Starting phenix.real_space_refine on Thu Aug 6 15:12:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzj_45069/08_2026/9bzj_45069_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzj_45069/08_2026/9bzj_45069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bzj_45069/08_2026/9bzj_45069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzj_45069/08_2026/9bzj_45069.map" model { file = "/net/cci-nas-00/data/ceres_data/9bzj_45069/08_2026/9bzj_45069_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzj_45069/08_2026/9bzj_45069_neut.cif" } resolution = 4.12 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.54, per 1000 atoms: 0.22 Number of scatterers: 16038 At special positions: 0 Unit cell: (93.288, 128.778, 130.806, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 676.4 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: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.986A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.954A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.665A 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: 4.850A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.627A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.073A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.677A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.645A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.730A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.027A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.069A 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: 3.546A 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: 3.669A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.876A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.360A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.200A 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: 7.902A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.394A 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: 6.478A pdb=" N LEU A 656 " --> pdb=" O ARG A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.185A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.228A 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: 4.050A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.749A 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: 2.05 Time building geometry restraints manager: 1.70 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: 4752 1.34 - 1.46: 3107 1.46 - 1.58: 8345 1.58 - 1.70: 26 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: 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=" O3B TTP B 801 " pdb=" PG TTP B 801 " ideal model delta sigma weight residual 1.748 1.610 0.138 2.00e-02 2.50e+03 4.78e+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 2.39e+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 1.19e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21527 2.09 - 4.18: 526 4.18 - 6.27: 64 6.27 - 8.36: 8 8.36 - 10.45: 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 110.54 116.59 -6.05 1.36e+00 5.41e-01 1.98e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.14 -4.43 1.15e+00 7.56e-01 1.48e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.82 -4.32 1.23e+00 6.61e-01 1.23e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.68 -3.97 1.15e+00 7.56e-01 1.19e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.54 3.65 1.06e+00 8.90e-01 1.18e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.05: 9088 25.05 - 50.09: 655 50.09 - 75.14: 127 75.14 - 100.18: 26 100.18 - 125.23: 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 -98.21 125.23 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 -134.28 12.28 0 2.50e+00 1.60e-01 2.41e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2137 0.094 - 0.187: 189 0.187 - 0.281: 29 0.281 - 0.374: 3 0.374 - 0.468: 2 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.48e+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 4.65e+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 2.90e+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 4.10e-02 2.70e+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 1.13e-02 2.23e+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 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 169 " 0.017 2.00e-02 2.50e+03 9.83e-03 1.93e+00 pdb=" CG TYR C 169 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 169 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 169 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 169 " 0.009 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 130 2.51 - 3.11: 11553 3.11 - 3.70: 27047 3.70 - 4.30: 41558 4.30 - 4.90: 65430 Nonbonded interactions: 145718 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.991 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.013 3.040 ... (remaining 145713 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.480 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 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 10.445 22134 Z= 0.471 Chirality : 0.058 0.468 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.680 125.230 6202 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.34 % Allowed : 15.38 % Favored : 83.28 % 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: 0.55 (0.18), residues: 1932 helix: 0.58 (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 0.003 0.000 ARG D 225 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.33 (16386) covalent geometry : angle 0.78738 / 0.47 (22134) hydrogen bonds : bond 0.15420 / 9.51 ( 871) hydrogen bonds : angle 6.51774 / 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 1022 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 999 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8162 (p) cc_final: 0.7957 (m) REVERT: A 12 LEU cc_start: 0.8765 (mt) cc_final: 0.8508 (mp) REVERT: A 55 LEU cc_start: 0.8884 (mt) cc_final: 0.8609 (mt) REVERT: A 76 ASP cc_start: 0.8076 (m-30) cc_final: 0.7579 (m-30) REVERT: A 152 SER cc_start: 0.8599 (p) cc_final: 0.8233 (p) REVERT: A 157 LEU cc_start: 0.9275 (tp) cc_final: 0.8868 (tp) REVERT: A 172 LEU cc_start: 0.9261 (mp) cc_final: 0.8972 (mp) REVERT: A 186 ILE cc_start: 0.9098 (mt) cc_final: 0.8890 (mt) REVERT: A 188 ILE cc_start: 0.9093 (mt) cc_final: 0.8806 (mt) REVERT: A 192 LEU cc_start: 0.9318 (mt) cc_final: 0.8866 (mt) REVERT: A 211 GLU cc_start: 0.6249 (mt-10) cc_final: 0.5871 (tp30) REVERT: A 236 TYR cc_start: 0.7661 (t80) cc_final: 0.7385 (t80) REVERT: A 238 ASP cc_start: 0.7874 (p0) cc_final: 0.7546 (p0) REVERT: A 259 ASN cc_start: 0.8087 (m-40) cc_final: 0.7626 (m-40) REVERT: A 265 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8518 (mmmt) REVERT: A 322 MET cc_start: 0.7756 (mmp) cc_final: 0.6238 (mmm) REVERT: A 326 PHE cc_start: 0.8518 (m-10) cc_final: 0.7947 (m-80) REVERT: A 355 TYR cc_start: 0.7427 (m-80) cc_final: 0.7214 (m-80) REVERT: A 367 VAL cc_start: 0.8652 (m) cc_final: 0.8435 (p) REVERT: A 373 ILE cc_start: 0.9100 (mt) cc_final: 0.8789 (mt) REVERT: A 377 LYS cc_start: 0.8839 (mttt) cc_final: 0.8497 (mttm) REVERT: A 407 ILE cc_start: 0.8904 (mt) cc_final: 0.8460 (mt) REVERT: A 415 ASN cc_start: 0.8025 (t0) cc_final: 0.7708 (t0) REVERT: A 417 LEU cc_start: 0.8059 (tt) cc_final: 0.7706 (tt) REVERT: A 418 ASN cc_start: 0.8250 (m-40) cc_final: 0.7391 (m110) REVERT: A 435 SER cc_start: 0.9330 (p) cc_final: 0.8992 (t) REVERT: A 447 ASN cc_start: 0.8127 (m-40) cc_final: 0.7811 (m-40) REVERT: A 480 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7749 (mt-10) REVERT: A 490 THR cc_start: 0.8511 (m) cc_final: 0.8188 (m) REVERT: A 500 ILE cc_start: 0.9187 (mt) cc_final: 0.8967 (mt) REVERT: A 546 LEU cc_start: 0.9075 (mt) cc_final: 0.8846 (mt) REVERT: A 550 MET cc_start: 0.7295 (mtm) cc_final: 0.7029 (mtm) REVERT: A 594 VAL cc_start: 0.8906 (m) cc_final: 0.8577 (t) REVERT: A 597 ILE cc_start: 0.8719 (pt) cc_final: 0.8393 (pt) REVERT: A 644 ILE cc_start: 0.8381 (mt) cc_final: 0.7911 (mt) REVERT: A 653 SER cc_start: 0.9125 (OUTLIER) cc_final: 0.8844 (p) REVERT: B 12 LEU cc_start: 0.8951 (mt) cc_final: 0.8661 (mp) REVERT: B 51 LEU cc_start: 0.8137 (tp) cc_final: 0.7882 (tp) REVERT: B 147 GLN cc_start: 0.7969 (mt0) cc_final: 0.7602 (mt0) REVERT: B 175 VAL cc_start: 0.8898 (t) cc_final: 0.8630 (t) REVERT: B 204 SER cc_start: 0.8988 (m) cc_final: 0.7912 (t) REVERT: B 261 PHE cc_start: 0.8606 (t80) cc_final: 0.8317 (t80) REVERT: B 265 LYS cc_start: 0.8801 (mmtt) cc_final: 0.7941 (mmmt) REVERT: B 286 ASP cc_start: 0.6400 (OUTLIER) cc_final: 0.6150 (m-30) REVERT: B 315 ASP cc_start: 0.8332 (p0) cc_final: 0.7901 (p0) REVERT: B 326 PHE cc_start: 0.8294 (m-10) cc_final: 0.8068 (m-10) REVERT: B 362 ASP cc_start: 0.6386 (m-30) cc_final: 0.5899 (m-30) REVERT: B 366 LYS cc_start: 0.8586 (ptpp) cc_final: 0.8324 (ptpp) REVERT: B 373 ILE cc_start: 0.9116 (mt) cc_final: 0.8849 (mt) REVERT: B 384 GLU cc_start: 0.9052 (pm20) cc_final: 0.8320 (pm20) REVERT: B 387 GLN cc_start: 0.7898 (mt0) cc_final: 0.7608 (mt0) REVERT: B 425 ILE cc_start: 0.8783 (mt) cc_final: 0.8517 (mt) REVERT: B 467 ASN cc_start: 0.8197 (t0) cc_final: 0.7932 (t0) REVERT: B 494 MET cc_start: 0.7579 (mtp) cc_final: 0.7126 (mtp) REVERT: B 496 ASN cc_start: 0.7642 (t0) cc_final: 0.7391 (t0) REVERT: B 500 ILE cc_start: 0.9131 (mt) cc_final: 0.8901 (mt) REVERT: B 561 LEU cc_start: 0.8484 (tp) cc_final: 0.8127 (tp) REVERT: B 570 MET cc_start: 0.6811 (mtm) cc_final: 0.6473 (mtm) REVERT: B 605 THR cc_start: 0.7613 (m) cc_final: 0.6865 (m) REVERT: B 640 MET cc_start: 0.7912 (tpp) cc_final: 0.7137 (tpp) REVERT: B 644 ILE cc_start: 0.8666 (mt) cc_final: 0.8258 (mt) REVERT: C 43 THR cc_start: 0.4801 (p) cc_final: 0.4481 (m) REVERT: C 92 PHE cc_start: 0.6653 (t80) cc_final: 0.6166 (t80) REVERT: C 96 MET cc_start: 0.4835 (mmm) cc_final: 0.4402 (mmm) REVERT: C 169 TYR cc_start: 0.4145 (m-80) cc_final: 0.3717 (m-80) REVERT: C 185 MET cc_start: 0.3037 (mtp) cc_final: 0.2625 (ptt) REVERT: C 195 LEU cc_start: 0.7441 (tt) cc_final: 0.7188 (tt) REVERT: D 95 MET cc_start: 0.1774 (tmm) cc_final: 0.0973 (tmm) REVERT: D 151 ILE cc_start: 0.5937 (mm) cc_final: 0.5201 (mm) REVERT: D 178 PHE cc_start: 0.4551 (m-80) cc_final: 0.4120 (m-80) REVERT: D 194 ILE cc_start: 0.6906 (mt) cc_final: 0.6615 (mt) REVERT: D 286 VAL cc_start: 0.2691 (t) cc_final: 0.1557 (p) outliers start: 23 outliers final: 6 residues processed: 1010 average time/residue: 0.1181 time to fit residues: 174.4298 Evaluate side-chains 677 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 669 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.0970 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 9.