Starting phenix.real_space_refine on Thu Aug 6 15:05:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bze_45065/08_2026/9bze_45065_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bze_45065/08_2026/9bze_45065.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bze_45065/08_2026/9bze_45065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bze_45065/08_2026/9bze_45065.map" model { file = "/net/cci-nas-00/data/ceres_data/9bze_45065/08_2026/9bze_45065_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bze_45065/08_2026/9bze_45065_neut.cif" } resolution = 4.19 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 2.63, per 1000 atoms: 0.16 Number of scatterers: 16038 At special positions: 0 Unit cell: (96.33, 142.974, 129.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 638.7 milliseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.104A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.985A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.954A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.665A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.949A 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: 4.118A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.074A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.580A 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: 3.872A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.644A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.729A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.027A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.118A 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: 4.068A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A 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: 4.876A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.359A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.477A 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: 6.716A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.477A 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: 6.064A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.049A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.563A 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: 8.344A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.04 Time building geometry restraints manager: 1.60 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: 4876 1.34 - 1.46: 3021 1.46 - 1.58: 8308 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" O3B TTP B 801 " pdb=" PG TTP B 801 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" O3B TTP A 803 " pdb=" PG TTP A 803 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.061 1.25e-02 6.40e+03 2.35e+01 bond pdb=" O3A TTP A 803 " pdb=" PB TTP A 803 " ideal model delta sigma weight residual 1.675 1.606 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.608 0.067 2.00e-02 2.50e+03 1.14e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21528 2.09 - 4.17: 524 4.17 - 6.26: 65 6.26 - 8.35: 8 8.35 - 10.44: 9 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.66 -6.12 1.36e+00 5.41e-01 2.03e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.11 -4.40 1.15e+00 7.56e-01 1.46e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.89 -4.39 1.23e+00 6.61e-01 1.27e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.69 -3.98 1.15e+00 7.56e-01 1.20e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.53 3.66 1.06e+00 8.90e-01 1.19e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.05: 9093 25.05 - 50.10: 652 50.10 - 75.15: 125 75.15 - 100.20: 26 100.20 - 125.25: 2 Dihedral angle restraints: 9898 sinusoidal: 4140 harmonic: 5758 Sorted by residual: dihedral pdb=" O4' GDP A 802 " pdb=" C1' GDP A 802 " pdb=" N9 GDP A 802 " pdb=" C8 GDP A 802 " ideal model delta sinusoidal sigma weight residual 27.02 -98.22 125.25 1 2.00e+01 2.50e-03 3.78e+01 dihedral pdb=" O4' GDP B 804 " pdb=" C1' GDP B 804 " pdb=" N9 GDP B 804 " pdb=" C8 GDP B 804 " ideal model delta sinusoidal sigma weight residual 27.02 -95.59 122.61 1 2.00e+01 2.50e-03 3.69e+01 dihedral pdb=" C VAL C 125 " pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual -122.00 -134.30 12.30 0 2.50e+00 1.60e-01 2.42e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2137 0.093 - 0.187: 192 0.187 - 0.280: 26 0.280 - 0.373: 3 0.373 - 0.466: 2 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.43e+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 4.59e+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 2.97e+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 4.13e-02 2.73e+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 " 0.018 2.00e-02 2.50e+03 1.12e-02 2.21e+00 pdb=" CG PHE D 92 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 179 " -0.017 2.00e-02 2.50e+03 9.87e-03 1.95e+00 pdb=" CG TYR D 179 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR D 179 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 179 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR D 179 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 179 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR D 179 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 179 " -0.005 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 128 2.51 - 3.11: 11548 3.11 - 3.70: 27036 3.70 - 4.30: 41567 4.30 - 4.90: 65484 Nonbonded interactions: 145763 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.911 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 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 145758 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: 0.890 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.830 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.139 16386 Z= 0.334 Angle : 0.787 10.436 22134 Z= 0.472 Chirality : 0.058 0.466 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.634 125.246 6202 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.34 % Allowed : 15.27 % Favored : 83.39 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (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 0.021 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.009 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.33 (16386) covalent geometry : angle 0.78745 / 0.47 (22134) hydrogen bonds : bond 0.15421 / 9.51 ( 871) hydrogen bonds : angle 6.51768 / 4.65 ( 2571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1038 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 1015 time to evaluate : 0.394 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: A 41 ILE cc_start: 0.8698 (mm) cc_final: 0.8400 (mm) REVERT: A 51 LEU cc_start: 0.8139 (tp) cc_final: 0.7856 (tp) REVERT: A 81 PHE cc_start: 0.8260 (m-80) cc_final: 0.8001 (m-10) REVERT: A 123 SER cc_start: 0.9320 (m) cc_final: 0.8886 (m) REVERT: A 157 LEU cc_start: 0.8978 (tp) cc_final: 0.8773 (tp) REVERT: A 172 LEU cc_start: 0.9490 (mp) cc_final: 0.9147 (mp) REVERT: A 181 ASP cc_start: 0.8241 (m-30) cc_final: 0.7581 (m-30) REVERT: A 211 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6381 (tp30) REVERT: A 258 ILE cc_start: 0.9219 (tp) cc_final: 0.8843 (tp) REVERT: A 265 LYS cc_start: 0.9075 (mmtt) cc_final: 0.8696 (mmmt) REVERT: A 267 ILE cc_start: 0.8833 (mp) cc_final: 0.8079 (pt) REVERT: A 315 ASP cc_start: 0.8472 (p0) cc_final: 0.7912 (p0) REVERT: A 344 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7247 (mt-10) REVERT: A 345 LYS cc_start: 0.8888 (tttt) cc_final: 0.8388 (ttmt) REVERT: A 362 ASP cc_start: 0.6076 (m-30) cc_final: 0.5768 (m-30) REVERT: A 365 ASN cc_start: 0.8288 (m-40) cc_final: 0.8044 (m-40) REVERT: A 377 LYS cc_start: 0.8818 (mttt) cc_final: 0.8463 (mttp) REVERT: A 378 PHE cc_start: 0.8896 (p90) cc_final: 0.8646 (p90) REVERT: A 387 GLN cc_start: 0.7497 (mt0) cc_final: 0.7156 (mt0) REVERT: A 408 SER cc_start: 0.8599 (p) cc_final: 0.8396 (p) REVERT: A 420 MET cc_start: 0.7468 (mmm) cc_final: 0.7258 (mmm) REVERT: A 435 SER cc_start: 0.9408 (p) cc_final: 0.8802 (p) REVERT: A 501 GLN cc_start: 0.8285 (tt0) cc_final: 0.8072 (tt0) REVERT: A 576 LEU cc_start: 0.8683 (mt) cc_final: 0.8130 (mt) REVERT: A 583 SER cc_start: 0.8180 (m) cc_final: 0.7861 (t) REVERT: A 590 SER cc_start: 0.9100 (p) cc_final: 0.8361 (p) REVERT: A 595 MET cc_start: 0.8050 (mmp) cc_final: 0.7671 (mmp) REVERT: A 670 ILE cc_start: 0.8913 (mt) cc_final: 0.8460 (mt) REVERT: A 687 THR cc_start: 0.7729 (m) cc_final: 0.7469 (m) REVERT: B 11 GLN cc_start: 0.7654 (mt0) cc_final: 0.6754 (mt0) REVERT: B 41 ILE cc_start: 0.8792 (mm) cc_final: 0.8338 (mm) REVERT: B 99 LYS cc_start: 0.9064 (mmtt) cc_final: 0.8421 (tppt) REVERT: B 127 LEU cc_start: 0.8999 (mt) cc_final: 0.8785 (mt) REVERT: B 147 GLN cc_start: 0.8314 (mt0) cc_final: 0.8003 (mt0) REVERT: B 172 LEU cc_start: 0.9343 (mp) cc_final: 0.8955 (mp) REVERT: B 175 VAL cc_start: 0.9207 (t) cc_final: 0.9007 (t) REVERT: B 177 ASP cc_start: 0.8671 (t0) cc_final: 0.8058 (t70) REVERT: B 181 ASP cc_start: 0.8122 (m-30) cc_final: 0.7639 (m-30) REVERT: B 192 LEU cc_start: 0.9272 (mt) cc_final: 0.8959 (mt) REVERT: B 204 SER cc_start: 0.9055 (m) cc_final: 0.8209 (t) REVERT: B 226 VAL cc_start: 0.9079 (t) cc_final: 0.8711 (t) REVERT: B 256 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7212 (tpt90) REVERT: B 288 PHE cc_start: 0.7689 (t80) cc_final: 0.7287 (t80) REVERT: B 315 ASP cc_start: 0.8777 (p0) cc_final: 0.8394 (p0) REVERT: B 322 MET cc_start: 0.7584 (mmm) cc_final: 0.6977 (mmm) REVERT: B 345 LYS cc_start: 0.8290 (tttt) cc_final: 0.7970 (ttpt) REVERT: B 346 LEU cc_start: 0.8863 (mt) cc_final: 0.8478 (mt) REVERT: B 359 MET cc_start: 0.8061 (ttt) cc_final: 0.7720 (ttt) REVERT: B 374 SER cc_start: 0.8716 (t) cc_final: 0.8478 (p) REVERT: B 381 LEU cc_start: 0.8730 (tp) cc_final: 0.8511 (tp) REVERT: B 387 GLN cc_start: 0.7301 (mt0) cc_final: 0.6892 (mt0) REVERT: B 417 LEU cc_start: 0.8819 (tp) cc_final: 0.8487 (tt) REVERT: B 418 ASN cc_start: 0.8302 (m-40) cc_final: 0.7799 (m-40) REVERT: B 425 ILE cc_start: 0.8954 (mt) cc_final: 0.8666 (mt) REVERT: B 474 GLN cc_start: 0.7992 (mt0) cc_final: 0.7702 (mt0) REVERT: B 494 MET cc_start: 0.7983 (mtp) cc_final: 0.7781 (mtp) REVERT: B 500 ILE cc_start: 0.9441 (mt) cc_final: 0.8999 (mt) REVERT: B 550 MET cc_start: 0.7876 (mtm) cc_final: 0.6885 (mtm) REVERT: B 587 VAL cc_start: 0.8690 (t) cc_final: 0.8459 (t) REVERT: B 597 ILE cc_start: 0.9427 (pt) cc_final: 0.9221 (pt) REVERT: B 644 ILE cc_start: 0.8904 (mt) cc_final: 0.8659 (mt) REVERT: B 655 THR cc_start: 0.9501 (m) cc_final: 0.9289 (t) REVERT: C 27 LYS cc_start: 0.8056 (ptmm) cc_final: 0.7833 (tmtt) REVERT: C 37 LEU cc_start: 0.5102 (mt) cc_final: 0.4489 (tp) REVERT: C 114 PRO cc_start: 0.5223 (Cg_endo) cc_final: 0.4845 (Cg_exo) REVERT: C 163 LEU cc_start: 0.6465 (tt) cc_final: 0.6189 (tt) REVERT: C 178 PHE cc_start: 0.4924 (m-80) cc_final: 0.4646 (m-80) REVERT: D 47 LEU cc_start: 0.5071 (mt) cc_final: 0.3954 (mp) REVERT: D 96 MET cc_start: 0.5835 (mmm) cc_final: 0.5523 (mmm) REVERT: D 141 LEU cc_start: 0.6273 (mt) cc_final: 0.5960 (mp) REVERT: D 186 GLN cc_start: 0.4627 (mm-40) cc_final: 0.3829 (mm-40) outliers start: 23 outliers final: 6 residues processed: 1020 average time/residue: 0.1219 time to fit residues: 179.6636 Evaluate side-chains 688 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 682 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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: 0.0060 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.0170 overall best weight: 0.5434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN A 312 GLN A 320 ASN A 361 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN B 19 GLN B 43 GLN B 61 ASN B 102 ASN B 191 GLN B 304 HIS B 320 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 HIS ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN C 263 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 186 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.130990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.095038 restraints weight = 39179.