Starting phenix.real_space_refine on Fri Jul 3 19:41:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bze_45065/07_2026/9bze_45065_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bze_45065/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9bze_45065/07_2026/9bze_45065_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bze_45065/07_2026/9bze_45065_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bze_45065/07_2026/9bze_45065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bze_45065/07_2026/9bze_45065.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.64, per 1000 atoms: 0.23 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: 1.33 Conformation dependent library (CDL) restraints added in 751.3 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: 0.44 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: 2.85 Time building geometry restraints manager: 1.79 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 3.060 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 3.060 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 3.060 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.991 3.060 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: 0.010 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.180 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.540 ------------------------------------------------------------------------------- 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 : 0.592 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: 0.8398 (mm) REVERT: A 51 LEU cc_start: 0.8139 (tp) cc_final: 0.7854 (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: 0.8885 (m) REVERT: A 157 LEU cc_start: 0.8978 (tp) cc_final: 0.8772 (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: 0.6378 (tp30) REVERT: A 258 ILE cc_start: 0.9219 (tp) cc_final: 0.8844 (tp) REVERT: A 265 LYS cc_start: 0.9075 (mmtt) cc_final: 0.8694 (mmmt) REVERT: A 267 ILE cc_start: 0.8833 (mp) cc_final: 0.8078 (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: 0.7248 (mt-10) REVERT: A 345 LYS cc_start: 0.8888 (tttt) cc_final: 0.8389 (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: 0.8046 (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: 0.7157 (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: 0.7259 (mmm) REVERT: A 435 SER cc_start: 0.9408 (p) cc_final: 0.8803 (p) REVERT: A 501 GLN cc_start: 0.8285 (tt0) cc_final: 0.8070 (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: 0.7860 (t) REVERT: A 590 SER cc_start: 0.9100 (p) cc_final: 0.8360 (p) REVERT: A 595 MET cc_start: 0.8050 (mmp) cc_final: 0.7669 (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: 0.7470 (m) REVERT: B 11 GLN cc_start: 0.7654 (mt0) cc_final: 0.6756 (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: 0.8783 (mt) REVERT: B 147 GLN cc_start: 0.8314 (mt0) cc_final: 0.8005 (mt0) REVERT: B 172 LEU cc_start: 0.9343 (mp) cc_final: 0.8954 (mp) REVERT: B 175 VAL cc_start: 0.9207 (t) cc_final: 0.9005 (t) REVERT: B 177 ASP cc_start: 0.8671 (t0) cc_final: 0.8057 (t70) REVERT: B 181 ASP cc_start: 0.8122 (m-30) cc_final: 0.7638 (m-30) REVERT: B 192 LEU cc_start: 0.9272 (mt) cc_final: 0.8958 (mt) REVERT: B 204 SER cc_start: 0.9055 (m) cc_final: 0.8213 (t) REVERT: B 226 VAL cc_start: 0.9079 (t) cc_final: 0.8712 (t) REVERT: B 256 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7209 (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: 0.6978 (mmm) REVERT: B 345 LYS cc_start: 0.8290 (tttt) cc_final: 0.7968 (ttpt) REVERT: B 346 LEU cc_start: 0.8863 (mt) cc_final: 0.8474 (mt) REVERT: B 359 MET cc_start: 0.8061 (ttt) cc_final: 0.7721 (ttt) REVERT: B 374 SER cc_start: 0.8716 (t) cc_final: 0.8477 (p) REVERT: B 381 LEU cc_start: 0.8730 (tp) cc_final: 0.8513 (tp) REVERT: B 387 GLN cc_start: 0.7301 (mt0) cc_final: 0.6895 (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: 0.7798 (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: 0.7701 (mt0) REVERT: B 494 MET cc_start: 0.7983 (mtp) cc_final: 0.7782 (mtp) REVERT: B 500 ILE cc_start: 0.9441 (mt) cc_final: 0.9000 (mt) REVERT: B 550 MET cc_start: 0.7876 (mtm) cc_final: 0.6887 (mtm) REVERT: B 587 VAL cc_start: 0.8690 (t) cc_final: 0.8460 (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: 0.8660 (mt) REVERT: B 655 THR cc_start: 0.9501 (m) cc_final: 0.9290 (t) REVERT: C 27 LYS cc_start: 0.8056 (ptmm) cc_final: 0.7832 (tmtt) REVERT: C 37 LEU cc_start: 0.5102 (mt) cc_final: 0.4503 (tp) REVERT: C 114 PRO cc_start: 0.5223 (Cg_endo) cc_final: 0.4829 (Cg_exo) REVERT: C 163 LEU cc_start: 0.6465 (tt) cc_final: 0.6191 (tt) REVERT: C 178 PHE cc_start: 0.4924 (m-80) cc_final: 0.4644 (m-80) REVERT: D 47 LEU cc_start: 0.5071 (mt) cc_final: 0.3946 (mp) REVERT: D 96 MET cc_start: 0.5835 (mmm) cc_final: 0.5505 (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: 0.3825 (mm-40) outliers start: 23 outliers final: 6 residues processed: 1020 average time/residue: 0.1332 time to fit residues: 195.2738 Evaluate side-chains 689 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 683 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 84 HIS C 85 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** 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 D 80 HIS D 186 GLN D 201 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.130595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.095846 restraints weight = 39048.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.099124 restraints weight = 20204.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.101609 restraints weight = 12599.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.103153 restraints weight = 8900.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.104144 restraints weight = 6842.862| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 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 = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (13 function evaluations) r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16386 Z= 0.149 Angle : 0.611 6.691 22134 Z= 0.328 Chirality : 0.043 0.240 2360 Planarity : 0.004 0.034 2818 Dihedral : 9.777 130.851 2290 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.17 % Allowed : 3.03 % Favored : 96.79 % 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: 1.20 (0.18), residues: 1932 helix: 1.29 (0.15), residues: 1110 sheet: -0.10 (0.39), residues: 138 loop : 0.36 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 331 TYR 0.021 0.002 TYR D 142 PHE 0.027 0.002 PHE C 168 TRP 0.030 0.002 TRP D 124 HIS 0.010 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (16386) covalent geometry : angle 0.61109 / 0.33 (22134) hydrogen bonds : bond 0.04599 / 2.93 ( 871) hydrogen bonds : angle 5.06004 / 3.64 ( 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 825 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 822 time to evaluate : 0.572 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: A 8 LYS cc_start: 0.9227 (tptp) cc_final: 0.8850 (tppt) REVERT: A 41 ILE cc_start: 0.9248 (mm) cc_final: 0.8818 (mm) REVERT: A 52 LYS cc_start: 0.9658 (tppt) cc_final: 0.9451 (tppp) REVERT: A 118 TYR cc_start: 0.9270 (t80) cc_final: 0.8969 (t80) REVERT: A 147 GLN cc_start: 0.9388 (mt0) cc_final: 0.8399 (mt0) REVERT: A 158 ASN cc_start: 0.9359 (m110) cc_final: 0.8992 (m-40) REVERT: A 162 LYS cc_start: 0.8801 (ttmm) cc_final: 0.8583 (ttmm) REVERT: A 195 LEU cc_start: 0.9602 (mt) cc_final: 0.9321 (mt) REVERT: A 227 MET cc_start: 0.9315 (mtm) cc_final: 0.9038 (mtm) REVERT: A 235 ARG cc_start: 0.9212 (ttm-80) cc_final: 0.8991 (ttm-80) REVERT: A 238 ASP cc_start: 0.8588 (p0) cc_final: 0.8025 (p0) REVERT: A 255 HIS cc_start: 0.8964 (t-90) cc_final: 0.8208 (t-90) REVERT: A 257 ASP cc_start: 0.9141 (m-30) cc_final: 0.8723 (m-30) REVERT: A 262 LEU cc_start: 0.9829 (mt) cc_final: 0.9565 (mt) REVERT: A 286 ASP cc_start: 0.8590 (m-30) cc_final: 0.8222 (m-30) REVERT: A 315 ASP cc_start: 0.8499 (p0) cc_final: 0.8298 (p0) REVERT: A 333 LYS cc_start: 0.9458 (tppt) cc_final: 0.9243 (tppp) REVERT: A 335 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7603 (mm-30) REVERT: A 359 MET cc_start: 0.8832 (ttp) cc_final: 0.8604 (ttp) REVERT: A 362 ASP cc_start: 0.7982 (m-30) cc_final: 0.7630 (m-30) REVERT: A 366 LYS cc_start: 0.9298 (mtmm) cc_final: 0.8831 (mtmm) REVERT: A 375 LYS cc_start: 0.8802 (mmtt) cc_final: 0.8458 (mmtm) REVERT: A 415 ASN cc_start: 0.9229 (t0) cc_final: 0.8662 (t0) REVERT: A 418 ASN cc_start: 0.9297 (OUTLIER) cc_final: 0.8862 (m110) REVERT: A 447 ASN cc_start: 0.8025 (m-40) cc_final: 0.7644 (t0) REVERT: A 456 LYS cc_start: 0.8603 (mtmm) cc_final: 0.8398 (mtmm) REVERT: A 466 MET cc_start: 0.8994 (ptt) cc_final: 0.8592 (ptt) REVERT: A 493 MET cc_start: 0.9118 (tmm) cc_final: 0.8688 (tmm) REVERT: A 494 MET cc_start: 0.9383 (mtp) cc_final: 0.9150 (mtp) REVERT: A 510 LYS cc_start: 0.8990 (mtpt) cc_final: 0.8589 (mtpt) REVERT: A 527 TYR cc_start: 0.8701 (t80) cc_final: 0.8363 (t80) REVERT: A 528 PHE cc_start: 0.9244 (m-80) cc_final: 0.8788 (m-80) REVERT: A 553 PRO cc_start: 0.9546 (Cg_exo) cc_final: 0.9061 (Cg_endo) REVERT: A 602 GLU cc_start: 0.7719 (pt0) cc_final: 0.7170 (pt0) REVERT: A 604 ARG cc_start: 0.8998 (mmm160) cc_final: 0.8700 (mmm-85) REVERT: A 645 GLN cc_start: 0.8687 (tp40) cc_final: 0.7816 (tp40) REVERT: A 657 PHE cc_start: 0.9055 (m-80) cc_final: 0.8656 (m-80) REVERT: A 669 ARG cc_start: 0.9165 (tpp-160) cc_final: 0.8806 (tpp-160) REVERT: A 680 LYS cc_start: 0.9163 (mttt) cc_final: 0.8461 (mttt) REVERT: B 8 LYS cc_start: 0.9446 (tptt) cc_final: 0.9030 (tppt) REVERT: B 12 LEU cc_start: 0.9574 (mt) cc_final: 0.9341 (mt) REVERT: B 51 LEU cc_start: 0.9416 (tp) cc_final: 0.9198 (tp) REVERT: B 147 GLN cc_start: 0.8642 (mt0) cc_final: 0.8192 (mt0) REVERT: B 184 ARG cc_start: 0.9399 (tpp80) cc_final: 0.9085 (tpp80) REVERT: B 191 GLN cc_start: 0.9202 (mm-40) cc_final: 0.8779 (mt0) REVERT: B 211 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8372 (mm-30) REVERT: B 236 TYR cc_start: 0.9241 (t80) cc_final: 0.8956 (t80) REVERT: B 279 SER cc_start: 0.7903 (m) cc_final: 0.7625 (t) REVERT: B 288 PHE cc_start: 0.9313 (t80) cc_final: 0.8826 (t80) REVERT: B 315 ASP cc_start: 0.8712 (p0) cc_final: 0.8137 (p0) REVERT: B 321 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8243 (tm-30) REVERT: B 322 MET cc_start: 0.8645 (mmm) cc_final: 0.8370 (mmm) REVERT: B 335 GLU cc_start: 0.8291 (mm-30) cc_final: 0.8067 (mm-30) REVERT: B 348 MET cc_start: 0.9478 (ptm) cc_final: 0.9149 (ptm) REVERT: B 374 SER cc_start: 0.8915 (t) cc_final: 0.7922 (p) REVERT: B 375 LYS cc_start: 0.9104 (mttm) cc_final: 0.8607 (mtpp) REVERT: B 390 GLN cc_start: 0.9203 (mt0) cc_final: 0.8992 (mm110) REVERT: B 393 SER cc_start: 0.9391 (m) cc_final: 0.9075 (p) REVERT: B 398 ASP cc_start: 0.7907 (t0) cc_final: 0.7642 (t0) REVERT: B 402 GLU cc_start: 0.8855 (tp30) cc_final: 0.8618 (tp30) REVERT: B 410 ASN cc_start: 0.8618 (m110) cc_final: 0.8064 (m110) REVERT: B 423 LYS cc_start: 0.9576 (mttt) cc_final: 0.9282 (mppt) REVERT: B 427 LYS cc_start: 0.9349 (mmmm) cc_final: 0.9067 (tppt) REVERT: B 474 GLN cc_start: 0.8683 (mt0) cc_final: 