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN A 232 ASN A 242 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 387 GLN B 390 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN B 676 HIS C 249 GLN C 263 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 136 GLN D 233 ASN D 249 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.134900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.098385 restraints weight = 37008.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.101510 restraints weight = 20436.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.103787 restraints weight = 13150.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.105054 restraints weight = 9686.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.105884 restraints weight = 7786.240| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 13 (18 function evaluations) r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 16386 Z= 0.280 Angle : 0.715 8.743 22134 Z= 0.384 Chirality : 0.047 0.328 2360 Planarity : 0.004 0.072 2818 Dihedral : 9.730 133.210 2290 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.12 % Allowed : 3.15 % Favored : 96.74 % 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: 0.96 (0.18), residues: 1932 helix: 1.05 (0.15), residues: 1130 sheet: -0.29 (0.40), residues: 150 loop : 0.39 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 225 TYR 0.019 0.002 TYR D 262 PHE 0.028 0.002 PHE D 320 TRP 0.047 0.003 TRP D 124 HIS 0.010 0.002 HIS A 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.28 (16386) covalent geometry : angle 0.71500 / 0.38 (22134) hydrogen bonds : bond 0.04744 / 3.01 ( 871) hydrogen bonds : angle 5.13389 / 3.66 ( 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 754 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 752 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.9295 (p0) cc_final: 0.9068 (p0) REVERT: A 31 GLU cc_start: 0.9291 (mm-30) cc_final: 0.9020 (mp0) REVERT: A 99 LYS cc_start: 0.9350 (mmtp) cc_final: 0.9079 (mmtp) REVERT: A 117 ARG cc_start: 0.9098 (mtp85) cc_final: 0.8805 (mtp85) REVERT: A 118 TYR cc_start: 0.9174 (t80) cc_final: 0.8954 (t80) REVERT: A 144 MET cc_start: 0.9149 (mtm) cc_final: 0.8807 (mtm) REVERT: A 147 GLN cc_start: 0.9007 (mt0) cc_final: 0.8338 (mt0) REVERT: A 172 LEU cc_start: 0.9628 (mp) cc_final: 0.9379 (mp) REVERT: A 204 SER cc_start: 0.9590 (m) cc_final: 0.9383 (t) REVERT: A 217 GLU cc_start: 0.9267 (mm-30) cc_final: 0.9040 (tp30) REVERT: A 236 TYR cc_start: 0.9206 (t80) cc_final: 0.8362 (t80) REVERT: A 276 LYS cc_start: 0.9229 (ptpp) cc_final: 0.8907 (mppt) REVERT: A 322 MET cc_start: 0.8702 (mmp) cc_final: 0.7660 (tpp) REVERT: A 326 PHE cc_start: 0.9609 (m-10) cc_final: 0.8855 (m-80) REVERT: A 333 LYS cc_start: 0.9148 (tmtt) cc_final: 0.8664 (tptt) REVERT: A 344 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8205 (mp0) REVERT: A 355 TYR cc_start: 0.9116 (m-80) cc_final: 0.8706 (m-80) REVERT: A 375 LYS cc_start: 0.9301 (mttm) cc_final: 0.8834 (mtpp) REVERT: A 405 LEU cc_start: 0.8817 (mt) cc_final: 0.8615 (mt) REVERT: A 407 ILE cc_start: 0.9275 (mt) cc_final: 0.8838 (mt) REVERT: A 428 THR cc_start: 0.9589 (m) cc_final: 0.9243 (m) REVERT: A 456 LYS cc_start: 0.9055 (mtmt) cc_final: 0.8802 (ptpt) REVERT: A 505 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8292 (mt-10) REVERT: A 515 ASP cc_start: 0.8846 (m-30) cc_final: 0.8624 (m-30) REVERT: A 550 MET cc_start: 0.7663 (mtm) cc_final: 0.7190 (mtm) REVERT: A 604 ARG cc_start: 0.8691 (mmp80) cc_final: 0.8378 (mmp80) REVERT: A 606 TYR cc_start: 0.7651 (m-80) cc_final: 0.7309 (m-80) REVERT: A 611 THR cc_start: 0.9173 (p) cc_final: 0.8288 (p) REVERT: A 632 MET cc_start: 0.8889 (mtp) cc_final: 0.8669 (mtp) REVERT: A 639 ASP cc_start: 0.8887 (m-30) cc_final: 0.8667 (m-30) REVERT: A 649 ASP cc_start: 0.8629 (p0) cc_final: 0.8410 (p0) REVERT: A 668 ASN cc_start: 0.9422 (m-40) cc_final: 0.9157 (m110) REVERT: A 683 TYR cc_start: 0.8415 (t80) cc_final: 0.8137 (t80) REVERT: B 51 LEU cc_start: 0.9406 (tp) cc_final: 0.9058 (tp) REVERT: B 71 LEU cc_start: 0.9481 (mm) cc_final: 0.9197 (mm) REVERT: B 95 MET cc_start: 0.9239 (tpp) cc_final: 0.8958 (tpp) REVERT: B 119 GLU cc_start: 0.9322 (mp0) cc_final: 0.9061 (mp0) REVERT: B 128 PHE cc_start: 0.9570 (t80) cc_final: 0.9331 (t80) REVERT: B 149 TYR cc_start: 0.9236 (t80) cc_final: 0.8870 (t80) REVERT: B 162 LYS cc_start: 0.9600 (tppt) cc_final: 0.9216 (mmmm) REVERT: B 172 LEU cc_start: 0.9341 (mp) cc_final: 0.8924 (mp) REVERT: B 173 LEU cc_start: 0.9651 (mt) cc_final: 0.9348 (mt) REVERT: B 186 ILE cc_start: 0.9756 (mt) cc_final: 0.9403 (mt) REVERT: B 190 MET cc_start: 0.9534 (mtm) cc_final: 0.9047 (mtm) REVERT: B 191 GLN cc_start: 0.9075 (mm-40) cc_final: 0.8818 (mm-40) REVERT: B 211 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8295 (mm-30) REVERT: B 223 VAL cc_start: 0.9408 (m) cc_final: 0.9068 (m) REVERT: B 227 MET cc_start: 0.9170 (mtt) cc_final: 0.8716 (mtt) REVERT: B 286 ASP cc_start: 0.8497 (m-30) cc_final: 0.7530 (m-30) REVERT: B 312 GLN cc_start: 0.9003 (pm20) cc_final: 0.8680 (pm20) REVERT: B 319 MET cc_start: 0.9104 (tpp) cc_final: 0.8761 (tpp) REVERT: B 362 ASP cc_start: 0.8699 (m-30) cc_final: 0.7653 (m-30) REVERT: B 370 ASN cc_start: 0.9504 (m-40) cc_final: 0.8995 (m-40) REVERT: B 390 GLN cc_start: 0.9138 (mt0) cc_final: 0.8885 (mm110) REVERT: B 393 SER cc_start: 0.9574 (t) cc_final: 0.9312 (p) REVERT: B 398 ASP cc_start: 0.8845 (t0) cc_final: 0.8609 (t70) REVERT: B 406 ASP cc_start: 0.8020 (m-30) cc_final: 0.7615 (m-30) REVERT: B 410 ASN cc_start: 0.8920 (m110) cc_final: 0.8644 (m110) REVERT: B 413 SER cc_start: 0.9581 (m) cc_final: 0.9189 (t) REVERT: B 415 ASN cc_start: 0.9562 (t0) cc_final: 0.9149 (t0) REVERT: B 446 ARG cc_start: 0.8381 (mtp85) cc_final: 0.8036 (mmm-85) REVERT: B 447 ASN cc_start: 0.8651 (m-40) cc_final: 0.7661 (m-40) REVERT: B 458 MET cc_start: 0.9463 (mmm) cc_final: 0.8859 (mmm) REVERT: B 467 ASN cc_start: 0.9217 (t0) cc_final: 0.9014 (t0) REVERT: B 493 MET cc_start: 0.9551 (tmm) cc_final: 0.9318 (tmm) REVERT: B 494 MET cc_start: 0.9433 (mtp) cc_final: 0.9003 (mtp) REVERT: B 558 TRP cc_start: 0.9286 (m100) cc_final: 0.8648 (m100) REVERT: B 574 TYR cc_start: 0.8649 (m-80) cc_final: 0.8279 (m-80) REVERT: B 602 GLU cc_start: 0.8267 (pt0) cc_final: 0.8003 (pt0) REVERT: B 615 MET cc_start: 0.9168 (mmp) cc_final: 0.8880 (mmp) REVERT: B 627 LYS cc_start: 0.9358 (tttp) cc_final: 0.8786 (tttp) REVERT: B 632 MET cc_start: 0.9080 (mtm) cc_final: 0.8442 (mtm) REVERT: B 636 LYS cc_start: 0.9697 (mmmm) cc_final: 0.9423 (mmmm) REVERT: B 640 MET cc_start: 0.9557 (tpp) cc_final: 0.8656 (tpp) REVERT: B 644 ILE cc_start: 0.9738 (mt) cc_final: 0.9492 (mt) REVERT: B 648 ILE cc_start: 0.9394 (mm) cc_final: 0.9090 (mm) REVERT: B 682 ILE cc_start: 0.9721 (mt) cc_final: 0.9368 (mt) REVERT: C 92 PHE cc_start: 0.8918 (t80) cc_final: 0.8686 (t80) REVERT: C 196 ARG cc_start: 0.8525 (ptp-110) cc_final: 0.8122 (ttm110) REVERT: C 233 ASN cc_start: 0.9089 (m110) cc_final: 0.8866 (m110) REVERT: D 47 LEU cc_start: 0.6576 (mt) cc_final: 0.6082 (mt) REVERT: D 137 MET cc_start: 0.6609 (mtm) cc_final: 0.6050 (mmp) REVERT: D 151 ILE cc_start: 0.7287 (mm) cc_final: 0.6731 (mm) REVERT: D 194 ILE cc_start: 0.9377 (mt) cc_final: 0.9135 (mt) outliers start: 2 outliers final: 0 residues processed: 752 average time/residue: 0.1126 time to fit residues: 126.4936 Evaluate side-chains 618 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 618 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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: 6.9990 chunk 131 optimal weight: 1.9990 chunk 164 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN B 645 GLN C 132 GLN C 249 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 128 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.131528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.092939 restraints weight = 40059.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.096604 restraints weight = 21024.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.098984 restraints weight = 13101.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.100688 restraints weight = 9173.