80) REVERT: D 244 GLU cc_start: 0.9109 (mp0) cc_final: 0.8851 (mm-30) REVERT: D 318 ASP cc_start: 0.9153 (t0) cc_final: 0.8854 (t70) outliers start: 0 outliers final: 0 residues processed: 664 average time/residue: 0.1238 time to fit residues: 123.4313 Evaluate side-chains 572 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 572 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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: 0.9990 chunk 62 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 189 optimal weight: 8.9990 chunk 181 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 chunk 16 optimal weight: 0.4980 chunk 54 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 50 optimal weight: 0.3980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 313 HIS ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.113958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.085080 restraints weight = 51184.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.088232 restraints weight = 30377.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.090397 restraints weight = 20590.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.092112 restraints weight = 15345.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.093334 restraints weight = 11947.799| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.8043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16386 Z= 0.157 Angle : 0.674 9.775 22134 Z= 0.358 Chirality : 0.045 0.373 2360 Planarity : 0.004 0.049 2818 Dihedral : 10.466 175.648 2242 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: 0.42 (0.18), residues: 1932 helix: 0.82 (0.15), residues: 1147 sheet: -0.51 (0.44), residues: 132 loop : -0.33 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 604 TYR 0.035 0.002 TYR D 174 PHE 0.031 0.002 PHE C 168 TRP 0.059 0.003 TRP D 124 HIS 0.014 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00348 (16386) covalent geometry : angle 0.67412 (22134) hydrogen bonds : bond 0.04075 ( 871) hydrogen bonds : angle 5.24398 ( 2571) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 668 time to evaluate : 0.611 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: A 8 LYS cc_start: 0.9243 (tptp) cc_final: 0.8772 (tppt) REVERT: A 15 GLU cc_start: 0.9222 (tp30) cc_final: 0.8757 (tp30) REVERT: A 116 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7530 (tt0) REVERT: A 119 GLU cc_start: 0.9069 (mp0) cc_final: 0.8761 (mp0) REVERT: A 136 LYS cc_start: 0.9574 (ttmm) cc_final: 0.9245 (ttpt) REVERT: A 144 MET cc_start: 0.8554 (mtm) cc_final: 0.8310 (mtm) REVERT: A 147 GLN cc_start: 0.8819 (mt0) cc_final: 0.8541 (mt0) REVERT: A 164 ARG cc_start: 0.8088 (ptm-80) cc_final: 0.6657 (ptm-80) REVERT: A 190 MET cc_start: 0.9128 (mtp) cc_final: 0.8903 (mtp) REVERT: A 221 LYS cc_start: 0.8952 (mmtm) cc_final: 0.8724 (mmtm) REVERT: A 236 TYR cc_start: 0.8952 (t80) cc_final: 0.8296 (t80) REVERT: A 261 PHE cc_start: 0.9144 (t80) cc_final: 0.8894 (t80) REVERT: A 280 ILE cc_start: 0.8559 (pt) cc_final: 0.8182 (mp) REVERT: A 286 ASP cc_start: 0.9239 (m-30) cc_final: 0.8844 (m-30) REVERT: A 307 TYR cc_start: 0.9535 (t80) cc_final: 0.9200 (t80) REVERT: A 322 MET cc_start: 0.9291 (mmm) cc_final: 0.8810 (tpp) REVERT: A 345 LYS cc_start: 0.8978 (tttt) cc_final: 0.8755 (tttt) REVERT: A 349 LEU cc_start: 0.9484 (mt) cc_final: 0.9215 (mt) REVERT: A 352 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8692 (tm-30) REVERT: A 359 MET cc_start: 0.8986 (ttp) cc_final: 0.8426 (ttp) REVERT: A 362 ASP cc_start: 0.8894 (m-30) cc_final: 0.8667 (m-30) REVERT: A 370 ASN cc_start: 0.9303 (m-40) cc_final: 0.8966 (m110) REVERT: A 377 LYS cc_start: 0.8593 (mttt) cc_final: 0.8110 (mtmt) REVERT: A 381 LEU cc_start: 0.9110 (tp) cc_final: 0.8663 (pt) REVERT: A 515 ASP cc_start: 0.9409 (m-30) cc_final: 0.9129 (m-30) REVERT: A 562 LYS cc_start: 0.9750 (ttmm) cc_final: 0.9529 (ttmm) REVERT: A 570 MET cc_start: 0.9234 (mtp) cc_final: 0.8849 (mtp) REVERT: A 598 MET cc_start: 0.9198 (ttt) cc_final: 0.8888 (ttt) REVERT: A 636 LYS cc_start: 0.9786 (mmtp) cc_final: 0.9557 (mmmm) REVERT: A 640 MET cc_start: 0.9419 (tpp) cc_final: 0.9103 (tpp) REVERT: A 646 GLN cc_start: 0.9164 (pm20) cc_final: 0.8819 (pm20) REVERT: A 647 HIS cc_start: 0.9214 (m-70) cc_final: 0.7657 (m170) REVERT: A 653 SER cc_start: 0.9004 (p) cc_final: 0.8724 (p) REVERT: A 655 THR cc_start: 0.9089 (m) cc_final: 0.8848 (t) REVERT: A 658 LEU cc_start: 0.9308 (mt) cc_final: 0.9094 (mt) REVERT: A 675 HIS cc_start: 0.9146 (t70) cc_final: 0.8788 (t70) REVERT: A 686 ARG cc_start: 0.7326 (tpt170) cc_final: 0.7105 (tpt170) REVERT: B 30 LYS cc_start: 0.9773 (tmtt) cc_final: 0.9346 (tptt) REVERT: B 67 GLU cc_start: 0.9196 (mp0) cc_final: 0.8914 (mp0) REVERT: B 82 LYS cc_start: 0.9531 (ptpp) cc_final: 0.9156 (ptpp) REVERT: B 95 MET cc_start: 0.9256 (tpp) cc_final: 0.8342 (tpp) REVERT: B 98 PHE cc_start: 0.9533 (t80) cc_final: 0.9213 (t80) REVERT: B 119 GLU cc_start: 0.9179 (mp0) cc_final: 0.8800 (mp0) REVERT: B 120 ASP cc_start: 0.9430 (m-30) cc_final: 0.9186 (m-30) REVERT: B 144 MET cc_start: 0.9390 (mtm) cc_final: 0.9067 (mtm) REVERT: B 147 GLN cc_start: 0.9513 (mt0) cc_final: 0.9247 (mt0) REVERT: B 184 ARG cc_start: 0.9298 (mmm-85) cc_final: 0.9042 (mmm-85) REVERT: B 187 ASP cc_start: 0.9420 (t70) cc_final: 0.9203 (t0) REVERT: B 211 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8376 (mm-30) REVERT: B 227 MET cc_start: 0.9178 (ttp) cc_final: 0.8927 (ttp) REVERT: B 235 ARG cc_start: 0.8711 (ttm110) cc_final: 0.8227 (ttm110) REVERT: B 250 TYR cc_start: 0.8577 (m-80) cc_final: 0.7395 (m-80) REVERT: B 260 ASP cc_start: 0.9423 (p0) cc_final: 0.9194 (p0) REVERT: B 263 ASP cc_start: 0.9134 (m-30) cc_final: 0.8767 (m-30) REVERT: B 283 VAL cc_start: 0.9518 (t) cc_final: 0.9189 (t) REVERT: B 286 ASP cc_start: 0.8883 (m-30) cc_final: 0.8088 (m-30) REVERT: B 290 GLU cc_start: 0.9178 (pp20) cc_final: 0.8855 (pp20) REVERT: B 291 LEU cc_start: 0.9513 (mt) cc_final: 0.9013 (mt) REVERT: B 317 MET cc_start: 0.8538 (ptm) cc_final: 0.8106 (ptm) REVERT: B 325 LYS cc_start: 0.8963 (mptt) cc_final: 0.8666 (tptt) REVERT: B 359 MET cc_start: 0.9008 (ttt) cc_final: 0.8522 (tmm) REVERT: B 362 ASP cc_start: 0.8723 (m-30) cc_final: 0.7639 (m-30) REVERT: B 375 LYS cc_start: 0.9238 (mmmm) cc_final: 0.8946 (mmmm) REVERT: B 379 SER cc_start: 0.9063 (t) cc_final: 0.8510 (t) REVERT: B 390 GLN cc_start: 0.9214 (mm110) cc_final: 0.8816 (mm-40) REVERT: B 415 ASN cc_start: 0.9454 (t0) cc_final: 0.8917 (t0) REVERT: B 416 ILE cc_start: 0.9660 (mt) cc_final: 0.9458 (mt) REVERT: B 418 ASN cc_start: 0.9161 (m110) cc_final: 0.8955 (m110) REVERT: B 420 MET cc_start: 0.9483 (mmm) cc_final: 0.9140 (mmm) REVERT: B 458 MET cc_start: 0.9433 (mmm) cc_final: 0.9170 (mmm) REVERT: B 469 HIS cc_start: 0.8817 (t-170) cc_final: 0.8589 (t70) REVERT: B 493 MET cc_start: 0.9127 (ppp) cc_final: 0.8842 (ppp) REVERT: B 494 MET cc_start: 0.9502 (mtt) cc_final: 0.9164 (mtt) REVERT: B 585 SER cc_start: 0.9256 (p) cc_final: 0.9027 (p) REVERT: B 586 TYR cc_start: 0.9330 (m-80) cc_final: 0.9049 (m-10) REVERT: B 606 TYR cc_start: 0.8506 (m-80) cc_final: 0.7865 (m-80) REVERT: B 613 TYR cc_start: 0.9121 (t80) cc_final: 0.8130 (t80) REVERT: B 615 MET cc_start: 0.8978 (mmp) cc_final: 0.8562 (mmp) REVERT: B 631 ASP cc_start: 0.9346 (t70) cc_final: 0.8924 (t0) REVERT: B 640 MET cc_start: 0.9311 (tpp) cc_final: 0.8763 (tpp) REVERT: B 641 ILE cc_start: 0.9711 (mm) cc_final: 0.9507 (mm) REVERT: B 679 ILE cc_start: 0.9592 (mm) cc_final: 0.9381 (mm) REVERT: C 17 PHE cc_start: 0.8373 (p90) cc_final: 0.7683 (p90) REVERT: C 20 MET cc_start: 0.8874 (ptp) cc_final: 0.8670 (pmm) REVERT: C 21 PHE cc_start: 0.9038 (m-10) cc_final: 0.8487 (m-80) REVERT: C 96 MET cc_start: 0.8422 (tpt) cc_final: 0.8093 (tpt) REVERT: C 105 TYR cc_start: 0.9008 (m-80) cc_final: 0.8487 (m-80) REVERT: C 112 LEU cc_start: 0.7709 (mt) cc_final: 0.7469 (pp) REVERT: C 122 PHE cc_start: 0.8611 (m-80) cc_final: 0.8264 (m-10) REVERT: C 157 MET cc_start: 0.9528 (ptm) cc_final: 0.9246 (ptm) REVERT: C 172 PHE cc_start: 0.9281 (m-80) cc_final: 0.8599 (m-80) REVERT: C 204 TYR cc_start: 0.8919 (t80) cc_final: 0.8525 (t80) REVERT: C 313 GLU cc_start: 0.9394 (mt-10) cc_final: 0.8643 (mm-30) REVERT: D 21 PHE cc_start: 0.8696 (m-10) cc_final: 0.8472 (m-10) REVERT: D 109 PHE cc_start: 0.8531 (m-80) cc_final: 0.7836 (m-80) REVERT: D 112 LEU cc_start: 0.8825 (mm) cc_final: 0.8079 (pp) REVERT: D 157 MET cc_start: 0.9522 (ptm) cc_final: 0.9267 (ppp) REVERT: D 166 PHE cc_start: 0.7765 (t80) cc_final: 0.7481 (t80) REVERT: D 169 TYR cc_start: 0.9033 (m-10) cc_final: 0.8710 (m-80) REVERT: D 172 PHE cc_start: 0.9379 (m-80) cc_final: 0.9061 (m-80) REVERT: D 177 TYR cc_start: 0.9286 (t80) cc_final: 0.8914 (t80) REVERT: D 179 TYR cc_start: 0.8445 (t80) cc_final: 0.7937 (t80) REVERT: D 185 MET cc_start: 0.5623 (mmp) cc_final: 0.5053 (mmm) REVERT: D 233 ASN cc_start: 0.8827 (m-40) cc_final: 0.8595 (m-40) REVERT: D 244 GLU cc_start: 0.9128 (mp0) cc_final: 0.8889 (mm-30) REVERT: D 318 ASP cc_start: 0.9088 (t0) cc_final: 0.8778 (t70) outliers start: 0 outliers final: 0 residues processed: 668 average time/residue: 0.1222 time to fit residues: 122.6564 Evaluate side-chains 572 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 572 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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: 7.9990 chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 232 ASN A 313 HIS ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.108834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.080111 restraints weight = 50094.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.083139 restraints weight = 30470.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.085354 restraints weight = 21345.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.086972 restraints weight = 15876.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.088222 restraints weight = 12547.870| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.8249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16386 Z= 0.158 Angle : 0.686 11.297 22134 Z= 0.366 Chirality : 0.045 0.350 2360 Planarity : 0.004 0.045 2818 Dihedral : 10.433 173.846 2242 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % 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: 0.47 (0.18), residues: 1932 helix: 0.83 (0.15), residues: 1141 sheet: -0.15 (0.45), residues: 114 loop : -0.32 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 161 TYR 0.030 0.002 TYR C 142 PHE 0.037 0.002 PHE C 109 TRP 0.057 0.003 TRP D 124 HIS 0.013 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00346 (16386) covalent geometry : angle 0.68609 (22134) hydrogen bonds : bond 0.04160 ( 871) hydrogen bonds : angle 5.27649 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3423.32 seconds wall clock time: 60 minutes 4.04 seconds (3604.04 seconds total)