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.098518 restraints weight = 20240.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.100823 restraints weight = 12889.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.102455 restraints weight = 9143.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.103508 restraints weight = 7026.812| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (15 function evaluations) r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16386 Z= 0.152 Angle : 0.610 6.973 22134 Z= 0.328 Chirality : 0.043 0.241 2360 Planarity : 0.004 0.032 2818 Dihedral : 9.793 130.571 2290 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.23 % Allowed : 2.91 % 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 are not related in a simple way. whole: 1.21 (0.18), residues: 1932 helix: 1.29 (0.15), residues: 1110 sheet: -0.08 (0.39), residues: 138 loop : 0.37 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 331 TYR 0.020 0.002 TYR D 174 PHE 0.034 0.002 PHE C 168 TRP 0.028 0.002 TRP D 124 HIS 0.010 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (16386) covalent geometry : angle 0.60963 / 0.33 (22134) hydrogen bonds : bond 0.04655 / 2.96 ( 871) hydrogen bonds : angle 5.05695 / 3.63 ( 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 823 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 819 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9236 (tptp) cc_final: 0.8853 (tppt) REVERT: A 29 ASP cc_start: 0.9214 (t0) cc_final: 0.8974 (t0) REVERT: A 41 ILE cc_start: 0.9244 (mm) cc_final: 0.8859 (mm) REVERT: A 118 TYR cc_start: 0.9273 (t80) cc_final: 0.8956 (t80) REVERT: A 147 GLN cc_start: 0.9384 (mt0) cc_final: 0.8374 (mt0) REVERT: A 158 ASN cc_start: 0.9358 (m110) cc_final: 0.8980 (m-40) REVERT: A 162 LYS cc_start: 0.8811 (ttmm) cc_final: 0.8581 (ttmm) REVERT: A 195 LEU cc_start: 0.9600 (mt) cc_final: 0.9327 (mt) REVERT: A 227 MET cc_start: 0.9326 (mtm) cc_final: 0.9047 (mtm) REVERT: A 235 ARG cc_start: 0.9209 (ttm-80) cc_final: 0.8995 (ttm-80) REVERT: A 238 ASP cc_start: 0.8600 (p0) cc_final: 0.7983 (p0) REVERT: A 255 HIS cc_start: 0.8960 (t-90) cc_final: 0.8118 (t-90) REVERT: A 257 ASP cc_start: 0.9155 (m-30) cc_final: 0.8702 (m-30) REVERT: A 262 LEU cc_start: 0.9824 (mt) cc_final: 0.9560 (mt) REVERT: A 286 ASP cc_start: 0.8576 (m-30) cc_final: 0.8204 (m-30) REVERT: A 291 LEU cc_start: 0.9651 (mt) cc_final: 0.9450 (mt) REVERT: A 333 LYS cc_start: 0.9455 (tppt) cc_final: 0.9247 (tppp) REVERT: A 335 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7595 (mm-30) REVERT: A 359 MET cc_start: 0.8851 (ttp) cc_final: 0.8645 (ttp) REVERT: A 362 ASP cc_start: 0.7960 (m-30) cc_final: 0.7604 (m-30) REVERT: A 366 LYS cc_start: 0.9292 (mtmm) cc_final: 0.8825 (mtmm) REVERT: A 375 LYS cc_start: 0.8835 (mmtt) cc_final: 0.8459 (mmtm) REVERT: A 415 ASN cc_start: 0.9243 (t0) cc_final: 0.8672 (t0) REVERT: A 418 ASN cc_start: 0.9300 (OUTLIER) cc_final: 0.8810 (m110) REVERT: A 447 ASN cc_start: 0.8004 (m-40) cc_final: 0.7631 (t0) REVERT: A 466 MET cc_start: 0.9020 (ptt) cc_final: 0.8621 (ptt) REVERT: A 493 MET cc_start: 0.9079 (tmm) cc_final: 0.8662 (tmm) REVERT: A 494 MET cc_start: 0.9372 (mtp) cc_final: 0.9148 (mtp) REVERT: A 510 LYS cc_start: 0.9002 (mtpt) cc_final: 0.8623 (mtpt) REVERT: A 527 TYR cc_start: 0.8713 (t80) cc_final: 0.8386 (t80) REVERT: A 528 PHE cc_start: 0.9242 (m-80) cc_final: 0.8775 (m-80) REVERT: A 553 PRO cc_start: 0.9541 (Cg_exo) cc_final: 0.9044 (Cg_endo) REVERT: A 602 GLU cc_start: 0.7713 (pt0) cc_final: 0.7057 (pt0) REVERT: A 645 GLN cc_start: 0.8668 (tp40) cc_final: 0.7819 (tp40) REVERT: A 657 PHE cc_start: 0.9031 (m-80) cc_final: 0.8641 (m-80) REVERT: A 669 ARG cc_start: 0.9162 (tpp-160) cc_final: 0.8818 (tpp-160) REVERT: A 680 LYS cc_start: 0.9164 (mttt) cc_final: 0.8474 (mttt) REVERT: B 8 LYS cc_start: 0.9449 (tptt) cc_final: 0.9032 (tppt) REVERT: B 12 LEU cc_start: 0.9563 (mt) cc_final: 0.9129 (mt) REVERT: B 15 GLU cc_start: 0.9274 (mt-10) cc_final: 0.9007 (mt-10) REVERT: B 51 LEU cc_start: 0.9434 (tp) cc_final: 0.9216 (tp) REVERT: B 147 GLN cc_start: 0.8626 (mt0) cc_final: 0.8174 (mt0) REVERT: B 184 ARG cc_start: 0.9398 (tpp80) cc_final: 0.9082 (tpp80) REVERT: B 191 GLN cc_start: 0.9213 (mm-40) cc_final: 0.8784 (mt0) REVERT: B 211 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8363 (mm-30) REVERT: B 236 TYR cc_start: 0.9250 (t80) cc_final: 0.8950 (t80) REVERT: B 279 SER cc_start: 0.7933 (m) cc_final: 0.7641 (t) REVERT: B 288 PHE cc_start: 0.9302 (t80) cc_final: 0.8811 (t80) REVERT: B 315 ASP cc_start: 0.8735 (p0) cc_final: 0.8163 (p0) REVERT: B 321 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8217 (tm-30) REVERT: B 322 MET cc_start: 0.8643 (mmm) cc_final: 0.8382 (mmm) REVERT: B 335 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8060 (mm-30) REVERT: B 348 MET cc_start: 0.9466 (ptm) cc_final: 0.9151 (ptm) REVERT: B 374 SER cc_start: 0.8917 (t) cc_final: 0.7926 (p) REVERT: B 375 LYS cc_start: 0.9114 (mttm) cc_final: 0.8621 (mtpp) REVERT: B 387 GLN cc_start: 0.9093 (mt0) cc_final: 0.8857 (mt0) REVERT: B 390 GLN cc_start: 0.9195 (mt0) cc_final: 0.8992 (mm110) REVERT: B 393 SER cc_start: 0.9375 (m) cc_final: 0.9068 (p) REVERT: B 398 ASP cc_start: 0.7892 (t0) cc_final: 0.7629 (t0) REVERT: B 410 ASN cc_start: 0.8602 (m110) cc_final: 0.8053 (m110) REVERT: B 423 LYS cc_start: 0.9574 (mttt) cc_final: 0.9243 (mppt) REVERT: B 427 LYS cc_start: 0.9337 (mmmm) cc_final: 0.9058 (tppt) REVERT: B 474 GLN cc_start: 0.8676 (mt0) cc_final: 0.8403 (mt0) REVERT: B 493 MET cc_start: 0.9666 (tmm) cc_final: 0.9333 (tmm) REVERT: B 516 GLN cc_start: 0.8821 (tp-100) cc_final: 0.8117 (tp40) REVERT: B 558 TRP cc_start: 0.9220 (m100) cc_final: 0.8564 (m100) REVERT: B 570 MET cc_start: 0.8474 (mtm) cc_final: 0.8163 (mtm) REVERT: B 576 LEU cc_start: 0.9073 (mt) cc_final: 0.8812 (mt) REVERT: B 612 TYR cc_start: 0.9074 (m-80) cc_final: 0.8525 (m-10) REVERT: B 639 ASP cc_start: 0.9202 (m-30) cc_final: 0.8808 (m-30) REVERT: B 640 MET cc_start: 0.9417 (tpp) cc_final: 0.9061 (tpp) REVERT: B 677 ARG cc_start: 0.9351 (mmm-85) cc_final: 0.9028 (mmm-85) REVERT: C 35 ILE cc_start: 0.6949 (tt) cc_final: 0.6702 (tt) REVERT: C 101 HIS cc_start: 0.7828 (m90) cc_final: 0.6063 (m90) REVERT: C 123 GLU cc_start: 0.9541 (mm-30) cc_final: 0.9295 (mm-30) REVERT: C 162 TYR cc_start: 0.9259 (m-10) cc_final: 0.8497 (m-10) REVERT: C 163 LEU cc_start: 0.9604 (tt) cc_final: 0.9189 (tt) REVERT: C 173 TYR cc_start: 0.7393 (t80) cc_final: 0.6437 (t80) REVERT: C 179 TYR cc_start: 0.8203 (t80) cc_final: 0.7852 (t80) REVERT: C 201 HIS cc_start: 0.9080 (m170) cc_final: 0.8722 (m90) REVERT: C 212 ILE cc_start: 0.8362 (mt) cc_final: 0.7887 (mt) REVERT: C 233 ASN cc_start: 0.9306 (m110) cc_final: 0.8667 (m110) REVERT: C 271 LEU cc_start: 0.7336 (mt) cc_final: 0.7134 (mt) REVERT: C 278 GLU cc_start: 0.8444 (mm-30) cc_final: 0.7676 (pm20) REVERT: D 20 MET cc_start: 0.8944 (mtm) cc_final: 0.8707 (mpp) REVERT: D 96 MET cc_start: 0.8992 (mmm) cc_final: 0.8759 (mmt) REVERT: D 148 ASP cc_start: 0.7349 (m-30) cc_final: 0.7027 (m-30) REVERT: D 186 GLN cc_start: 0.7656 (mm110) cc_final: 0.7119 (mm110) REVERT: D 230 ASP cc_start: 0.8915 (t70) cc_final: 0.8643 (t0) REVERT: D 281 ASP cc_start: 0.8124 (p0) cc_final: 0.7754 (t0) outliers start: 4 outliers final: 0 residues processed: 820 average time/residue: 0.1063 time to fit residues: 130.9168 Evaluate side-chains 676 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 675 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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: 9.9990 chunk 131 optimal weight: 0.6980 chunk 164 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 159 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 150 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 158 optimal weight: 0.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN B 19 GLN B 44 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN C 263 ASN D 28 GLN D 71 ASN D 127 GLN D 238 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.124037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.088066 restraints weight = 40814.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.091433 restraints weight = 20980.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.093721 restraints weight = 13133.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.095168 restraints weight = 9236.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.096302 restraints weight = 7155.828| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (17 function evaluations) r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16386 Z= 0.193 Angle : 0.590 7.594 22134 Z= 0.319 Chirality : 0.042 0.212 2360 Planarity : 0.004 0.037 2818 Dihedral : 9.033 134.332 2290 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.23 % Allowed : 2.86 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.19), residues: 1932 helix: 1.31 (0.15), residues: 1135 sheet: -0.08 (0.43), residues: 126 loop : 0.50 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 161 TYR 0.035 0.002 TYR B 574 PHE 0.031 0.002 PHE A 654 TRP 0.019 0.002 TRP D 124 HIS 0.006 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (16386) covalent geometry : angle 0.59048 / 0.32 (22134) hydrogen bonds : bond 0.04160 / 2.64 ( 871) hydrogen bonds : angle 4.87608 / 3.52 ( 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 754 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 750 time to evaluate : 0.366 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: A 8 LYS cc_start: 0.9242 (tptp) cc_final: 0.8885 (tppt) REVERT: A 12 LEU cc_start: 0.9643 (mt) cc_final: 0.9362 (mt) REVERT: A 95 MET cc_start: 0.9117 (mmm) cc_final: 0.8480 (mmm) REVERT: A 118 TYR cc_start: 0.9398 (t80) cc_final: 0.9160 (t80) REVERT: A 147 GLN cc_start: 0.9436 (mt0) cc_final: 0.8607 (mt0) REVERT: A 149 TYR cc_start: 0.9005 (t80) cc_final: 0.8717 (t80) REVERT: A 157 LEU cc_start: 0.9427 (tp) cc_final: 0.9155 (tp) REVERT: A 158 ASN cc_start: 0.9415 (m110) cc_final: 0.8995 (m-40) REVERT: A 164 ARG cc_start: 0.8885 (ptt90) cc_final: 0.7896 (ptm-80) REVERT: A 195 LEU cc_start: 0.9704 (mt) cc_final: 0.9430 (mt) REVERT: A 214 LYS cc_start: 0.8779 (tppt) cc_final: 0.8318 (mmtt) REVERT: A 223 VAL cc_start: 0.9734 (m) cc_final: 0.9229 (p) REVERT: A 227 MET cc_start: 0.9314 (mtm) cc_final: 0.8870 (mtm) REVERT: A 232 ASN cc_start: 0.8898 (m-40) cc_final: 0.8517 (m-40) REVERT: A 235 ARG cc_start: 0.9183 (ttm-80) cc_final: 0.8939 (ttm110) REVERT: A 238 ASP cc_start: 0.8457 (p0) cc_final: 0.8075 (p0) REVERT: A 252 ASN cc_start: 0.9485 (t0) cc_final: 0.9258 (t0) REVERT: A 255 HIS cc_start: 0.8753 (t-90) cc_final: 0.7923 (t-90) REVERT: A 257 ASP cc_start: 0.9101 (m-30) cc_final: 0.8796 (m-30) REVERT: A 262 LEU cc_start: 0.9843 (mt) cc_final: 0.9587 (mt) REVERT: A 263 ASP cc_start: 0.9241 (m-30) cc_final: 0.8952 (m-30) REVERT: A 270 ASP cc_start: 0.8907 (t0) cc_final: 0.8563 (t0) REVERT: A 276 LYS cc_start: 0.9301 (ttpp) cc_final: 0.9086 (tmtt) REVERT: A 322 MET cc_start: 0.8924 (tpt) cc_final: 0.8068 (tpt) REVERT: A 333 LYS cc_start: 0.9547 (tppt) cc_final: 0.9304 (tppp) REVERT: A 335 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7694 (mm-30) REVERT: A 344 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8804 (mt-10) REVERT: A 366 LYS cc_start: 0.9248 (mtmm) cc_final: 0.8863 (mtmm) REVERT: A 375 LYS cc_start: 0.8782 (mmtt) cc_final: 0.8241 (mmtm) REVERT: A 390 GLN cc_start: 0.8614 (mt0) cc_final: 0.8387 (mt0) REVERT: A 415 ASN cc_start: 0.9454 (t0) cc_final: 0.8956 (t0) REVERT: A 441 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8546 (mt-10) REVERT: A 459 LYS cc_start: 0.8947 (mttp) cc_final: 0.8529 (mtmt) REVERT: A 466 MET cc_start: 0.9171 (ptt) cc_final: 0.8761 (ptt) REVERT: A 491 PHE cc_start: 0.9666 (t80) cc_final: 0.9434 (t80) REVERT: A 493 MET cc_start: 0.9084 (tmm) cc_final: 0.8708 (tmm) REVERT: A 494 MET cc_start: 0.9381 (mtp) cc_final: 0.9061 (mtp) REVERT: A 515 ASP cc_start: 0.9018 (m-30) cc_final: 0.8663 (m-30) REVERT: A 601 ILE cc_start: 0.9564 (mm) cc_final: 0.9131 (mm) REVERT: A 604 ARG cc_start: 0.9114 (mmm160) cc_final: 0.8552 (mmp80) REVERT: A 640 MET cc_start: 0.9161 (tpp) cc_final: 0.8845 (tpp) REVERT: A 645 GLN cc_start: 0.9078 (tp40) cc_final: 0.8752 (tp40) REVERT: A 669 ARG cc_start: 0.9120 (tpp-160) cc_final: 0.8761 (tpp-160) REVERT: B 8 LYS cc_start: 0.9430 (tptt) cc_final: 0.8965 (tppt) REVERT: B 12 LEU cc_start: 0.9608 (mt) cc_final: 0.9304 (mt) REVERT: B 30 LYS cc_start: 0.9540 (tmtt) cc_final: 0.9335 (tmtt) REVERT: B 111 LYS cc_start: 0.9697 (mptt) cc_final: 0.9413 (mmtt) REVERT: B 117 ARG cc_start: 0.9376 (mmm-85) cc_final: 0.9042 (mmm-85) REVERT: B 119 GLU cc_start: 0.9305 (mp0) cc_final: 0.9070 (mp0) REVERT: B 150 GLN cc_start: 0.9424 (tp40) cc_final: 0.9031 (tp-100) REVERT: B 176 ASN cc_start: 0.8753 (t0) cc_final: 0.8519 (t0) REVERT: B 184 ARG cc_start: 0.9456 (tpp80) cc_final: 0.8932 (tpp80) REVERT: B 191 GLN cc_start: 0.9308 (mm-40) cc_final: 0.8855 (mt0) REVERT: B 211 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8514 (mm-30) REVERT: B 236 TYR cc_start: 0.9221 (t80) cc_final: 0.8958 (t80) REVERT: B 239 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8028 (tm-30) REVERT: B 252 ASN cc_start: 0.9216 (t0) cc_final: 0.8950 (t0) REVERT: B 288 PHE cc_start: 0.9416 (t80) cc_final: 0.9205 (t80) REVERT: B 322 MET cc_start: 0.8881 (mmm) cc_final: 0.8487 (mmm) REVERT: B 335 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8141 (mm-30) REVERT: B 350 ARG cc_start: 0.9192 (mmm-85) cc_final: 0.8952 (mmm-85) REVERT: B 358 ILE cc_start: 0.9700 (mm) cc_final: 0.9469 (mm) REVERT: B 374 SER cc_start: 0.9319 (t) cc_final: 0.8503 (p) REVERT: B 393 SER cc_start: 0.9383 (m) cc_final: 0.9035 (p) REVERT: B 398 ASP cc_start: 0.8207 (t0) cc_final: 0.7857 (t0) REVERT: B 410 ASN cc_start: 0.8941 (m110) cc_final: 0.8567 (m110) REVERT: B 423 LYS cc_start: 0.9595 (mttt) cc_final: 0.9354 (mppt) REVERT: B 493 MET cc_start: 0.9615 (tmm) cc_final: 0.9402 (tmm) REVERT: B 522 TYR cc_start: 0.9155 (m-10) cc_final: 0.8518 (m-10) REVERT: B 550 MET cc_start: 0.8180 (mtp) cc_final: 0.7886 (mtm) REVERT: B 565 VAL cc_start: 0.9800 (t) cc_final: 0.9589 (p) REVERT: B 570 MET cc_start: 0.8527 (mtm) cc_final: 0.7790 (mtm) REVERT: B 576 LEU cc_start: 0.9446 (mt) cc_final: 0.9076 (mt) REVERT: B 588 GLN cc_start: 0.9356 (mm-40) cc_final: 0.8874 (mm-40) REVERT: B 603 GLU cc_start: 0.8700 (tm-30) cc_final: 0.7859 (tp30) REVERT: B 639 ASP cc_start: 0.9150 (m-30) cc_final: 0.8772 (m-30) REVERT: B 640 MET cc_start: 0.9453 (tpp) cc_final: 0.9030 (tpp) REVERT: B 677 ARG cc_start: 0.9403 (mmm-85) cc_final: 0.9193 (mmm-85) REVERT: C 20 MET cc_start: 0.9503 (tmm) cc_final: 0.9117 (ptp) REVERT: C 21 PHE cc_start: 0.9165 (m-80) cc_final: 0.8541 (m-80) REVERT: C 107 ASN cc_start: 0.8837 (m110) cc_final: 0.8542 (t0) REVERT: C 108 ILE cc_start: 0.8817 (mt) cc_final: 0.8545 (mt) REVERT: C 162 TYR cc_start: 0.9344 (m-10) cc_final: 0.8607 (m-10) REVERT: C 163 LEU cc_start: 0.9681 (tt) cc_final: 0.9432 (pp) REVERT: C 173 TYR cc_start: 0.7350 (t80) cc_final: 0.6310 (t80) REVERT: C 179 TYR cc_start: 0.8239 (t80) cc_final: 0.7841 (t80) REVERT: C 185 MET cc_start: 0.5195 (mmm) cc_final: 0.3832 (mpp) REVERT: C 201 HIS cc_start: 0.9046 (m170) cc_final: 0.8634 (m170) REVERT: C 208 LEU cc_start: 0.8864 (mm) cc_final: 0.8556 (mm) REVERT: C 212 ILE cc_start: 0.8335 (mt) cc_final: 0.7721 (mt) REVERT: C 233 ASN cc_start: 0.9358 (m110) cc_final: 0.8758 (m110) REVERT: C 252 LEU cc_start: 0.7619 (mt) cc_final: 0.7355 (mt) REVERT: C 278 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8076 (pm20) REVERT: D 20 MET cc_start: 0.8954 (mtm) cc_final: 0.8705 (mpp) REVERT: D 148 ASP cc_start: 0.7186 (m-30) cc_final: 0.6977 (m-30) REVERT: D 176 LEU cc_start: 0.9609 (mt) cc_final: 0.9160 (tp) REVERT: D 186 GLN cc_start: 0.7791 (mm110) cc_final: 0.7472 (mm110) REVERT: D 201 HIS cc_start: 0.9221 (m170) cc_final: 0.8927 (m170) REVERT: D 219 GLU cc_start: 0.9135 (tp30) cc_final: 0.8875 (tp30) REVERT: D 266 LYS cc_start: 0.8755 (mmtp) cc_final: 0.8529 (mmmm) outliers start: 4 outliers final: 0 residues processed: 750 average time/residue: 0.1026 time to fit residues: 115.7232 Evaluate side-chains 630 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 630 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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: 1.9990 chunk 157 optimal weight: 20.0000 chunk 168 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 127 optimal weight: 0.0470 chunk 60 optimal weight: 0.6980 chunk 185 optimal weight: 8.9990 chunk 191 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 182 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN A 259 ASN A 320 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 28 GLN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.121701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.087857 restraints weight = 40454.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.091017 restraints weight = 20774.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.093234 restraints weight = 12926.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.094754 restraints weight = 9031.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.095783 restraints weight = 6838.553| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (15 function evaluations) r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16386 Z= 0.132 Angle : 0.559 8.070 22134 Z= 0.300 Chirality : 0.042 0.200 2360 Planarity : 0.003 0.042 2818 Dihedral : 8.623 134.800 2290 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.29 % Allowed : 2.04 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.19), residues: 1932 helix: 1.30 (0.15), residues: 1126 sheet: 0.24 (0.45), residues: 110 loop : 0.12 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 243 TYR 0.028 0.001 TYR C 174 PHE 0.043 0.002 PHE D 109 TRP 0.033 0.002 TRP D 124 HIS 0.007 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (16386) covalent geometry : angle 0.55860 / 0.30 (22134) hydrogen bonds : bond 0.03840 / 2.46 ( 871) hydrogen bonds : angle 4.75550 / 3.46 ( 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 744 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 739 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9224 (tptp) cc_final: 0.8888 (tppt) REVERT: A 12 LEU cc_start: 0.9607 (mt) cc_final: 0.9404 (mt) REVERT: A 95 MET cc_start: 0.9051 (mmm) cc_final: 0.8638 (tpp) REVERT: A 147 GLN cc_start: 0.9353 (mt0) cc_final: 0.8598 (mt0) REVERT: A 149 TYR cc_start: 0.8978 (t80) cc_final: 0.8653 (t80) REVERT: A 158 ASN cc_start: 0.9351 (m110) cc_final: 0.8855 (m-40) REVERT: A 195 LEU cc_start: 0.9670 (mt) cc_final: 0.9372 (mt) REVERT: A 223 VAL cc_start: 0.9751 (m) cc_final: 0.9299 (p) REVERT: A 227 MET cc_start: 0.9249 (mtm) cc_final: 0.8863 (mtm) REVERT: A 232 ASN cc_start: 0.8988 (m-40) cc_final: 0.8552 (m-40) REVERT: A 238 ASP cc_start: 0.8470 (p0) cc_final: 0.8091 (p0) REVERT: A 257 ASP cc_start: 0.9053 (m-30) cc_final: 0.8762 (m-30) REVERT: A 262 LEU cc_start: 0.9853 (mt) cc_final: 0.9634 (mt) REVERT: A 270 ASP cc_start: 0.8935 (t0) cc_final: 0.8649 (t0) REVERT: A 301 PHE cc_start: 0.9164 (m-80) cc_final: 0.8898 (m-10) REVERT: A 314 MET cc_start: 0.9117 (ttp) cc_final: 0.8767 (tmm) REVERT: A 322 MET cc_start: 0.8638 (tpt) cc_final: 0.8180 (tpp) REVERT: A 344 GLU cc_start: 0.9281 (mt-10) cc_final: 0.8735 (mt-10) REVERT: A 349 LEU cc_start: 0.9667 (mt) cc_final: 0.9427 (mt) REVERT: A 366 LYS cc_start: 0.9187 (mtmm) cc_final: 0.8957 (mtmm) REVERT: A 375 LYS cc_start: 0.8761 (mmtt) cc_final: 0.8247 (mmtm) REVERT: A 415 ASN cc_start: 0.9436 (t0) cc_final: 0.8860 (t0) REVERT: A 459 LYS cc_start: 0.8948 (mttp) cc_final: 0.8543 (mtmt) REVERT: A 466 MET cc_start: 0.9012 (ptt) cc_final: 0.8657 (ptt) REVERT: A 493 MET cc_start: 0.9049 (tmm) cc_final: 0.8596 (tmm) REVERT: A 494 MET cc_start: 0.9322 (mtp) cc_final: 0.8994 (mtp) REVERT: A 510 LYS cc_start: 0.9253 (mtpt) cc_final: 0.9004 (mtmt) REVERT: A 515 ASP cc_start: 0.8928 (m-30) cc_final: 0.8550 (m-30) REVERT: A 528 PHE cc_start: 0.9182 (m-80) cc_final: 0.8876 (m-10) REVERT: A 543 ILE cc_start: 0.9587 (mp) cc_final: 0.9168 (mt) REVERT: A 595 MET cc_start: 0.9056 (mmp) cc_final: 0.8656 (mmp) REVERT: A 598 MET cc_start: 0.8472 (mtm) cc_final: 0.8118 (mtm) REVERT: A 601 ILE cc_start: 0.9367 (mm) cc_final: 0.9071 (mm) REVERT: A 604 ARG cc_start: 0.9136 (mmm160) cc_final: 0.8464 (mmp80) REVERT: A 645 GLN cc_start: 0.9074 (tp40) cc_final: 0.8741 (tp40) REVERT: A 655 THR cc_start: 0.9434 (t) cc_final: 0.9076 (t) REVERT: A 667 LEU cc_start: 0.9281 (tt) cc_final: 0.9049 (tt) REVERT: A 669 ARG cc_start: 0.9051 (tpp-160) cc_final: 0.8459 (tpp-160) REVERT: B 8 LYS cc_start: 0.9410 (tptt) cc_final: 0.8946 (tppt) REVERT: B 30 LYS cc_start: 0.9540 (tmtt) cc_final: 0.9339 (tmtt) REVERT: B 87 LYS cc_start: 0.9354 (tptm) cc_final: 0.9146 (tptt) REVERT: B 109 ASN cc_start: 0.9257 (m110) cc_final: 0.8841 (m-40) REVERT: B 111 LYS cc_start: 0.9690 (mptt) cc_final: 0.9437 (mmtt) REVERT: B 117 ARG cc_start: 0.9388 (mmm-85) cc_final: 0.9117 (mmm-85) REVERT: B 119 GLU cc_start: 0.9270 (mp0) cc_final: 0.9017 (mp0) REVERT: B 150 GLN cc_start: 0.9457 (tp40) cc_final: 0.9145 (tp-100) REVERT: B 172 LEU cc_start: 0.9288 (mp) cc_final: 0.9058 (mp) REVERT: B 176 ASN cc_start: 0.8630 (t0) cc_final: 0.8337 (t0) REVERT: B 181 ASP cc_start: 0.8716 (m-30) cc_final: 0.8363 (m-30) REVERT: B 184 ARG cc_start: 0.9411 (tpp80) cc_final: 0.9006 (tpp80) REVERT: B 235 ARG cc_start: 0.9345 (ttm110) cc_final: 0.8808 (ptp-110) REVERT: B 239 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8010 (tm-30) REVERT: B 252 ASN cc_start: 0.9291 (t0) cc_final: 0.9062 (t0) REVERT: B 288 PHE cc_start: 0.9323 (t80) cc_final: 0.9092 (t80) REVERT: B 322 MET cc_start: 0.8904 (mmm) cc_final: 0.8671 (mmm) REVERT: B 335 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8157 (mm-30) REVERT: B 348 MET cc_start: 0.9450 (ptm) cc_final: 0.9152 (ptp) REVERT: B 352 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8455 (mm-30) REVERT: B 358 ILE