0.8404 (mt0) REVERT: B 493 MET cc_start: 0.9666 (tmm) cc_final: 0.9342 (tmm) REVERT: B 516 GLN cc_start: 0.8843 (tp-100) cc_final: 0.8139 (tp-100) REVERT: B 558 TRP cc_start: 0.9212 (m100) cc_final: 0.8564 (m100) REVERT: B 576 LEU cc_start: 0.9068 (mt) cc_final: 0.8816 (mt) REVERT: B 612 TYR cc_start: 0.9075 (m-80) cc_final: 0.8517 (m-10) REVERT: B 639 ASP cc_start: 0.9207 (m-30) cc_final: 0.8824 (m-30) REVERT: B 640 MET cc_start: 0.9427 (tpp) cc_final: 0.9087 (tpp) REVERT: B 677 ARG cc_start: 0.9358 (mmm-85) cc_final: 0.9081 (mmm-85) REVERT: C 90 LEU cc_start: 0.9618 (mt) cc_final: 0.9388 (mt) REVERT: C 101 HIS cc_start: 0.7450 (m90) cc_final: 0.6318 (m90) REVERT: C 123 GLU cc_start: 0.9537 (mm-30) cc_final: 0.9274 (mm-30) REVERT: C 162 TYR cc_start: 0.9215 (m-10) cc_final: 0.8444 (m-10) REVERT: C 163 LEU cc_start: 0.9657 (tt) cc_final: 0.9251 (tt) REVERT: C 173 TYR cc_start: 0.7439 (t80) cc_final: 0.6429 (t80) REVERT: C 179 TYR cc_start: 0.8196 (t80) cc_final: 0.7753 (t80) REVERT: C 212 ILE cc_start: 0.8450 (mt) cc_final: 0.8001 (mt) REVERT: C 229 ILE cc_start: 0.6314 (mt) cc_final: 0.5997 (mm) REVERT: C 233 ASN cc_start: 0.9293 (m110) cc_final: 0.8644 (m110) REVERT: C 278 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7644 (pm20) REVERT: D 20 MET cc_start: 0.8909 (mtm) cc_final: 0.8680 (mpp) REVERT: D 148 ASP cc_start: 0.7312 (m-30) cc_final: 0.6988 (m-30) REVERT: D 168 PHE cc_start: 0.9032 (m-80) cc_final: 0.8587 (m-80) REVERT: D 186 GLN cc_start: 0.7663 (mm110) cc_final: 0.7130 (mm110) REVERT: D 198 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7705 (mm-30) REVERT: D 230 ASP cc_start: 0.8903 (t70) cc_final: 0.8629 (t0) outliers start: 3 outliers final: 0 residues processed: 823 average time/residue: 0.1195 time to fit residues: 147.0292 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 : 0.585 ------------------------------------------------------------------------------- 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: 0.9990 chunk 164 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 182 optimal weight: 0.9980 chunk 159 optimal weight: 20.0000 chunk 91 optimal weight: 0.8980 chunk 150 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN C 249 GLN C 263 ASN D 28 GLN D 238 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.126259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.091040 restraints weight = 40168.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.094298 restraints weight = 20914.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.096683 restraints weight = 12924.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.098210 restraints weight = 9110.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.099292 restraints weight = 6993.495| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16386 Z= 0.142 Angle : 0.564 7.351 22134 Z= 0.305 Chirality : 0.042 0.201 2360 Planarity : 0.003 0.042 2818 Dihedral : 8.880 132.868 2290 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.23 % Allowed : 2.68 % Favored : 97.09 % 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: 1.29 (0.19), residues: 1932 helix: 1.31 (0.15), residues: 1137 sheet: 0.15 (0.43), residues: 118 loop : 0.38 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 243 TYR 0.028 0.002 TYR B 626 PHE 0.031 0.002 PHE A 654 TRP 0.019 0.002 TRP D 124 HIS 0.007 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (16386) covalent geometry : angle 0.56446 / 0.30 (22134) hydrogen bonds : bond 0.04091 / 2.58 ( 871) hydrogen bonds : angle 4.83251 / 3.49 ( 2571) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 745 time to evaluate : 0.474 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: A 8 LYS cc_start: 0.9247 (tptp) cc_final: 0.8841 (tppt) REVERT: A 12 LEU cc_start: 0.9621 (mt) cc_final: 0.9365 (mt) REVERT: A 118 TYR cc_start: 0.9341 (t80) cc_final: 0.9045 (t80) REVERT: A 147 GLN cc_start: 0.9455 (mt0) cc_final: 0.8673 (mt0) REVERT: A 157 LEU cc_start: 0.9384 (tp) cc_final: 0.9036 (tp) REVERT: A 158 ASN cc_start: 0.9398 (m110) cc_final: 0.9036 (m-40) REVERT: A 195 LEU cc_start: 0.9705 (mt) cc_final: 0.9397 (mt) REVERT: A 214 LYS cc_start: 0.8740 (tppt) cc_final: 0.8497 (tppt) REVERT: A 218 ASN cc_start: 0.9225 (t0) cc_final: 0.8921 (t0) REVERT: A 223 VAL cc_start: 0.9709 (m) cc_final: 0.9201 (p) REVERT: A 227 MET cc_start: 0.9282 (mtm) cc_final: 0.8855 (mtm) REVERT: A 235 ARG cc_start: 0.9131 (ttm-80) cc_final: 0.8905 (ttm110) REVERT: A 238 ASP cc_start: 0.8517 (p0) cc_final: 0.8152 (p0) REVERT: A 252 ASN cc_start: 0.9403 (t0) cc_final: 0.9103 (t0) REVERT: A 255 HIS cc_start: 0.8720 (t-90) cc_final: 0.7875 (t-90) REVERT: A 257 ASP cc_start: 0.9019 (m-30) cc_final: 0.8664 (m-30) REVERT: A 262 LEU cc_start: 0.9825 (mt) cc_final: 0.9591 (mt) REVERT: A 263 ASP cc_start: 0.9269 (m-30) cc_final: 0.9057 (m-30) REVERT: A 270 ASP cc_start: 0.8887 (t0) cc_final: 0.8560 (t0) REVERT: A 322 MET cc_start: 0.8741 (tpt) cc_final: 0.8086 (tpp) REVERT: A 333 LYS cc_start: 0.9526 (tppt) cc_final: 0.9264 (tppp) REVERT: A 335 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7704 (mm-30) REVERT: A 344 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8832 (mt-10) REVERT: A 366 LYS cc_start: 0.9273 (mtmm) cc_final: 0.8725 (mtmm) REVERT: A 375 LYS cc_start: 0.8686 (mmtt) cc_final: 0.8210 (mmtm) REVERT: A 390 GLN cc_start: 0.8502 (mt0) cc_final: 0.8281 (mt0) REVERT: A 405 LEU cc_start: 0.9168 (mt) cc_final: 0.8923 (mt) REVERT: A 415 ASN cc_start: 0.9476 (t0) cc_final: 0.8982 (t0) REVERT: A 447 ASN cc_start: 0.8133 (m-40) cc_final: 0.7720 (t0) REVERT: A 459 LYS cc_start: 0.8865 (mttp) cc_final: 0.8457 (mtmt) REVERT: A 466 MET cc_start: 0.9105 (ptt) cc_final: 0.8669 (ptt) REVERT: A 468 LEU cc_start: 0.9679 (tp) cc_final: 0.9440 (tp) REVERT: A 474 GLN cc_start: 0.9137 (mt0) cc_final: 0.8885 (mm-40) REVERT: A 493 MET cc_start: 0.9111 (tmm) cc_final: 0.8654 (tmm) REVERT: A 494 MET cc_start: 0.9379 (mtp) cc_final: 0.9004 (mtp) REVERT: A 527 TYR cc_start: 0.8834 (t80) cc_final: 0.8563 (t80) REVERT: A 528 PHE cc_start: 0.9278 (m-80) cc_final: 0.8880 (m-80) REVERT: A 553 PRO cc_start: 0.9545 (Cg_exo) cc_final: 0.9076 (Cg_endo) REVERT: A 601 ILE cc_start: 0.9575 (mm) cc_final: 0.9135 (mm) REVERT: A 602 GLU cc_start: 0.7618 (pt0) cc_final: 0.7368 (pt0) REVERT: A 640 MET cc_start: 0.9126 (tpp) cc_final: 0.8891 (tpp) REVERT: A 645 GLN cc_start: 0.8950 (tp40) cc_final: 0.8166 (tp40) REVERT: A 669 ARG cc_start: 0.9096 (tpp-160) cc_final: 0.8476 (tpp-160) REVERT: A 680 LYS cc_start: 0.9034 (mttt) cc_final: 0.8435 (mttt) REVERT: B 8 LYS cc_start: 0.9460 (tptt) cc_final: 0.9013 (tppt) REVERT: B 30 LYS cc_start: 0.9540 (tmtt) cc_final: 0.9329 (tmtt) REVERT: B 41 ILE cc_start: 0.9378 (mm) cc_final: 0.9058 (mm) REVERT: B 94 PHE cc_start: 0.9262 (t80) cc_final: 0.9060 (t80) REVERT: B 111 LYS cc_start: 0.9677 (mptt) cc_final: 0.9457 (mmtt) REVERT: B 117 ARG cc_start: 0.9354 (mmm-85) cc_final: 0.8997 (mmm-85) REVERT: B 119 GLU cc_start: 0.9233 (mp0) cc_final: 0.9023 (mp0) REVERT: B 176 ASN cc_start: 0.8571 (t0) cc_final: 0.8324 (t0) REVERT: B 184 ARG cc_start: 0.9472 (tpp80) cc_final: 0.8918 (tpp80) REVERT: B 202 ASN cc_start: 0.9232 (t0) cc_final: 0.8984 (t0) REVERT: B 214 LYS cc_start: 0.8542 (mmtm) cc_final: 0.8278 (mmtt) REVERT: B 235 ARG cc_start: 0.9390 (ttm110) cc_final: 0.8899 (ttm110) REVERT: B 236 TYR cc_start: 0.9169 (t80) cc_final: 0.8884 (t80) REVERT: B 239 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8041 (tm-30) REVERT: B 322 MET cc_start: 0.8874 (mmm) cc_final: 0.8532 (mmm) REVERT: B 335 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8057 (mm-30) REVERT: B 350 ARG cc_start: 0.9102 (mmm-85) cc_final: 0.8874 (mmm-85) REVERT: B 375 LYS cc_start: 0.8995 (mttm) cc_final: 0.8513 (mtpp) REVERT: B 386 LEU cc_start: 0.9513 (mt) cc_final: 0.9103 (mt) REVERT: B 387 GLN cc_start: 0.9049 (mt0) cc_final: 0.8384 (mp10) REVERT: B 393 SER cc_start: 0.9395 (m) cc_final: 0.9039 (p) REVERT: B 398 ASP cc_start: 0.8074 (t0) cc_final: 0.7760 (t0) REVERT: B 407 ILE cc_start: 0.8995 (mp) cc_final: 0.8680 (mp) REVERT: B 410 ASN cc_start: 0.8818 (m110) cc_final: 0.8332 (m110) REVERT: B 436 LEU cc_start: 0.9580 (mt) cc_final: 0.9362 (mt) REVERT: B 493 MET cc_start: 0.9640 (tmm) cc_final: 0.9400 (tmm) REVERT: B 522 TYR cc_start: 0.9098 (m-10) cc_final: 0.8693 (m-10) REVERT: B 543 ILE cc_start: 0.9728 (mm) cc_final: 0.9440 (mm) REVERT: B 558 TRP cc_start: 0.9349 (m100) cc_final: 0.8804 (m100) REVERT: B 576 LEU cc_start: 0.9322 (mt) cc_final: 0.8883 (mt) REVERT: B 610 LYS cc_start: 0.8959 (ptmt) cc_final: 0.8524 (ttpp) REVERT: B 612 TYR cc_start: 0.9136 (m-80) cc_final: 0.8503 (m-80) REVERT: B 615 MET cc_start: 0.9244 (mmp) cc_final: 0.9010 (mmp) REVERT: B 639 ASP cc_start: 0.9153 (m-30) cc_final: 0.8782 (m-30) REVERT: B 640 MET cc_start: 0.9458 (tpp) cc_final: 0.9024 (tpp) REVERT: B 658 LEU cc_start: 0.9322 (mm) cc_final: 0.9113 (mp) REVERT: C 20 MET cc_start: 0.9486 (tmm) cc_final: 0.9103 (ptp) REVERT: C 21 PHE cc_start: 0.9132 (m-80) cc_final: 0.8776 (m-80) REVERT: C 101 HIS cc_start: 0.7259 (m90) cc_final: 0.6460 (m90) REVERT: C 162 TYR cc_start: 0.9272 (m-10) cc_final: 0.8410 (m-10) REVERT: C 163 LEU cc_start: 0.9697 (tt) cc_final: 0.9283 (tt) REVERT: C 173 TYR cc_start: 0.7437 (t80) cc_final: 0.6413 (t80) REVERT: C 179 TYR cc_start: 0.8110 (t80) cc_final: 0.7791 (t80) REVERT: C 185 MET cc_start: 0.5180 (mmm) cc_final: 0.3843 (mpp) REVERT: C 208 LEU cc_start: 0.8608 (mm) cc_final: 0.8327 (mm) REVERT: C 212 ILE cc_start: 0.8211 (mt) cc_final: 0.7678 (mt) REVERT: C 229 ILE cc_start: 0.6559 (mt) cc_final: 0.5973 (mm) REVERT: C 233 ASN cc_start: 0.9394 (m110) cc_final: 0.8837 (m110) REVERT: C 252 LEU cc_start: 0.7557 (mt) cc_final: 0.7201 (mt) REVERT: C 270 ASN cc_start: 0.8784 (m110) cc_final: 0.8575 (m-40) REVERT: C 278 GLU cc_start: 0.8530 (mm-30) cc_final: 0.7969 (pm20) REVERT: D 20 MET cc_start: 0.8947 (mtm) cc_final: 0.8708 (mpp) REVERT: D 148 ASP cc_start: 0.7223 (m-30) cc_final: 0.6880 (m-30) REVERT: D 176 LEU cc_start: 0.9588 (mt) cc_final: 0.9152 (tp) REVERT: D 186 GLN cc_start: 0.7694 (mm110) cc_final: 0.7173 (mm110) REVERT: D 201 HIS cc_start: 0.9339 (m-70) cc_final: 0.8995 (m-70) REVERT: D 219 GLU cc_start: 0.9159 (tp30) cc_final: 0.8860 (tp30) REVERT: D 266 LYS cc_start: 0.8752 (mmtp) cc_final: 0.8551 (mmmm) outliers start: 4 outliers final: 0 residues processed: 745 average time/residue: 0.1204 time to fit residues: 134.3149 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 : 0.545 ------------------------------------------------------------------------------- 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: 7.9990 chunk 157 optimal weight: 8.9990 chunk 168 optimal weight: 0.6980 chunk 89 optimal weight: 9.9990 chunk 127 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 185 optimal weight: 20.0000 chunk 191 optimal weight: 8.9990 chunk 159 optimal weight: 20.0000 chunk 182 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN A 232 ASN A 259 ASN A 320 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN C 263 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.122794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.088341 restraints weight = 40731.