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.101802 restraints weight = 6927.866| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16386 Z= 0.190 Angle : 0.598 7.128 22134 Z= 0.323 Chirality : 0.043 0.206 2360 Planarity : 0.004 0.044 2818 Dihedral : 9.267 134.063 2290 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.17 % Allowed : 2.45 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.18), residues: 1932 helix: 1.10 (0.15), residues: 1129 sheet: -0.46 (0.39), residues: 148 loop : 0.31 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 225 TYR 0.028 0.002 TYR C 174 PHE 0.023 0.002 PHE B 261 TRP 0.032 0.002 TRP D 124 HIS 0.004 0.001 HIS C 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (16386) covalent geometry : angle 0.59799 / 0.32 (22134) hydrogen bonds : bond 0.04208 / 2.68 ( 871) hydrogen bonds : angle 4.90695 / 3.48 ( 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 703 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 700 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ASN cc_start: 0.9275 (t0) cc_final: 0.9036 (t0) REVERT: A 77 ILE cc_start: 0.9596 (pt) cc_final: 0.9332 (mp) REVERT: A 95 MET cc_start: 0.9320 (mmm) cc_final: 0.8798 (tpp) REVERT: A 99 LYS cc_start: 0.9399 (mmtp) cc_final: 0.9036 (mmtp) REVERT: A 117 ARG cc_start: 0.9136 (mtp85) cc_final: 0.8767 (mtp85) REVERT: A 139 GLU cc_start: 0.9449 (mm-30) cc_final: 0.9112 (tp30) REVERT: A 144 MET cc_start: 0.9150 (mtm) cc_final: 0.8748 (mtm) REVERT: A 147 GLN cc_start: 0.9015 (mt0) cc_final: 0.8300 (mt0) REVERT: A 172 LEU cc_start: 0.9648 (mp) cc_final: 0.9339 (mp) REVERT: A 204 SER cc_start: 0.9542 (m) cc_final: 0.9163 (t) REVERT: A 227 MET cc_start: 0.9393 (mtp) cc_final: 0.8990 (mtp) REVERT: A 276 LYS cc_start: 0.9232 (ptpp) cc_final: 0.8919 (mptt) REVERT: A 317 MET cc_start: 0.8963 (ptm) cc_final: 0.8395 (ptm) REVERT: A 322 MET cc_start: 0.9015 (mmp) cc_final: 0.7968 (tpp) REVERT: A 326 PHE cc_start: 0.9665 (m-10) cc_final: 0.8937 (m-80) REVERT: A 333 LYS cc_start: 0.9138 (tmtt) cc_final: 0.8590 (tptt) REVERT: A 361 GLN cc_start: 0.8971 (tp40) cc_final: 0.8730 (tp-100) REVERT: A 402 GLU cc_start: 0.8718 (tp30) cc_final: 0.8491 (tp30) REVERT: A 403 ILE cc_start: 0.9432 (mm) cc_final: 0.8941 (mm) REVERT: A 405 LEU cc_start: 0.8985 (mt) cc_final: 0.8763 (mt) REVERT: A 407 ILE cc_start: 0.9349 (mt) cc_final: 0.8776 (mt) REVERT: A 428 THR cc_start: 0.9629 (m) cc_final: 0.9295 (m) REVERT: A 447 ASN cc_start: 0.8674 (m110) cc_final: 0.8393 (m-40) REVERT: A 456 LYS cc_start: 0.9108 (mtmt) cc_final: 0.8809 (ptpt) REVERT: A 505 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8592 (mt-10) REVERT: A 550 MET cc_start: 0.8085 (mtm) cc_final: 0.7769 (mtm) REVERT: A 604 ARG cc_start: 0.8751 (mmp80) cc_final: 0.8418 (mmp80) REVERT: A 606 TYR cc_start: 0.7758 (m-80) cc_final: 0.7389 (m-80) REVERT: A 611 THR cc_start: 0.9101 (p) cc_final: 0.8429 (t) REVERT: A 615 MET cc_start: 0.9217 (mmp) cc_final: 0.8710 (mmp) REVERT: A 636 LYS cc_start: 0.9754 (mmtm) cc_final: 0.9551 (mmmm) REVERT: A 639 ASP cc_start: 0.8953 (m-30) cc_final: 0.8751 (m-30) REVERT: A 668 ASN cc_start: 0.9447 (m-40) cc_final: 0.9194 (m-40) REVERT: B 51 LEU cc_start: 0.9457 (tp) cc_final: 0.9096 (tp) REVERT: B 55 LEU cc_start: 0.9804 (mt) cc_final: 0.9587 (mt) REVERT: B 71 LEU cc_start: 0.9476 (mm) cc_final: 0.9207 (mm) REVERT: B 95 MET cc_start: 0.9017 (tpp) cc_final: 0.8511 (tpp) REVERT: B 106 LEU cc_start: 0.9591 (tp) cc_final: 0.9385 (tp) REVERT: B 116 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8245 (mt-10) REVERT: B 119 GLU cc_start: 0.9277 (mp0) cc_final: 0.8969 (mp0) REVERT: B 139 GLU cc_start: 0.9357 (mm-30) cc_final: 0.9137 (mm-30) REVERT: B 149 TYR cc_start: 0.9235 (t80) cc_final: 0.8779 (t80) REVERT: B 162 LYS cc_start: 0.9595 (tppt) cc_final: 0.8593 (mmmt) REVERT: B 172 LEU cc_start: 0.9311 (mp) cc_final: 0.8993 (mp) REVERT: B 191 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8626 (mm-40) REVERT: B 211 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8320 (mm-30) REVERT: B 223 VAL cc_start: 0.9480 (m) cc_final: 0.9197 (m) REVERT: B 227 MET cc_start: 0.8951 (mtt) cc_final: 0.8549 (mtt) REVERT: B 250 TYR cc_start: 0.9154 (m-80) cc_final: 0.8849 (m-80) REVERT: B 257 ASP cc_start: 0.8777 (m-30) cc_final: 0.8349 (m-30) REVERT: B 263 ASP cc_start: 0.9201 (m-30) cc_final: 0.8839 (m-30) REVERT: B 266 LYS cc_start: 0.9474 (mtpp) cc_final: 0.9108 (mttp) REVERT: B 286 ASP cc_start: 0.8598 (m-30) cc_final: 0.7684 (m-30) REVERT: B 321 GLU cc_start: 0.8825 (pp20) cc_final: 0.8557 (pp20) REVERT: B 362 ASP cc_start: 0.8623 (m-30) cc_final: 0.7613 (m-30) REVERT: B 370 ASN cc_start: 0.9494 (m-40) cc_final: 0.8932 (m-40) REVERT: B 379 SER cc_start: 0.9239 (t) cc_final: 0.8748 (t) REVERT: B 390 GLN cc_start: 0.9177 (mt0) cc_final: 0.8824 (mm110) REVERT: B 393 SER cc_start: 0.9608 (t) cc_final: 0.9334 (p) REVERT: B 398 ASP cc_start: 0.8648 (t0) cc_final: 0.8439 (t70) REVERT: B 410 ASN cc_start: 0.8970 (m110) cc_final: 0.8670 (m110) REVERT: B 413 SER cc_start: 0.9616 (m) cc_final: 0.9248 (t) REVERT: B 414 LEU cc_start: 0.9690 (mt) cc_final: 0.9481 (mt) REVERT: B 415 ASN cc_start: 0.9662 (t0) cc_final: 0.9121 (t0) REVERT: B 447 ASN cc_start: 0.8600 (m-40) cc_final: 0.7384 (m-40) REVERT: B 467 ASN cc_start: 0.9221 (t0) cc_final: 0.9002 (t0) REVERT: B 493 MET cc_start: 0.9602 (tmm) cc_final: 0.9336 (tmm) REVERT: B 505 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8518 (mt-10) REVERT: B 516 GLN cc_start: 0.9049 (tp-100) cc_final: 0.8785 (tp-100) REVERT: B 602 GLU cc_start: 0.8199 (pt0) cc_final: 0.7624 (pt0) REVERT: B 603 GLU cc_start: 0.7728 (tp30) cc_final: 0.7433 (tp30) REVERT: B 615 MET cc_start: 0.9201 (mmp) cc_final: 0.8907 (mmp) REVERT: B 627 LYS cc_start: 0.9396 (tttp) cc_final: 0.9027 (tttt) REVERT: B 628 GLU cc_start: 0.8589 (mm-30) cc_final: 0.7215 (mm-30) REVERT: B 640 MET cc_start: 0.9601 (tpp) cc_final: 0.8865 (tpp) REVERT: B 648 ILE cc_start: 0.9362 (mm) cc_final: 0.9102 (mm) REVERT: B 667 LEU cc_start: 0.9598 (tp) cc_final: 0.9217 (tp) REVERT: B 682 ILE cc_start: 0.9647 (mt) cc_final: 0.9357 (mt) REVERT: C 233 ASN cc_start: 0.9223 (m110) cc_final: 0.9001 (m110) REVERT: D 137 MET cc_start: 0.7070 (mtm) cc_final: 0.6449 (mmp) REVERT: D 149 ASP cc_start: 0.9037 (m-30) cc_final: 0.8747 (m-30) REVERT: D 151 ILE cc_start: 0.6729 (mm) cc_final: 0.6405 (mm) REVERT: D 185 MET cc_start: 0.4676 (mmp) cc_final: 0.4012 (tpp) REVERT: D 196 ARG cc_start: 0.8951 (ttm110) cc_final: 0.8742 (ttm110) REVERT: D 263 ASN cc_start: 0.8819 (m-40) cc_final: 0.8445 (m-40) outliers start: 3 outliers final: 1 residues processed: 701 average time/residue: 0.1088 time to fit residues: 114.8321 Evaluate side-chains 623 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 622 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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: 0.7980 chunk 157 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 chunk 60 optimal weight: 0.0970 chunk 185 optimal weight: 10.0000 chunk 191 optimal weight: 20.0000 chunk 159 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 93 optimal weight: 0.0270 overall best weight: 1.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN A 365 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 HIS ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN B 645 GLN C 249 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 ASN D 127 GLN ** D 132 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 = 0.3712 r_free = 0.3712 target = 0.133354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.094475 restraints weight = 39924.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.098122 restraints weight = 21079.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.100532 restraints weight = 13098.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.102141 restraints weight = 9162.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.103231 restraints weight = 6982.359| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 11 (18 function evaluations) r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.6040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16386 Z= 0.177 Angle : 0.600 14.110 22134 Z= 0.321 Chirality : 0.043 0.209 2360 Planarity : 0.004 0.046 2818 Dihedral : 8.940 135.725 2290 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.12 % Allowed : 1.86 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.19), residues: 1932 helix: 1.14 (0.15), residues: 1135 sheet: -0.69 (0.37), residues: 150 loop : 0.10 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 446 TYR 0.043 0.002 TYR B 574 PHE 0.027 0.002 PHE D 178 TRP 0.015 0.001 TRP D 124 HIS 0.006 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (16386) covalent geometry : angle 0.60038 / 0.32 (22134) hydrogen bonds : bond 0.04000 / 2.56 ( 871) hydrogen bonds : angle 4.92593 / 3.52 ( 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 681 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 679 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.9541 (mm) cc_final: 0.9244 (mm) REVERT: A 14 ASN cc_start: 0.9346 (m-40) cc_final: 0.9046 (m110) REVERT: A 77 ILE cc_start: 0.9610 (pt) cc_final: 0.9377 (mp) REVERT: A 95 MET cc_start: 0.9274 (mmm) cc_final: 0.8775 (tpp) REVERT: A 99 LYS cc_start: 0.9453 (mmtp) cc_final: 0.9071 (mmtp) REVERT: A 118 TYR cc_start: 0.9166 (t80) cc_final: 0.8899 (t80) REVERT: A 139 GLU cc_start: 0.9430 (mm-30) cc_final: 0.9076 (tp30) REVERT: A 147 GLN cc_start: 0.9043 (mt0) cc_final: 0.8536 (mt0) REVERT: A 172 LEU cc_start: 0.9658 (mp) cc_final: 0.9293 (mp) REVERT: A 204 SER cc_start: 0.9512 (m) cc_final: 0.9267 (t) REVERT: A 227 MET cc_start: 0.9379 (mtp) cc_final: 0.8959 (mtp) REVERT: A 315 ASP cc_start: 0.9091 (p0) cc_final: 0.8777 (p0) REVERT: A 320 ASN cc_start: 0.9036 (t0) cc_final: 0.8564 (t0) REVERT: A 333 LYS cc_start: 0.9173 (tmtt) cc_final: 0.8639 (tptt) REVERT: A 361 GLN cc_start: 0.8988 (tp40) cc_final: 0.8598 (tp-100) REVERT: A 376 VAL cc_start: 0.9088 (t) cc_final: 0.8766 (t) REVERT: A 405 LEU cc_start: 0.8946 (mt) cc_final: 0.8718 (mt) REVERT: A 407 ILE cc_start: 0.9372 (mt) cc_final: 0.8878 (mt) REVERT: A 447 ASN cc_start: 0.8643 (m110) cc_final: 0.8282 (m-40) REVERT: A 456 LYS cc_start: 0.9086 (mtmt) cc_final: 0.8794 (ptpt) REVERT: A 458 MET cc_start: 0.9089 (mmp) cc_final: 0.8618 (mmp) REVERT: A 501 GLN cc_start: 0.9364 (tt0) cc_final: 0.8581 (tm-30) REVERT: A 505 GLU cc_start: 0.8907 (mt-10) cc_final: 0.7965 (mt-10) REVERT: A 606 TYR cc_start: 0.7752 (m-80) cc_final: 0.7460 (m-80) REVERT: A 611 THR cc_start: 0.9112 (p) cc_final: 0.8356 (t) REVERT: A 615 MET cc_start: 0.9229 (mmp) cc_final: 0.8907 (mmp) REVERT: A 672 LEU cc_start: 0.9407 (mt) cc_final: 0.9189 (mt) REVERT: A 683 TYR cc_start: 0.8683 (t80) cc_final: 0.8278 (t80) REVERT: B 51 LEU cc_start: 0.9396 (tp) cc_final: 0.9025 (tp) REVERT: B 55 LEU cc_start: 0.9803 (mt) cc_final: 0.9584 (mt) REVERT: B 67 GLU cc_start: 0.9229 (tm-30) cc_final: 0.8783 (tm-30) REVERT: B 71 LEU cc_start: 0.9502 (mm) cc_final: 0.9299 (mm) REVERT: B 95 MET cc_start: 0.9078 (tpp) cc_final: 0.8611 (tpp) REVERT: B 116 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8332 (mt-10) REVERT: B 119 GLU cc_start: 0.9248 (mp0) cc_final: 0.8916 (mp0) REVERT: B 139 GLU cc_start: 0.9313 (mm-30) cc_final: 0.9107 (mm-30) REVERT: B 149 TYR cc_start: 0.9288 (t80) cc_final: 0.8747 (t80) REVERT: B 191 GLN cc_start: 0.8942 (mm-40) cc_final: 0.8488 (mm-40) REVERT: B 209 LYS cc_start: 0.9063 (tppt) cc_final: 0.8832 (tptp) REVERT: B 211 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8285 (mm-30) REVERT: B 214 LYS cc_start: 0.8329 (mttm) cc_final: 0.8125 (mmtt) REVERT: B 235 ARG cc_start: 0.9121 (tpp80) cc_final: 0.8799 (mtt-85) REVERT: B 250 TYR cc_start: 0.9045 (m-80) cc_final: 0.8654 (m-80) REVERT: B 263 ASP cc_start: 0.9202 (m-30) cc_final: 0.8857 (m-30) REVERT: B 266 LYS cc_start: 0.9482 (mtpp) cc_final: 0.9106 (mtmm) REVERT: B 286 ASP cc_start: 0.8500 (m-30) cc_final: 0.7590 (m-30) REVERT: B 312 GLN cc_start: 0.8929 (pm20) cc_final: 0.8708 (pm20) REVERT: B 321 GLU cc_start: 0.8880 (pp20) cc_final: 0.8243 (pp20) REVERT: B 322 MET cc_start: 0.9264 (tpt) cc_final: 0.8947 (mmm) REVERT: B 362 ASP cc_start: 0.8611 (m-30) cc_final: 0.7538 (m-30) REVERT: B 370 ASN cc_start: 0.9541 (m-40) cc_final: 0.8990 (m110) REVERT: B 373 ILE cc_start: 0.9552 (mt) cc_final: 0.8936 (tp) REVERT: B 379 SER cc_start: 0.9113 (t) cc_final: 0.8732 (t) REVERT: B 386 LEU cc_start: 0.9237 (mt) cc_final: 0.8907 (mt) REVERT: B 390 GLN cc_start: 0.9156 (mt0) cc_final: 0.8668 (mm110) REVERT: B 393 SER cc_start: 0.9639 (t) cc_final: 0.9343 (p) REVERT: B 398 ASP cc_start: 0.8649 (t0) cc_final: 0.8417 (t70) REVERT: B 403 ILE cc_start: 0.9539 (mp) cc_final: 0.9211 (tp) REVERT: B 410 ASN cc_start: 0.9019 (m110) cc_final: 0.8807 (m110) REVERT: B 413 SER cc_start: 0.9611 (m) cc_final: 0.9275 (t) REVERT: B 414 LEU cc_start: 0.9723 (mt) cc_final: 0.9519 (mt) REVERT: B 415 ASN cc_start: 0.9664 (t0) cc_final: 0.9152 (t0) REVERT: B 447 ASN cc_start: 0.8604 (m-40) cc_final: 0.7148 (m-40) REVERT: B 460 SER cc_start: 0.9449 (t) cc_final: 0.8900 (t) REVERT: B 467 ASN cc_start: 0.9214 (t0) cc_final: 0.8958 (t0) REVERT: B 493 MET cc_start: 0.9614 (tmm) cc_final: 0.9350 (tmm) REVERT: B 494 MET cc_start: 0.9433 (mtp) cc_final: 0.9197 (mtp) REVERT: B 601 ILE cc_start: 0.9532 (mm) cc_final: 0.9028 (mm) REVERT: B 610 LYS cc_start: 0.9182 (tttm) cc_final: 0.8842 (tmtt) REVERT: B 615 MET cc_start: 0.9170 (mmp) cc_final: 0.8865 (mmp) REVERT: B 627 LYS cc_start: 0.9326 (tttp) cc_final: 0.8946 (tttt) REVERT: B 640 MET cc_start: 0.9616 (tpp) cc_final: 0.9191 (tpp) REVERT: B 646 GLN cc_start: 0.9187 (pt0) cc_final: 0.8972 (pt0) REVERT: B 650 GLN cc_start: 0.8481 (mt0) cc_final: 0.7886 (mm-40) REVERT: B 655 THR cc_start: 0.9610 (m) cc_final: 0.9308 (t) REVERT: B 667 LEU cc_start: 0.9570 (tp) cc_final: 0.9159 (tp) REVERT: C 55 TYR cc_start: 0.8495 (t80) cc_final: 0.7783 (t80) REVERT: C 110 MET cc_start: 0.7932 (mtm) cc_final: 0.7702 (mtm) REVERT: C 233 ASN cc_start: 0.9251 (m110) cc_final: 0.9019 (m110) REVERT: D 120 GLU cc_start: 0.9415 (tm-30) cc_final: 0.9182 (pp20) REVERT: D 151 ILE cc_start: 0.6817 (mm) cc_final: 0.6425 (mm) REVERT: D 162 TYR cc_start: 0.9294 (m-10) cc_final: 0.8597 (m-10) REVERT: D 230 ASP cc_start: 0.8815 (t0) cc_final: 0.8502 (t70) REVERT: D 231 LEU cc_start: 0.8928 (mt) cc_final: 0.8383 (pp) outliers start: 2 outliers final: 0 residues processed: 680 average time/residue: 0.1106 time to fit residues: 113.6789 Evaluate side-chains 612 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 612 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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: 5.9990 chunk 46 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN B 588 GLN C 127 GLN C 249 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.131215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.092405 restraints weight = 40223.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.096023 restraints weight = 21057.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.098363 restraints weight = 13240.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.099922 restraints weight = 9343.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.101025 restraints weight = 7179.624| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.6439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16386 Z= 0.187 Angle : 0.589 8.297 22134 Z= 0.320 Chirality : 0.043 0.229 2360 Planarity : 0.004 0.058 2818 Dihedral : 8.829 138.163 2290 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.23 % Allowed : 2.39 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.18), residues: 1932 helix: 1.07 (0.15), residues: 1127 sheet: -0.73 (0.38), residues: 148 loop : 0.05 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 274 TYR 0.025 0.001 TYR B 574 PHE 0.022 0.002 PHE D 178 TRP 0.009 0.002 TRP D 124 HIS 0.005 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 (16386) covalent geometry : angle 0.58932 / 0.32 (22134) hydrogen bonds : bond 0.03937 / 2.50 ( 871) hydrogen bonds : angle 4.89241 / 3.49 ( 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 673 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 669 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.9568 (mm) cc_final: 0.9315 (mm) REVERT: A 14 ASN cc_start: 0.9432 (m-40) cc_final: 0.9085 (m110) REVERT: A 95 MET cc_start: 0.9267 (mmm) cc_final: 0.8833 (tpp) REVERT: A 99 LYS cc_start: 0.9513 (mmtp) cc_final: 0.9113 (mmtp) REVERT: A 139 GLU cc_start: 0.9415 (mm-30) cc_final: 0.9093 (tp30) REVERT: A 144 MET cc_start: 0.9065 (mtm) cc_final: 0.8578 (mtm) REVERT: A 147 GLN cc_start: 0.9065 (mt0) cc_final: 0.8345 (mt0) REVERT: A 172 LEU cc_start: 0.9639 (mp) cc_final: 0.9226 (mp) REVERT: A 204 SER cc_start: 0.9518 (m) cc_final: 0.9283 (t) REVERT: A 227 MET cc_start: 0.9389 (mtp) cc_final: 0.8999 (mtp) REVERT: A 290 GLU cc_start: 0.8853 (tp30) cc_final: 0.8592 (tm-30) REVERT: A 315 ASP cc_start: 0.9145 (p0) cc_final: 0.8775 (p0) REVERT: A 317 MET cc_start: 0.8822 (ptm) cc_final: 0.7803 (ptm) REVERT: A 320 ASN cc_start: 0.8936 (t0) cc_final: 0.8659 (t0) REVERT: A 333 LYS cc_start: 0.9160 (tmtt) cc_final: 0.8728 (tptp) REVERT: A 357 TYR cc_start: 0.8894 (m-10) cc_final: 0.8596 (m-10) REVERT: A 361 GLN cc_start: 0.8981 (tp40) cc_final: 0.8582 (tp-100) REVERT: A 402 GLU cc_start: 0.8756 (tp30) cc_final: 0.8538 (tp30) REVERT: A 407 ILE cc_start: 0.9312 (mt) cc_final: 0.8858 (mt) REVERT: A 413 SER cc_start: 0.9403 (m) cc_final: 0.9197 (m) REVERT: A 418 ASN cc_start: 0.9092 (m-40) cc_final: 0.8552 (m-40) REVERT: A 447 ASN cc_start: 0.8642 (m110) cc_final: 0.8166 (m-40) REVERT: A 458 MET cc_start: 0.9122 (mmp) cc_final: 0.8588 (mmp) REVERT: A 494 MET cc_start: 0.9307 (mmt) cc_final: 0.8994 (mmt) REVERT: A 501 GLN cc_start: 0.9370 (tt0) cc_final: 0.8815 (tm-30) REVERT: A 505 GLU cc_start: 0.8933 (mt-10) cc_final: 0.7728 (mt-10) REVERT: A 515 ASP cc_start: 0.8829 (m-30) cc_final: 0.8622 (m-30) REVERT: A 550 MET cc_start: 0.8129 (mtm) cc_final: 0.7916 (mtm) REVERT: A 604 ARG cc_start: 0.8897 (mmp80) cc_final: 0.8613 (mmp80) REVERT: A 606 TYR cc_start: 0.7941 (m-80) cc_final: 0.7531 (m-80) REVERT: A 611 THR cc_start: 0.9126 (p) cc_final: 0.8322 (t) REVERT: A 640 MET cc_start: 0.9388 (tpp) cc_final: 0.8898 (tpp) REVERT: A 672 LEU cc_start: 0.9411 (mt) cc_final: 0.9195 (mt) REVERT: A 683 TYR cc_start: 0.8736 (t80) cc_final: 0.8239 (t80) REVERT: B 51 LEU cc_start: 0.9393 (tp) cc_final: 0.9014 (tp) REVERT: B 55 LEU cc_start: 0.9834 (mt) cc_final: 0.9596 (mt) REVERT: B 67 GLU cc_start: 0.9276 (tm-30) cc_final: 0.8799 (tm-30) REVERT: B 95 MET cc_start: 0.9094 (tpp) cc_final: 0.8572 (tpp) REVERT: B 116 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8441 (mt-10) REVERT: B 119 GLU cc_start: 0.9271 (mp0) cc_final: 0.8936 (mp0) REVERT: B 149 TYR cc_start: 0.9340 (t80) cc_final: 0.8754 (t80) REVERT: B 173 LEU cc_start: 0.9627 (mt) cc_final: 0.9372 (mt) REVERT: B 191 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8535 (mm-40) REVERT: B 209 LYS cc_start: 0.9155 (tppt) cc_final: 0.8910 (tptp) REVERT: B 211 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8440 (mm-30) REVERT: B 223 VAL cc_start: 0.9249 (m) cc_final: 0.8677 (m) REVERT: B 235 ARG cc_start: 0.9219 (tpp80) cc_final: 0.8828 (mtt-85) REVERT: B 257 ASP cc_start: 0.9033 (m-30) cc_final: 0.8609 (m-30) REVERT: B 258 ILE cc_start: 0.9497 (tp) cc_final: 0.9277 (tp) REVERT: B 286 ASP cc_start: 0.8520 (m-30) cc_final: 0.7596 (m-30) REVERT: B 290 GLU cc_start: 0.9217 (tp30) cc_final: 0.9010 (tp30) REVERT: B 308 LYS cc_start: 0.9578 (mtpp) cc_final: 0.9237 (mtpp) REVERT: B 312 GLN cc_start: 0.8685 (pm20) cc_final: 0.8484 (pm20) REVERT: B 316 GLU cc_start: 0.9240 (tt0) cc_final: 0.8936 (tt0) REVERT: B 319 MET cc_start: 0.9027 (tpp) cc_final: 0.8713 (tpp) REVERT: B 321 GLU cc_start: 0.8948 (pp20) cc_final: 0.8379 (pp20) REVERT: B 322 MET cc_start: 0.9331 (tpt) cc_final: 0.8964 (mmm) REVERT: B 362 ASP cc_start: 0.8670 (m-30) cc_final: 0.7597 (m-30) REVERT: B 373 ILE cc_start: 0.9568 (mt) cc_final: 0.9069 (tp) REVERT: B 386 LEU cc_start: 0.9417 (mt) cc_final: 0.8702 (mt) REVERT: B 390 GLN cc_start: 0.8971 (mt0) cc_final: 0.8638 (mm110) REVERT: B 392 SER cc_start: 0.9267 (m) cc_final: 0.9039 (m) REVERT: B 398 ASP cc_start: 0.8667 (t0) cc_final: 0.8407 (t70) REVERT: B 403 ILE cc_start: 0.9547 (mp) cc_final: 0.9217 (tp) REVERT: B 413 SER cc_start: 0.9655 (m) cc_final: 0.9309 (t) REVERT: B 415 ASN cc_start: 0.9651 (t0) cc_final: 0.8714 (t0) REVERT: B 418 ASN cc_start: 0.9312 (m-40) cc_final: 0.8847 (m-40) REVERT: B 447 ASN cc_start: 0.8571 (m-40) cc_final: 0.7004 (m-40) REVERT: B 467 ASN cc_start: 0.9186 (t0) cc_final: 0.8958 (t0) REVERT: B 493 MET cc_start: 0.9595 (tmm) cc_final: 0.9349 (tmm) REVERT: B 494 MET cc_start: 0.9416 (mtp) cc_final: 0.9131 (ttm) REVERT: B 501 GLN cc_start: 0.9444 (tt0) cc_final: 0.9175 (tt0) REVERT: B 505 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8387 (mt-10) REVERT: B 601 ILE cc_start: 0.9582 (mm) cc_final: 0.9102 (mm) REVERT: B 610 LYS cc_start: 0.9059 (tttm) cc_final: 0.8746 (tttm) REVERT: B 615 MET cc_start: 0.9236 (mmp) cc_final: 0.8905 (mmp) REVERT: B 627 LYS cc_start: 0.9371 (tttp) cc_final: 0.8936 (tttp) REVERT: B 632 MET cc_start: 0.8991 (mtp) cc_final: 0.8721 (mtp) REVERT: B 640 MET cc_start: 0.9581 (tpp) cc_final: 0.9182 (tpp) REVERT: B 648 ILE cc_start: 0.9356 (mm) cc_final: 0.9128 (mm) REVERT: B 650 GLN cc_start: 0.8384 (mt0) cc_final: 0.7688 (mm-40) REVERT: B 655 THR cc_start: 0.9637 (m) cc_final: 0.9419 (t) REVERT: B 667 LEU cc_start: 0.9656 (tp) cc_final: 0.9315 (tp) REVERT: B 668 ASN cc_start: 0.9431 (m-40) cc_final: 0.9148 (m110) REVERT: B 671 ASP cc_start: 0.8856 (m-30) cc_final: 0.8618 (m-30) REVERT: C 55 TYR cc_start: 0.8298 (t80) cc_final: 0.7786 (t80) REVERT: C 110 MET cc_start: 0.7763 (mtm) cc_final: 0.7530 (mtm) REVERT: C 183 LYS cc_start: 0.4984 (mppt) cc_final: 0.4553 (ptmt) REVERT: C 241 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8139 (pm20) REVERT: D 74 MET cc_start: 0.4598 (tmm) cc_final: 0.4003 (tmm) REVERT: D 151 ILE cc_start: 0.6858 (mm) cc_final: 0.6641 (mm) REVERT: D 174 TYR cc_start: 0.8342 (t80) cc_final: 0.7716 (t80) REVERT: D 194 ILE cc_start: 0.8842 (mt) cc_final: 0.8640 (mt) REVERT: D 196 ARG cc_start: 0.8909 (ttm110) cc_final: 0.8697 (ttm110) outliers start: 4 outliers final: 0 residues processed: 672 average time/residue: 0.1022 time to fit residues: 103.4200 Evaluate side-chains 593 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 592 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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: 5.9990 chunk 183 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 172 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN A 242 GLN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN B 588 GLN B 645 GLN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN C 263 ASN D 28 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 119 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.128637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.090954 restraints weight = 40955.