cc_start: 0.9670 (mm) cc_final: 0.9465 (mm) REVERT: B 393 SER cc_start: 0.9395 (m) cc_final: 0.9078 (p) REVERT: B 410 ASN cc_start: 0.8953 (m110) cc_final: 0.8544 (m110) REVERT: B 423 LYS cc_start: 0.9556 (mttt) cc_final: 0.9305 (mtpt) REVERT: B 427 LYS cc_start: 0.9320 (mmmm) cc_final: 0.9080 (mmmm) REVERT: B 468 LEU cc_start: 0.9666 (tp) cc_final: 0.9455 (tp) REVERT: B 522 TYR cc_start: 0.9134 (m-10) cc_final: 0.8539 (m-10) REVERT: B 550 MET cc_start: 0.8200 (mtp) cc_final: 0.7903 (mtm) REVERT: B 558 TRP cc_start: 0.9382 (m100) cc_final: 0.8573 (m100) REVERT: B 570 MET cc_start: 0.9148 (mtp) cc_final: 0.7697 (mtp) REVERT: B 576 LEU cc_start: 0.9443 (mt) cc_final: 0.9000 (mt) REVERT: B 588 GLN cc_start: 0.9352 (mm-40) cc_final: 0.8931 (mm-40) REVERT: B 639 ASP cc_start: 0.9055 (m-30) cc_final: 0.8742 (m-30) REVERT: B 640 MET cc_start: 0.9400 (tpp) cc_final: 0.8968 (tpp) REVERT: B 680 LYS cc_start: 0.9111 (mttt) cc_final: 0.8760 (mttt) REVERT: C 20 MET cc_start: 0.9466 (tmm) cc_final: 0.9115 (ptp) REVERT: C 101 HIS cc_start: 0.8003 (m90) cc_final: 0.6558 (m90) REVERT: C 107 ASN cc_start: 0.8933 (m110) cc_final: 0.8697 (t0) REVERT: C 108 ILE cc_start: 0.8780 (mt) cc_final: 0.8511 (mt) REVERT: C 109 PHE cc_start: 0.7701 (m-80) cc_final: 0.7444 (m-80) REVERT: C 162 TYR cc_start: 0.9323 (m-10) cc_final: 0.8584 (m-10) REVERT: C 173 TYR cc_start: 0.7515 (t80) cc_final: 0.6683 (t80) REVERT: C 179 TYR cc_start: 0.8478 (t80) cc_final: 0.7919 (t80) REVERT: C 185 MET cc_start: 0.5336 (mmm) cc_final: 0.4160 (mpp) REVERT: C 208 LEU cc_start: 0.8784 (mm) cc_final: 0.8552 (mm) REVERT: C 233 ASN cc_start: 0.9406 (m110) cc_final: 0.8860 (m110) REVERT: C 252 LEU cc_start: 0.7571 (mt) cc_final: 0.7279 (mt) REVERT: C 260 ILE cc_start: 0.6895 (pt) cc_final: 0.6679 (pt) REVERT: C 271 LEU cc_start: 0.8435 (mt) cc_final: 0.8043 (mt) REVERT: C 278 GLU cc_start: 0.8515 (mm-30) cc_final: 0.7982 (pm20) REVERT: D 20 MET cc_start: 0.8951 (mtm) cc_final: 0.8728 (mpp) REVERT: D 137 MET cc_start: 0.7698 (mtt) cc_final: 0.7495 (mtt) REVERT: D 138 ILE cc_start: 0.9755 (mm) cc_final: 0.9479 (mm) REVERT: D 148 ASP cc_start: 0.7213 (m-30) cc_final: 0.6892 (m-30) REVERT: D 186 GLN cc_start: 0.7620 (mm110) cc_final: 0.7299 (mm110) REVERT: D 219 GLU cc_start: 0.9139 (tp30) cc_final: 0.8871 (tp30) REVERT: D 266 LYS cc_start: 0.8807 (mmtp) cc_final: 0.8592 (mmmm) REVERT: D 315 LEU cc_start: 0.9297 (tp) cc_final: 0.9023 (pt) outliers start: 5 outliers final: 0 residues processed: 739 average time/residue: 0.1104 time to fit residues: 123.2905 Evaluate side-chains 629 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 629 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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: 6.9990 chunk 46 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN A 259 ASN A 320 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 GLN D 186 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.116906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.082586 restraints weight = 41988.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.085705 restraints weight = 21682.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.087822 restraints weight = 13531.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.089284 restraints weight = 9531.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.090291 restraints weight = 7307.198| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.6068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16386 Z= 0.244 Angle : 0.641 11.794 22134 Z= 0.339 Chirality : 0.044 0.288 2360 Planarity : 0.004 0.052 2818 Dihedral : 8.749 137.553 2290 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.06 % Allowed : 1.98 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.19), residues: 1932 helix: 1.27 (0.15), residues: 1122 sheet: 0.20 (0.42), residues: 100 loop : 0.04 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 235 TYR 0.036 0.002 TYR D 142 PHE 0.027 0.002 PHE D 168 TRP 0.032 0.002 TRP D 124 HIS 0.006 0.002 HIS D 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.24 (16386) covalent geometry : angle 0.64120 / 0.34 (22134) hydrogen bonds : bond 0.04040 / 2.58 ( 871) hydrogen bonds : angle 4.86700 / 3.53 ( 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 726 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 725 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9259 (tptp) cc_final: 0.8944 (tppt) REVERT: A 30 LYS cc_start: 0.9509 (tptp) cc_final: 0.9255 (tptp) REVERT: A 95 MET cc_start: 0.9154 (mmm) cc_final: 0.8841 (tpp) REVERT: A 107 LYS cc_start: 0.9182 (mttm) cc_final: 0.8918 (mtpp) REVERT: A 117 ARG cc_start: 0.9148 (ttm-80) cc_final: 0.8899 (ttm-80) REVERT: A 129 PHE cc_start: 0.9532 (m-10) cc_final: 0.9274 (m-80) REVERT: A 147 GLN cc_start: 0.9377 (mt0) cc_final: 0.8583 (mt0) REVERT: A 149 TYR cc_start: 0.9109 (t80) cc_final: 0.8622 (t80) REVERT: A 158 ASN cc_start: 0.9305 (m110) cc_final: 0.9102 (m-40) REVERT: A 195 LEU cc_start: 0.9701 (mt) cc_final: 0.9441 (mt) REVERT: A 214 LYS cc_start: 0.8873 (tppt) cc_final: 0.8643 (tppt) REVERT: A 223 VAL cc_start: 0.9757 (m) cc_final: 0.9184 (p) REVERT: A 227 MET cc_start: 0.9328 (mtm) cc_final: 0.8861 (mtm) REVERT: A 232 ASN cc_start: 0.8800 (m-40) cc_final: 0.8123 (m-40) REVERT: A 238 ASP cc_start: 0.8412 (p0) cc_final: 0.8055 (p0) REVERT: A 255 HIS cc_start: 0.8754 (t-90) cc_final: 0.7698 (t-90) REVERT: A 257 ASP cc_start: 0.9073 (m-30) cc_final: 0.8779 (m-30) REVERT: A 262 LEU cc_start: 0.9892 (mt) cc_final: 0.9637 (mt) REVERT: A 270 ASP cc_start: 0.9046 (t0) cc_final: 0.8769 (t0) REVERT: A 301 PHE cc_start: 0.9270 (m-80) cc_final: 0.9060 (m-10) REVERT: A 322 MET cc_start: 0.9119 (tpt) cc_final: 0.8799 (mmm) REVERT: A 333 LYS cc_start: 0.9557 (tppt) cc_final: 0.9214 (tppp) REVERT: A 335 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7199 (mm-30) REVERT: A 344 GLU cc_start: 0.9306 (mt-10) cc_final: 0.8751 (mt-10) REVERT: A 349 LEU cc_start: 0.9693 (mt) cc_final: 0.9478 (mt) REVERT: A 366 LYS cc_start: 0.9242 (mtmm) cc_final: 0.8999 (mtmm) REVERT: A 375 LYS cc_start: 0.8740 (mmtt) cc_final: 0.8227 (mmtm) REVERT: A 390 GLN cc_start: 0.8815 (mt0) cc_final: 0.8602 (mt0) REVERT: A 393 SER cc_start: 0.9380 (m) cc_final: 0.9066 (t) REVERT: A 415 ASN cc_start: 0.9364 (t0) cc_final: 0.8863 (t0) REVERT: A 459 LYS cc_start: 0.8954 (mttp) cc_final: 0.8523 (mtmt) REVERT: A 466 MET cc_start: 0.9085 (ptt) cc_final: 0.8813 (ptt) REVERT: A 493 MET cc_start: 0.8985 (tmm) cc_final: 0.8516 (tmm) REVERT: A 494 MET cc_start: 0.9338 (mtp) cc_final: 0.8984 (mtp) REVERT: A 501 GLN cc_start: 0.9338 (tt0) cc_final: 0.8656 (tm-30) REVERT: A 515 ASP cc_start: 0.8979 (m-30) cc_final: 0.8672 (m-30) REVERT: A 561 LEU cc_start: 0.9337 (tp) cc_final: 0.9001 (tp) REVERT: A 598 MET cc_start: 0.8348 (mtm) cc_final: 0.8099 (mtm) REVERT: A 601 ILE cc_start: 0.9623 (mm) cc_final: 0.9135 (mm) REVERT: A 645 GLN cc_start: 0.9242 (tp40) cc_final: 0.8826 (tp40) REVERT: A 654 PHE cc_start: 0.9524 (t80) cc_final: 0.8961 (t80) REVERT: A 669 ARG cc_start: 0.9104 (tpp-160) cc_final: 0.8730 (tpp-160) REVERT: B 8 LYS cc_start: 0.9427 (tptt) cc_final: 0.8976 (tppt) REVERT: B 30 LYS cc_start: 0.9531 (tmtt) cc_final: 0.9330 (tmtt) REVERT: B 55 LEU cc_start: 0.9763 (mt) cc_final: 0.9561 (mt) REVERT: B 58 LEU cc_start: 0.9778 (mt) cc_final: 0.9567 (mt) REVERT: B 88 LYS cc_start: 0.9440 (mptt) cc_final: 0.9209 (mmtt) REVERT: B 119 GLU cc_start: 0.9373 (mp0) cc_final: 0.9074 (mp0) REVERT: B 150 GLN cc_start: 0.9511 (tp40) cc_final: 0.9269 (tp-100) REVERT: B 167 LEU cc_start: 0.9110 (mt) cc_final: 0.8663 (mt) REVERT: B 172 LEU cc_start: 0.9431 (mp) cc_final: 0.9151 (mp) REVERT: B 176 ASN cc_start: 0.8799 (t0) cc_final: 0.8582 (t0) REVERT: B 181 ASP cc_start: 0.8699 (m-30) cc_final: 0.8321 (m-30) REVERT: B 184 ARG cc_start: 0.9370 (tpp80) cc_final: 0.8767 (tpp80) REVERT: B 187 ASP cc_start: 0.9148 (t0) cc_final: 0.8926 (t0) REVERT: B 211 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8096 (mm-30) REVERT: B 238 ASP cc_start: 0.8396 (t0) cc_final: 0.8016 (t70) REVERT: B 239 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8033 (tm-30) REVERT: B 252 ASN cc_start: 0.9420 (t0) cc_final: 0.9063 (t0) REVERT: B 322 MET cc_start: 0.9074 (mmm) cc_final: 0.8824 (mmm) REVERT: B 335 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8203 (mm-30) REVERT: B 348 MET cc_start: 0.9457 (ptm) cc_final: 0.8950 (ptp) REVERT: B 393 SER cc_start: 0.9404 (m) cc_final: 0.9088 (p) REVERT: B 402 GLU cc_start: 0.9027 (tp30) cc_final: 0.8819 (tp30) REVERT: B 410 ASN cc_start: 0.9016 (m-40) cc_final: 0.8758 (m-40) REVERT: B 494 MET cc_start: 0.9460 (mtp) cc_final: 0.9055 (mmt) REVERT: B 505 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8353 (mt-10) REVERT: B 550 MET cc_start: 0.8156 (mtp) cc_final: 0.7812 (mtm) REVERT: B 570 MET cc_start: 0.9058 (mtp) cc_final: 0.8350 (mtp) REVERT: B 588 GLN cc_start: 0.9338 (mm-40) cc_final: 0.8961 (mm-40) REVERT: B 599 GLU cc_start: 0.9044 (pm20) cc_final: 0.8754 (pm20) REVERT: B 639 ASP cc_start: 0.9148 (m-30) cc_final: 0.8839 (m-30) REVERT: B 640 MET cc_start: 0.9242 (tpp) cc_final: 0.8816 (tpp) REVERT: B 664 THR cc_start: 0.8880 (p) cc_final: 0.8231 (p) REVERT: B 668 ASN cc_start: 0.9068 (m110) cc_final: 0.8791 (m110) REVERT: B 683 TYR cc_start: 0.8940 (t80) cc_final: 0.8596 (t80) REVERT: C 20 MET cc_start: 0.9520 (tmm) cc_final: 0.9109 (ptp) REVERT: C 89 VAL cc_start: 0.6193 (t) cc_final: 0.5989 (t) REVERT: C 101 HIS cc_start: 0.8011 (m90) cc_final: 0.6787 (m90) REVERT: C 108 ILE cc_start: 0.8779 (mt) cc_final: 0.8485 (mt) REVERT: C 110 MET cc_start: 0.5535 (mpp) cc_final: 0.5208 (mpp) REVERT: C 158 VAL cc_start: 0.9692 (t) cc_final: 0.9203 (t) REVERT: C 162 TYR cc_start: 0.9360 (m-10) cc_final: 0.8670 (m-10) REVERT: C 173 TYR cc_start: 0.7431 (t80) cc_final: 0.6492 (t80) REVERT: C 177 TYR cc_start: 0.9140 (t80) cc_final: 0.8919 (t80) REVERT: C 179 TYR cc_start: 0.8565 (t80) cc_final: 0.8047 (t80) REVERT: C 185 MET cc_start: 0.5527 (mmm) cc_final: 0.5296 (mmp) REVERT: C 201 HIS cc_start: 0.9219 (m90) cc_final: 0.8662 (m90) REVERT: C 208 LEU cc_start: 0.8948 (mm) cc_final: 0.8702 (mm) REVERT: C 212 ILE cc_start: 0.8398 (mm) cc_final: 0.7802 (mm) REVERT: C 233 ASN cc_start: 0.9393 (m110) cc_final: 0.8835 (m110) REVERT: C 252 LEU cc_start: 0.7606 (mt) cc_final: 0.7289 (mt) REVERT: C 278 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8298 (pm20) REVERT: D 20 MET cc_start: 0.8971 (mtm) cc_final: 0.8712 (mpp) REVERT: D 148 ASP cc_start: 0.7000 (m-30) cc_final: 0.6697 (m-30) REVERT: D 176 LEU cc_start: 0.9634 (mt) cc_final: 0.9314 (tp) REVERT: D 201 HIS cc_start: 0.9394 (m170) cc_final: 0.9086 (m170) REVERT: D 207 LEU cc_start: 0.8478 (mt) cc_final: 0.8266 (mt) REVERT: D 219 GLU cc_start: 0.9167 (tp30) cc_final: 0.8942 (tp30) REVERT: D 266 LYS cc_start: 0.8838 (mmtp) cc_final: 0.8617 (mmmm) REVERT: D 269 MET cc_start: 0.8750 (ppp) cc_final: 0.8541 (ppp) REVERT: D 270 ASN cc_start: 0.8655 (m-40) cc_final: 0.8405 (m-40) outliers start: 1 outliers final: 1 residues processed: 726 average time/residue: 0.1144 time to fit residues: 125.4421 Evaluate side-chains 633 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 632 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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: 6.9990 chunk 183 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 52 optimal weight: 0.1980 chunk 28 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN A 34 HIS A 313 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN B 645 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.120811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.086277 restraints weight = 41497.