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.091623 restraints weight = 20941.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.093803 restraints weight = 13244.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.095324 restraints weight = 9282.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.096205 restraints weight = 7050.034| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16386 Z= 0.139 Angle : 0.554 8.069 22134 Z= 0.297 Chirality : 0.042 0.197 2360 Planarity : 0.003 0.065 2818 Dihedral : 8.526 134.482 2290 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.29 % Allowed : 2.27 % Favored : 97.44 % 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: 1.22 (0.19), residues: 1932 helix: 1.31 (0.15), residues: 1135 sheet: 0.00 (0.43), residues: 118 loop : 0.28 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 243 TYR 0.026 0.001 TYR C 174 PHE 0.026 0.002 PHE D 109 TRP 0.032 0.002 TRP D 124 HIS 0.008 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (16386) covalent geometry : angle 0.55373 / 0.30 (22134) hydrogen bonds : bond 0.03866 / 2.46 ( 871) hydrogen bonds : angle 4.73697 / 3.44 ( 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 721 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 716 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9246 (tptp) cc_final: 0.8909 (tppt) REVERT: A 12 LEU cc_start: 0.9619 (mt) cc_final: 0.9404 (mt) REVERT: A 118 TYR cc_start: 0.9372 (t80) cc_final: 0.9169 (t80) REVERT: A 147 GLN cc_start: 0.9319 (mt0) cc_final: 0.8563 (mt0) REVERT: A 149 TYR cc_start: 0.8945 (t80) cc_final: 0.8712 (t80) REVERT: A 161 ARG cc_start: 0.8073 (ttm110) cc_final: 0.7473 (mmm-85) REVERT: A 195 LEU cc_start: 0.9683 (mt) cc_final: 0.9385 (mt) REVERT: A 223 VAL cc_start: 0.9739 (m) cc_final: 0.9300 (p) REVERT: A 227 MET cc_start: 0.9249 (mtm) cc_final: 0.8880 (mtm) REVERT: A 238 ASP cc_start: 0.8467 (p0) cc_final: 0.8127 (p0) REVERT: A 257 ASP cc_start: 0.9016 (m-30) cc_final: 0.8741 (m-30) REVERT: A 262 LEU cc_start: 0.9840 (mt) cc_final: 0.9600 (mt) REVERT: A 270 ASP cc_start: 0.8925 (t0) cc_final: 0.8617 (t0) REVERT: A 307 TYR cc_start: 0.9521 (t80) cc_final: 0.9287 (t80) REVERT: A 316 GLU cc_start: 0.8947 (tp30) cc_final: 0.8526 (tp30) REVERT: A 333 LYS cc_start: 0.9555 (tppt) cc_final: 0.9134 (tptp) REVERT: A 344 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8775 (mt-10) REVERT: A 366 LYS cc_start: 0.9161 (mtmm) cc_final: 0.8929 (mtmm) REVERT: A 375 LYS cc_start: 0.8652 (mmtt) cc_final: 0.8190 (mmtm) REVERT: A 390 GLN cc_start: 0.8653 (mt0) cc_final: 0.8371 (mt0) REVERT: A 405 LEU cc_start: 0.9234 (mt) cc_final: 0.8972 (mt) REVERT: A 415 ASN cc_start: 0.9408 (t0) cc_final: 0.8754 (t0) REVERT: A 459 LYS cc_start: 0.8911 (mttp) cc_final: 0.8521 (mtmt) REVERT: A 466 MET cc_start: 0.9085 (ptt) cc_final: 0.8712 (ptt) REVERT: A 474 GLN cc_start: 0.9226 (mt0) cc_final: 0.8917 (mm-40) REVERT: A 493 MET cc_start: 0.9069 (tmm) cc_final: 0.8611 (tmm) REVERT: A 494 MET cc_start: 0.9345 (mtp) cc_final: 0.9033 (mtp) REVERT: A 506 ILE cc_start: 0.9708 (mm) cc_final: 0.9476 (mm) REVERT: A 515 ASP cc_start: 0.8968 (m-30) cc_final: 0.8579 (m-30) REVERT: A 543 ILE cc_start: 0.9582 (mp) cc_final: 0.9142 (mt) REVERT: A 595 MET cc_start: 0.9020 (mmp) cc_final: 0.8582 (mmp) REVERT: A 598 MET cc_start: 0.8517 (mtm) cc_final: 0.8163 (mtm) REVERT: A 601 ILE cc_start: 0.9423 (mm) cc_final: 0.8800 (tp) REVERT: A 604 ARG cc_start: 0.9196 (mmm-85) cc_final: 0.8633 (mmp80) REVERT: A 645 GLN cc_start: 0.9040 (tp40) cc_final: 0.8754 (tp40) REVERT: A 650 GLN cc_start: 0.8710 (mt0) cc_final: 0.8503 (mt0) REVERT: A 669 ARG cc_start: 0.9054 (tpp-160) cc_final: 0.8493 (tpp-160) REVERT: B 8 LYS cc_start: 0.9447 (tptt) cc_final: 0.8983 (tppt) REVERT: B 30 LYS cc_start: 0.9531 (tmtt) cc_final: 0.9326 (tmtt) REVERT: B 87 LYS cc_start: 0.9315 (tptt) cc_final: 0.9075 (tptt) REVERT: B 109 ASN cc_start: 0.9261 (m110) cc_final: 0.8783 (m-40) REVERT: B 111 LYS cc_start: 0.9692 (mptt) cc_final: 0.9429 (mmtt) REVERT: B 119 GLU cc_start: 0.9279 (mp0) cc_final: 0.9006 (mp0) REVERT: B 172 LEU cc_start: 0.9266 (mp) cc_final: 0.9046 (mp) REVERT: B 173 LEU cc_start: 0.9360 (mt) cc_final: 0.9138 (mt) REVERT: B 176 ASN cc_start: 0.8613 (t0) cc_final: 0.8314 (t0) REVERT: B 181 ASP cc_start: 0.8698 (m-30) cc_final: 0.8322 (m-30) REVERT: B 184 ARG cc_start: 0.9408 (tpp80) cc_final: 0.9003 (tpp80) REVERT: B 202 ASN cc_start: 0.9294 (t0) cc_final: 0.9065 (t0) REVERT: B 211 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8378 (mm-30) REVERT: B 214 LYS cc_start: 0.8572 (mmtm) cc_final: 0.8305 (mmtt) REVERT: B 235 ARG cc_start: 0.9388 (ttm110) cc_final: 0.8795 (ttm110) REVERT: B 236 TYR cc_start: 0.9184 (t80) cc_final: 0.8973 (t80) REVERT: B 239 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8263 (tm-30) REVERT: B 252 ASN cc_start: 0.9252 (t0) cc_final: 0.9009 (t0) REVERT: B 270 ASP cc_start: 0.8841 (t0) cc_final: 0.8612 (t0) REVERT: B 286 ASP cc_start: 0.8951 (m-30) cc_final: 0.8591 (m-30) REVERT: B 288 PHE cc_start: 0.9371 (t80) cc_final: 0.9063 (t80) REVERT: B 322 MET cc_start: 0.8913 (mmm) cc_final: 0.8705 (mmm) REVERT: B 335 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8123 (mm-30) REVERT: B 358 ILE cc_start: 0.9647 (mm) cc_final: 0.9371 (mm) REVERT: B 362 ASP cc_start: 0.8967 (m-30) cc_final: 0.8665 (m-30) REVERT: B 390 GLN cc_start: 0.9014 (mm110) cc_final: 0.8638 (mm-40) REVERT: B 393 SER cc_start: 0.9381 (m) cc_final: 0.9073 (p) REVERT: B 410 ASN cc_start: 0.8924 (m110) cc_final: 0.8550 (m110) REVERT: B 468 LEU cc_start: 0.9672 (tp) cc_final: 0.9470 (tp) REVERT: B 493 MET cc_start: 0.9588 (tmm) cc_final: 0.9388 (tmm) REVERT: B 543 ILE cc_start: 0.9741 (mm) cc_final: 0.9422 (mm) REVERT: B 575 ARG cc_start: 0.8792 (mtm-85) cc_final: 0.8270 (mtm-85) REVERT: B 576 LEU cc_start: 0.9395 (mt) cc_final: 0.8942 (mt) REVERT: B 606 TYR cc_start: 0.8122 (m-80) cc_final: 0.7823 (m-10) REVERT: B 631 ASP cc_start: 0.9424 (m-30) cc_final: 0.9223 (m-30) REVERT: B 640 MET cc_start: 0.9432 (tpp) cc_final: 0.8986 (tpp) REVERT: C 20 MET cc_start: 0.9520 (tmm) cc_final: 0.9094 (ptp) REVERT: C 21 PHE cc_start: 0.9107 (m-80) cc_final: 0.8766 (m-80) REVERT: C 69 GLN cc_start: 0.9359 (tp-100) cc_final: 0.9154 (tp-100) REVERT: C 74 MET cc_start: 0.7306 (mtt) cc_final: 0.6775 (mtt) REVERT: C 90 LEU cc_start: 0.9562 (mt) cc_final: 0.9167 (mt) REVERT: C 93 MET cc_start: 0.8795 (ttp) cc_final: 0.8441 (tmm) REVERT: C 101 HIS cc_start: 0.6841 (m90) cc_final: 0.6174 (m90) REVERT: C 162 TYR cc_start: 0.9318 (m-10) cc_final: 0.8569 (m-10) REVERT: C 163 LEU cc_start: 0.9712 (tt) cc_final: 0.9479 (pp) REVERT: C 168 PHE cc_start: 0.8922 (m-80) cc_final: 0.8613 (m-80) REVERT: C 173 TYR cc_start: 0.7483 (t80) cc_final: 0.6559 (t80) REVERT: C 179 TYR cc_start: 0.8437 (t80) cc_final: 0.7897 (t80) REVERT: C 185 MET cc_start: 0.5407 (mmm) cc_final: 0.4271 (mpp) REVERT: C 233 ASN cc_start: 0.9407 (m110) cc_final: 0.8878 (m-40) REVERT: C 237 GLU cc_start: 0.9601 (mm-30) cc_final: 0.9333 (pp20) REVERT: C 252 LEU cc_start: 0.7567 (mt) cc_final: 0.7316 (mt) REVERT: C 271 LEU cc_start: 0.8126 (mt) cc_final: 0.7489 (mt) REVERT: C 278 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8025 (pm20) REVERT: D 20 MET cc_start: 0.8954 (mtm) cc_final: 0.8732 (mpp) REVERT: D 96 MET cc_start: 0.8851 (mmm) cc_final: 0.8635 (mmm) REVERT: D 138 ILE cc_start: 0.9742 (mm) cc_final: 0.9468 (mm) REVERT: D 139 VAL cc_start: 0.7874 (p) cc_final: 0.7205 (p) REVERT: D 148 ASP cc_start: 0.7349 (m-30) cc_final: 0.7036 (m-30) REVERT: D 176 LEU cc_start: 0.9559 (mt) cc_final: 0.9148 (tp) REVERT: D 185 MET cc_start: 0.5730 (ppp) cc_final: 0.5401 (mmm) REVERT: D 186 GLN cc_start: 0.7740 (mm110) cc_final: 0.7470 (mm110) REVERT: D 201 HIS cc_start: 0.9363 (m-70) cc_final: 0.9016 (m-70) REVERT: D 219 GLU cc_start: 0.9132 (tp30) cc_final: 0.8853 (tp30) REVERT: D 266 LYS cc_start: 0.8850 (mmtp) cc_final: 0.8639 (mmmm) outliers start: 5 outliers final: 0 residues processed: 717 average time/residue: 0.1165 time to fit residues: 126.3923 Evaluate side-chains 632 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 632 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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: 0.8980 chunk 46 optimal weight: 0.7980 chunk 120 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 168 optimal weight: 50.0000 chunk 157 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 320 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 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN C 263 ASN D 127 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 = 0.3582 r_free = 0.3582 target = 0.122388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.087886 restraints weight = 41531.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.091163 restraints weight = 21109.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.093351 restraints weight = 13170.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.094879 restraints weight = 9218.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.095874 restraints weight = 6997.871| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.5913 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= 0.145 Angle : 0.557 9.071 22134 Z= 0.297 Chirality : 0.042 0.169 2360 Planarity : 0.004 0.048 2818 Dihedral : 8.387 135.872 2290 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.12 % Allowed : 1.57 % Favored : 98.31 % 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 (0.19), residues: 1932 helix: 1.36 (0.16), residues: 1135 sheet: 0.03 (0.43), residues: 110 loop : 0.15 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 243 TYR 0.029 0.001 TYR C 174 PHE 0.022 0.002 PHE A 261 TRP 0.035 0.002 TRP D 124 HIS 0.006 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (16386) covalent geometry : angle 0.55742 / 0.30 (22134) hydrogen bonds : bond 0.03797 / 2.42 ( 871) hydrogen bonds : angle 4.70543 / 3.41 ( 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 730 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 728 time to evaluate : 0.568 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: 0.9254 (tptp) cc_final: 0.8921 (tppt) REVERT: A 12 LEU cc_start: 0.9596 (mt) cc_final: 0.9396 (mt) REVERT: A 30 LYS cc_start: 0.9459 (tptp) cc_final: 0.9255 (tptp) REVERT: A 67 GLU cc_start: 0.9344 (mp0) cc_final: 0.9138 (pm20) REVERT: A 107 LYS cc_start: 0.9157 (mttm) cc_final: 0.8739 (mtpp) REVERT: A 129 PHE cc_start: 0.9573 (m-10) cc_final: 0.9343 (m-80) REVERT: A 147 GLN cc_start: 0.9282 (mt0) cc_final: 0.8511 (mt0) REVERT: A 149 TYR cc_start: 0.8956 (t80) cc_final: 0.8646 (t80) REVERT: A 158 ASN cc_start: 0.9404 (m-40) cc_final: 0.9114 (m-40) REVERT: A 161 ARG cc_start: 0.8075 (ttm110) cc_final: 0.7574 (mmm-85) REVERT: A 164 ARG cc_start: 0.9058 (ptt90) cc_final: 0.8316 (ptm-80) REVERT: A 172 LEU cc_start: 0.9500 (mp) cc_final: 0.9068 (mp) REVERT: A 195 LEU cc_start: 0.9726 (mt) cc_final: 0.9481 (mt) REVERT: A 214 LYS cc_start: 0.8736 (tppt) cc_final: 0.8505 (tppt) REVERT: A 223 VAL cc_start: 0.9740 (m) cc_final: 0.9222 (p) REVERT: A 227 MET cc_start: 0.9280 (mtm) cc_final: 0.8829 (mtm) REVERT: A 232 ASN cc_start: 0.8913 (m110) cc_final: 0.8521 (m-40) REVERT: A 238 ASP cc_start: 0.8476 (p0) cc_final: 0.8125 (p0) REVERT: A 255 HIS cc_start: 0.8582 (t-90) cc_final: 0.8053 (t-90) REVERT: A 257 ASP cc_start: 0.9031 (m-30) cc_final: 0.8671 (m-30) REVERT: A 262 LEU cc_start: 0.9881 (mt) cc_final: 0.9629 (mt) REVERT: A 263 ASP cc_start: 0.9212 (m-30) cc_final: 0.8999 (m-30) REVERT: A 270 ASP cc_start: 0.8937 (t0) cc_final: 0.8653 (t0) REVERT: A 301 PHE cc_start: 0.9050 (m-10) cc_final: 0.8598 (m-10) REVERT: A 316 GLU cc_start: 0.8943 (tp30) cc_final: 0.8429 (tp30) REVERT: A 322 MET cc_start: 0.8568 (tpt) cc_final: 0.8252 (tpt) REVERT: A 344 GLU cc_start: 0.9264 (mt-10) cc_final: 0.8736 (mt-10) REVERT: A 345 LYS cc_start: 0.9820 (ttpt) cc_final: 0.9479 (ttmt) REVERT: A 349 LEU cc_start: 0.9673 (mt) cc_final: 0.9429 (mt) REVERT: A 366 LYS cc_start: 0.9199 (mtmm) cc_final: 0.8974 (mtmm) REVERT: A 375 LYS cc_start: 0.8691 (mmtt) cc_final: 0.8176 (mmtm) REVERT: A 379 SER cc_start: 0.9335 (t) cc_final: 0.9123 (t) REVERT: A 390 GLN cc_start: 0.8696 (mt0) cc_final: 0.8496 (mt0) REVERT: A 393 SER cc_start: 0.9435 (m) cc_final: 0.8942 (p) REVERT: A 402 GLU cc_start: 0.8075 (mp0) cc_final: 0.7804 (mp0) REVERT: A 415 ASN cc_start: 0.9364 (t0) cc_final: 0.8898 (t0) REVERT: A 420 MET cc_start: 0.9194 (tpp) cc_final: 0.8834 (ttm) REVERT: A 459 LYS cc_start: 0.8995 (mttp) cc_final: 0.8484 (mtmt) REVERT: A 466 MET cc_start: 0.9012 (ptt) cc_final: 0.8697 (ptt) REVERT: A 474 GLN cc_start: 0.9234 (mt0) cc_final: 0.8929 (mm-40) REVERT: A 491 PHE cc_start: 0.9647 (t80) cc_final: 0.9328 (t80) REVERT: A 493 MET cc_start: 0.9031 (tmm) cc_final: 0.8575 (tmm) REVERT: A 494 MET cc_start: 0.9328 (mtp) cc_final: 0.9017 (mtp) REVERT: A 501 GLN cc_start: 0.9319 (tt0) cc_final: 0.8606 (tm-30) REVERT: A 515 ASP cc_start: 0.8949 (m-30) cc_final: 0.8560 (m-30) REVERT: A 561 LEU cc_start: 0.9349 (tp) cc_final: 0.8794 (tp) REVERT: A 595 MET cc_start: 0.9039 (mmp) cc_final: 0.8464 (mmp) REVERT: A 598 MET cc_start: 0.8375 (mtm) cc_final: 0.8156 (mtm) REVERT: A 601 ILE cc_start: 0.9589 (mm) cc_final: 0.9291 (mm) REVERT: A 604 ARG cc_start: 0.9208 (mmm-85) cc_final: 0.8697 (mmp80) REVERT: A 615 MET cc_start: 0.9016 (mmm) cc_final: 0.8790 (mmm) REVERT: A 645 GLN cc_start: 0.9112 (tp40) cc_final: 0.8779 (tp40) REVERT: A 669 ARG cc_start: 0.9061 (tpp-160) cc_final: 0.8621 (tpp-160) REVERT: B 8 LYS cc_start: 0.9428 (tptt) cc_final: 0.8970 (tppt) REVERT: B 12 LEU cc_start: 0.9581 (mt) cc_final: 0.9262 (mt) REVERT: B 30 LYS cc_start: 0.9524 (tmtt) cc_final: 0.9314 (tmtt) REVERT: B 58 LEU cc_start: 0.9772 (mt) cc_final: 0.9564 (mt) REVERT: B 87 LYS cc_start: 0.9325 (tptt) cc_final: 0.8994 (tptt) REVERT: B 88 LYS cc_start: 0.9419 (mptt) cc_final: 0.9146 (mmtt) REVERT: B 106 LEU cc_start: 0.9124 (tt) cc_final: 0.8870 (tt) REVERT: B 119 GLU cc_start: 0.9276 (mp0) cc_final: 0.9001 (mp0) REVERT: B 167 LEU cc_start: 0.8708 (mt) cc_final: 0.8378 (mt) REVERT: B 172 LEU cc_start: 0.9309 (mp) cc_final: 0.9079 (mp) REVERT: B 173 LEU cc_start: 0.9376 (mt) cc_final: 0.9141 (mt) REVERT: B 176 ASN cc_start: 0.8688 (t0) cc_final: 0.8418 (t0) REVERT: B 181 ASP cc_start: 0.8613 (m-30) cc_final: 0.8218 (m-30) REVERT: B 184 ARG cc_start: 0.9374 (tpp80) cc_final: 0.8895 (tpp80) REVERT: B 211 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8211 (mm-30) REVERT: B 214 LYS cc_start: 0.8661 (mmtm) cc_final: 0.8357 (mmtm) REVERT: B 235 ARG cc_start: 0.9377 (ttm110) cc_final: 0.8907 (ttm110) REVERT: B 236 TYR cc_start: 0.9181 (t80) cc_final: 0.8949 (t80) REVERT: B 239 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8279 (tm-30) REVERT: B 252 ASN cc_start: 0.9309 (t0) cc_final: 0.9014 (t0) REVERT: B 270 ASP cc_start: 0.8870 (t0) cc_final: 0.8670 (p0) REVERT: B 286 ASP cc_start: 0.8952 (m-30) cc_final: 0.8545 (m-30) REVERT: B 322 MET cc_start: 0.9067 (mmm) cc_final: 0.8791 (mmm) REVERT: B 335 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8150 (mm-30) REVERT: B 348 MET cc_start: 0.9481 (ptp) cc_final: 0.9152 (ptp) REVERT: B 358 ILE cc_start: 0.9684 (mm) cc_final: 0.9452 (mm) REVERT: B 362 ASP cc_start: 0.8964 (m-30) cc_final: 0.8496 (m-30) REVERT: B 390 GLN cc_start: 0.9069 (mm110) cc_final: 0.8781 (mm-40) REVERT: B 393 SER cc_start: 0.9422 (m) cc_final: 0.9108 (p) REVERT: B 407 ILE cc_start: 0.9149 (mp) cc_final: 0.8869 (mp) REVERT: B 410 ASN cc_start: 0.8957 (m110) cc_final: 0.8660 (m110) REVERT: B 427 LYS cc_start: 0.9441 (ttmm) cc_final: 0.9174 (ptpp) REVERT: B 543 ILE cc_start: 0.9729 (mm) cc_final: 0.9403 (mm) REVERT: B 558 TRP cc_start: 0.9521 (m100) cc_final: 0.8620 (m100) REVERT: B 575 ARG cc_start: 0.8796 (mtm-85) cc_final: 0.8506 (mtm-85) REVERT: B 606 TYR cc_start: 0.7950 (m-80) cc_final: 0.7687 (m-10) REVERT: B 639 ASP cc_start: 0.9036 (m-30) cc_final: 0.8806 (m-30) REVERT: B 640 MET cc_start: 0.9329 (tpp) cc_final: 0.8863 (tpp) REVERT: B 664 THR cc_start: 0.8908 (p) cc_final: 0.8328 (p) REVERT: C 20 MET cc_start: 0.9536 (tmm) cc_final: 0.9095 (ptp) REVERT: C 21 PHE cc_start: 0.9157 (m-80) cc_final: 0.8891 (m-80) REVERT: C 74 MET cc_start: 0.7459 (mtt) cc_final: 0.7119 (mtt) REVERT: C 90 LEU cc_start: 0.9602 (mt) cc_final: 0.9232 (mt) REVERT: C 93 MET cc_start: 0.8745 (ttp) cc_final: 0.8447 (tmm) REVERT: C 101 HIS cc_start: 0.7010 (m90) cc_final: 0.6285 (m90) REVERT: C 163 LEU cc_start: 0.9717 (tt) cc_final: 0.9511 (pp) REVERT: C 168 PHE cc_start: 0.8800 (m-80) cc_final: 0.8586 (m-80) REVERT: C 173 TYR cc_start: 0.7544 (t80) cc_final: 0.6616 (t80) REVERT: C 177 TYR cc_start: 0.9141 (t80) cc_final: 0.8926 (t80) REVERT: C 179 TYR cc_start: 0.8480 (t80) cc_final: 0.7896 (t80) REVERT: C 185 MET cc_start: 0.5469 (mmm) cc_final: 0.4485 (mpp) REVERT: C 212 ILE cc_start: 0.8265 (mm) cc_final: 0.7664 (mm) REVERT: C 233 ASN cc_start: 0.9443 (m110) cc_final: 0.8882 (m110) REVERT: C 252 LEU cc_start: 0.7556 (mt) cc_final: 0.7264 (mt) REVERT: C 260 ILE cc_start: 0.6894 (pt) cc_final: 0.6668 (pt) REVERT: C 270 ASN cc_start: 0.8452 (m110) cc_final: 0.8102 (m-40) REVERT: C 278 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8149 (pm20) REVERT: C 317 ASP cc_start: 0.9167 (t0) cc_final: 0.8950 (t0) REVERT: C 321 TYR cc_start: 0.8684 (m-80) cc_final: 0.8416 (m-80) REVERT: D 20 MET cc_start: 0.8970 (mtm) cc_final: 0.8717 (mpp) REVERT: D 139 VAL cc_start: 0.8165 (p) cc_final: 0.7682 (p) REVERT: D 148 ASP cc_start: 0.7016 (m-30) cc_final: 0.6680 (m-30) REVERT: D 186 GLN cc_start: 0.7801 (mm-40) cc_final: 0.7417 (mm-40) REVERT: D 219 GLU cc_start: 0.9125 (tp30) cc_final: 0.8878 (tp30) outliers start: 2 outliers final: 1 residues processed: 729 average time/residue: 0.1173 time to fit residues: 128.4073 Evaluate side-chains 643 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 642 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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: 9.9990 chunk 183 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 172 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN A 34 HIS ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN B 150 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 ASN B 410 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.118932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.084594 restraints weight = 41808.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.087627 restraints weight = 21545.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.089785 restraints weight = 13825.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.091282 restraints weight = 9633.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.092308 restraints weight = 7338.234| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 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 = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.6221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16386 Z= 0.190 Angle : 0.588 7.817 22134 Z= 0.313 Chirality : 0.043 0.258 2360 Planarity : 0.003 0.043 2818 Dihedral : 8.379 137.426 2290 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.19), residues: 1932 helix: 1.43 (0.16), residues: 1133 sheet: -0.62 (0.39), residues: 132 loop : 0.24 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 243 TYR 0.029 0.002 TYR C 174 PHE 0.024 0.002 PHE D 168 TRP 0.039 0.002 TRP D 124 HIS 0.027 0.002 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (16386) covalent geometry : angle 0.58790 / 0.31 (22134) hydrogen bonds : bond 0.03874 / 2.45 ( 871) hydrogen bonds : angle 4.70689 / 3.42 ( 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 737 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 737 time to evaluate : 0.529 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: 0.9248 (tptp) cc_final: 0.8969 (tppt) REVERT: A 12 LEU cc_start: 0.9603 (mt) cc_final: 0.9376 (mt) REVERT: A 27 ASP cc_start: 0.9105 (p0) cc_final: 0.8874 (p0) REVERT: A 95 MET cc_start: 0.9089 (mmm) cc_final: 0.8743 (tpp) REVERT: A 107 LYS cc_start: 0.9180 (mttm) cc_final: 0.8800 (mtpp) REVERT: A 110 ASP cc_start: 0.9591 (p0) cc_final: 0.9370 (p0) REVERT: A 147 GLN cc_start: 0.9318 (mt0) cc_final: 0.8573 (mt0) REVERT: A 149 TYR cc_start: 0.9177 (t80) cc_final: 0.8694 (t80) REVERT: A 158 ASN cc_start: 0.9439 (m-40) cc_final: 0.9167 (m-40) REVERT: A 161 ARG cc_start: 0.8344 (ttm110) cc_final: 0.7786 (mmm-85) REVERT: A 164 ARG cc_start: 0.9180 (ptt90) cc_final: 0.8328 (ptm-80) REVERT: A 172 LEU cc_start: 0.9514 (mp) cc_final: 0.9155 (mp) REVERT: A 195 LEU cc_start: 0.9718 (mt) cc_final: 0.9473 (mt) REVERT: A 223 VAL cc_start: 0.9763 (m) cc_final: 0.9317 (p) REVERT: A 227 MET cc_start: 0.9287 (mtm) cc_final: 0.8895 (mtm) REVERT: A 232 ASN cc_start: 0.8923 (m110) cc_final: 0.8431 (m-40) REVERT: A 235 ARG cc_start: 0.9347 (ttm-80) cc_final: 0.9014 (ttm-80) REVERT: A 238 ASP cc_start: 0.8247 (p0) cc_final: 0.7698 (p0) REVERT: A 252 ASN cc_start: 0.9458 (t0) cc_final: 0.9237 (t0) REVERT: A 255 HIS cc_start: 0.8626 (t-90) cc_final: 0.8265 (t-90) REVERT: A 257 ASP cc_start: 0.9046 (m-30) cc_final: 0.8764 (m-30) REVERT: A 262 LEU cc_start: 0.9889 (mt) cc_final: 0.9634 (mt) REVERT: A 263 ASP cc_start: 0.9207 (m-30) cc_final: 0.8991 (m-30) REVERT: A 270 ASP cc_start: 0.9017 (t0) cc_final: 0.8710 (t0) REVERT: A 301 PHE cc_start: 0.9214 (m-10) cc_final: 0.8717 (m-10) REVERT: A 316 GLU cc_start: 0.9000 (tp30) cc_final: 0.8538 (tp30) REVERT: A 322 MET cc_start: 0.8671 (tpt) cc_final: 0.8332 (tpt) REVERT: A 333 LYS cc_start: 0.9585 (tppt) cc_final: 0.9244 (tppp) REVERT: A 335 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7942 (mm-30) REVERT: A 344 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8705 (mt-10) REVERT: A 345 LYS cc_start: 0.9821 (ttpt) cc_final: 0.9454 (ttmt) REVERT: A 349 LEU cc_start: 0.9689 (mt) cc_final: 0.9446 (mt) REVERT: A 375 LYS cc_start: 0.8694 (mmtt) cc_final: 0.8173 (mmtm) REVERT: A 393 SER cc_start: 0.9364 (m) cc_final: 0.8730 (t) REVERT: A 401 ASP cc_start: 0.9358 (m-30) cc_final: 0.8797 (m-30) REVERT: A 402 GLU cc_start: 0.8112 (mp0) cc_final: 0.7907 (mp0) REVERT: A 407 ILE cc_start: 0.9273 (mt) cc_final: 0.9054 (mt) REVERT: A 415 ASN cc_start: 0.9382 (t0) cc_final: 0.8955 (t0) REVERT: A 446 ARG cc_start: 0.8140 (ptp-110) cc_final: 0.7748 (ttm110) REVERT: A 459 LYS cc_start: 0.8987 (mttp) cc_final: 0.8549 (mtmt) REVERT: A 466 MET cc_start: 0.9043 (ptt) cc_final: 0.8699 (ptt) REVERT: A 474 GLN cc_start: 0.9261 (mt0) cc_final: 0.8930 (mm-40) REVERT: A 493 MET cc_start: 0.9008 (tmm) cc_final: 0.8513 (tmm) REVERT: A 494 MET cc_start: 0.9303 (mtp) cc_final: 0.8951 (mtp) REVERT: A 501 GLN cc_start: 0.9357 (tt0) cc_final: 0.8746 (tm-30) REVERT: A 512 GLU cc_start: 0.8793 (pm20) cc_final: 0.8582 (pm20) REVERT: A 515 ASP cc_start: 0.8917 (m-30) cc_final: 0.8574 (m-30) REVERT: A 561 LEU cc_start: 0.9411 (tp) cc_final: 0.8927 (tp) REVERT: A 601 ILE cc_start: 0.9437 (mm) cc_final: 0.8906 (tp) REVERT: A 615 MET cc_start: 0.9086 (mmm) cc_final: 0.8799 (mmm) REVERT: A 633 ASP cc_start: 0.9192 (t0) cc_final: 0.8587 (t70) REVERT: A 645 GLN cc_start: 0.9165 (tp40) cc_final: 0.8818 (tp40) REVERT: A 654 PHE cc_start: 0.9473 (t80) cc_final: 0.9205 (t80) REVERT: A 669 ARG cc_start: 0.9034 (tpp-160) cc_final: 0.8545 (tpp80) REVERT: A 677 ARG cc_start: 0.9089 (tpp80) cc_final: 0.8791 (tpp80) REVERT: B 8 LYS cc_start: 0.9440 (tptt) cc_final: 0.9013 (tppt) REVERT: B 12 LEU cc_start: 0.9611 (mt) cc_final: 0.9344 (mt) REVERT: B 16 ILE cc_start: 0.9694 (mm) cc_final: 0.9462 (tp) REVERT: B 20 LYS cc_start: 0.9617 (tmtt) cc_final: 0.9391 (tptp) REVERT: B 21 ASP cc_start: 0.8591 (t70) cc_final: 0.8325 (t0) REVERT: B 30 LYS cc_start: 0.9531 (tmtt) cc_final: 0.9313 (tmtt) REVERT: B 58 LEU cc_start: 0.9767 (mt) cc_final: 0.9560 (mt) REVERT: B 87 LYS cc_start: 0.9390 (tptt) cc_final: 0.9132 (tptm) REVERT: B 88 LYS cc_start: 0.9431 (mptt) cc_final: 0.9188 (mmtt) REVERT: B 119 GLU cc_start: 0.9330 (mp0) cc_final: 0.9028 (mp0) REVERT: B 167 LEU cc_start: 0.8960 (mt) cc_final: 0.8525 (mt) REVERT: B 172 LEU cc_start: 0.9330 (mp) cc_final: 0.9102 (mp) REVERT: B 173 LEU cc_start: 0.9374 (mt) cc_final: 0.9133 (mt) REVERT: B 176 ASN cc_start: 0.8782 (t0) cc_final: 0.8539 (t0) REVERT: B 181 ASP cc_start: 0.8643 (m-30) cc_final: 0.8282 (m-30) REVERT: B 184 ARG cc_start: 0.9376 (tpp80) cc_final: 0.8784 (tpp80) REVERT: B 211 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8226 (mm-30) REVERT: B 235 ARG cc_start: 0.9174 (ttm110) cc_final: 0.8861 (ttm110) REVERT: B 239 GLN cc_start: 0.8846 (tm-30) cc_final: 0.8310 (tm-30) REVERT: B 252 ASN cc_start: 0.9330 (t0) cc_final: 0.9010 (t0) REVERT: B 286 ASP cc_start: 0.8875 (m-30) cc_final: 0.8376 (m-30) REVERT: B 322 MET cc_start: 0.9071 (mmm) cc_final: 0.8800 (mmm) REVERT: B 335 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8256 (mm-30) REVERT: B 358 ILE cc_start: 0.9671 (mm) cc_final: 0.9446 (mm) REVERT: B 362 ASP cc_start: 0.8931 (m-30) cc_final: 0.8268 (m-30) REVERT: B 387 GLN cc_start: 0.9014 (mt0) cc_final: 0.8594 (mp10) REVERT: B 393 SER cc_start: 0.9427 (m) cc_final: 0.9129 (p) REVERT: B 403 ILE cc_start: 0.8858 (tp) cc_final: 0.8655 (tp) REVERT: B 407 ILE cc_start: 0.9109 (mp) cc_final: 0.8677 (mp) REVERT: B 410 ASN cc_start: 0.9025 (m-40) cc_final: 0.8819 (m-40) REVERT: B 415 ASN cc_start: 0.9370 (t0) cc_final: 0.8913 (t0) REVERT: B 426 GLU cc_start: 0.9024 (pm20) cc_final: 0.8811 (pm20) REVERT: B 491 PHE cc_start: 0.9605 (t80) cc_final: 0.9238 (t80) REVERT: B 494 MET cc_start: 0.9391 (mtp) cc_final: 0.9077 (mmt) REVERT: B 543 ILE cc_start: 0.9735 (mm) cc_final: 0.9401 (mm) REVERT: B 639 ASP cc_start: 0.9049 (m-30) cc_final: 0.8833 (m-30) REVERT: B 640 MET cc_start: 0.9227 (tpp) cc_final: 0.8663 (tpp) REVERT: B 664 THR cc_start: 0.8754 (p) cc_final: 0.8443 (p) REVERT: B 686 ARG cc_start: 0.8581 (ttm110) cc_final: 0.8152 (mtt90) REVERT: C 20 MET cc_start: 0.9543 (tmm) cc_final: 0.9068 (ptp) REVERT: C 37 LEU cc_start: 0.2373 (tp) cc_final: 0.2170 (tp) REVERT: C 74 MET cc_start: 0.7500 (mtt) cc_final: 0.7279 (mtt) REVERT: C 90 LEU cc_start: 0.9620 (mt) cc_final: 0.9296 (mt) REVERT: C 93 MET cc_start: 0.8729 (ttp) cc_final: 0.8506 (tmm) REVERT: C 101 HIS cc_start: 0.7202 (m90) cc_final: 0.6330 (m90) REVERT: C 129 LYS cc_start: 0.9448 (ttpp) cc_final: 0.9174 (tptt) REVERT: C 168 PHE cc_start: 0.8861 (m-80) cc_final: 0.8539 (m-80) REVERT: C 173 TYR cc_start: 0.7511 (t80) cc_final: 0.6629 (t80) REVERT: C 177 TYR cc_start: 0.9121 (t80) cc_final: 0.8914 (t80) REVERT: C 179 TYR cc_start: 0.8552 (t80) cc_final: 0.7922 (t80) REVERT: C 185 MET cc_start: 0.5497 (mmm) cc_final: 0.4588 (mpp) REVERT: C 208 LEU cc_start: 0.8834 (mm) cc_final: 0.8568 (mm) REVERT: C 212 ILE cc_start: 0.8208 (mm) cc_final: 0.7567 (mm) REVERT: C 252 LEU cc_start: 0.7545 (mt) cc_final: 0.7249 (mt) REVERT: C 278 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8274 (pm20) REVERT: D 20 MET cc_start: 0.9000 (mtm) cc_final: 0.8709 (mpp) REVERT: D 148 ASP cc_start: 0.7002 (m-30) cc_final: 0.6689 (m-30) REVERT: D 176 LEU cc_start: 0.9611 (mt) cc_final: 0.9212 (tp) REVERT: D 185 MET cc_start: 0.5354 (ppp) cc_final: 0.4253 (mmm) REVERT: D 219 GLU cc_start: 0.9169 (tp30) cc_final: 0.8938 (tp30) REVERT: D 270 ASN cc_start: 0.8712 (m-40) cc_final: 0.8471 (m-40) outliers start: 0 outliers final: 0 residues processed: 737 average time/residue: 0.1209 time to fit residues: 133.5228 Evaluate side-chains 635 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 635 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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: 0.1980 chunk 51 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 186 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 156 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 447 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 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 28 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 GLN D 28 GLN D 132 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.121297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.087410 restraints weight = 41218.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.090551 restraints weight = 21022.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.092634 restraints weight = 13099.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.094070 restraints weight = 9234.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.095097 restraints weight = 7075.748| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.6497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16386 Z= 0.151 Angle : 0.578 6.904 22134 Z= 0.308 Chirality : 0.042 0.225 2360 Planarity : 0.003 0.044 2818 Dihedral : 8.364 137.637 2290 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: 1.12 (0.19), residues: 1932 helix: 1.34 (0.15), residues: 1137 sheet: -0.12 (0.42), residues: 110 loop : 0.02 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 243 TYR 0.027 0.001 TYR D 142 PHE 0.024 0.002 PHE D 168 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 0.00334 / 0.15 (16386) covalent geometry : angle 0.57801 / 0.31 (22134) hydrogen bonds : bond 0.03783 / 2.40 ( 871) hydrogen bonds : angle 4.71576 / 3.41 ( 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 716 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 716 time to evaluate : 0.568 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: A 8 LYS cc_start: 0.9271 (tptp) cc_final: 0.8989 (tppt) REVERT: A 12 LEU cc_start: 0.9605 (mt) cc_final: 0.9358 (mt) REVERT: A 30 LYS cc_start: 0.9492 (tptp) cc_final: 0.9260 (tptp) REVERT: A 95 MET cc_start: 0.9054 (mmm) cc_final: 0.8669 (tpp) REVERT: A 107 LYS cc_start: 0.9222 (mttm) cc_final: 0.8926 (mtpp) REVERT: A 147 GLN cc_start: 0.9283 (mt0) cc_final: 0.8278 (mt0) REVERT: A 149 TYR cc_start: 0.9200 (t80) cc_final: 0.8737 (t80) REVERT: A 158 ASN cc_start: 0.9460 (m-40) cc_final: 0.9185 (m-40) REVERT: A 161 ARG cc_start: 0.8409 (ttm110) cc_final: 0.7850 (mmm-85) REVERT: A 164 ARG cc_start: 0.9178 (ptt90) cc_final: 0.8354 (ptm-80) REVERT: A 172 LEU cc_start: 0.9593 (mp) cc_final: 0.9092 (mp) REVERT: A 179 LEU cc_start: 0.9571 (tp) cc_final: 0.9351 (tp) REVERT: A 195 LEU cc_start: 0.9716 (mt) cc_final: 0.9480 (mt) REVERT: A 223 VAL cc_start: 0.9750 (m) cc_final: 0.9265 (p) REVERT: A 227 MET cc_start: 0.9271 (mtm) cc_final: 0.8829 (mtm) REVERT: A 232 ASN cc_start: 0.8860 (m110) cc_final: 0.8645 (m-40) REVERT: A 238 ASP cc_start: 0.8081 (p0) cc_final: 0.7811 (p0) REVERT: A 255 HIS cc_start: 0.8695 (t-90) cc_final: 0.8329 (t-90) REVERT: A 257 ASP cc_start: 0.9056 (m-30) cc_final: 0.8739 (m-30) REVERT: A 262 LEU cc_start: 0.9895 (mt) cc_final: 0.9625 (mt) REVERT: A 263 ASP cc_start: 0.9216 (m-30) cc_final: 0.8997 (m-30) REVERT: A 301 PHE cc_start: 0.9163 (m-10) cc_final: 0.8661 (m-10) REVERT: A 316 GLU cc_start: 0.9035 (tp30) cc_final: 0.8516 (tp30) REVERT: A 318 ASP cc_start: 0.9334 (t0) cc_final: 0.9119 (t0) REVERT: A 333 LYS cc_start: 0.9586 (tppt) cc_final: 0.9271 (tppp) REVERT: A 335 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8022 (mm-30) REVERT: A 344 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8651 (mt-10) REVERT: A 345 LYS cc_start: 0.9807 (ttpt) cc_final: 0.9450 (ttmt) REVERT: A 349 LEU cc_start: 0.9686 (mt) cc_final: 0.9435 (mt) REVERT: A 366 LYS cc_start: 0.9439 (mtmm) cc_final: 0.9167 (mtmm) REVERT: A 371 ASN cc_start: 0.8741 (m-40) cc_final: 0.8174 (m-40) REVERT: A 375 LYS cc_start: 0.8740 (mmtt) cc_final: 0.8409 (mmtm) REVERT: A 390 GLN cc_start: 0.8809 (mt0) cc_final: 0.8579 (mt0) REVERT: A 393 SER cc_start: 0.9259 (m) cc_final: 0.8949 (t) REVERT: A 407 ILE cc_start: 0.9299 (mt) cc_final: 0.9046 (mt) REVERT: A 415 ASN cc_start: 0.9393 (t0) cc_final: 0.8383 (t0) REVERT: A 418 ASN cc_start: 0.9091 (m110) cc_final: 0.8404 (m-40) REVERT: A 420 MET cc_start: 0.9253 (tpp) cc_final: 0.8914 (ttm) REVERT: A 459 LYS cc_start: 0.8986 (mttp) cc_final: 0.8373 (mtmm) REVERT: A 466 MET cc_start: 0.8998 (ptt) cc_final: 0.8736 (ptt) REVERT: A 474 GLN cc_start: 0.9270 (mt0) cc_final: 0.8967 (mm-40) REVERT: A 493 MET cc_start: 0.8991 (tmm) cc_final: 0.8678 (tmm) REVERT: A 494 MET cc_start: 0.9296 (mtp) cc_final: 0.8975 (mtp) REVERT: A 501 GLN cc_start: 0.9348 (tt0) cc_final: 0.8748 (tm-30) REVERT: A 515 ASP cc_start: 0.8940 (m-30) cc_final: 0.8567 (m-30) REVERT: A 561 LEU cc_start: 0.9427 (tp) cc_final: 0.8992 (tp) REVERT: A 601 ILE cc_start: 0.9606 (mm) cc_final: 0.8901 (tp) REVERT: A 615 MET cc_start: 0.9115 (mmm) cc_final: 0.8795 (mmm) REVERT: A 645 GLN cc_start: 0.9176 (tp40) cc_final: 0.8868 (tp40) REVERT: A 654 PHE cc_start: 0.9451 (t80) cc_final: 0.9207 (t80) REVERT: A 669 ARG cc_start: 0.9046 (tpp-160) cc_final: 0.8561 (tpp80) REVERT: B 8 LYS cc_start: 0.9454 (tptt) cc_final: 0.9024 (tppt) REVERT: B 12 LEU cc_start: 0.9617 (mt) cc_final: 0.9337 (mt) REVERT: B 16 ILE cc_start: 0.9696 (mm) cc_final: 0.9455 (tp) REVERT: B 30 LYS cc_start: 0.9519 (tmtt) cc_final: 0.9302 (tmtt) REVERT: B 55 LEU cc_start: 0.9786 (mt) cc_final: 0.9584 (mt) REVERT: B 58 LEU cc_start: 