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.094370 restraints weight = 21290.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.096600 restraints weight = 13377.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.098141 restraints weight = 9489.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.099161 restraints weight = 7318.739| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.6933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 16386 Z= 0.270 Angle : 0.675 8.492 22134 Z= 0.363 Chirality : 0.045 0.234 2360 Planarity : 0.004 0.051 2818 Dihedral : 8.947 146.033 2290 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.06 % Allowed : 1.63 % 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: 0.69 (0.19), residues: 1932 helix: 0.97 (0.15), residues: 1115 sheet: -0.78 (0.38), residues: 152 loop : 0.11 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 446 TYR 0.030 0.002 TYR D 130 PHE 0.025 0.002 PHE A 171 TRP 0.011 0.002 TRP D 124 HIS 0.005 0.002 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.27 (16386) covalent geometry : angle 0.67537 / 0.36 (22134) hydrogen bonds : bond 0.04164 / 2.64 ( 871) hydrogen bonds : angle 5.12303 / 3.67 ( 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 663 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 662 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.9629 (mm) cc_final: 0.9389 (mm) REVERT: A 14 ASN cc_start: 0.9522 (m-40) cc_final: 0.9173 (m110) REVERT: A 30 LYS cc_start: 0.9127 (tptt) cc_final: 0.8896 (tptp) REVERT: A 54 LYS cc_start: 0.9637 (ttmm) cc_final: 0.9265 (mtmm) REVERT: A 95 MET cc_start: 0.9229 (mmm) cc_final: 0.8906 (tpp) REVERT: A 99 LYS cc_start: 0.9582 (mmtp) cc_final: 0.9139 (mmtp) REVERT: A 119 GLU cc_start: 0.8985 (mp0) cc_final: 0.8604 (mp0) REVERT: A 120 ASP cc_start: 0.8933 (m-30) cc_final: 0.8711 (m-30) REVERT: A 139 GLU cc_start: 0.9405 (mm-30) cc_final: 0.9102 (tp30) REVERT: A 144 MET cc_start: 0.9074 (mtm) cc_final: 0.8565 (mtm) REVERT: A 147 GLN cc_start: 0.9158 (mt0) cc_final: 0.8519 (mt0) REVERT: A 166 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8425 (mm-30) REVERT: A 172 LEU cc_start: 0.9699 (mp) cc_final: 0.9313 (mp) REVERT: A 224 VAL cc_start: 0.9651 (m) cc_final: 0.9400 (p) REVERT: A 227 MET cc_start: 0.9408 (mtp) cc_final: 0.8946 (mtp) REVERT: A 290 GLU cc_start: 0.8908 (tp30) cc_final: 0.8544 (tp30) REVERT: A 315 ASP cc_start: 0.8995 (p0) cc_final: 0.8733 (p0) REVERT: A 318 ASP cc_start: 0.9054 (t0) cc_final: 0.7521 (t0) REVERT: A 319 MET cc_start: 0.8974 (ttp) cc_final: 0.8507 (tmm) REVERT: A 333 LYS cc_start: 0.9368 (tmtt) cc_final: 0.8894 (tptp) REVERT: A 348 MET cc_start: 0.9077 (ptp) cc_final: 0.8664 (ptp) REVERT: A 357 TYR cc_start: 0.8903 (m-10) cc_final: 0.8547 (m-10) REVERT: A 361 GLN cc_start: 0.9076 (tp40) cc_final: 0.8638 (tp-100) REVERT: A 402 GLU cc_start: 0.8824 (tp30) cc_final: 0.8558 (tp30) REVERT: A 403 ILE cc_start: 0.9484 (mm) cc_final: 0.8998 (mm) REVERT: A 407 ILE cc_start: 0.9317 (mt) cc_final: 0.8832 (mt) REVERT: A 427 LYS cc_start: 0.9194 (ptpp) cc_final: 0.8902 (ptpp) REVERT: A 447 ASN cc_start: 0.8526 (m-40) cc_final: 0.8022 (m-40) REVERT: A 458 MET cc_start: 0.9135 (mmp) cc_final: 0.8589 (mmp) REVERT: A 505 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8240 (mt-10) REVERT: A 515 ASP cc_start: 0.8810 (m-30) cc_final: 0.8494 (m-30) REVERT: A 561 LEU cc_start: 0.9661 (tp) cc_final: 0.9457 (tp) REVERT: A 586 TYR cc_start: 0.9007 (m-80) cc_final: 0.8492 (m-80) REVERT: A 602 GLU cc_start: 0.7965 (pt0) cc_final: 0.6733 (pt0) REVERT: A 640 MET cc_start: 0.9384 (tpp) cc_final: 0.9061 (tpp) REVERT: A 672 LEU cc_start: 0.9436 (mt) cc_final: 0.9232 (mt) REVERT: A 683 TYR cc_start: 0.8669 (t80) cc_final: 0.7785 (t80) REVERT: B 51 LEU cc_start: 0.9452 (tp) cc_final: 0.9110 (tp) REVERT: B 55 LEU cc_start: 0.9842 (mt) cc_final: 0.9584 (mt) REVERT: B 67 GLU cc_start: 0.9341 (tm-30) cc_final: 0.8887 (tm-30) REVERT: B 95 MET cc_start: 0.9175 (tpp) cc_final: 0.8911 (tpp) REVERT: B 115 LEU cc_start: 0.9604 (mp) cc_final: 0.9389 (mp) REVERT: B 116 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8703 (mt-10) REVERT: B 117 ARG cc_start: 0.9000 (mtp85) cc_final: 0.8489 (mtp85) REVERT: B 119 GLU cc_start: 0.9321 (mp0) cc_final: 0.8948 (mp0) REVERT: B 147 GLN cc_start: 0.9364 (mt0) cc_final: 0.9051 (mt0) REVERT: B 149 TYR cc_start: 0.9403 (t80) cc_final: 0.8783 (t80) REVERT: B 174 GLU cc_start: 0.7843 (tp30) cc_final: 0.7398 (tp30) REVERT: B 209 LYS cc_start: 0.9190 (tppt) cc_final: 0.8932 (tptp) REVERT: B 211 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8398 (mm-30) REVERT: B 223 VAL cc_start: 0.9274 (m) cc_final: 0.8742 (m) REVERT: B 235 ARG cc_start: 0.9222 (tpp80) cc_final: 0.8785 (mtt-85) REVERT: B 257 ASP cc_start: 0.8986 (m-30) cc_final: 0.8648 (m-30) REVERT: B 258 ILE cc_start: 0.9550 (tp) cc_final: 0.9293 (tp) REVERT: B 263 ASP cc_start: 0.9134 (m-30) cc_final: 0.8558 (m-30) REVERT: B 266 LYS cc_start: 0.9408 (mtpp) cc_final: 0.9173 (mttm) REVERT: B 286 ASP cc_start: 0.8566 (m-30) cc_final: 0.7537 (m-30) REVERT: B 319 MET cc_start: 0.9010 (tpp) cc_final: 0.8689 (tpp) REVERT: B 321 GLU cc_start: 0.8880 (pp20) cc_final: 0.8402 (pp20) REVERT: B 322 MET cc_start: 0.9449 (tpt) cc_final: 0.9114 (mmm) REVERT: B 362 ASP cc_start: 0.8697 (m-30) cc_final: 0.7705 (m-30) REVERT: B 373 ILE cc_start: 0.9605 (mt) cc_final: 0.9398 (tp) REVERT: B 393 SER cc_start: 0.9624 (t) cc_final: 0.9301 (p) REVERT: B 398 ASP cc_start: 0.8691 (t0) cc_final: 0.8447 (t70) REVERT: B 403 ILE cc_start: 0.9547 (mp) cc_final: 0.9197 (tp) REVERT: B 413 SER cc_start: 0.9569 (m) cc_final: 0.9219 (t) REVERT: B 415 ASN cc_start: 0.9630 (t0) cc_final: 0.8982 (t0) REVERT: B 445 ILE cc_start: 0.9288 (mp) cc_final: 0.8544 (mp) REVERT: B 446 ARG cc_start: 0.7374 (mmp80) cc_final: 0.6986 (mmp80) REVERT: B 447 ASN cc_start: 0.8652 (m-40) cc_final: 0.8387 (m-40) REVERT: B 463 LEU cc_start: 0.9764 (tp) cc_final: 0.9557 (tp) REVERT: B 493 MET cc_start: 0.9604 (tmm) cc_final: 0.9293 (tmm) REVERT: B 505 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8384 (mt-10) REVERT: B 601 ILE cc_start: 0.9599 (mm) cc_final: 0.9119 (mm) REVERT: B 610 LYS cc_start: 0.9085 (tttm) cc_final: 0.8799 (tttm) REVERT: B 615 MET cc_start: 0.9191 (mmp) cc_final: 0.8839 (mmp) REVERT: B 627 LYS cc_start: 0.9418 (tttp) cc_final: 0.9065 (tttp) REVERT: B 633 ASP cc_start: 0.8960 (t0) cc_final: 0.8582 (t0) REVERT: B 640 MET cc_start: 0.9509 (tpp) cc_final: 0.9102 (tpp) REVERT: B 646 GLN cc_start: 0.9464 (pt0) cc_final: 0.9181 (pm20) REVERT: B 667 LEU cc_start: 0.9621 (tp) cc_final: 0.9265 (tp) REVERT: B 668 ASN cc_start: 0.9484 (m-40) cc_final: 0.9187 (m110) REVERT: B 671 ASP cc_start: 0.8923 (m-30) cc_final: 0.8619 (m-30) REVERT: C 55 TYR cc_start: 0.8257 (t80) cc_final: 0.7818 (t80) REVERT: C 110 MET cc_start: 0.7861 (mtm) cc_final: 0.7594 (mtm) REVERT: C 183 LYS cc_start: 0.5483 (mppt) cc_final: 0.5023 (ptmt) REVERT: C 269 MET cc_start: 0.5911 (tmm) cc_final: 0.5538 (ppp) REVERT: D 74 MET cc_start: 0.4788 (tmm) cc_final: 0.4292 (tmm) REVERT: D 151 ILE cc_start: 0.7072 (mm) cc_final: 0.6861 (mm) REVERT: D 163 LEU cc_start: 0.8991 (tp) cc_final: 0.8618 (tp) REVERT: D 168 PHE cc_start: 0.9070 (m-10) cc_final: 0.8766 (m-80) REVERT: D 174 TYR cc_start: 0.8322 (t80) cc_final: 0.7864 (t80) REVERT: D 196 ARG cc_start: 0.8944 (ttm110) cc_final: 0.8705 (ttm110) outliers start: 1 outliers final: 0 residues processed: 663 average time/residue: 0.1082 time to fit residues: 108.4148 Evaluate side-chains 588 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 588 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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: 3.9990 chunk 51 optimal weight: 0.0170 chunk 74 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 645 GLN C 127 GLN C 249 GLN D 24 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.132466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.094450 restraints weight = 40069.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.098042 restraints weight = 21053.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.100343 restraints weight = 13108.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.101968 restraints weight = 9218.