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.089474 restraints weight = 21621.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.091630 restraints weight = 13393.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.093008 restraints weight = 9401.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.094092 restraints weight = 7249.593| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.6353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16386 Z= 0.127 Angle : 0.583 8.067 22134 Z= 0.310 Chirality : 0.042 0.216 2360 Planarity : 0.003 0.048 2818 Dihedral : 8.462 138.332 2290 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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 are not related in a simple way. whole: 1.06 (0.19), residues: 1932 helix: 1.26 (0.15), residues: 1136 sheet: -0.01 (0.42), residues: 110 loop : 0.02 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 243 TYR 0.034 0.001 TYR D 142 PHE 0.026 0.002 PHE C 166 TRP 0.035 0.001 TRP D 124 HIS 0.006 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (16386) covalent geometry : angle 0.58340 / 0.31 (22134) hydrogen bonds : bond 0.03808 / 2.43 ( 871) hydrogen bonds : angle 4.80709 / 3.50 ( 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 740 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 740 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9245 (tptp) cc_final: 0.8924 (tppt) REVERT: A 12 LEU cc_start: 0.9619 (mt) cc_final: 0.9359 (mt) REVERT: A 95 MET cc_start: 0.9040 (mmm) cc_final: 0.8698 (tpp) REVERT: A 112 LYS cc_start: 0.9438 (ptpt) cc_final: 0.9174 (ptpp) REVERT: A 147 GLN cc_start: 0.9284 (mt0) cc_final: 0.8528 (mt0) REVERT: A 149 TYR cc_start: 0.9117 (t80) cc_final: 0.8827 (t80) REVERT: A 172 LEU cc_start: 0.9542 (mp) cc_final: 0.9058 (mp) REVERT: A 195 LEU cc_start: 0.9684 (mt) cc_final: 0.9426 (mt) REVERT: A 214 LYS cc_start: 0.8849 (tppt) cc_final: 0.8599 (tppt) REVERT: A 223 VAL cc_start: 0.9760 (m) cc_final: 0.9266 (p) REVERT: A 227 MET cc_start: 0.9259 (mtm) cc_final: 0.8904 (mtm) REVERT: A 231 ASP cc_start: 0.8832 (t0) cc_final: 0.8622 (t0) REVERT: A 255 HIS cc_start: 0.8656 (t-90) cc_final: 0.8091 (t-90) REVERT: A 257 ASP cc_start: 0.9071 (m-30) cc_final: 0.8772 (m-30) REVERT: A 262 LEU cc_start: 0.9886 (mt) cc_final: 0.9640 (mt) REVERT: A 270 ASP cc_start: 0.8985 (t0) cc_final: 0.8676 (t0) REVERT: A 322 MET cc_start: 0.9002 (tpt) cc_final: 0.8570 (mmm) REVERT: A 344 GLU cc_start: 0.9269 (mt-10) cc_final: 0.8654 (mt-10) REVERT: A 345 LYS cc_start: 0.9808 (ttpt) cc_final: 0.9466 (ttmt) REVERT: A 349 LEU cc_start: 0.9686 (mt) cc_final: 0.9426 (mt) REVERT: A 366 LYS cc_start: 0.9223 (mtmm) cc_final: 0.8976 (mtmm) REVERT: A 375 LYS cc_start: 0.8653 (mmtt) cc_final: 0.8148 (mmtm) REVERT: A 390 GLN cc_start: 0.8803 (mt0) cc_final: 0.8570 (mt0) REVERT: A 393 SER cc_start: 0.9306 (m) cc_final: 0.8971 (t) REVERT: A 407 ILE cc_start: 0.9231 (mt) cc_final: 0.8921 (mt) REVERT: A 415 ASN cc_start: 0.9336 (t0) cc_final: 0.8849 (t0) REVERT: A 459 LYS cc_start: 0.8970 (mttp) cc_final: 0.8531 (mtmt) REVERT: A 466 MET cc_start: 0.9018 (ptt) cc_final: 0.8686 (ptt) REVERT: A 471 TYR cc_start: 0.9120 (t80) cc_final: 0.8662 (t80) REVERT: A 493 MET cc_start: 0.8959 (tmm) cc_final: 0.8471 (tmm) REVERT: A 494 MET cc_start: 0.9294 (mtp) cc_final: 0.8895 (mtp) REVERT: A 501 GLN cc_start: 0.9322 (tt0) cc_final: 0.8749 (tm-30) REVERT: A 515 ASP cc_start: 0.8892 (m-30) cc_final: 0.8518 (m-30) REVERT: A 561 LEU cc_start: 0.9314 (tp) cc_final: 0.8953 (tp) REVERT: A 595 MET cc_start: 0.8829 (mmp) cc_final: 0.8572 (mmp) REVERT: A 601 ILE cc_start: 0.9608 (mm) cc_final: 0.9256 (mm) REVERT: A 604 ARG cc_start: 0.9198 (mmm-85) cc_final: 0.8645 (mmp80) REVERT: A 645 GLN cc_start: 0.9161 (tp40) cc_final: 0.8818 (tp-100) REVERT: A 650 GLN cc_start: 0.8825 (mt0) cc_final: 0.8443 (mt0) REVERT: A 669 ARG cc_start: 0.9046 (tpp-160) cc_final: 0.8661 (tpp-160) REVERT: B 8 LYS cc_start: 0.9415 (tptt) cc_final: 0.8988 (tppt) REVERT: B 12 LEU cc_start: 0.9566 (mt) cc_final: 0.9307 (mt) REVERT: B 20 LYS cc_start: 0.9648 (tmtt) cc_final: 0.9424 (tptp) REVERT: B 21 ASP cc_start: 0.8565 (t70) cc_final: 0.8292 (t0) REVERT: B 30 LYS cc_start: 0.9536 (tmtt) cc_final: 0.9324 (tmtt) REVERT: B 55 LEU cc_start: 0.9779 (mt) cc_final: 0.9571 (mt) REVERT: B 58 LEU cc_start: 0.9762 (mt) cc_final: 0.9561 (mt) REVERT: B 87 LYS cc_start: 0.9357 (tptm) cc_final: 0.9084 (tppt) REVERT: B 88 LYS cc_start: 0.9371 (mptt) cc_final: 0.9120 (mmtt) REVERT: B 119 GLU cc_start: 0.9317 (mp0) cc_final: 0.9033 (mp0) REVERT: B 167 LEU cc_start: 0.9107 (mt) cc_final: 0.8753 (mt) REVERT: B 172 LEU cc_start: 0.9343 (mp) cc_final: 0.9052 (mp) REVERT: B 176 ASN cc_start: 0.8718 (t0) cc_final: 0.8491 (t0) REVERT: B 181 ASP cc_start: 0.8733 (m-30) cc_final: 0.8318 (m-30) REVERT: B 184 ARG cc_start: 0.9421 (tpp80) cc_final: 0.9155 (tpp80) REVERT: B 191 GLN cc_start: 0.9317 (mm-40) cc_final: 0.9003 (mt0) REVERT: B 211 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8091 (mm-30) REVERT: B 235 ARG cc_start: 0.9316 (ttm110) cc_final: 0.8807 (mtm-85) REVERT: B 238 ASP cc_start: 0.8373 (t0) cc_final: 0.8003 (t70) REVERT: B 239 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8069 (tm-30) REVERT: B 252 ASN cc_start: 0.9417 (t0) cc_final: 0.9053 (t0) REVERT: B 319 MET cc_start: 0.9239 (mmm) cc_final: 0.8853 (mmm) REVERT: B 321 GLU cc_start: 0.8637 (pp20) cc_final: 0.8254 (pp20) REVERT: B 322 MET cc_start: 0.9095 (mmm) cc_final: 0.8517 (mmm) REVERT: B 335 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8379 (mm-30) REVERT: B 348 MET cc_start: 0.9380 (ptm) cc_final: 0.9138 (ptp) REVERT: B 357 TYR cc_start: 0.8427 (m-80) cc_final: 0.7984 (m-80) REVERT: B 358 ILE cc_start: 0.9651 (mm) cc_final: 0.9448 (mm) REVERT: B 374 SER cc_start: 0.9398 (t) cc_final: 0.8825 (p) REVERT: B 393 SER cc_start: 0.9402 (m) cc_final: 0.9193 (p) REVERT: B 467 ASN cc_start: 0.8041 (m110) cc_final: 0.7785 (m110) REVERT: B 522 TYR cc_start: 0.9047 (m-10) cc_final: 0.8122 (m-10) REVERT: B 550 MET cc_start: 0.8284 (mtp) cc_final: 0.7796 (mtm) REVERT: B 570 MET cc_start: 0.8923 (mtp) cc_final: 0.7720 (mtp) REVERT: B 576 LEU cc_start: 0.9461 (mt) cc_final: 0.9103 (mt) REVERT: B 639 ASP cc_start: 0.9117 (m-30) cc_final: 0.8806 (m-30) REVERT: B 640 MET cc_start: 0.9254 (tpp) cc_final: 0.8571 (tpp) REVERT: C 20 MET cc_start: 0.9555 (tmm) cc_final: 0.9063 (ptp) REVERT: C 69 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8450 (tm-30) REVERT: C 101 HIS cc_start: 0.7941 (m90) cc_final: 0.6704 (m90) REVERT: C 110 MET cc_start: 0.5578 (mpp) cc_final: 0.5276 (mpp) REVERT: C 173 TYR cc_start: 0.7541 (t80) cc_final: 0.6788 (t80) REVERT: C 177 TYR cc_start: 0.9173 (t80) cc_final: 0.8929 (t80) REVERT: C 185 MET cc_start: 0.5452 (mmm) cc_final: 0.4648 (mpp) REVERT: C 201 HIS cc_start: 0.9305 (m90) cc_final: 0.8745 (m90) REVERT: C 208 LEU cc_start: 0.8913 (mm) cc_final: 0.8652 (mm) REVERT: C 212 ILE cc_start: 0.8297 (mm) cc_final: 0.7712 (mm) REVERT: C 233 ASN cc_start: 0.9404 (m110) cc_final: 0.8876 (m110) REVERT: C 252 LEU cc_start: 0.7576 (mt) cc_final: 0.7261 (mt) REVERT: C 278 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8339 (pm20) REVERT: C 321 TYR cc_start: 0.8888 (m-80) cc_final: 0.8612 (m-80) REVERT: D 20 MET cc_start: 0.8997 (mtm) cc_final: 0.8684 (mpp) REVERT: D 137 MET cc_start: 0.8307 (mtt) cc_final: 0.8080 (mtt) REVERT: D 148 ASP cc_start: 0.7063 (m-30) cc_final: 0.6759 (m-30) REVERT: D 219 GLU cc_start: 0.9181 (tp30) cc_final: 0.8957 (tp30) REVERT: D 270 ASN cc_start: 0.8628 (m-40) cc_final: 0.8428 (m-40) REVERT: D 315 LEU cc_start: 0.9290 (tp) cc_final: 0.9026 (pt) outliers start: 0 outliers final: 0 residues processed: 740 average time/residue: 0.1057 time to fit residues: 118.1439 Evaluate side-chains 640 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 640 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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: 5.9990 chunk 51 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN ** A 410 ASN ** 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 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 HIS ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.118975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.085064 restraints weight = 41388.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.088104 restraints weight = 21418.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.090197 restraints weight = 13545.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.091675 restraints weight = 9512.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.092666 restraints weight = 7268.063| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.6619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16386 Z= 0.159 Angle : 0.592 9.732 22134 Z= 0.315 Chirality : 0.042 0.204 2360 Planarity : 0.004 0.060 2818 Dihedral : 8.402 139.088 2290 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.19), residues: 1932 helix: 1.19 (0.15), residues: 1138 sheet: 0.19 (0.44), residues: 100 loop : -0.02 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 235 TYR 0.034 0.002 TYR D 142 PHE 0.027 0.002 PHE C 166 TRP 0.038 0.002 TRP D 124 HIS 0.006 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (16386) covalent geometry : angle 0.59160 / 0.31 (22134) hydrogen bonds : bond 0.03795 / 2.42 ( 871) hydrogen bonds : angle 4.81543 / 3.51 ( 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 717 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 717 time to evaluate : 0.623 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: A 8 LYS cc_start: 0.9216 (tptp) cc_final: 0.8935 (tppt) REVERT: A 12 LEU cc_start: 0.9622 (mt) cc_final: 0.9356 (mt) REVERT: A 95 MET cc_start: 0.9072 (mmm) cc_final: 0.8693 (tpp) REVERT: A 107 LYS cc_start: 0.9214 (mttm) cc_final: 0.8817 (mtpp) REVERT: A 147 GLN cc_start: 0.9274 (mt0) cc_final: 0.8299 (mt0) REVERT: A 149 TYR cc_start: 0.9321 (t80) cc_final: 0.8715 (t80) REVERT: A 158 ASN cc_start: 0.9293 (m110) cc_final: 0.9057 (m-40) REVERT: A 164 ARG cc_start: 0.8730 (ptm-80) cc_final: 0.7628 (ptm-80) REVERT: A 172 LEU cc_start: 0.9545 (mp) cc_final: 0.9196 (mp) REVERT: A 195 LEU cc_start: 0.9680 (mt) cc_final: 0.9416 (mt) REVERT: A 223 VAL cc_start: 0.9754 (m) cc_final: 0.9213 (p) REVERT: A 227 MET cc_start: 0.9286 (mtm) cc_final: 0.8848 (mtm) REVERT: A 255 HIS cc_start: 0.8638 (t-90) cc_final: 0.8324 (t-90) REVERT: A 257 ASP cc_start: 0.9088 (m-30) cc_final: 0.8812 (m-30) REVERT: A 262 LEU cc_start: 0.9901 (mt) cc_final: 0.9659 (mt) REVERT: A 263 ASP cc_start: 0.9355 (m-30) cc_final: 0.9090 (m-30) REVERT: A 270 ASP cc_start: 0.9028 (t0) cc_final: 0.8723 (t0) REVERT: A 301 PHE cc_start: 0.9134 (m-10) cc_final: 0.8664 (m-10) REVERT: A 322 MET cc_start: 0.8797 (tpt) cc_final: 0.8386 (mmm) REVERT: A 335 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8125 (mm-30) REVERT: A 344 GLU cc_start: 0.9282 (mt-10) cc_final: 0.8632 (mt-10) REVERT: A 345 LYS cc_start: 