0.9773 (mt) cc_final: 0.9561 (mt) REVERT: B 87 LYS cc_start: 0.9391 (tptt) cc_final: 0.9176 (tptm) REVERT: B 88 LYS cc_start: 0.9391 (mptt) cc_final: 0.9183 (mmtt) REVERT: B 99 LYS cc_start: 0.9584 (tppt) cc_final: 0.9319 (tppt) REVERT: B 119 GLU cc_start: 0.9324 (mp0) cc_final: 0.9017 (mp0) REVERT: B 167 LEU cc_start: 0.9061 (mt) cc_final: 0.8574 (mt) REVERT: B 172 LEU cc_start: 0.9310 (mp) cc_final: 0.9048 (mp) REVERT: B 173 LEU cc_start: 0.9398 (mt) cc_final: 0.9144 (mt) REVERT: B 176 ASN cc_start: 0.8805 (t0) cc_final: 0.8568 (t0) REVERT: B 181 ASP cc_start: 0.8684 (m-30) cc_final: 0.8279 (m-30) REVERT: B 184 ARG cc_start: 0.9426 (tpp80) cc_final: 0.9149 (tpp80) REVERT: B 211 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8108 (mm-30) REVERT: B 239 GLN cc_start: 0.8835 (tm-30) cc_final: 0.8239 (tm-30) REVERT: B 252 ASN cc_start: 0.9341 (t0) cc_final: 0.9010 (t0) REVERT: B 286 ASP cc_start: 0.8869 (m-30) cc_final: 0.8361 (m-30) REVERT: B 322 MET cc_start: 0.9077 (mmm) cc_final: 0.8755 (mmm) REVERT: B 335 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8267 (mm-30) REVERT: B 362 ASP cc_start: 0.8917 (m-30) cc_final: 0.8222 (m-30) REVERT: B 384 GLU cc_start: 0.8797 (pm20) cc_final: 0.8399 (pm20) REVERT: B 387 GLN cc_start: 0.8968 (mt0) cc_final: 0.8469 (mp10) REVERT: B 393 SER cc_start: 0.9413 (m) cc_final: 0.9175 (p) REVERT: B 407 ILE cc_start: 0.9094 (mp) cc_final: 0.8654 (mp) REVERT: B 415 ASN cc_start: 0.9290 (t0) cc_final: 0.9054 (t0) REVERT: B 427 LYS cc_start: 0.9387 (ptpp) cc_final: 0.8926 (ptpp) REVERT: B 543 ILE cc_start: 0.9742 (mm) cc_final: 0.9407 (mm) REVERT: B 606 TYR cc_start: 0.7861 (m-80) cc_final: 0.7392 (m-80) REVERT: B 639 ASP cc_start: 0.9005 (m-30) cc_final: 0.8753 (m-30) REVERT: B 640 MET cc_start: 0.9194 (tpp) cc_final: 0.8561 (tpp) REVERT: B 667 LEU cc_start: 0.9404 (tp) cc_final: 0.9001 (tp) REVERT: B 680 LYS cc_start: 0.9150 (mttt) cc_final: 0.8752 (mttt) REVERT: C 20 MET cc_start: 0.9518 (tmm) cc_final: 0.9076 (ptp) REVERT: C 90 LEU cc_start: 0.9612 (mt) cc_final: 0.9254 (mt) REVERT: C 101 HIS cc_start: 0.7125 (m90) cc_final: 0.6452 (m170) REVERT: C 129 LYS cc_start: 0.9406 (ttpp) cc_final: 0.9189 (tptt) REVERT: C 173 TYR cc_start: 0.7498 (t80) cc_final: 0.6650 (t80) REVERT: C 177 TYR cc_start: 0.9117 (t80) cc_final: 0.8916 (t80) REVERT: C 179 TYR cc_start: 0.8594 (t80) cc_final: 0.7936 (t80) REVERT: C 185 MET cc_start: 0.5954 (mmm) cc_final: 0.5043 (mpp) REVERT: C 212 ILE cc_start: 0.8250 (mm) cc_final: 0.7621 (mm) REVERT: C 252 LEU cc_start: 0.7526 (mt) cc_final: 0.7234 (mt) REVERT: C 278 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8369 (pm20) REVERT: D 20 MET cc_start: 0.8996 (mtm) cc_final: 0.8680 (mpp) REVERT: D 148 ASP cc_start: 0.7047 (m-30) cc_final: 0.6725 (m-30) REVERT: D 219 GLU cc_start: 0.9170 (tp30) cc_final: 0.8937 (tp30) REVERT: D 233 ASN cc_start: 0.8758 (m110) cc_final: 0.8541 (p0) outliers start: 0 outliers final: 0 residues processed: 716 average time/residue: 0.1202 time to fit residues: 128.6768 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 : 0.583 ------------------------------------------------------------------------------- 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: 5.9990 chunk 19 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN A 320 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 GLN C 136 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 HIS D 270 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.114478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.080499 restraints weight = 42940.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.083444 restraints weight = 22320.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.085420 restraints weight = 14036.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.086789 restraints weight = 9997.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.087693 restraints weight = 7735.793| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.6772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16386 Z= 0.281 Angle : 0.680 9.772 22134 Z= 0.360 Chirality : 0.045 0.256 2360 Planarity : 0.004 0.054 2818 Dihedral : 8.622 140.086 2290 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.19), residues: 1932 helix: 1.14 (0.15), residues: 1145 sheet: 0.15 (0.43), residues: 100 loop : -0.21 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 274 TYR 0.032 0.002 TYR D 142 PHE 0.033 0.002 PHE C 227 TRP 0.043 0.002 TRP D 124 HIS 0.011 0.002 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.28 (16386) covalent geometry : angle 0.67986 / 0.36 (22134) hydrogen bonds : bond 0.04006 / 2.57 ( 871) hydrogen bonds : angle 4.96032 / 3.60 ( 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 697 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 697 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9235 (tptp) cc_final: 0.8972 (tppt) REVERT: A 12 LEU cc_start: 0.9607 (mt) cc_final: 0.9329 (mt) REVERT: A 30 LYS cc_start: 0.9518 (tptp) cc_final: 0.9303 (tptp) REVERT: A 95 MET cc_start: 0.9133 (mmm) cc_final: 0.8861 (tpp) REVERT: A 107 LYS cc_start: 0.9252 (mttm) cc_final: 0.8868 (mtpp) REVERT: A 128 PHE cc_start: 0.9490 (t80) cc_final: 0.9140 (t80) REVERT: A 139 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8851 (mp0) REVERT: A 143 LEU cc_start: 0.9403 (tp) cc_final: 0.9172 (tp) REVERT: A 147 GLN cc_start: 0.9420 (mt0) cc_final: 0.8495 (mt0) REVERT: A 149 TYR cc_start: 0.9322 (t80) cc_final: 0.8579 (t80) REVERT: A 158 ASN cc_start: 0.9495 (m-40) cc_final: 0.9245 (m-40) REVERT: A 161 ARG cc_start: 0.8466 (ttm110) cc_final: 0.8085 (mmm-85) REVERT: A 172 LEU cc_start: 0.9618 (mp) cc_final: 0.9262 (mp) REVERT: A 181 ASP cc_start: 0.8843 (m-30) cc_final: 0.8343 (m-30) REVERT: A 195 LEU cc_start: 0.9706 (mt) cc_final: 0.9450 (mt) REVERT: A 214 LYS cc_start: 0.8742 (tppt) cc_final: 0.8388 (mmtt) REVERT: A 223 VAL cc_start: 0.9786 (m) cc_final: 0.9277 (p) REVERT: A 227 MET cc_start: 0.9292 (mtm) cc_final: 0.8954 (mtm) REVERT: A 232 ASN cc_start: 0.8929 (m110) cc_final: 0.8483 (m110) REVERT: A 238 ASP cc_start: 0.7940 (p0) cc_final: 0.7703 (p0) REVERT: A 255 HIS cc_start: 0.8772 (t-90) cc_final: 0.7699 (t-90) REVERT: A 257 ASP cc_start: 0.9036 (m-30) cc_final: 0.8640 (m-30) REVERT: A 262 LEU cc_start: 0.9902 (mt) cc_final: 0.9661 (mt) REVERT: A 276 LYS cc_start: 0.9324 (mptt) cc_final: 0.9018 (mmmm) REVERT: A 301 PHE cc_start: 0.9273 (m-10) cc_final: 0.8834 (m-10) REVERT: A 333 LYS cc_start: 0.9596 (tppt) cc_final: 0.9237 (tppp) REVERT: A 335 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8176 (mm-30) REVERT: A 344 GLU cc_start: 0.9310 (mt-10) cc_final: 0.8718 (mt-10) REVERT: A 349 LEU cc_start: 0.9720 (mt) cc_final: 0.9494 (mt) REVERT: A 375 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8584 (mmtm) REVERT: A 390 GLN cc_start: 0.8967 (mt0) cc_final: 0.8726 (mt0) REVERT: A 393 SER cc_start: 0.9232 (m) cc_final: 0.8676 (p) REVERT: A 402 GLU cc_start: 0.8216 (mp0) cc_final: 0.7936 (mp0) REVERT: A 407 ILE cc_start: 0.9326 (mt) cc_final: 0.9092 (mt) REVERT: A 415 ASN cc_start: 0.9369 (t0) cc_final: 0.8437 (t0) REVERT: A 418 ASN cc_start: 0.9187 (m110) cc_final: 0.8442 (m-40) REVERT: A 446 ARG cc_start: 0.8418 (ptp-110) cc_final: 0.8119 (ttm110) REVERT: A 459 LYS cc_start: 0.8981 (mttp) cc_final: 0.8410 (mtmm) REVERT: A 466 MET cc_start: 0.9090 (ptt) cc_final: 0.8821 (ptt) REVERT: A 493 MET cc_start: 0.8944 (tmm) cc_final: 0.8600 (tmm) REVERT: A 494 MET cc_start: 0.9268 (mtp) cc_final: 0.8959 (mtp) REVERT: A 501 GLN cc_start: 0.9358 (tt0) cc_final: 0.8742 (tm-30) REVERT: A 515 ASP cc_start: 0.8958 (m-30) cc_final: 0.8691 (m-30) REVERT: A 561 LEU cc_start: 0.9465 (tp) cc_final: 0.9038 (tp) REVERT: A 583 SER cc_start: 0.9085 (m) cc_final: 0.8769 (t) REVERT: A 601 ILE cc_start: 0.9639 (mm) cc_final: 0.9030 (tp) REVERT: A 615 MET cc_start: 0.9131 (mmm) cc_final: 0.8806 (mmm) REVERT: A 634 MET cc_start: 0.9088 (mmm) cc_final: 0.8828 (mmt) REVERT: A 645 GLN cc_start: 0.9296 (tp40) cc_final: 0.8983 (tp40) REVERT: A 669 ARG cc_start: 0.9095 (tpp-160) cc_final: 0.8872 (tpp-160) REVERT: B 8 LYS cc_start: 0.9438 (tptt) cc_final: 0.9043 (tppt) REVERT: B 12 LEU cc_start: 0.9634 (mt) cc_final: 0.9386 (mt) REVERT: B 16 ILE cc_start: 0.9702 (mm) cc_final: 0.9498 (tp) REVERT: B 30 LYS cc_start: 0.9518 (tmtt) cc_final: 0.9311 (tmtt) REVERT: B 55 LEU cc_start: 0.9771 (mt) cc_final: 0.9548 (mt) REVERT: B 87 LYS cc_start: 0.9455 (tptt) cc_final: 0.9171 (tppt) REVERT: B 88 LYS cc_start: 0.9395 (mptt) cc_final: 0.9178 (mmtt) REVERT: B 98 PHE cc_start: 0.9507 (t80) cc_final: 0.9243 (t80) REVERT: B 119 GLU cc_start: 0.9341 (mp0) cc_final: 0.9006 (mp0) REVERT: B 143 LEU cc_start: 0.9366 (tp) cc_final: 0.9141 (tp) REVERT: B 148 GLU cc_start: 0.9004 (mp0) cc_final: 0.8655 (mp0) REVERT: B 149 TYR cc_start: 0.9122 (t80) cc_final: 0.8729 (t80) REVERT: B 150 GLN cc_start: 0.9445 (tp-100) cc_final: 0.9219 (tp-100) REVERT: B 167 LEU cc_start: 0.9314 (mt) cc_final: 0.8879 (mt) REVERT: B 173 LEU cc_start: 0.9380 (mt) cc_final: 0.9036 (mt) REVERT: B 181 ASP cc_start: 0.8608 (m-30) cc_final: 0.8215 (m-30) REVERT: B 184 ARG cc_start: 0.9427 (tpp80) cc_final: 0.9019 (tpp80) REVERT: B 211 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8095 (mm-30) REVERT: B 238 ASP cc_start: 0.8405 (t0) cc_final: 0.7835 (t70) REVERT: B 239 GLN cc_start: 0.8820 (tm-30) cc_final: 0.8157 (tm-30) REVERT: B 252 ASN cc_start: 0.9397 (t0) cc_final: 0.8891 (t0) REVERT: B 263 ASP cc_start: 0.9328 (m-30) cc_final: 0.8942 (m-30) REVERT: B 286 ASP cc_start: 0.8913 (m-30) cc_final: 0.8509 (m-30) REVERT: B 322 MET cc_start: 0.9070 (mmm) cc_final: 0.8845 (mmm) REVERT: B 335 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8234 (mm-30) REVERT: B 385 VAL cc_start: 0.9193 (t) cc_final: 0.8936 (m) REVERT: B 393 SER cc_start: 0.9443 (m) cc_final: 0.9163 (p) REVERT: B 403 ILE cc_start: 0.8985 (tp) cc_final: 0.8745 (tp) REVERT: B 407 ILE cc_start: 0.9254 (mp) cc_final: 0.8984 (mp) REVERT: B 410 ASN cc_start: 0.8939 (m-40) cc_final: 0.8737 (m-40) REVERT: B 415 ASN cc_start: 0.9339 (t0) cc_final: 0.9105 (t0) REVERT: B 427 LYS cc_start: 0.9443 (ptpp) cc_final: 0.8937 (ptpp) REVERT: B 543 ILE cc_start: 0.9756 (mm) cc_final: 0.9524 (mm) REVERT: B 606 TYR cc_start: 0.8157 (m-80) cc_final: 0.7826 (m-80) REVERT: B 615 MET cc_start: 0.9330 (mmp) cc_final: 0.9046 (mmp) REVERT: B 639 ASP cc_start: 0.9033 (m-30) cc_final: 0.8827 (m-30) REVERT: B 640 MET cc_start: 0.9004 (tpp) cc_final: 0.8458 (tpp) REVERT: B 664 THR cc_start: 0.9061 (p) cc_final: 0.8519 (p) REVERT: B 667 LEU cc_start: 0.9307 (tp) cc_final: 0.9030 (tp) REVERT: B 671 ASP cc_start: 0.9020 (m-30) cc_final: 0.8814 (m-30) REVERT: B 680 LYS cc_start: 0.9051 (mttt) cc_final: 0.8767 (mttt) REVERT: C 17 PHE cc_start: 0.9038 (p90) cc_final: 0.8697 (p90) REVERT: C 20 MET cc_start: 0.9595 (tmm) cc_final: 0.9284 (tmm) REVERT: C 74 MET cc_start: 0.7075 (mtm) cc_final: 0.6536 (mtm) REVERT: C 101 HIS cc_start: 0.7514 (m90) cc_final: 0.6788 (m90) REVERT: C 173 TYR cc_start: 0.7356 (t80) cc_final: 0.6585 (t80) REVERT: C 177 TYR cc_start: 0.9141 (t80) cc_final: 0.8939 (t80) REVERT: C 185 MET cc_start: 0.6301 (mmm) cc_final: 0.5542 (mpp) REVERT: C 252 LEU cc_start: 0.7437 (mt) cc_final: 0.7124 (mt) REVERT: C 278 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8452 (pm20) REVERT: D 20 MET cc_start: 0.9066 (mtm) cc_final: 0.8730 (mpp) REVERT: D 148 ASP cc_start: 0.6954 (m-30) cc_final: 0.6664 (m-30) REVERT: D 176 LEU cc_start: 0.9641 (mt) cc_final: 0.9307 (tp) REVERT: D 219 GLU cc_start: 0.9237 (tp30) cc_final: 0.9030 (tp30) REVERT: D 240 LEU cc_start: 0.7785 (mt) cc_final: 0.7392 (mt) REVERT: D 270 ASN cc_start: 0.8619 (m110) cc_final: 0.8418 (m110) outliers start: 0 outliers final: 0 residues processed: 697 average time/residue: 0.1108 time to fit residues: 115.9718 Evaluate side-chains 610 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 610 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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: 0.6980 chunk 133 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN A 313 HIS A 320 ASN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 GLN C 263 ASN D 201 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.121414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.087657 restraints weight = 41511.