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.103060 restraints weight = 7058.571| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.7130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16386 Z= 0.165 Angle : 0.602 7.787 22134 Z= 0.325 Chirality : 0.044 0.226 2360 Planarity : 0.004 0.050 2818 Dihedral : 8.593 146.224 2290 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.06 % Allowed : 1.57 % 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: 0.84 (0.19), residues: 1932 helix: 1.06 (0.15), residues: 1115 sheet: -0.77 (0.38), residues: 152 loop : 0.23 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 274 TYR 0.035 0.002 TYR C 242 PHE 0.024 0.002 PHE B 156 TRP 0.013 0.001 TRP A 9 HIS 0.005 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (16386) covalent geometry : angle 0.60222 / 0.33 (22134) hydrogen bonds : bond 0.03905 / 2.48 ( 871) hydrogen bonds : angle 4.96445 / 3.56 ( 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 674 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 673 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.9620 (mm) cc_final: 0.9340 (mm) REVERT: A 14 ASN cc_start: 0.9405 (m-40) cc_final: 0.9099 (m-40) REVERT: A 16 ILE cc_start: 0.9332 (mm) cc_final: 0.9066 (mm) REVERT: A 27 ASP cc_start: 0.9375 (p0) cc_final: 0.9138 (p0) REVERT: A 30 LYS cc_start: 0.9155 (tptt) cc_final: 0.8928 (tptp) REVERT: A 54 LYS cc_start: 0.9647 (ttmm) cc_final: 0.9292 (mtmm) REVERT: A 95 MET cc_start: 0.9226 (mmm) cc_final: 0.8781 (tpp) REVERT: A 99 LYS cc_start: 0.9586 (mmtp) cc_final: 0.9125 (mmtp) REVERT: A 119 GLU cc_start: 0.8944 (mp0) cc_final: 0.8526 (mp0) REVERT: A 128 PHE cc_start: 0.9511 (t80) cc_final: 0.9283 (t80) REVERT: A 139 GLU cc_start: 0.9390 (mm-30) cc_final: 0.9062 (tp30) REVERT: A 144 MET cc_start: 0.9028 (mtm) cc_final: 0.8490 (mtm) REVERT: A 147 GLN cc_start: 0.9052 (mt0) cc_final: 0.8706 (mt0) REVERT: A 150 GLN cc_start: 0.9230 (tm-30) cc_final: 0.8723 (tm-30) REVERT: A 166 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8359 (mm-30) REVERT: A 172 LEU cc_start: 0.9653 (mp) cc_final: 0.9274 (mp) REVERT: A 224 VAL cc_start: 0.9631 (m) cc_final: 0.9388 (p) REVERT: A 227 MET cc_start: 0.9332 (mtp) cc_final: 0.8953 (mtp) REVERT: A 251 LEU cc_start: 0.9450 (tp) cc_final: 0.9238 (tp) REVERT: A 278 LEU cc_start: 0.9287 (tp) cc_final: 0.9033 (tp) REVERT: A 290 GLU cc_start: 0.8863 (tp30) cc_final: 0.8538 (tp30) REVERT: A 315 ASP cc_start: 0.8828 (p0) cc_final: 0.8310 (p0) REVERT: A 319 MET cc_start: 0.8645 (ttp) cc_final: 0.8403 (ttp) REVERT: A 320 ASN cc_start: 0.8747 (t0) cc_final: 0.8533 (t0) REVERT: A 322 MET cc_start: 0.8947 (mtm) cc_final: 0.7565 (mtm) REVERT: A 333 LYS cc_start: 0.9358 (tmtt) cc_final: 0.8909 (tptp) REVERT: A 348 MET cc_start: 0.9038 (ptp) cc_final: 0.8614 (ptp) REVERT: A 357 TYR cc_start: 0.8872 (m-10) cc_final: 0.8552 (m-10) REVERT: A 361 GLN cc_start: 0.8941 (tp40) cc_final: 0.8504 (tp-100) REVERT: A 395 THR cc_start: 0.9613 (p) cc_final: 0.9352 (p) REVERT: A 402 GLU cc_start: 0.8735 (tp30) cc_final: 0.8523 (tp30) REVERT: A 403 ILE cc_start: 0.9456 (mm) cc_final: 0.8906 (mm) REVERT: A 407 ILE cc_start: 0.9267 (mt) cc_final: 0.8846 (mt) REVERT: A 413 SER cc_start: 0.9436 (m) cc_final: 0.9232 (m) REVERT: A 418 ASN cc_start: 0.9027 (m-40) cc_final: 0.8625 (m-40) REVERT: A 427 LYS cc_start: 0.9187 (ptpp) cc_final: 0.8820 (ptpp) REVERT: A 447 ASN cc_start: 0.8445 (m-40) cc_final: 0.8016 (m-40) REVERT: A 458 MET cc_start: 0.9122 (mmp) cc_final: 0.8599 (mmp) REVERT: A 472 LEU cc_start: 0.9479 (mt) cc_final: 0.9243 (mp) REVERT: A 494 MET cc_start: 0.9357 (mmt) cc_final: 0.8846 (mmt) REVERT: A 501 GLN cc_start: 0.9412 (tt0) cc_final: 0.8835 (tm-30) REVERT: A 505 GLU cc_start: 0.8910 (mt-10) cc_final: 0.7788 (mt-10) REVERT: A 515 ASP cc_start: 0.8765 (m-30) cc_final: 0.8398 (m-30) REVERT: A 586 TYR cc_start: 0.8984 (m-80) cc_final: 0.8580 (m-80) REVERT: A 602 GLU cc_start: 0.7948 (pt0) cc_final: 0.6481 (pt0) REVERT: A 604 ARG cc_start: 0.8894 (mmp80) cc_final: 0.8568 (mmp80) REVERT: A 606 TYR cc_start: 0.7985 (m-80) cc_final: 0.7533 (m-80) REVERT: A 611 THR cc_start: 0.9256 (p) cc_final: 0.8377 (t) REVERT: A 615 MET cc_start: 0.9213 (mmp) cc_final: 0.8814 (mmp) REVERT: A 640 MET cc_start: 0.9367 (tpp) cc_final: 0.9077 (tpp) REVERT: A 683 TYR cc_start: 0.8707 (t80) cc_final: 0.8007 (t80) REVERT: B 40 TYR cc_start: 0.9259 (t80) cc_final: 0.9044 (t80) REVERT: B 51 LEU cc_start: 0.9353 (tp) cc_final: 0.9023 (tp) REVERT: B 55 LEU cc_start: 0.9845 (mt) cc_final: 0.9577 (mt) REVERT: B 67 GLU cc_start: 0.9315 (tm-30) cc_final: 0.8877 (tm-30) REVERT: B 82 LYS cc_start: 0.9488 (mmmm) cc_final: 0.9200 (mmtt) REVERT: B 95 MET cc_start: 0.9157 (tpp) cc_final: 0.8821 (tpp) REVERT: B 98 PHE cc_start: 0.9571 (t80) cc_final: 0.9169 (t80) REVERT: B 116 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8186 (mt-10) REVERT: B 119 GLU cc_start: 0.9289 (mp0) cc_final: 0.8929 (mp0) REVERT: B 128 PHE cc_start: 0.9694 (t80) cc_final: 0.9468 (t80) REVERT: B 149 TYR cc_start: 0.9444 (t80) cc_final: 0.8743 (t80) REVERT: B 174 GLU cc_start: 0.8041 (tp30) cc_final: 0.7674 (tp30) REVERT: B 191 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8422 (mt0) REVERT: B 209 LYS cc_start: 0.9129 (tppt) cc_final: 0.8876 (tptp) REVERT: B 211 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8477 (mm-30) REVERT: B 235 ARG cc_start: 0.9238 (tpp80) cc_final: 0.9021 (tpp80) REVERT: B 257 ASP cc_start: 0.8996 (m-30) cc_final: 0.8694 (m-30) REVERT: B 258 ILE cc_start: 0.9527 (tp) cc_final: 0.9305 (tp) REVERT: B 263 ASP cc_start: 0.9079 (m-30) cc_final: 0.8569 (m-30) REVERT: B 266 LYS cc_start: 0.9542 (mtpp) cc_final: 0.9075 (mttp) REVERT: B 286 ASP cc_start: 0.8585 (m-30) cc_final: 0.7614 (m-30) REVERT: B 290 GLU cc_start: 0.9299 (tp30) cc_final: 0.9001 (tp30) REVERT: B 322 MET cc_start: 0.9405 (tpt) cc_final: 0.9034 (mmp) REVERT: B 362 ASP cc_start: 0.8649 (m-30) cc_final: 0.7640 (m-30) REVERT: B 373 ILE cc_start: 0.9556 (mt) cc_final: 0.9199 (tp) REVERT: B 386 LEU cc_start: 0.9449 (mt) cc_final: 0.8870 (mt) REVERT: B 390 GLN cc_start: 0.9094 (mt0) cc_final: 0.8877 (mm110) REVERT: B 393 SER cc_start: 0.9584 (t) cc_final: 0.9290 (p) REVERT: B 398 ASP cc_start: 0.8647 (t0) cc_final: 0.8403 (t70) REVERT: B 413 SER cc_start: 0.9560 (m) cc_final: 0.9169 (t) REVERT: B 415 ASN cc_start: 0.9563 (t0) cc_final: 0.8978 (t0) REVERT: B 434 ASP cc_start: 0.8970 (m-30) cc_final: 0.8761 (m-30) REVERT: B 445 ILE cc_start: 0.9360 (mp) cc_final: 0.8721 (mp) REVERT: B 446 ARG cc_start: 0.7442 (mmp80) cc_final: 0.7053 (mmp80) REVERT: B 447 ASN cc_start: 0.8603 (m-40) cc_final: 0.7294 (m-40) REVERT: B 463 LEU cc_start: 0.9755 (tp) cc_final: 0.9533 (tp) REVERT: B 493 MET cc_start: 0.9579 (tmm) cc_final: 0.9274 (tmm) REVERT: B 501 GLN cc_start: 0.9404 (tt0) cc_final: 0.9107 (tt0) REVERT: B 505 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8412 (mt-10) REVERT: B 601 ILE cc_start: 0.9545 (mm) cc_final: 0.9050 (mm) REVERT: B 610 LYS cc_start: 0.9084 (tttm) cc_final: 0.8794 (tttm) REVERT: B 615 MET cc_start: 0.9178 (mmp) cc_final: 0.8840 (mmp) REVERT: B 627 LYS cc_start: 0.9409 (tttp) cc_final: 0.8944 (tttp) REVERT: B 633 ASP cc_start: 0.8836 (t0) cc_final: 0.8400 (t0) REVERT: B 640 MET cc_start: 0.9494 (tpp) cc_final: 0.9133 (tpp) REVERT: B 650 GLN cc_start: 0.8215 (mt0) cc_final: 0.7736 (mm-40) REVERT: B 655 THR cc_start: 0.9620 (m) cc_final: 0.9365 (t) REVERT: B 667 LEU cc_start: 0.9639 (tp) cc_final: 0.9307 (tp) REVERT: B 668 ASN cc_start: 0.9442 (m-40) cc_final: 0.9159 (m110) REVERT: B 671 ASP cc_start: 0.8853 (m-30) cc_final: 0.8548 (m-30) REVERT: C 96 MET cc_start: 0.7674 (mmm) cc_final: 0.6519 (mmm) REVERT: C 110 MET cc_start: 0.7842 (mtm) cc_final: 0.7595 (mtm) REVERT: C 183 LYS cc_start: 0.5374 (mppt) cc_final: 0.4914 (ptmt) REVERT: C 197 ASP cc_start: 0.9119 (m-30) cc_final: 0.8905 (m-30) REVERT: C 269 MET cc_start: 0.5869 (tmm) cc_final: 0.5573 (ppp) REVERT: D 151 ILE cc_start: 0.6927 (mm) cc_final: 0.6718 (mm) REVERT: D 174 TYR cc_start: 0.8262 (t80) cc_final: 0.7716 (t80) outliers start: 1 outliers final: 1 residues processed: 673 average time/residue: 0.1082 time to fit residues: 110.0160 Evaluate side-chains 611 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 610 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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: 0.8980 chunk 99 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 134 optimal weight: 0.8980 chunk 153 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN C 263 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.134970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.096617 restraints weight = 40512.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.100201 restraints weight = 21002.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.102532 restraints weight = 13059.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.104145 restraints weight = 9223.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.105239 restraints weight = 7077.848| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.7338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16386 Z= 0.154 Angle : 0.602 6.999 22134 Z= 0.326 Chirality : 0.044 0.226 2360 Planarity : 0.004 0.044 2818 Dihedral : 8.248 146.083 2290 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.06 % Allowed : 0.70 % Favored : 99.24 % 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: 1.06 (0.15), residues: 1117 sheet: -0.74 (0.39), residues: 152 loop : 0.24 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 274 TYR 0.022 0.001 TYR D 130 PHE 0.032 0.002 PHE D 168 TRP 0.011 0.001 TRP A 9 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (16386) covalent geometry : angle 0.60160 / 0.33 (22134) hydrogen bonds : bond 0.03835 / 2.45 ( 871) hydrogen bonds : angle 4.94855 / 3.53 ( 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 672 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 671 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.9632 (mm) cc_final: 0.9340 (mm) REVERT: A 14 ASN cc_start: 0.9436 (m-40) cc_final: 0.9200 (m-40) REVERT: A 16 ILE cc_start: 0.9265 (mm) cc_final: 0.9058 (mm) REVERT: A 27 ASP cc_start: 0.9380 (p0) cc_final: 0.9140 (p0) REVERT: A 30 LYS cc_start: 0.9159 (tptt) cc_final: 0.8930 (tptp) REVERT: A 95 MET cc_start: 0.9225 (mmm) cc_final: 0.8895 (tpp) REVERT: A 99 LYS cc_start: 0.9593 (mmtp) cc_final: 0.9292 (mmtp) REVERT: A 101 TYR cc_start: 0.9440 (m-80) cc_final: 