0.9819 (ttpt) cc_final: 0.9465 (ttmt) REVERT: A 349 LEU cc_start: 0.9686 (mt) cc_final: 0.9409 (mt) REVERT: A 366 LYS cc_start: 0.9275 (mtmm) cc_final: 0.9007 (mtmm) REVERT: A 371 ASN cc_start: 0.8798 (m-40) cc_final: 0.8476 (m-40) REVERT: A 375 LYS cc_start: 0.8748 (mmtt) cc_final: 0.8411 (mmtm) REVERT: A 390 GLN cc_start: 0.8795 (mt0) cc_final: 0.8589 (mt0) REVERT: A 393 SER cc_start: 0.9293 (m) cc_final: 0.8002 (p) REVERT: A 402 GLU cc_start: 0.8133 (mp0) cc_final: 0.7110 (mp0) REVERT: A 407 ILE cc_start: 0.9323 (mt) cc_final: 0.9090 (mt) REVERT: A 415 ASN cc_start: 0.9329 (t0) cc_final: 0.8249 (t0) REVERT: A 418 ASN cc_start: 0.9125 (m110) cc_final: 0.8443 (m-40) REVERT: A 459 LYS cc_start: 0.8974 (mttp) cc_final: 0.8520 (mtmt) REVERT: A 493 MET cc_start: 0.8931 (tmm) cc_final: 0.8599 (tmm) REVERT: A 494 MET cc_start: 0.9315 (mtp) cc_final: 0.8961 (mtp) REVERT: A 501 GLN cc_start: 0.9343 (tt0) cc_final: 0.8781 (tm-30) REVERT: A 515 ASP cc_start: 0.8947 (m-30) cc_final: 0.8601 (m-30) REVERT: A 561 LEU cc_start: 0.9370 (tp) cc_final: 0.8924 (tp) REVERT: A 604 ARG cc_start: 0.9231 (mmm-85) cc_final: 0.8724 (mmp80) REVERT: A 615 MET cc_start: 0.9197 (mmm) cc_final: 0.8858 (mmm) REVERT: A 645 GLN cc_start: 0.9149 (tp40) cc_final: 0.8852 (tp40) REVERT: A 650 GLN cc_start: 0.8806 (mt0) cc_final: 0.8465 (mt0) REVERT: A 654 PHE cc_start: 0.9328 (t80) cc_final: 0.8736 (t80) REVERT: A 669 ARG cc_start: 0.9078 (tpp-160) cc_final: 0.8861 (tpp-160) REVERT: B 8 LYS cc_start: 0.9407 (tptt) cc_final: 0.8987 (tppt) REVERT: B 12 LEU cc_start: 0.9580 (mt) cc_final: 0.9314 (mt) REVERT: B 30 LYS cc_start: 0.9535 (tmtt) cc_final: 0.9326 (tmtt) REVERT: B 55 LEU cc_start: 0.9781 (mt) cc_final: 0.9579 (mt) REVERT: B 58 LEU cc_start: 0.9786 (mt) cc_final: 0.9582 (mt) REVERT: B 87 LYS cc_start: 0.9404 (tptm) cc_final: 0.9161 (tppt) REVERT: B 107 LYS cc_start: 0.9459 (mmmt) cc_final: 0.8883 (mmmt) REVERT: B 111 LYS cc_start: 0.9682 (mptt) cc_final: 0.9393 (mmtt) REVERT: B 119 GLU cc_start: 0.9341 (mp0) cc_final: 0.9050 (mp0) REVERT: B 167 LEU cc_start: 0.9132 (mt) cc_final: 0.8834 (mt) REVERT: B 172 LEU cc_start: 0.9391 (mp) cc_final: 0.9113 (mp) REVERT: B 181 ASP cc_start: 0.8673 (m-30) cc_final: 0.8297 (m-30) REVERT: B 184 ARG cc_start: 0.9377 (tpp80) cc_final: 0.9074 (tpp80) REVERT: B 191 GLN cc_start: 0.9400 (mm-40) cc_final: 0.8980 (mt0) REVERT: B 235 ARG cc_start: 0.9186 (ttm110) cc_final: 0.8624 (mtm-85) REVERT: B 238 ASP cc_start: 0.8421 (t0) cc_final: 0.7800 (t70) REVERT: B 239 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8298 (tm-30) REVERT: B 252 ASN cc_start: 0.9439 (t0) cc_final: 0.9089 (t0) REVERT: B 263 ASP cc_start: 0.9288 (m-30) cc_final: 0.8829 (m-30) REVERT: B 319 MET cc_start: 0.9215 (mmm) cc_final: 0.8804 (mmm) REVERT: B 321 GLU cc_start: 0.8652 (pp20) cc_final: 0.8312 (pp20) REVERT: B 322 MET cc_start: 0.9050 (mmm) cc_final: 0.8360 (mmm) REVERT: B 335 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8401 (mm-30) REVERT: B 348 MET cc_start: 0.9430 (ptm) cc_final: 0.8932 (ptt) REVERT: B 374 SER cc_start: 0.9461 (t) cc_final: 0.8873 (p) REVERT: B 393 SER cc_start: 0.9398 (m) cc_final: 0.9173 (p) REVERT: B 410 ASN cc_start: 0.9024 (m-40) cc_final: 0.8749 (m-40) REVERT: B 494 MET cc_start: 0.9360 (mtp) cc_final: 0.9085 (mmt) REVERT: B 522 TYR cc_start: 0.9041 (m-10) cc_final: 0.8364 (m-10) REVERT: B 550 MET cc_start: 0.8308 (mtp) cc_final: 0.7994 (mtm) REVERT: B 570 MET cc_start: 0.8971 (mtp) cc_final: 0.7593 (mtp) REVERT: B 604 ARG cc_start: 0.9141 (tpp80) cc_final: 0.8832 (tpp80) REVERT: B 610 LYS cc_start: 0.8623 (tmmt) cc_final: 0.8037 (tmmt) REVERT: B 612 TYR cc_start: 0.8949 (m-80) cc_final: 0.8565 (m-80) REVERT: B 639 ASP cc_start: 0.9046 (m-30) cc_final: 0.8800 (m-30) REVERT: B 640 MET cc_start: 0.9150 (tpp) cc_final: 0.8577 (tpp) REVERT: B 667 LEU cc_start: 0.9403 (tp) cc_final: 0.8893 (tp) REVERT: B 668 ASN cc_start: 0.9121 (m-40) cc_final: 0.8908 (m-40) REVERT: C 20 MET cc_start: 0.9564 (tmm) cc_final: 0.9025 (ptp) REVERT: C 69 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8191 (tm-30) REVERT: C 101 HIS cc_start: 0.8036 (m90) cc_final: 0.6803 (m90) REVERT: C 110 MET cc_start: 0.5306 (mpp) cc_final: 0.4958 (mpp) REVERT: C 173 TYR cc_start: 0.7661 (t80) cc_final: 0.6940 (t80) REVERT: C 177 TYR cc_start: 0.9127 (t80) cc_final: 0.8885 (t80) REVERT: C 179 TYR cc_start: 0.8139 (t80) cc_final: 0.7742 (t80) REVERT: C 185 MET cc_start: 0.5832 (mmm) cc_final: 0.4501 (mpp) REVERT: C 201 HIS cc_start: 0.9329 (m90) cc_final: 0.8682 (m90) REVERT: C 208 LEU cc_start: 0.8921 (mm) cc_final: 0.8715 (mt) REVERT: C 252 LEU cc_start: 0.7531 (mt) cc_final: 0.7183 (mt) REVERT: C 271 LEU cc_start: 0.9041 (tp) cc_final: 0.8675 (mt) REVERT: C 278 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8376 (pm20) REVERT: D 20 MET cc_start: 0.9007 (mtm) cc_final: 0.8677 (mpp) REVERT: D 148 ASP cc_start: 0.7039 (m-30) cc_final: 0.6718 (m-30) REVERT: D 176 LEU cc_start: 0.9597 (mt) cc_final: 0.9248 (tp) REVERT: D 201 HIS cc_start: 0.9403 (m170) cc_final: 0.9168 (m170) REVERT: D 219 GLU cc_start: 0.9180 (tp30) cc_final: 0.8957 (tp30) outliers start: 0 outliers final: 0 residues processed: 717 average time/residue: 0.1062 time to fit residues: 114.9301 Evaluate side-chains 631 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 631 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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: 7.9990 chunk 99 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 158 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN A 320 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN B 180 ASN B 363 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.117902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.083639 restraints weight = 42483.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.086705 restraints weight = 22054.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.088815 restraints weight = 13785.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.090171 restraints weight = 9731.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.091225 restraints weight = 7522.322| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.6875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16386 Z= 0.220 Angle : 0.651 9.170 22134 Z= 0.347 Chirality : 0.044 0.373 2360 Planarity : 0.004 0.052 2818 Dihedral : 8.600 140.179 2290 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.19), residues: 1932 helix: 1.08 (0.15), residues: 1141 sheet: 0.27 (0.44), residues: 100 loop : -0.17 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 243 TYR 0.030 0.002 TYR D 142 PHE 0.024 0.002 PHE A 301 TRP 0.041 0.002 TRP D 124 HIS 0.007 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.22 (16386) covalent geometry : angle 0.65104 / 0.35 (22134) hydrogen bonds : bond 0.03961 / 2.50 ( 871) hydrogen bonds : angle 4.96968 / 3.63 ( 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 711 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 711 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9219 (tptp) cc_final: 0.8939 (tppt) REVERT: A 12 LEU cc_start: 0.9614 (mt) cc_final: 0.9355 (mt) REVERT: A 71 LEU cc_start: 0.9714 (mt) cc_final: 0.9511 (mt) REVERT: A 95 MET cc_start: 0.9161 (mmm) cc_final: 0.8764 (tpp) REVERT: A 107 LYS cc_start: 0.9196 (mttm) cc_final: 0.8937 (mtpp) REVERT: A 147 GLN cc_start: 0.9388 (mt0) cc_final: 0.8490 (mt0) REVERT: A 149 TYR cc_start: 0.9287 (t80) cc_final: 0.8644 (t80) REVERT: A 158 ASN cc_start: 0.9359 (m110) cc_final: 0.9150 (m-40) REVERT: A 164 ARG cc_start: 0.9004 (ptm-80) cc_final: 0.7599 (ptm-80) REVERT: A 195 LEU cc_start: 0.9655 (mt) cc_final: 0.9391 (mt) REVERT: A 214 LYS cc_start: 0.8889 (mmpt) cc_final: 0.8661 (mmtt) REVERT: A 223 VAL cc_start: 0.9793 (m) cc_final: 0.9291 (p) REVERT: A 227 MET cc_start: 0.9255 (mtm) cc_final: 0.8940 (mtm) REVERT: A 232 ASN cc_start: 0.9125 (m110) cc_final: 0.8759 (m110) REVERT: A 255 HIS cc_start: 0.8609 (t-90) cc_final: 0.7680 (t-90) REVERT: A 257 ASP cc_start: 0.9031 (m-30) cc_final: 0.8724 (m-30) REVERT: A 262 LEU cc_start: 0.9899 (mt) cc_final: 0.9676 (mt) REVERT: A 301 PHE cc_start: 0.9252 (m-10) cc_final: 0.8738 (m-10) REVERT: A 322 MET cc_start: 0.8787 (tpt) cc_final: 0.8524 (mmm) REVERT: A 333 LYS cc_start: 0.9608 (tppt) cc_final: 0.9210 (tppp) REVERT: A 335 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8031 (mm-30) REVERT: A 344 GLU cc_start: 0.9304 (mt-10) cc_final: 0.8697 (mt-10) REVERT: A 345 LYS cc_start: 0.9819 (ttpt) cc_final: 0.9448 (ttmt) REVERT: A 349 LEU cc_start: 0.9696 (mt) cc_final: 0.9451 (mt) REVERT: A 365 ASN cc_start: 0.9210 (m-40) cc_final: 0.8838 (m-40) REVERT: A 366 LYS cc_start: 0.9315 (mtmm) cc_final: 0.9064 (mtmm) REVERT: A 375 LYS cc_start: 0.8899 (mmtt) cc_final: 0.8683 (mmtm) REVERT: A 390 GLN cc_start: 0.8912 (mt0) cc_final: 0.8682 (mt0) REVERT: A 393 SER cc_start: 0.9291 (m) cc_final: 0.8154 (t) REVERT: A 402 GLU cc_start: 0.8215 (mp0) cc_final: 0.7435 (mp0) REVERT: A 415 ASN cc_start: 0.9364 (t0) cc_final: 0.8526 (t0) REVERT: A 418 ASN cc_start: 0.9186 (m110) cc_final: 0.8579 (m110) REVERT: A 459 LYS cc_start: 0.8965 (mttp) cc_final: 0.8525 (mtmt) REVERT: A 466 MET cc_start: 0.9129 (ptt) cc_final: 0.8922 (ptt) REVERT: A 493 MET cc_start: 0.8941 (tmm) cc_final: 0.8576 (tmm) REVERT: A 494 MET cc_start: 0.9287 (mtp) cc_final: 0.8918 (mtp) REVERT: A 501 GLN cc_start: 0.9343 (tt0) cc_final: 0.8785 (tm-30) REVERT: A 515 ASP cc_start: 0.8966 (m-30) cc_final: 0.8748 (m-30) REVERT: A 561 LEU cc_start: 0.9446 (tp) cc_final: 0.9061 (tp) REVERT: A 601 ILE cc_start: 0.9626 (mm) cc_final: 0.9341 (mm) REVERT: A 615 MET cc_start: 0.9195 (mmm) cc_final: 0.8833 (mmm) REVERT: A 645 GLN cc_start: 0.9199 (tp40) cc_final: 0.8927 (tp40) REVERT: A 654 PHE cc_start: 0.9362 (t80) cc_final: 0.8752 (t80) REVERT: A 669 ARG cc_start: 0.9080 (tpp-160) cc_final: 0.8862 (tpp-160) REVERT: B 8 LYS cc_start: 0.9411 (tptt) cc_final: 0.8999 (tppt) REVERT: B 12 LEU cc_start: 0.9592 (mt) cc_final: 0.9324 (mt) REVERT: B 30 LYS cc_start: 0.9534 (tmtt) cc_final: 0.9328 (tmtt) REVERT: B 55 LEU cc_start: 0.9776 (mt) cc_final: 0.9556 (mt) REVERT: B 88 LYS cc_start: 0.9239 (tttp) cc_final: 0.8976 (tptt) REVERT: B 98 PHE cc_start: 0.9324 (t80) cc_final: 0.8961 (t80) REVERT: B 107 LYS cc_start: 0.9286 (mmmt) cc_final: 0.8892 (mmmt) REVERT: B 119 GLU cc_start: 0.9333 (mp0) cc_final: 0.9001 (mp0) REVERT: B 143 LEU cc_start: 0.9295 (tp) cc_final: 0.8373 (tp) REVERT: B 148 GLU cc_start: 0.8839 (mp0) cc_final: 0.7744 (mp0) REVERT: B 149 TYR cc_start: 0.9060 (t80) cc_final: 0.8690 (t80) REVERT: B 173 LEU cc_start: 0.9379 (mt) cc_final: 0.9146 (mt) REVERT: B 181 ASP cc_start: 0.8526 (m-30) cc_final: 0.8111 (m-30) REVERT: B 191 GLN cc_start: 0.9374 (mm-40) cc_final: 0.9064 (mt0) REVERT: B 235 ARG cc_start: 0.9153 (ttm110) cc_final: 0.8495 (ttm110) REVERT: B 238 ASP cc_start: 0.8399 (t0) cc_final: 0.7814 (t70) REVERT: B 239 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8212 (tm-30) REVERT: B 252 ASN cc_start: 0.9502 (t0) cc_final: 0.9287 (t0) REVERT: B 263 ASP cc_start: 0.9313 (m-30) cc_final: 0.8876 (m-30) REVERT: B 279 SER cc_start: 0.8581 (m) cc_final: 0.8374 (t) REVERT: B 319 MET cc_start: 0.9243 (mmm) cc_final: 0.8813 (mmm) REVERT: B 322 MET cc_start: 0.9078 (mmm) cc_final: 0.8496 (mmm) REVERT: B 335 