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.090797 restraints weight = 21247.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.092909 restraints weight = 13123.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.094337 restraints weight = 9174.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.095333 restraints weight = 6989.406| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.6969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16386 Z= 0.135 Angle : 0.626 9.694 22134 Z= 0.328 Chirality : 0.043 0.233 2360 Planarity : 0.004 0.057 2818 Dihedral : 8.298 138.715 2290 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: 0.79 (0.19), residues: 1932 helix: 1.17 (0.15), residues: 1149 sheet: -0.61 (0.40), residues: 134 loop : -0.25 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 243 TYR 0.035 0.002 TYR D 142 PHE 0.026 0.002 PHE B 492 TRP 0.044 0.002 TRP D 124 HIS 0.012 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (16386) covalent geometry : angle 0.62605 / 0.33 (22134) hydrogen bonds : bond 0.03871 / 2.48 ( 871) hydrogen bonds : angle 4.82899 / 3.52 ( 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 714 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 714 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9215 (tptp) cc_final: 0.8925 (tppt) REVERT: A 12 LEU cc_start: 0.9594 (mt) cc_final: 0.9259 (mt) REVERT: A 95 MET cc_start: 0.9099 (mmm) cc_final: 0.8764 (tpp) REVERT: A 107 LYS cc_start: 0.9222 (mttm) cc_final: 0.8858 (mtpp) REVERT: A 128 PHE cc_start: 0.9556 (t80) cc_final: 0.9209 (t80) REVERT: A 147 GLN cc_start: 0.9306 (mt0) cc_final: 0.8516 (mt0) REVERT: A 149 TYR cc_start: 0.9259 (t80) cc_final: 0.8736 (t80) REVERT: A 158 ASN cc_start: 0.9453 (m-40) cc_final: 0.9170 (m-40) REVERT: A 166 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8437 (mm-30) REVERT: A 172 LEU cc_start: 0.9570 (mp) cc_final: 0.9190 (mp) REVERT: A 176 ASN cc_start: 0.8724 (t0) cc_final: 0.8028 (m-40) REVERT: A 179 LEU cc_start: 0.9673 (tp) cc_final: 0.9464 (tp) REVERT: A 181 ASP cc_start: 0.8846 (m-30) cc_final: 0.8462 (m-30) REVERT: A 195 LEU cc_start: 0.9705 (mt) cc_final: 0.9439 (mt) REVERT: A 214 LYS cc_start: 0.8626 (tppt) cc_final: 0.8261 (mmtt) REVERT: A 223 VAL cc_start: 0.9773 (m) cc_final: 0.9198 (p) REVERT: A 227 MET cc_start: 0.9311 (mtm) cc_final: 0.8870 (mtm) REVERT: A 232 ASN cc_start: 0.8831 (m110) cc_final: 0.8329 (m110) REVERT: A 238 ASP cc_start: 0.7925 (p0) cc_final: 0.7663 (p0) REVERT: A 255 HIS cc_start: 0.8766 (t-90) cc_final: 0.8188 (t-90) REVERT: A 257 ASP cc_start: 0.9084 (m-30) cc_final: 0.8808 (m-30) REVERT: A 262 LEU cc_start: 0.9891 (mt) cc_final: 0.9616 (mt) REVERT: A 284 ILE cc_start: 0.9136 (mm) cc_final: 0.8916 (mm) REVERT: A 301 PHE cc_start: 0.9124 (m-10) cc_final: 0.8668 (m-10) REVERT: A 316 GLU cc_start: 0.8963 (tp30) cc_final: 0.8358 (tp30) REVERT: A 318 ASP cc_start: 0.9320 (t0) cc_final: 0.9102 (t0) REVERT: A 333 LYS cc_start: 0.9582 (tppt) cc_final: 0.9201 (tppp) REVERT: A 335 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7930 (mm-30) REVERT: A 344 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8588 (mt-10) REVERT: A 345 LYS cc_start: 0.9816 (ttpt) cc_final: 0.9451 (ttmt) REVERT: A 349 LEU cc_start: 0.9709 (mt) cc_final: 0.9462 (mt) REVERT: A 375 LYS cc_start: 0.9018 (mmtt) cc_final: 0.8667 (mmtm) REVERT: A 390 GLN cc_start: 0.8845 (mt0) cc_final: 0.8612 (mt0) REVERT: A 391 VAL cc_start: 0.9190 (p) cc_final: 0.8716 (m) REVERT: A 393 SER cc_start: 0.9168 (m) cc_final: 0.7889 (p) REVERT: A 402 GLU cc_start: 0.8164 (mp0) cc_final: 0.7152 (mp0) REVERT: A 407 ILE cc_start: 0.9341 (mt) cc_final: 0.9111 (mt) REVERT: A 415 ASN cc_start: 0.9340 (t0) cc_final: 0.8985 (t0) REVERT: A 420 MET cc_start: 0.9122 (tpp) cc_final: 0.8795 (ttm) REVERT: A 446 ARG cc_start: 0.8391 (ptp-110) cc_final: 0.8056 (ttm110) REVERT: A 459 LYS cc_start: 0.9031 (mttp) cc_final: 0.8386 (mtmm) REVERT: A 466 MET cc_start: 0.9068 (ptt) cc_final: 0.8797 (ptt) REVERT: A 474 GLN cc_start: 0.9341 (mt0) cc_final: 0.9044 (mm-40) REVERT: A 493 MET cc_start: 0.8977 (tmm) cc_final: 0.8636 (tmm) REVERT: A 494 MET cc_start: 0.9266 (mtp) cc_final: 0.8935 (mtp) REVERT: A 501 GLN cc_start: 0.9354 (tt0) cc_final: 0.8803 (tm-30) REVERT: A 515 ASP cc_start: 0.8909 (m-30) cc_final: 0.8571 (m-30) REVERT: A 550 MET cc_start: 0.8692 (mmt) cc_final: 0.8470 (mmt) REVERT: A 561 LEU cc_start: 0.9407 (tp) cc_final: 0.8957 (tp) REVERT: A 601 ILE cc_start: 0.9401 (mm) cc_final: 0.9062 (tp) REVERT: A 604 ARG cc_start: 0.9220 (mmm-85) cc_final: 0.8737 (mmp80) REVERT: A 615 MET cc_start: 0.9157 (mmm) cc_final: 0.8875 (mmm) REVERT: A 645 GLN cc_start: 0.9174 (tp40) cc_final: 0.8938 (tp40) REVERT: A 669 ARG cc_start: 0.8973 (tpp-160) cc_final: 0.8683 (tpp-160) REVERT: A 671 ASP cc_start: 0.8991 (m-30) cc_final: 0.8774 (m-30) REVERT: B 8 LYS cc_start: 0.9448 (tptt) cc_final: 0.9090 (tppt) REVERT: B 12 LEU cc_start: 0.9631 (mt) cc_final: 0.9384 (mt) REVERT: B 30 LYS cc_start: 0.9507 (tmtt) cc_final: 0.9293 (tmtt) REVERT: B 55 LEU cc_start: 0.9786 (mt) cc_final: 0.9584 (mt) REVERT: B 87 LYS cc_start: 0.9382 (tptt) cc_final: 0.9082 (tppt) REVERT: B 98 PHE cc_start: 0.9374 (t80) cc_final: 0.9166 (t80) REVERT: B 119 GLU cc_start: 0.9264 (mp0) cc_final: 0.8955 (mp0) REVERT: B 128 PHE cc_start: 0.9568 (t80) cc_final: 0.9299 (t80) REVERT: B 139 GLU cc_start: 0.9339 (mp0) cc_final: 0.8983 (mp0) REVERT: B 143 LEU cc_start: 0.9262 (tp) cc_final: 0.8353 (tp) REVERT: B 148 GLU cc_start: 0.8985 (mp0) cc_final: 0.7853 (mp0) REVERT: B 149 TYR cc_start: 0.9004 (t80) cc_final: 0.8804 (t80) REVERT: B 167 LEU cc_start: 0.9283 (mt) cc_final: 0.8830 (mt) REVERT: B 173 LEU cc_start: 0.9382 (mt) cc_final: 0.9091 (mt) REVERT: B 181 ASP cc_start: 0.8558 (m-30) cc_final: 0.8122 (m-30) REVERT: B 211 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8000 (mm-30) REVERT: B 238 ASP cc_start: 0.8389 (t0) cc_final: 0.7797 (t70) REVERT: B 239 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8314 (tm-30) REVERT: B 252 ASN cc_start: 0.9331 (t0) cc_final: 0.8856 (t0) REVERT: B 263 ASP cc_start: 0.9227 (m-30) cc_final: 0.8926 (m-30) REVERT: B 286 ASP cc_start: 0.8907 (m-30) cc_final: 0.8550 (m-30) REVERT: B 314 MET cc_start: 0.8996 (tmm) cc_final: 0.8752 (tmm) REVERT: B 322 MET cc_start: 0.9084 (mmm) cc_final: 0.8750 (mmm) REVERT: B 335 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8258 (mm-30) REVERT: B 358 ILE cc_start: 0.9649 (mm) cc_final: 0.9423 (mm) REVERT: B 384 GLU cc_start: 0.8829 (pm20) cc_final: 0.8345 (pm20) REVERT: B 393 SER cc_start: 0.9337 (m) cc_final: 0.8950 (p) REVERT: B 402 GLU cc_start: 0.8929 (tp30) cc_final: 0.8657 (tp30) REVERT: B 410 ASN cc_start: 0.8946 (m-40) cc_final: 0.8634 (m-40) REVERT: B 427 LYS cc_start: 0.9367 (ptpp) cc_final: 0.8713 (ptpp) REVERT: B 522 TYR cc_start: 0.9059 (m-10) cc_final: 0.8725 (m-10) REVERT: B 543 ILE cc_start: 0.9741 (mm) cc_final: 0.9426 (mm) REVERT: B 576 LEU cc_start: 0.9339 (mt) cc_final: 0.9057 (mt) REVERT: B 585 SER cc_start: 0.9137 (p) cc_final: 0.8687 (t) REVERT: B 591 THR cc_start: 0.9108 (p) cc_final: 0.8901 (p) REVERT: B 615 MET cc_start: 0.9254 (mmp) cc_final: 0.8942 (mmp) REVERT: B 639 ASP cc_start: 0.9011 (m-30) cc_final: 0.8805 (m-30) REVERT: B 640 MET cc_start: 0.9096 (tpp) cc_final: 0.8503 (tpp) REVERT: B 664 THR cc_start: 0.8973 (p) cc_final: 0.8481 (p) REVERT: B 668 ASN cc_start: 0.9131 (m-40) cc_final: 0.8912 (m-40) REVERT: B 671 ASP cc_start: 0.8976 (m-30) cc_final: 0.8753 (m-30) REVERT: B 680 LYS cc_start: 0.8945 (mttt) cc_final: 0.8690 (mttt) REVERT: C 17 PHE cc_start: 0.8991 (p90) cc_final: 0.8652 (p90) REVERT: C 20 MET cc_start: 0.9569 (tmm) cc_final: 0.9293 (tmm) REVERT: C 74 MET cc_start: 0.6689 (mtm) cc_final: 0.6047 (mtm) REVERT: C 101 HIS cc_start: 0.7395 (m90) cc_final: 0.6839 (m90) REVERT: C 118 ILE cc_start: 0.9289 (pt) cc_final: 0.8753 (pt) REVERT: C 121 VAL cc_start: 0.8593 (p) cc_final: 0.8008 (p) REVERT: C 122 PHE cc_start: 0.8017 (m-80) cc_final: 0.7597 (m-80) REVERT: C 162 TYR cc_start: 0.9339 (m-10) cc_final: 0.8208 (m-80) REVERT: C 173 TYR cc_start: 0.7500 (t80) cc_final: 0.6891 (t80) REVERT: C 174 TYR cc_start: 0.7674 (t80) cc_final: 0.7039 (t80) REVERT: C 179 TYR cc_start: 0.8335 (t80) cc_final: 0.7924 (t80) REVERT: C 185 MET cc_start: 0.6192 (mmm) cc_final: 0.4921 (mpp) REVERT: C 231 LEU cc_start: 0.8979 (mt) cc_final: 0.8468 (pp) REVERT: C 271 LEU cc_start: 0.8424 (pp) cc_final: 0.8114 (pp) REVERT: C 278 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8394 (pm20) REVERT: C 317 ASP cc_start: 0.9125 (t0) cc_final: 0.8891 (t0) REVERT: C 321 TYR cc_start: 0.9015 (m-80) cc_final: 0.8733 (m-80) REVERT: D 20 MET cc_start: 0.9060 (mtm) cc_final: 0.8709 (mpp) REVERT: D 148 ASP cc_start: 0.7006 (m-30) cc_final: 0.6695 (m-30) REVERT: D 219 GLU cc_start: 0.9182 (tp30) cc_final: 0.8965 (tp30) REVERT: D 233 ASN cc_start: 0.8787 (m110) cc_final: 0.8564 (p0) outliers start: 0 outliers final: 0 residues processed: 714 average time/residue: 0.1149 time to fit residues: 123.7106 Evaluate side-chains 627 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 627 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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: 0.9980 chunk 62 optimal weight: 0.0970 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 189 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 165 optimal weight: 0.0270 chunk 16 optimal weight: 0.5980 chunk 54 optimal weight: 0.0980 chunk 132 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 GLN A 320 ASN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.125307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.091156 restraints weight = 41250.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.094444 restraints weight = 21298.