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8433 (mm-30) REVERT: B 348 MET cc_start: 0.9429 (ptm) cc_final: 0.8978 (ptp) REVERT: B 393 SER cc_start: 0.9374 (m) cc_final: 0.8994 (p) REVERT: B 402 GLU cc_start: 0.8978 (tp30) cc_final: 0.8725 (tp30) REVERT: B 410 ASN cc_start: 0.9006 (m-40) cc_final: 0.8736 (m-40) REVERT: B 494 MET cc_start: 0.9415 (mtp) cc_final: 0.9066 (mmt) REVERT: B 522 TYR cc_start: 0.9053 (m-10) cc_final: 0.8565 (m-10) REVERT: B 550 MET cc_start: 0.8257 (mtp) cc_final: 0.7790 (mtm) REVERT: B 570 MET cc_start: 0.9042 (mtp) cc_final: 0.7713 (mtp) REVERT: B 573 SER cc_start: 0.9682 (p) cc_final: 0.9419 (p) REVERT: B 604 ARG cc_start: 0.9154 (tpp80) cc_final: 0.8917 (tpp80) REVERT: B 634 MET cc_start: 0.9453 (mmm) cc_final: 0.8983 (mpp) REVERT: B 639 ASP cc_start: 0.9047 (m-30) cc_final: 0.8810 (m-30) REVERT: B 640 MET cc_start: 0.9116 (tpp) cc_final: 0.8553 (tpp) REVERT: B 668 ASN cc_start: 0.9182 (m-40) cc_final: 0.8981 (m-40) REVERT: B 671 ASP cc_start: 0.9061 (m-30) cc_final: 0.8844 (m-30) REVERT: C 17 PHE cc_start: 0.8998 (p90) cc_final: 0.8692 (p90) REVERT: C 20 MET cc_start: 0.9598 (tmm) cc_final: 0.9331 (tmm) REVERT: C 37 LEU cc_start: 0.2591 (tp) cc_final: 0.2346 (tp) REVERT: C 69 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7890 (tm-30) REVERT: C 101 HIS cc_start: 0.7859 (m90) cc_final: 0.6872 (m90) REVERT: C 173 TYR cc_start: 0.7719 (t80) cc_final: 0.7154 (t80) REVERT: C 174 TYR cc_start: 0.7906 (t80) cc_final: 0.7417 (t80) REVERT: C 177 TYR cc_start: 0.9145 (t80) cc_final: 0.8904 (t80) REVERT: C 179 TYR cc_start: 0.8185 (t80) cc_final: 0.7886 (t80) REVERT: C 185 MET cc_start: 0.6203 (mmm) cc_final: 0.4826 (mpp) REVERT: C 201 HIS cc_start: 0.9400 (m90) cc_final: 0.8680 (m90) REVERT: C 233 ASN cc_start: 0.9429 (m110) cc_final: 0.8742 (m110) REVERT: C 252 LEU cc_start: 0.7414 (mt) cc_final: 0.7209 (mt) REVERT: C 271 LEU cc_start: 0.9126 (tp) cc_final: 0.8776 (mt) REVERT: C 278 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8460 (pm20) REVERT: D 20 MET cc_start: 0.9052 (mtm) cc_final: 0.8698 (mpp) REVERT: D 148 ASP cc_start: 0.7013 (m-30) cc_final: 0.6723 (m-30) REVERT: D 154 PHE cc_start: 0.7989 (t80) cc_final: 0.7680 (t80) REVERT: D 176 LEU cc_start: 0.9572 (mt) cc_final: 0.9305 (tp) REVERT: D 219 GLU cc_start: 0.9207 (tp30) cc_final: 0.8999 (tp30) REVERT: D 224 LEU cc_start: 0.8377 (mt) cc_final: 0.8063 (mt) REVERT: D 240 LEU cc_start: 0.7879 (mt) cc_final: 0.7604 (mt) REVERT: D 270 ASN cc_start: 0.8661 (m-40) cc_final: 0.8425 (m-40) outliers start: 0 outliers final: 0 residues processed: 711 average time/residue: 0.1054 time to fit residues: 113.7848 Evaluate side-chains 633 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 633 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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: 0.9980 chunk 133 optimal weight: 0.0870 chunk 149 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 100 optimal weight: 0.0020 chunk 88 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.5766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN A 19 GLN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 ASN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN C 263 ASN D 270 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.122826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.088900 restraints weight = 41140.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.092072 restraints weight = 21281.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.094255 restraints weight = 13190.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.095730 restraints weight = 9210.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.096788 restraints weight = 6989.270| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.7106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16386 Z= 0.129 Angle : 0.622 9.149 22134 Z= 0.327 Chirality : 0.043 0.289 2360 Planarity : 0.004 0.057 2818 Dihedral : 8.230 138.966 2290 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.19), residues: 1932 helix: 1.01 (0.15), residues: 1155 sheet: 0.27 (0.45), residues: 100 loop : -0.20 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 243 TYR 0.028 0.001 TYR D 142 PHE 0.026 0.002 PHE B 492 TRP 0.042 0.002 TRP D 124 HIS 0.006 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (16386) covalent geometry : angle 0.62208 / 0.33 (22134) hydrogen bonds : bond 0.03816 / 2.44 ( 871) hydrogen bonds : angle 4.90271 / 3.57 ( 2571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 741 time to evaluate : 0.376 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: A 8 LYS cc_start: 0.9197 (tptp) cc_final: 0.8875 (tppt) REVERT: A 12 LEU cc_start: 0.9605 (mt) cc_final: 0.9239 (mt) REVERT: A 107 LYS cc_start: 0.9187 (mttm) cc_final: 0.8823 (mtpp) REVERT: A 110 ASP cc_start: 0.9477 (p0) cc_final: 0.9226 (p0) REVERT: A 128 PHE cc_start: 0.9557 (t80) cc_final: 0.9347 (t80) REVERT: A 139 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8822 (mp0) REVERT: A 147 GLN cc_start: 0.9252 (mt0) cc_final: 0.8285 (mt0) REVERT: A 149 TYR cc_start: 0.9225 (t80) cc_final: 0.8809 (t80) REVERT: A 172 LEU cc_start: 0.9537 (mp) cc_final: 0.9110 (mp) REVERT: A 179 LEU cc_start: 0.9650 (tp) cc_final: 0.9448 (tp) REVERT: A 181 ASP cc_start: 0.8912 (m-30) cc_final: 0.8432 (m-30) REVERT: A 195 LEU cc_start: 0.9637 (mt) cc_final: 0.9373 (mt) REVERT: A 214 LYS cc_start: 0.8894 (mmpt) cc_final: 0.8627 (mmtt) REVERT: A 223 VAL cc_start: 0.9756 (m) cc_final: 0.9191 (p) REVERT: A 227 MET cc_start: 0.9295 (mtm) cc_final: 0.8842 (mtm) REVERT: A 231 ASP cc_start: 0.8740 (t70) cc_final: 0.8460 (t0) REVERT: A 238 ASP cc_start: 0.8109 (p0) cc_final: 0.7768 (p0) REVERT: A 252 ASN cc_start: 0.9438 (t0) cc_final: 0.9228 (t0) REVERT: A 255 HIS cc_start: 0.8580 (t-90) cc_final: 0.8179 (t-90) REVERT: A 257 ASP cc_start: 0.9082 (m-30) cc_final: 0.8778 (m-30) REVERT: A 262 LEU cc_start: 0.9878 (mt) cc_final: 0.9616 (mt) REVERT: A 263 ASP cc_start: 0.9288 (m-30) cc_final: 0.9003 (m-30) REVERT: A 295 ASP cc_start: 0.9429 (t0) cc_final: 0.9193 (t0) REVERT: A 301 PHE cc_start: 0.9086 (m-10) cc_final: 0.8524 (m-10) REVERT: A 333 LYS cc_start: 0.9562 (tppt) cc_final: 0.9176 (tppp) REVERT: A 335 GLU cc_start: 0.8434 (mm-30) cc_final: 0.7895 (mm-30) REVERT: A 344 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8567 (mt-10) REVERT: A 345 LYS cc_start: 0.9808 (ttpt) cc_final: 0.9454 (ttmt) REVERT: A 349 LEU cc_start: 0.9688 (mt) cc_final: 0.9438 (mt) REVERT: A 365 ASN cc_start: 0.9319 (m-40) cc_final: 0.8988 (m-40) REVERT: A 366 LYS cc_start: 0.9261 (mtmm) cc_final: 0.9032 (mtmm) REVERT: A 390 GLN cc_start: 0.8796 (mt0) cc_final: 0.8588 (mt0) REVERT: A 393 SER cc_start: 0.9309 (m) cc_final: 0.7807 (p) REVERT: A 401 ASP cc_start: 0.9440 (m-30) cc_final: 0.8720 (m-30) REVERT: A 402 GLU cc_start: 0.8242 (mp0) cc_final: 0.7253 (mp0) REVERT: A 407 ILE cc_start: 0.9306 (mt) cc_final: 0.9051 (mt) REVERT: A 415 ASN cc_start: 0.9348 (t0) cc_final: 0.8423 (t0) REVERT: A 418 ASN cc_start: 0.9142 (m110) cc_final: 0.8527 (m-40) REVERT: A 459 LYS cc_start: 0.8958 (mttp) cc_final: 0.8453 (mtmm) REVERT: A 466 MET cc_start: 0.9041 (ptt) cc_final: 0.8828 (ptt) REVERT: A 474 GLN cc_start: 0.9351 (mt0) cc_final: 0.9135 (mm110) REVERT: A 493 MET cc_start: 0.8913 (tmm) cc_final: 0.8538 (tmm) REVERT: A 494 MET cc_start: 0.9271 (mtp) cc_final: 0.8918 (mtp) REVERT: A 501 GLN cc_start: 0.9340 (tt0) cc_final: 0.8804 (tm-30) REVERT: A 515 ASP cc_start: 0.8914 (m-30) cc_final: 0.8589 (m-30) REVERT: A 550 MET cc_start: 0.8835 (mmt) cc_final: 0.8471 (mmt) REVERT: A 561 LEU cc_start: 0.9377 (tp) cc_final: 0.9023 (tp) REVERT: A 601 ILE cc_start: 0.9399 (mm) cc_final: 0.9192 (mm) REVERT: A 615 MET cc_start: 0.9236 (mmm) cc_final: 0.8911 (mmm) REVERT: A 633 ASP cc_start: 0.9090 (t0) cc_final: 0.8575 (t0) REVERT: A 645 GLN cc_start: 0.9121 (tp40) cc_final: 0.8765 (tp-100) REVERT: A 654 PHE cc_start: 0.9239 (t80) cc_final: 0.8915 (t80) REVERT: A 669 ARG cc_start: 0.9003 (tpp-160) cc_final: 0.8799 (tpp-160) REVERT: B 8 LYS cc_start: 0.9416 (tptt) cc_final: 0.9057 (tppt) REVERT: B 12 LEU cc_start: 0.9570 (mt) cc_final: 0.9317 (mt) REVERT: B 20 LYS cc_start: 0.9637 (tmtt) cc_final: 0.9407 (tptp) REVERT: B 21 ASP cc_start: 0.8526 (t70) cc_final: 0.8230 (t0) REVERT: B 30 LYS cc_start: 0.9528 (tmtt) cc_final: 0.9311 (tmtt) REVERT: B 98 PHE cc_start: 0.9363 (t80) cc_final: 0.8837 (t80) REVERT: B 111 LYS cc_start: 0.9635 (mptt) cc_final: 0.9360 (mmtt) REVERT: B 119 GLU cc_start: 0.9235 (mp0) cc_final: 0.8970 (mp0) REVERT: B 143 LEU cc_start: 0.9239 (tp) cc_final: 0.8554 (tp) REVERT: B 148 GLU cc_start: 0.8941 (mp0) cc_final: 0.8093 (pm20) REVERT: B 167 LEU cc_start: 0.9143 (mt) cc_final: 0.8824 (mt) REVERT: B 173 LEU cc_start: 0.9420 (mt) cc_final: 0.9193 (mt) REVERT: B 181 ASP cc_start: 0.8576 (m-30) cc_final: 0.8214 (m-30) REVERT: B 191 GLN cc_start: 0.9312 (mm-40) cc_final: 0.8954 (mt0) REVERT: B 236 TYR cc_start: 0.9192 (t80) cc_final: 0.8885 (t80) REVERT: B 238 ASP cc_start: 0.8438 (t0) cc_final: 0.7771 (t70) REVERT: B 239 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8355 (tm-30) REVERT: B 252 ASN cc_start: 0.9505 (t0) cc_final: 0.9289 (t0) REVERT: B 263 ASP cc_start: 0.9167 (m-30) cc_final: 0.8738 (m-30) REVERT: B 276 LYS cc_start: 0.9118 (ptpt) cc_final: 0.8912 (ptmm) REVERT: B 321 GLU cc_start: 0.8674 (pp20) cc_final: 0.8312 (pp20) REVERT: B 322 MET cc_start: 0.9070 (mmm) cc_final: 0.8363 (mmm) REVERT: B 335 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8233 (mm-30) REVERT: B 374 SER cc_start: 0.9416 (t) cc_final: 0.8825 (p) REVERT: B 384 GLU cc_start: 0.8762 (pm20) cc_final: 0.8221 (pm20) REVERT: B 393 SER cc_start: 0.9354 (m) cc_final: 0.9064 (p) REVERT: B 402 GLU cc_start: 0.8927 (tp30) cc_final: 0.8682 (tp30) REVERT: B 410 ASN cc_start: 0.8990 (m-40) cc_final: 0.8520 (m-40) REVERT: B 522 TYR cc_start: 0.9028 (m-10) cc_final: 0.8402 (m-10) REVERT: B 550 MET cc_start: 0.8333 (mtp) cc_final: 0.7995 (mtm) REVERT: B 570 MET cc_start: 0.8903 (mtp) cc_final: 0.7414 (mtp) REVERT: B 573 SER cc_start: 0.9630 (p) cc_final: 0.9315 (p) REVERT: B 576 LEU cc_start: 0.9473 (mt) cc_final: 0.9210 (mt) REVERT: B 639 ASP cc_start: 0.9018 (m-30) cc_final: 0.8761 (m-30) REVERT: B 640 MET cc_start: 0.9157 (tpp) cc_final: 0.8519 (tpp) REVERT: B 667 LEU cc_start: 0.9305 (tp) cc_final: 0.8873 (tp) REVERT: B 671 ASP cc_start: 0.9001 (m-30) cc_final: 0.8726 (m-30) REVERT: B 680 LYS cc_start: 0.9221 (mttt) cc_final: 0.8912 (mtpt) REVERT: C 17 PHE cc_start: 0.8976 (p90) cc_final: 0.8720 (p90) REVERT: C 20 MET cc_start: 0.9559 (tmm) cc_final: 0.9303 (tmm) REVERT: C 37 LEU cc_start: 0.2634 (tp) cc_final: 0.2402 (tp) REVERT: C 69 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7444 (pp30) REVERT: C 74 MET cc_start: 0.8974 (mmm) cc_final: 0.8773 (mpp) REVERT: C 101 HIS cc_start: 0.7673 (m90) cc_final: 0.6788 (m90) REVERT: C 118 ILE cc_start: 0.9146 (pt) cc_final: 0.8634 (pt) REVERT: C 122 PHE cc_start: 0.7987 (m-80) cc_final: 0.7527 (m-80) REVERT: C 173 TYR cc_start: 0.7831 (t80) cc_final: 0.7177 (t80) REVERT: C 177 TYR cc_start: 0.9113 (t80) cc_final: 0.8855 (t80) REVERT: C 179 TYR cc_start: 0.8184 (t80) cc_final: 0.7828 (t80) REVERT: C 185 MET cc_start: 0.6111 (mmm) cc_final: 0.4917 (mpp) REVERT: C 201 HIS cc_start: 0.9315 (m90) cc_final: 0.8600 (m90) REVERT: C 233 ASN cc_start: 0.9415 (m110) cc_final: 0.8905 (m110) REVERT: C 252 LEU cc_start: 0.7328 (mt) cc_final: 0.6996 (mt) REVERT: C 278 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8487 (pm20) REVERT: C 321 TYR cc_start: 0.9020 (m-80) cc_final: 0.8633 (m-80) REVERT: D 20 MET cc_start: 0.9027 (mtm) cc_final: 0.8666 (mpp) REVERT: D 148 ASP cc_start: 0.7000 (m-30) cc_final: 0.6690 (m-30) REVERT: D 154 PHE cc_start: 0.7888 (t80) cc_final: 0.7679 (t80) REVERT: D 219 GLU cc_start: 0.9194 (tp30) cc_final: 0.8967 (tp30) REVERT: D 224 LEU cc_start: 0.8328 (mt) cc_final: 0.7976 (mt) outliers start: 0 outliers final: 0 residues processed: 741 average time/residue: 0.0985 time to fit residues: 111.2652 Evaluate side-chains 640 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 640 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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: 0.6980 chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 189 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 165 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 ASN A 320 ASN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.123549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.090273 restraints weight = 41624.