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.096645 restraints weight = 13442.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.098204 restraints weight = 9410.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.099174 restraints weight = 7177.276| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.7260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16386 Z= 0.128 Angle : 0.629 10.527 22134 Z= 0.330 Chirality : 0.043 0.256 2360 Planarity : 0.004 0.056 2818 Dihedral : 8.017 139.206 2290 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.19), residues: 1932 helix: 1.21 (0.16), residues: 1140 sheet: -0.49 (0.40), residues: 134 loop : -0.12 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 243 TYR 0.029 0.001 TYR D 142 PHE 0.025 0.002 PHE B 492 TRP 0.045 0.002 TRP D 124 HIS 0.027 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (16386) covalent geometry : angle 0.62940 / 0.33 (22134) hydrogen bonds : bond 0.03819 / 2.46 ( 871) hydrogen bonds : angle 4.82610 / 3.51 ( 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 709 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 709 time to evaluate : 0.408 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: A 8 LYS cc_start: 0.9219 (tptp) cc_final: 0.8911 (tppt) REVERT: A 12 LEU cc_start: 0.9600 (mt) cc_final: 0.9251 (mt) REVERT: A 95 MET cc_start: 0.9095 (mmm) cc_final: 0.8728 (tpp) REVERT: A 107 LYS cc_start: 0.9200 (mttm) cc_final: 0.8792 (mmmt) REVERT: A 129 PHE cc_start: 0.9490 (m-10) cc_final: 0.9237 (m-10) REVERT: A 139 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8804 (mp0) REVERT: A 147 GLN cc_start: 0.9277 (mt0) cc_final: 0.8519 (mt0) REVERT: A 149 TYR cc_start: 0.9205 (t80) cc_final: 0.8680 (t80) REVERT: A 158 ASN cc_start: 0.9394 (m-40) cc_final: 0.9153 (m-40) REVERT: A 166 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8484 (mm-30) REVERT: A 172 LEU cc_start: 0.9519 (mp) cc_final: 0.9180 (mp) REVERT: A 176 ASN cc_start: 0.8795 (t0) cc_final: 0.8182 (m-40) REVERT: A 181 ASP cc_start: 0.8750 (m-30) cc_final: 0.8390 (m-30) REVERT: A 195 LEU cc_start: 0.9693 (mt) cc_final: 0.9432 (mt) REVERT: A 214 LYS cc_start: 0.8599 (tppt) cc_final: 0.8254 (mmtt) REVERT: A 223 VAL cc_start: 0.9775 (m) cc_final: 0.9221 (p) REVERT: A 227 MET cc_start: 0.9238 (mtm) cc_final: 0.8888 (mtm) REVERT: A 232 ASN cc_start: 0.8693 (m110) cc_final: 0.8208 (m-40) REVERT: A 252 ASN cc_start: 0.9435 (t0) cc_final: 0.9187 (t0) REVERT: A 255 HIS cc_start: 0.8628 (t-90) cc_final: 0.8372 (t-90) REVERT: A 257 ASP cc_start: 0.9008 (m-30) cc_final: 0.8757 (m-30) REVERT: A 259 ASN cc_start: 0.9476 (m-40) cc_final: 0.9209 (m-40) REVERT: A 262 LEU cc_start: 0.9889 (mt) cc_final: 0.9645 (mt) REVERT: A 263 ASP cc_start: 0.9303 (m-30) cc_final: 0.8917 (m-30) REVERT: A 276 LYS cc_start: 0.9345 (mptt) cc_final: 0.9030 (mmmt) REVERT: A 301 PHE cc_start: 0.9082 (m-10) cc_final: 0.8546 (m-10) REVERT: A 307 TYR cc_start: 0.9504 (t80) cc_final: 0.9301 (t80) REVERT: A 316 GLU cc_start: 0.8950 (tp30) cc_final: 0.8309 (tp30) REVERT: A 318 ASP cc_start: 0.9317 (t0) cc_final: 0.9032 (t0) REVERT: A 333 LYS cc_start: 0.9562 (tppt) cc_final: 0.9235 (tppp) REVERT: A 335 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7854 (mm-30) REVERT: A 344 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8533 (mt-10) REVERT: A 345 LYS cc_start: 0.9832 (ttpt) cc_final: 0.9487 (ttmt) REVERT: A 349 LEU cc_start: 0.9655 (mt) cc_final: 0.9407 (mt) REVERT: A 365 ASN cc_start: 0.9336 (m-40) cc_final: 0.8789 (m110) REVERT: A 375 LYS cc_start: 0.8976 (mmtt) cc_final: 0.8705 (mmtm) REVERT: A 379 SER cc_start: 0.9310 (t) cc_final: 0.8949 (t) REVERT: A 391 VAL cc_start: 0.9148 (p) cc_final: 0.8708 (m) REVERT: A 393 SER cc_start: 0.9143 (m) cc_final: 0.8638 (p) REVERT: A 402 GLU cc_start: 0.8057 (mp0) cc_final: 0.7618 (mp0) REVERT: A 407 ILE cc_start: 0.9319 (mt) cc_final: 0.9063 (mt) REVERT: A 415 ASN cc_start: 0.9327 (t0) cc_final: 0.8976 (t0) REVERT: A 420 MET cc_start: 0.9062 (tpp) cc_final: 0.8784 (ttm) REVERT: A 421 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8418 (tm-30) REVERT: A 459 LYS cc_start: 0.9017 (mttp) cc_final: 0.8322 (mtmm) REVERT: A 466 MET cc_start: 0.8934 (ptt) cc_final: 0.8701 (ptt) REVERT: A 471 TYR cc_start: 0.9062 (t80) cc_final: 0.8593 (t80) REVERT: A 474 GLN cc_start: 0.9324 (mt0) cc_final: 0.9046 (mm-40) REVERT: A 493 MET cc_start: 0.8942 (tmm) cc_final: 0.8592 (tmm) REVERT: A 494 MET cc_start: 0.9251 (mtp) cc_final: 0.8869 (mtp) REVERT: A 501 GLN cc_start: 0.9347 (tt0) cc_final: 0.8816 (tm-30) REVERT: A 515 ASP cc_start: 0.8853 (m-30) cc_final: 0.8498 (m-30) REVERT: A 550 MET cc_start: 0.8715 (mmt) cc_final: 0.8152 (mmm) REVERT: A 561 LEU cc_start: 0.9394 (tp) cc_final: 0.8937 (tp) REVERT: A 615 MET cc_start: 0.9246 (mmm) cc_final: 0.8923 (mmm) REVERT: A 636 LYS cc_start: 0.9333 (mmtm) cc_final: 0.9073 (mmmt) REVERT: A 640 MET cc_start: 0.9243 (tpp) cc_final: 0.8727 (tpp) REVERT: A 645 GLN cc_start: 0.9096 (tp40) cc_final: 0.8857 (tp-100) REVERT: A 646 GLN cc_start: 0.9361 (pt0) cc_final: 0.9107 (pt0) REVERT: A 654 PHE cc_start: 0.9297 (t80) cc_final: 0.8805 (t80) REVERT: A 686 ARG cc_start: 0.8394 (mmm-85) cc_final: 0.7329 (mtm180) REVERT: B 8 LYS cc_start: 0.9438 (tptt) cc_final: 0.9074 (tppt) REVERT: B 12 LEU cc_start: 0.9635 (mt) cc_final: 0.9365 (mt) REVERT: B 16 ILE cc_start: 0.9653 (mm) cc_final: 0.9407 (tp) REVERT: B 30 LYS cc_start: 0.9509 (tmtt) cc_final: 0.9287 (tmtt) REVERT: B 55 LEU cc_start: 0.9799 (mt) cc_final: 0.9598 (mt) REVERT: B 87 LYS cc_start: 0.9289 (tptt) cc_final: 0.9086 (tppt) REVERT: B 88 LYS cc_start: 0.8406 (tttp) cc_final: 0.8203 (tttm) REVERT: B 98 PHE cc_start: 0.9511 (t80) cc_final: 0.9055 (t80) REVERT: B 99 LYS cc_start: 0.9419 (tppt) cc_final: 0.9103 (tppt) REVERT: B 111 LYS cc_start: 0.9644 (mptt) cc_final: 0.9385 (mmtt) REVERT: B 119 GLU cc_start: 0.9186 (mp0) cc_final: 0.8938 (mp0) REVERT: B 128 PHE cc_start: 0.9549 (t80) cc_final: 0.9271 (t80) REVERT: B 139 GLU cc_start: 0.9277 (mp0) cc_final: 0.8979 (mp0) REVERT: B 143 LEU cc_start: 0.9119 (tp) cc_final: 0.8366 (tp) REVERT: B 148 GLU cc_start: 0.8949 (mp0) cc_final: 0.7890 (mp0) REVERT: B 149 TYR cc_start: 0.9037 (t80) cc_final: 0.8651 (t80) REVERT: B 167 LEU cc_start: 0.9234 (mt) cc_final: 0.8633 (mt) REVERT: B 181 ASP cc_start: 0.8514 (m-30) cc_final: 0.8030 (m-30) REVERT: B 211 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7977 (mm-30) REVERT: B 235 ARG cc_start: 0.9297 (ttm110) cc_final: 0.8835 (ttm110) REVERT: B 238 ASP cc_start: 0.8436 (t0) cc_final: 0.7866 (t70) REVERT: B 239 GLN cc_start: 0.8934 (tm-30) cc_final: 0.8399 (tm-30) REVERT: B 252 ASN cc_start: 0.9321 (t0) cc_final: 0.9087 (t0) REVERT: B 263 ASP cc_start: 0.9209 (m-30) cc_final: 0.8896 (m-30) REVERT: B 286 ASP cc_start: 0.8816 (m-30) cc_final: 0.8416 (m-30) REVERT: B 322 MET cc_start: 0.9011 (mmm) cc_final: 0.8679 (mmm) REVERT: B 335 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8199 (mm-30) REVERT: B 357 TYR cc_start: 0.8258 (m-80) cc_final: 0.7793 (m-80) REVERT: B 384 GLU cc_start: 0.8785 (pm20) cc_final: 0.8443 (pm20) REVERT: B 402 GLU cc_start: 0.8986 (tp30) cc_final: 0.8785 (tp30) REVERT: B 410 ASN cc_start: 0.8941 (m-40) cc_final: 0.8526 (m-40) REVERT: B 427 LYS cc_start: 0.9398 (ptpp) cc_final: 0.8700 (ptpp) REVERT: B 522 TYR cc_start: 0.8935 (m-10) cc_final: 0.8656 (m-80) REVERT: B 543 ILE cc_start: 0.9736 (mm) cc_final: 0.9519 (mm) REVERT: B 576 LEU cc_start: 0.9332 (mt) cc_final: 0.9068 (mt) REVERT: B 639 ASP cc_start: 0.8981 (m-30) cc_final: 0.8768 (m-30) REVERT: B 640 MET cc_start: 0.9182 (tpp) cc_final: 0.8603 (tpp) REVERT: B 664 THR cc_start: 0.9018 (p) cc_final: 0.8419 (p) REVERT: B 668 ASN cc_start: 0.9061 (m-40) cc_final: 0.8788 (m-40) REVERT: B 671 ASP cc_start: 0.8931 (m-30) cc_final: 0.8651 (m-30) REVERT: B 680 LYS cc_start: 0.8810 (mttt) cc_final: 0.8517 (mttt) REVERT: C 17 PHE cc_start: 0.8974 (p90) cc_final: 0.8600 (p90) REVERT: C 20 MET cc_start: 0.9563 (tmm) cc_final: 0.9300 (tmm) REVERT: C 74 MET cc_start: 0.6308 (mtm) cc_final: 0.5416 (mtm) REVERT: C 101 HIS cc_start: 0.7466 (m90) cc_final: 0.6420 (m170) REVERT: C 118 ILE cc_start: 0.9074 (pt) cc_final: 0.8590 (pt) REVERT: C 122 PHE cc_start: 0.8067 (m-80) cc_final: 0.7630 (m-80) REVERT: C 143 LYS cc_start: 0.8512 (pptt) cc_final: 0.8214 (pttm) REVERT: C 162 TYR cc_start: 0.9311 (m-10) cc_final: 0.8251 (m-80) REVERT: C 173 TYR cc_start: 0.7793 (t80) cc_final: 0.7159 (t80) REVERT: C 174 TYR cc_start: 0.7550 (t80) cc_final: 0.6976 (t80) REVERT: C 177 TYR cc_start: 0.9142 (t80) cc_final: 0.8855 (t80) REVERT: C 179 TYR cc_start: 0.8220 (t80) cc_final: 0.7843 (t80) REVERT: C 185 MET cc_start: 0.6135 (mmm) cc_final: 0.4822 (mpp) REVERT: C 231 LEU cc_start: 0.8979 (mt) cc_final: 0.8485 (pp) REVERT: C 271 LEU cc_start: 0.8330 (pp) cc_final: 0.7993 (pp) REVERT: C 278 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8493 (pm20) REVERT: C 321 TYR cc_start: 0.9024 (m-80) cc_final: 0.8772 (m-80) REVERT: D 20 MET cc_start: 0.9027 (mtm) cc_final: 0.8673 (mpp) REVERT: D 148 ASP cc_start: 0.7089 (m-30) cc_final: 0.6794 (m-30) REVERT: D 219 GLU cc_start: 0.9191 (tp30) cc_final: 0.8970 (tp30) REVERT: D 270 ASN cc_start: 0.8637 (m110) cc_final: 0.8382 (m110) outliers start: 0 outliers final: 0 residues processed: 709 average time/residue: 0.1199 time to fit residues: 127.9874 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 : 0.602 ------------------------------------------------------------------------------- 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: 0.7980 chunk 1 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 39 optimal weight: 0.0670 chunk 25 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 GLN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.125292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.091680 restraints weight = 41094.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.094842 restraints weight = 21345.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.097189 restraints weight = 13231.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.098651 restraints weight = 9252.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.099612 restraints weight = 7089.004| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.7405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16386 Z= 0.129 Angle : 0.634 10.726 22134 Z= 0.331 Chirality : 0.044 0.239 2360 Planarity : 0.004 0.055 2818 Dihedral : 7.891 139.862 2290 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.19), residues: 1932 helix: 1.11 (0.16), residues: 1153 sheet: -0.51 (0.39), residues: 138 loop : -0.19 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 243 TYR 0.036 0.001 TYR D 174 PHE 0.024 0.002 PHE B 491 TRP 0.044 0.002 TRP D 124 HIS 0.010 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (16386) covalent geometry : angle 0.63431 / 0.33 (22134) hydrogen bonds : bond 0.03819 / 2.46 ( 871) hydrogen bonds : angle 4.77230 / 3.48 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3349.47 seconds wall clock time: 58 minutes 56.16 seconds (3536.16 seconds total)