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.093326 restraints weight = 21497.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.095411 restraints weight = 13358.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.096891 restraints weight = 9314.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.097901 restraints weight = 7079.172| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.7284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16386 Z= 0.138 Angle : 0.624 8.819 22134 Z= 0.332 Chirality : 0.043 0.276 2360 Planarity : 0.004 0.061 2818 Dihedral : 8.116 139.837 2290 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.19), residues: 1932 helix: 1.04 (0.15), residues: 1142 sheet: 0.23 (0.46), residues: 100 loop : -0.28 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 235 TYR 0.030 0.001 TYR D 174 PHE 0.030 0.002 PHE D 109 TRP 0.040 0.002 TRP D 124 HIS 0.007 0.001 HIS A 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (16386) covalent geometry : angle 0.62412 / 0.33 (22134) hydrogen bonds : bond 0.03831 / 2.47 ( 871) hydrogen bonds : angle 4.91903 / 3.59 ( 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 716 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 716 time to evaluate : 0.580 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: A 8 LYS cc_start: 0.9188 (tptp) cc_final: 0.8894 (tppt) REVERT: A 12 LEU cc_start: 0.9510 (mt) cc_final: 0.9175 (mt) REVERT: A 107 LYS cc_start: 0.9221 (mttm) cc_final: 0.8847 (mtpp) REVERT: A 147 GLN cc_start: 0.9284 (mt0) cc_final: 0.8754 (mt0) REVERT: A 149 TYR cc_start: 0.9130 (t80) cc_final: 0.8633 (t80) REVERT: A 181 ASP cc_start: 0.8756 (m-30) cc_final: 0.8248 (m-30) REVERT: A 195 LEU cc_start: 0.9630 (mt) cc_final: 0.9361 (mt) REVERT: A 223 VAL cc_start: 0.9763 (m) cc_final: 0.9218 (p) REVERT: A 227 MET cc_start: 0.9240 (mtm) cc_final: 0.8871 (mtm) REVERT: A 231 ASP cc_start: 0.8657 (t70) cc_final: 0.8255 (t0) REVERT: A 257 ASP cc_start: 0.9035 (m-30) cc_final: 0.8737 (m-30) REVERT: A 262 LEU cc_start: 0.9879 (mt) cc_final: 0.9622 (mt) REVERT: A 263 ASP cc_start: 0.9291 (m-30) cc_final: 0.8990 (m-30) REVERT: A 276 LYS cc_start: 0.9283 (tmtt) cc_final: 0.8930 (tptp) REVERT: A 301 PHE cc_start: 0.9090 (m-10) cc_final: 0.8504 (m-10) REVERT: A 322 MET cc_start: 0.9177 (tpt) cc_final: 0.8261 (mmm) REVERT: A 333 LYS cc_start: 0.9564 (tppt) cc_final: 0.9197 (tppp) REVERT: A 335 GLU cc_start: 0.8449 (mm-30) cc_final: 0.7895 (mm-30) REVERT: A 344 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8549 (mt-10) REVERT: A 345 LYS cc_start: 0.9806 (ttpt) cc_final: 0.9464 (ttmt) REVERT: A 349 LEU cc_start: 0.9698 (mt) cc_final: 0.9440 (mt) REVERT: A 365 ASN cc_start: 0.9303 (m-40) cc_final: 0.8886 (m-40) REVERT: A 366 LYS cc_start: 0.9235 (mtmm) cc_final: 0.9013 (mtmm) REVERT: A 375 LYS cc_start: 0.9103 (mmtt) cc_final: 0.8718 (mmtp) REVERT: A 390 GLN cc_start: 0.8893 (mt0) cc_final: 0.8669 (mt0) REVERT: A 393 SER cc_start: 0.9342 (m) cc_final: 0.8869 (p) REVERT: A 402 GLU cc_start: 0.8211 (mp0) cc_final: 0.7930 (mp0) REVERT: A 415 ASN cc_start: 0.9361 (t0) cc_final: 0.8567 (t0) REVERT: A 418 ASN cc_start: 0.9196 (m110) cc_final: 0.8546 (m-40) REVERT: A 459 LYS cc_start: 0.8842 (mttp) cc_final: 0.8485 (mtmt) REVERT: A 466 MET cc_start: 0.8950 (ptt) cc_final: 0.8741 (ptt) REVERT: A 474 GLN cc_start: 0.9346 (mt0) cc_final: 0.9136 (mm110) REVERT: A 493 MET cc_start: 0.8888 (tmm) cc_final: 0.8523 (tmm) REVERT: A 494 MET cc_start: 0.9283 (mtp) cc_final: 0.8894 (mtp) REVERT: A 515 ASP cc_start: 0.8866 (m-30) cc_final: 0.8502 (m-30) REVERT: A 539 LYS cc_start: 0.9276 (mmpt) cc_final: 0.9055 (mmmt) REVERT: A 550 MET cc_start: 0.8836 (mmt) cc_final: 0.8472 (mmt) REVERT: A 561 LEU cc_start: 0.9376 (tp) cc_final: 0.9022 (tp) REVERT: A 601 ILE cc_start: 0.9567 (mm) cc_final: 0.9270 (mm) REVERT: A 615 MET cc_start: 0.9228 (mmm) cc_final: 0.8861 (mmm) REVERT: A 645 GLN cc_start: 0.9139 (tp40) cc_final: 0.8862 (tp40) REVERT: A 654 PHE cc_start: 0.9359 (t80) cc_final: 0.8887 (t80) REVERT: B 8 LYS cc_start: 0.9415 (tptt) cc_final: 0.9048 (tppt) REVERT: B 12 LEU cc_start: 0.9586 (mt) cc_final: 0.9332 (mt) REVERT: B 20 LYS cc_start: 0.9652 (tmtt) cc_final: 0.9422 (tptp) REVERT: B 21 ASP cc_start: 0.8551 (t70) cc_final: 0.8260 (t0) REVERT: B 30 LYS cc_start: 0.9526 (tmtt) cc_final: 0.9303 (tmtt) REVERT: B 88 LYS cc_start: 0.9077 (tttp) cc_final: 0.8707 (tttt) REVERT: B 98 PHE cc_start: 0.9457 (t80) cc_final: 0.9002 (t80) REVERT: B 99 LYS cc_start: 0.9407 (tppt) cc_final: 0.9101 (tppt) REVERT: B 111 LYS cc_start: 0.9612 (mptt) cc_final: 0.9329 (mmtt) REVERT: B 119 GLU cc_start: 0.9186 (mp0) cc_final: 0.8907 (mp0) REVERT: B 143 LEU cc_start: 0.9131 (tp) cc_final: 0.8387 (tp) REVERT: B 148 GLU cc_start: 0.8836 (mp0) cc_final: 0.7798 (mp0) REVERT: B 167 LEU cc_start: 0.9150 (mt) cc_final: 0.8808 (mt) REVERT: B 181 ASP cc_start: 0.8501 (m-30) cc_final: 0.8097 (m-30) REVERT: B 191 GLN cc_start: 0.9258 (mm-40) cc_final: 0.8935 (mt0) REVERT: B 211 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8049 (mm-30) REVERT: B 236 TYR cc_start: 0.9204 (t80) cc_final: 0.8914 (t80) REVERT: B 238 ASP cc_start: 0.8577 (t0) cc_final: 0.8035 (t70) REVERT: B 239 GLN cc_start: 0.8973 (tm-30) cc_final: 0.8326 (tm-30) REVERT: B 263 ASP cc_start: 0.9123 (m-30) cc_final: 0.8695 (m-30) REVERT: B 270 ASP cc_start: 0.8626 (p0) cc_final: 0.8317 (p0) REVERT: B 321 GLU cc_start: 0.8700 (pp20) cc_final: 0.8360 (pp20) REVERT: B 322 MET cc_start: 0.9034 (mmm) cc_final: 0.8320 (mmm) REVERT: B 335 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8281 (mm-30) REVERT: B 355 TYR cc_start: 0.8789 (m-10) cc_final: 0.8578 (m-10) REVERT: B 357 TYR cc_start: 0.7984 (m-80) cc_final: 0.7651 (m-80) REVERT: B 374 SER cc_start: 0.9446 (t) cc_final: 0.8860 (p) REVERT: B 379 SER cc_start: 0.9205 (t) cc_final: 0.8986 (t) REVERT: B 384 GLU cc_start: 0.8729 (pm20) cc_final: 0.8280 (pm20) REVERT: B 393 SER cc_start: 0.9365 (m) cc_final: 0.9111 (p) REVERT: B 402 GLU cc_start: 0.8931 (tp30) cc_final: 0.8713 (tp30) REVERT: B 410 ASN cc_start: 0.8987 (m-40) cc_final: 0.8468 (m-40) REVERT: B 440 SER cc_start: 0.9455 (p) cc_final: 0.9204 (p) REVERT: B 522 TYR cc_start: 0.9005 (m-10) cc_final: 0.8426 (m-10) REVERT: B 550 MET cc_start: 0.8325 (mtp) cc_final: 0.7927 (mtm) REVERT: B 570 MET cc_start: 0.8891 (mtp) cc_final: 0.7341 (mtp) REVERT: B 576 LEU cc_start: 0.9454 (mt) cc_final: 0.9188 (mt) REVERT: B 585 SER cc_start: 0.9266 (p) cc_final: 0.8857 (t) REVERT: B 639 ASP cc_start: 0.9016 (m-30) cc_final: 0.8586 (m-30) REVERT: B 640 MET cc_start: 0.9161 (tpp) cc_final: 0.8557 (tpp) REVERT: B 671 ASP cc_start: 0.8992 (m-30) cc_final: 0.8773 (m-30) REVERT: B 680 LYS cc_start: 0.9154 (mttt) cc_final: 0.8950 (mtpt) REVERT: C 17 PHE cc_start: 0.9039 (p90) cc_final: 0.8719 (p90) REVERT: C 20 MET cc_start: 0.9562 (tmm) cc_final: 0.9304 (tmm) REVERT: C 37 LEU cc_start: 0.2625 (tp) cc_final: 0.2373 (tp) REVERT: C 101 HIS cc_start: 0.7791 (m90) cc_final: 0.6887 (m90) REVERT: C 118 ILE cc_start: 0.9108 (pt) cc_final: 0.8589 (pt) REVERT: C 122 PHE cc_start: 0.8081 (m-80) cc_final: 0.7571 (m-80) REVERT: C 173 TYR cc_start: 0.7875 (t80) cc_final: 0.7654 (t80) REVERT: C 174 TYR cc_start: 0.7925 (t80) cc_final: 0.7278 (t80) REVERT: C 177 TYR cc_start: 0.9116 (t80) cc_final: 0.8912 (t80) REVERT: C 179 TYR cc_start: 0.8223 (t80) cc_final: 0.7786 (t80) REVERT: C 185 MET cc_start: 0.5960 (mmm) cc_final: 0.4828 (mpp) REVERT: C 201 HIS cc_start: 0.9330 (m90) cc_final: 0.8684 (m90) REVERT: C 233 ASN cc_start: 0.9448 (m110) cc_final: 0.8931 (m110) REVERT: C 278 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8455 (pm20) REVERT: C 321 TYR cc_start: 0.8981 (m-80) cc_final: 0.8658 (m-80) REVERT: D 20 MET cc_start: 0.9004 (mtm) cc_final: 0.8771 (mpp) REVERT: D 109 PHE cc_start: 0.8409 (m-80) cc_final: 0.7681 (m-80) REVERT: D 148 ASP cc_start: 0.7115 (m-30) cc_final: 0.6820 (m-30) REVERT: D 219 GLU cc_start: 0.9194 (tp30) cc_final: 0.8967 (tp30) REVERT: D 224 LEU cc_start: 0.8323 (mt) cc_final: 0.8010 (mt) REVERT: D 270 ASN cc_start: 0.8652 (m110) cc_final: 0.8397 (m110) outliers start: 0 outliers final: 0 residues processed: 716 average time/residue: 0.0968 time to fit residues: 105.7105 Evaluate side-chains 630 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 630 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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: 1.9990 chunk 1 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 34 optimal weight: 0.0980 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 GLN A 180 ASN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN D 28 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.123759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.090369 restraints weight = 41074.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.093504 restraints weight = 21383.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.095689 restraints weight = 13603.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.097230 restraints weight = 9492.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.098293 restraints weight = 7216.908| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (27 function evaluations) r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.7417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16386 Z= 0.137 Angle : 0.634 9.085 22134 Z= 0.335 Chirality : 0.044 0.248 2360 Planarity : 0.004 0.062 2818 Dihedral : 8.038 140.773 2290 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.19), residues: 1932 helix: 0.94 (0.15), residues: 1167 sheet: -0.62 (0.42), residues: 134 loop : -0.20 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 164 TYR 0.028 0.001 TYR B 394 PHE 0.043 0.002 PHE B 129 TRP 0.045 0.002 TRP D 124 HIS 0.006 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (16386) covalent geometry : angle 0.63416 / 0.33 (22134) hydrogen bonds : bond 0.03801 / 2.45 ( 871) hydrogen bonds : angle 4.91807 / 3.59 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2990.51 seconds wall clock time: 52 minutes 37.79 seconds (3157.79 seconds total)