0.9034 (m-10) REVERT: A 119 GLU cc_start: 0.8898 (mp0) cc_final: 0.8485 (mp0) REVERT: A 122 ILE cc_start: 0.9703 (mp) cc_final: 0.9503 (mp) REVERT: A 139 GLU cc_start: 0.9395 (mm-30) cc_final: 0.9040 (tp30) REVERT: A 144 MET cc_start: 0.9030 (mtm) cc_final: 0.8486 (mtm) REVERT: A 147 GLN cc_start: 0.9073 (mt0) cc_final: 0.8598 (mt0) REVERT: A 172 LEU cc_start: 0.9661 (mp) cc_final: 0.9298 (mp) REVERT: A 218 ASN cc_start: 0.9271 (t0) cc_final: 0.9050 (m-40) REVERT: A 224 VAL cc_start: 0.9616 (m) cc_final: 0.9345 (p) REVERT: A 227 MET cc_start: 0.9323 (mtp) cc_final: 0.8919 (mtp) REVERT: A 264 THR cc_start: 0.9406 (p) cc_final: 0.8591 (p) REVERT: A 290 GLU cc_start: 0.8873 (tp30) cc_final: 0.8457 (tp30) REVERT: A 318 ASP cc_start: 0.8446 (t0) cc_final: 0.8113 (t0) REVERT: A 320 ASN cc_start: 0.8639 (t0) cc_final: 0.8387 (t0) REVERT: A 322 MET cc_start: 0.8720 (mtm) cc_final: 0.7962 (mtm) REVERT: A 333 LYS cc_start: 0.9357 (tmtt) cc_final: 0.8915 (tptp) REVERT: A 348 MET cc_start: 0.9063 (ptp) cc_final: 0.8626 (ptp) REVERT: A 357 TYR cc_start: 0.8866 (m-10) cc_final: 0.8487 (m-10) REVERT: A 361 GLN cc_start: 0.8915 (tp40) cc_final: 0.8497 (tp-100) REVERT: A 405 LEU cc_start: 0.8973 (mt) cc_final: 0.8675 (mt) REVERT: A 407 ILE cc_start: 0.9340 (mt) cc_final: 0.8924 (mt) REVERT: A 427 LYS cc_start: 0.9166 (ptpp) cc_final: 0.8915 (ptpp) REVERT: A 447 ASN cc_start: 0.8331 (m-40) cc_final: 0.7846 (m-40) REVERT: A 458 MET cc_start: 0.9078 (mmp) cc_final: 0.8639 (mmp) REVERT: A 468 LEU cc_start: 0.9586 (tp) cc_final: 0.9384 (tp) REVERT: A 472 LEU cc_start: 0.9484 (mt) cc_final: 0.9271 (mp) REVERT: A 494 MET cc_start: 0.9313 (mmt) cc_final: 0.8825 (mmt) REVERT: A 501 GLN cc_start: 0.9426 (tt0) cc_final: 0.8850 (tm-30) REVERT: A 505 GLU cc_start: 0.8891 (mt-10) cc_final: 0.7762 (mt-10) REVERT: A 515 ASP cc_start: 0.8763 (m-30) cc_final: 0.8374 (m-30) REVERT: A 604 ARG cc_start: 0.8905 (mmp80) cc_final: 0.8615 (mmp80) REVERT: A 615 MET cc_start: 0.9209 (mmp) cc_final: 0.8794 (mmm) REVERT: A 640 MET cc_start: 0.9376 (tpp) cc_final: 0.9074 (tpp) REVERT: A 683 TYR cc_start: 0.8684 (t80) cc_final: 0.7893 (t80) REVERT: B 51 LEU cc_start: 0.9343 (tp) cc_final: 0.9005 (tp) REVERT: B 55 LEU cc_start: 0.9838 (mt) cc_final: 0.9553 (mt) REVERT: B 67 GLU cc_start: 0.9297 (tm-30) cc_final: 0.8799 (tm-30) REVERT: B 82 LYS cc_start: 0.9503 (mmmm) cc_final: 0.9191 (mmtt) REVERT: B 95 MET cc_start: 0.9146 (tpp) cc_final: 0.8581 (tpp) REVERT: B 98 PHE cc_start: 0.9570 (t80) cc_final: 0.9178 (t80) REVERT: B 119 GLU cc_start: 0.9283 (mp0) cc_final: 0.8928 (mp0) REVERT: B 128 PHE cc_start: 0.9683 (t80) cc_final: 0.9468 (t80) REVERT: B 149 TYR cc_start: 0.9436 (t80) cc_final: 0.8770 (t80) REVERT: B 166 GLU cc_start: 0.9032 (tp30) cc_final: 0.8777 (tp30) REVERT: B 174 GLU cc_start: 0.8073 (tp30) cc_final: 0.7822 (tp30) REVERT: B 191 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8371 (mt0) REVERT: B 209 LYS cc_start: 0.9144 (tppt) cc_final: 0.8890 (tptp) REVERT: B 211 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8435 (mm-30) REVERT: B 235 ARG cc_start: 0.9256 (tpp80) cc_final: 0.9018 (tpp80) REVERT: B 257 ASP cc_start: 0.8994 (m-30) cc_final: 0.8691 (m-30) REVERT: B 258 ILE cc_start: 0.9535 (tp) cc_final: 0.9324 (tp) REVERT: B 286 ASP cc_start: 0.8562 (m-30) cc_final: 0.7593 (m-30) REVERT: B 290 GLU cc_start: 0.9249 (tp30) cc_final: 0.9015 (tp30) REVERT: B 312 GLN cc_start: 0.8623 (pm20) cc_final: 0.8230 (pm20) REVERT: B 317 MET cc_start: 0.9056 (ptm) cc_final: 0.8575 (ptm) REVERT: B 322 MET cc_start: 0.9352 (tpt) cc_final: 0.8958 (mmm) REVERT: B 362 ASP cc_start: 0.8667 (m-30) cc_final: 0.7595 (m-30) REVERT: B 373 ILE cc_start: 0.9531 (mt) cc_final: 0.9076 (tp) REVERT: B 386 LEU cc_start: 0.9420 (mt) cc_final: 0.8889 (mt) REVERT: B 390 GLN cc_start: 0.9089 (mt0) cc_final: 0.8741 (mm110) REVERT: B 393 SER cc_start: 0.9584 (t) cc_final: 0.9296 (p) REVERT: B 398 ASP cc_start: 0.8644 (t0) cc_final: 0.8375 (t70) REVERT: B 406 ASP cc_start: 0.8078 (m-30) cc_final: 0.7823 (m-30) REVERT: B 413 SER cc_start: 0.9542 (m) cc_final: 0.9241 (t) REVERT: B 415 ASN cc_start: 0.9548 (t0) cc_final: 0.8917 (t0) REVERT: B 425 ILE cc_start: 0.9459 (mt) cc_final: 0.9179 (mt) REVERT: B 434 ASP cc_start: 0.8994 (m-30) cc_final: 0.8791 (m-30) REVERT: B 445 ILE cc_start: 0.9386 (mp) cc_final: 0.8756 (mp) REVERT: B 446 ARG cc_start: 0.7497 (mmp80) cc_final: 0.7109 (mmp80) REVERT: B 447 ASN cc_start: 0.8589 (m-40) cc_final: 0.7156 (m-40) REVERT: B 493 MET cc_start: 0.9586 (tmm) cc_final: 0.9262 (tmm) REVERT: B 501 GLN cc_start: 0.9420 (tt0) cc_final: 0.9099 (tt0) REVERT: B 505 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8383 (mt-10) REVERT: B 586 TYR cc_start: 0.9130 (m-80) cc_final: 0.8898 (m-80) REVERT: B 601 ILE cc_start: 0.9534 (mm) cc_final: 0.9062 (mm) REVERT: B 610 LYS cc_start: 0.9154 (tttm) cc_final: 0.8819 (tmtt) REVERT: B 615 MET cc_start: 0.9209 (mmp) cc_final: 0.8856 (mmp) REVERT: B 627 LYS cc_start: 0.9382 (tttp) cc_final: 0.8898 (tttp) REVERT: B 628 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8001 (mm-30) REVERT: B 632 MET cc_start: 0.8905 (mtp) cc_final: 0.8705 (mtp) REVERT: B 633 ASP cc_start: 0.8692 (t0) cc_final: 0.8319 (t0) REVERT: B 640 MET cc_start: 0.9512 (tpp) cc_final: 0.9175 (tpp) REVERT: B 650 GLN cc_start: 0.8256 (mt0) cc_final: 0.7802 (mm-40) REVERT: B 655 THR cc_start: 0.9587 (m) cc_final: 0.9364 (t) REVERT: B 667 LEU cc_start: 0.9615 (tp) cc_final: 0.9223 (tp) REVERT: B 668 ASN cc_start: 0.9417 (m-40) cc_final: 0.9150 (m110) REVERT: B 671 ASP cc_start: 0.8832 (m-30) cc_final: 0.8568 (m-30) REVERT: C 18 THR cc_start: 0.7892 (p) cc_final: 0.7674 (p) REVERT: C 96 MET cc_start: 0.7679 (mmm) cc_final: 0.6532 (mmm) REVERT: C 110 MET cc_start: 0.7732 (mtm) cc_final: 0.7526 (mtm) REVERT: C 197 ASP cc_start: 0.9135 (m-30) cc_final: 0.8902 (m-30) REVERT: D 74 MET cc_start: 0.4209 (tmm) cc_final: 0.3945 (tmm) REVERT: D 109 PHE cc_start: 0.8120 (m-80) cc_final: 0.7459 (m-80) REVERT: D 117 THR cc_start: 0.7730 (t) cc_final: 0.7459 (t) REVERT: D 137 MET cc_start: 0.8812 (mmp) cc_final: 0.8607 (mmp) REVERT: D 174 TYR cc_start: 0.8308 (t80) cc_final: 0.7732 (t80) REVERT: D 212 ILE cc_start: 0.8221 (pt) cc_final: 0.8001 (pt) REVERT: D 233 ASN cc_start: 0.8749 (m110) cc_final: 0.8440 (m110) outliers start: 1 outliers final: 0 residues processed: 672 average time/residue: 0.1065 time to fit residues: 108.1091 Evaluate side-chains 605 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 605 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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: 1.9990 chunk 133 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 49 optimal weight: 0.0010 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN B 645 GLN D 69 GLN D 119 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.133573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.096216 restraints weight = 40223.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.099805 restraints weight = 20829.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.102160 restraints weight = 12873.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.103756 restraints weight = 9021.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.104844 restraints weight = 6897.791| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.7594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16386 Z= 0.133 Angle : 0.607 9.117 22134 Z= 0.327 Chirality : 0.044 0.201 2360 Planarity : 0.004 0.046 2818 Dihedral : 8.071 146.817 2290 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.12 % Allowed : 0.41 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.19), residues: 1932 helix: 1.07 (0.15), residues: 1130 sheet: -0.73 (0.38), residues: 146 loop : 0.09 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 243 TYR 0.018 0.001 TYR D 174 PHE 0.032 0.002 PHE D 168 TRP 0.012 0.001 TRP D 124 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (16386) covalent geometry : angle 0.60682 / 0.33 (22134) hydrogen bonds : bond 0.03814 / 2.45 ( 871) hydrogen bonds : angle 4.96232 / 3.57 ( 2571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 680 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.9649 (mm) cc_final: 0.9347 (mm) REVERT: A 16 ILE cc_start: 0.9249 (mm) cc_final: 0.9011 (mm) REVERT: A 30 LYS cc_start: 0.9205 (tptt) cc_final: 0.8971 (tptp) REVERT: A 95 MET cc_start: 0.9123 (mmm) cc_final: 0.8880 (tpp) REVERT: A 99 LYS cc_start: 0.9582 (mmtp) cc_final: 0.9293 (mmtp) REVERT: A 107 LYS cc_start: 0.9077 (mttm) cc_final: 0.8848 (mmmt) REVERT: A 119 GLU cc_start: 0.8885 (mp0) cc_final: 0.8505 (mp0) REVERT: A 172 LEU cc_start: 0.9632 (mp) cc_final: 0.9251 (mp) REVERT: A 218 ASN cc_start: 0.9249 (t0) cc_final: 0.8993 (m-40) REVERT: A 227 MET cc_start: 0.9344 (mtp) cc_final: 0.8966 (mtp) REVERT: A 235 ARG cc_start: 0.9157 (ttm-80) cc_final: 0.8899 (mmm-85) REVERT: A 251 LEU cc_start: 0.9506 (tp) cc_final: 0.9169 (tp) REVERT: A 255 HIS cc_start: 0.8693 (t-90) cc_final: 0.8301 (t-90) REVERT: A 259 ASN cc_start: 0.9118 (m-40) cc_final: 0.8764 (m-40) REVERT: A 291 LEU cc_start: 0.9537 (mt) cc_final: 0.9150 (mt) REVERT: A 318 ASP cc_start: 0.8167 (t0) cc_final: 0.7750 (t0) REVERT: A 322 MET cc_start: 0.8722 (mtm) cc_final: 0.7773 (mtm) REVERT: A 333 LYS cc_start: 0.9364 (tmtt) cc_final: 0.8938 (tptp) REVERT: A 345 LYS cc_start: 0.9470 (tttt) cc_final: 0.9184 (ttpt) REVERT: A 348 MET cc_start: 0.9122 (ptp) cc_final: 0.8663 (ptp) REVERT: A 357 TYR cc_start: 0.8833 (m-10) cc_final: 0.8400 (m-10) REVERT: A 361 GLN cc_start: 0.8901 (tp40) cc_final: 0.8517 (tp-100) REVERT: A 370 ASN cc_start: 0.9410 (m110) cc_final: 0.9118 (m110) REVERT: A 376 VAL cc_start: 0.9120 (t) cc_final: 0.8832 (t) REVERT: A 403 ILE cc_start: 0.9415 (mm) cc_final: 0.9149 (mm) REVERT: A 405 LEU cc_start: 0.8812 (mt) cc_final: 0.8512 (mt) REVERT: A 407 ILE cc_start: 0.9227 (mt) cc_final: 0.8816 (mt) REVERT: A 427 LYS cc_start: 0.9148 (ptpp) cc_final: 0.8893 (ptpp) REVERT: A 447 ASN cc_start: 0.8231 (m-40) cc_final: 0.7737 (m-40) REVERT: A 458 MET cc_start: 0.8977 (mmp) cc_final: 0.8557 (mmp) REVERT: A 472 LEU cc_start: 0.9481 (mt) cc_final: 0.9268 (mt) REVERT: A 494 MET cc_start: 0.9245 (mmt) cc_final: 0.8787 (mmt) REVERT: A 505 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8269 (mt-10) REVERT: A 515 ASP cc_start: 0.8755 (m-30) cc_final: 0.8340 (m-30) REVERT: A 604 ARG cc_start: 0.8876 (mmp80) cc_final: 0.8379 (mmp80) REVERT: A 615 MET cc_start: 0.9211 (mmp) cc_final: 0.8874 (mmp) REVERT: A 640 MET cc_start: 0.9380 (tpp) cc_final: 0.9145 (tpp) REVERT: A 683 TYR cc_start: 0.8433 (t80) cc_final: 0.7397 (t80) REVERT: B 40 TYR cc_start: 0.9303 (t80) cc_final: 0.9014 (t80) REVERT: B 51 LEU cc_start: 0.9275 (tp) cc_final: 0.8961 (tp) REVERT: B 55 LEU cc_start: 0.9839 (mt) cc_final: 0.9579 (mt) REVERT: B 67 GLU cc_start: 0.9339 (tm-30) cc_final: 0.8949 (tm-30) REVERT: B 82 LYS cc_start: 0.9513 (mmmm) cc_final: 0.9162 (mmtt) REVERT: B 95 MET cc_start: 0.9076 (tpp) cc_final: 0.8540 (tpp) REVERT: B 107 LYS cc_start: 0.9395 (mttp) cc_final: 0.9110 (mmmm) REVERT: B 116 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8354 (mt-10) REVERT: B 119 GLU cc_start: 0.9256 (mp0) cc_final: 0.8915 (mp0) REVERT: B 128 PHE cc_start: 0.9669 (t80) cc_final: 0.9456 (t80) REVERT: B 149 TYR cc_start: 0.9471 (t80) cc_final: 0.8749 (t80) REVERT: B 174 GLU cc_start: 0.8197 (tp30) cc_final: 0.7955 (tp30) REVERT: B 209 LYS cc_start: 0.9093 (tppt) cc_final: 0.8836 (tptp) REVERT: B 211 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8382 (mm-30) REVERT: B 235 ARG cc_start: 0.9267 (tpp80) cc_final: 0.8808 (mtm-85) REVERT: B 257 ASP cc_start: 0.9015 (m-30) cc_final: 0.8723 (m-30) REVERT: B 258 ILE cc_start: 0.9526 (tp) cc_final: 0.9317 (tp) REVERT: B 276 LYS cc_start: 0.9352 (mmtm) cc_final: 0.8923 (mmtm) REVERT: B 286 ASP cc_start: 0.8613 (m-30) cc_final: 0.7662 (m-30) REVERT: B 290 GLU cc_start: 0.9239 (tp30) cc_final: 0.8961 (tp30) REVERT: B 312 GLN cc_start: 0.8662 (pm20) cc_final: 0.8314 (pm20) REVERT: B 317 MET cc_start: 0.8997 (ptm) cc_final: 0.8622 (ptm) REVERT: B 322 MET cc_start: 0.9308 (tpt) cc_final: 0.8929 (mmm) REVERT: B 362 ASP cc_start: 0.8638 (m-30) cc_final: 0.7578 (m-30) REVERT: B 373 ILE cc_start: 0.9493 (mt) cc_final: 0.9024 (tp) REVERT: B 386 LEU cc_start: 0.9448 (mt) cc_final: 0.8825 (mt) REVERT: B 390 GLN cc_start: 0.9054 (mt0) cc_final: 0.8712 (mm110) REVERT: B 393 SER cc_start: 0.9570 (t) cc_final: 0.9276 (p) REVERT: B 398 ASP cc_start: 0.8599 (t0) cc_final: 0.8239 (t0) REVERT: B 413 SER cc_start: 0.9616 (m) cc_final: 0.9256 (t) REVERT: B 415 ASN cc_start: 0.9596 (t0) cc_final: 0.9119 (t0) REVERT: B 445 ILE cc_start: 0.9341 (mp) cc_final: 0.8729 (mp) REVERT: B 446 ARG cc_start: 0.7544 (mmp80) cc_final: 0.7185 (mmp80) REVERT: B 458 MET cc_start: 0.9313 (mmm) cc_final: 0.8633 (mmm) REVERT: B 467 ASN cc_start: 0.9041 (t0) cc_final: 0.8794 (t0) REVERT: B 493 MET cc_start: 0.9556 (tmm) cc_final: 0.9246 (tmm) REVERT: B 501 GLN cc_start: 0.9439 (tt0) cc_final: 0.9139 (tt0) REVERT: B 505 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8497 (mt-10) REVERT: B 601 ILE cc_start: 0.9501 (mm) cc_final: 0.8995 (mm) REVERT: B 610 LYS cc_start: 0.9274 (tttm) cc_final: 0.8965 (tmtt) REVERT: B 615 MET cc_start: 0.9262 (mmp) cc_final: 0.8817 (mmp) REVERT: B 618 LEU cc_start: 0.9233 (mt) cc_final: 0.8865 (mt) REVERT: B 627 LYS cc_start: 0.9337 (tttp) cc_final: 0.8841 (tttp) REVERT: B 628 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7913 (mm-30) REVERT: B 632 MET cc_start: 0.8902 (mtp) cc_final: 0.8641 (mtp) REVERT: B 633 ASP cc_start: 0.8682 (t0) cc_final: 0.7872 (t0) REVERT: B 636 LYS cc_start: 0.9608 (mmtp) cc_final: 0.9260 (mmtp) REVERT: B 640 MET cc_start: 0.9519 (tpp) cc_final: 0.9139 (tpp) REVERT: B 650 GLN cc_start: 0.8161 (mt0) cc_final: 0.7803 (mm-40) REVERT: B 655 THR cc_start: 0.9650 (m) cc_final: 0.9324 (t) REVERT: B 667 LEU cc_start: 0.9595 (tp) cc_final: 0.9213 (tp) REVERT: B 668 ASN cc_start: 0.9406 (m-40) cc_final: 0.9140 (m110) REVERT: B 671 ASP cc_start: 0.8802 (m-30) cc_final: 0.8509 (m-30) REVERT: C 96 MET cc_start: 0.7811 (mmm) cc_final: 0.6774 (mmm) REVERT: C 197 ASP cc_start: 0.9167 (m-30) cc_final: 0.8870 (m-30) REVERT: C 233 ASN cc_start: 0.9259 (m110) cc_final: 0.9019 (m110) REVERT: D 27 LYS cc_start: 0.8498 (ptmm) cc_final: 0.8261 (ptpp) REVERT: D 96 MET cc_start: -0.2041 (mmt) cc_final: -0.2408 (mmt) REVERT: D 137 MET cc_start: 0.8756 (mmp) cc_final: 0.8380 (ptp) REVERT: D 172 PHE cc_start: 0.8961 (m-80) cc_final: 0.8571 (m-80) REVERT: D 174 TYR cc_start: 0.8351 (t80) cc_final: 0.7809 (t80) REVERT: D 185 MET cc_start: 0.5819 (mmp) cc_final: 0.5545 (mmp) REVERT: D 212 ILE cc_start: 0.8294 (pt) cc_final: 0.7780 (pt) outliers start: 2 outliers final: 0 residues processed: 682 average time/residue: 0.1010 time to fit residues: 103.8085 Evaluate side-chains 604 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 604 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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: 5.9990 chunk 62 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 189 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 54 optimal weight: 0.1980 chunk 132 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN A 25 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.133373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.095878 restraints weight = 40895.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.099413 restraints weight = 21566.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.101720 restraints weight = 13516.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.103322 restraints weight = 9533.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.104321 restraints weight = 7308.611| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.7722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16386 Z= 0.177 Angle : 0.638 8.797 22134 Z= 0.344 Chirality : 0.045 0.288 2360 Planarity : 0.004 0.044 2818 Dihedral : 8.261 146.891 2290 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 1932 helix: 1.05 (0.15), residues: 1127 sheet: -0.62 (0.41), residues: 134 loop : 0.05 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 243 TYR 0.022 0.002 TYR C 130 PHE 0.039 0.002 PHE D 109 TRP 0.012 0.001 TRP D 124 HIS 0.005 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (16386) covalent geometry : angle 0.63780 / 0.34 (22134) hydrogen bonds : bond 0.03860 / 2.48 ( 871) hydrogen bonds : angle 5.01944 / 3.60 ( 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 658 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 658 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.9200 (tptt) cc_final: 0.8967 (tptp) REVERT: A 95 MET cc_start: 0.9086 (mmm) cc_final: 0.8872 (tpp) REVERT: A 99 LYS cc_start: 0.9600 (mmtp) cc_final: 0.9308 (mmtp) REVERT: A 119 GLU cc_start: 0.8874 (mp0) cc_final: 0.8503 (mp0) REVERT: A 122 ILE cc_start: 0.9693 (mp) cc_final: 0.9484 (mp) REVERT: A 139 GLU cc_start: 0.9364 (tp30) cc_final: 0.9015 (tp30) REVERT: A 144 MET cc_start: 0.8936 (mtm) cc_final: 0.8430 (mtm) REVERT: A 172 LEU cc_start: 0.9636 (mp) cc_final: 0.9214 (mp) REVERT: A 218 ASN cc_start: 0.9204 (t0) cc_final: 0.8998 (m-40) REVERT: A 227 MET cc_start: 0.9288 (mtp) cc_final: 0.8945 (mtp) REVERT: A 235 ARG cc_start: 0.9154 (ttm-80) cc_final: 0.8887 (mmm-85) REVERT: A 259 ASN cc_start: 0.9093 (m-40) cc_final: 0.8703 (m-40) REVERT: A 264 THR cc_start: 0.9510 (p) cc_final: 0.9303 (p) REVERT: A 274 ARG cc_start: 0.8680 (tpp-160) cc_final: 0.8202 (tpm170) REVERT: A 318 ASP cc_start: 0.8475 (t0) cc_final: 0.8164 (t0) REVERT: A 322 MET cc_start: 0.8646 (mtm) cc_final: 0.7750 (mtm) REVERT: A 333 LYS cc_start: 0.9370 (tmtt) cc_final: 0.8959 (tptp) REVERT: A 345 LYS cc_start: 0.9561 (tttt) cc_final: 0.9211 (ttpt) REVERT: A 348 MET cc_start: 0.9050 (ptp) cc_final: 0.8618 (ptp) REVERT: A 357 TYR cc_start: 0.8809 (m-10) cc_final: 0.8374 (m-10) REVERT: A 361 GLN cc_start: 0.8855 (tp40) cc_final: 0.8531 (tp-100) REVERT: A 370 ASN cc_start: 0.9433 (m110) cc_final: 0.8885 (m110) REVERT: A 376 VAL cc_start: 0.9167 (t) cc_final: 0.8869 (t) REVERT: A 407 ILE cc_start: 0.9271 (mt) cc_final: 0.8868 (mt) REVERT: A 413 SER cc_start: 0.9368 (m) cc_final: 0.9138 (m) REVERT: A 427 LYS cc_start: 0.9102 (ptpp) cc_final: 0.8843 (ptpp) REVERT: A 447 ASN cc_start: 0.8298 (m-40) cc_final: 0.7895 (m-40) REVERT: A 472 LEU cc_start: 0.9475 (mt) cc_final: 0.9257 (mt) REVERT: A 494 MET cc_start: 0.9131 (mmt) cc_final: 0.8636 (mmt) REVERT: A 505 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8265 (mt-10) REVERT: A 515 ASP cc_start: 0.8693 (m-30) cc_final: 0.8382 (m-30) REVERT: A 604 ARG cc_start: 0.8864 (mmp80) cc_final: 0.8554 (mmp80) REVERT: A 610 LYS cc_start: 0.8781 (ttmm) cc_final: 0.8287 (mmtt) REVERT: A 615 MET cc_start: 0.9163 (mmp) cc_final: 0.8857 (mmp) REVERT: A 640 MET cc_start: 0.9271 (tpp) cc_final: 0.9065 (tpp) REVERT: A 675 HIS cc_start: 0.9430 (t70) cc_final: 0.9006 (t70) REVERT: A 683 TYR cc_start: 0.8478 (t80) cc_final: 0.7544 (t80) REVERT: B 51 LEU cc_start: 0.9315 (tp) cc_final: 0.8996 (tp) REVERT: B 55 LEU cc_start: 0.9838 (mt) cc_final: 0.9578 (mt) REVERT: B 67 GLU cc_start: 0.9350 (tm-30) cc_final: 0.8963 (tm-30) REVERT: B 82 LYS cc_start: 0.9505 (mmmm) cc_final: 0.9164 (mmtt) REVERT: B 95 MET cc_start: 0.9008 (tpp) cc_final: 0.8646 (tpp) REVERT: B 98 PHE cc_start: 0.9557 (t80) cc_final: 0.9025 (t80) REVERT: B 107 LYS cc_start: 0.9398 (mttp) cc_final: 0.9130 (mmmm) REVERT: B 116 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8290 (mt-10) REVERT: B 119 GLU cc_start: 0.9286 (mp0) cc_final: 0.8942 (mp0) REVERT: B 149 TYR cc_start: 0.9486 (t80) cc_final: 0.8819 (t80) REVERT: B 161 ARG cc_start: 0.8412 (mtp85) cc_final: 0.8043 (mtt180) REVERT: B 174 GLU cc_start: 0.8114 (tp30) cc_final: 0.7716 (tp30) REVERT: B 209 LYS cc_start: 0.9126 (tppt) cc_final: 0.8865 (tptp) REVERT: B 211 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8484 (mm-30) REVERT: B 235 ARG cc_start: 0.9244 (tpp80) cc_final: 0.8815 (mtm-85) REVERT: B 257 ASP cc_start: 0.8923 (m-30) cc_final: 0.8647 (m-30) REVERT: B 258 ILE cc_start: 0.9532 (tp) cc_final: 0.9322 (tp) REVERT: B 263 ASP cc_start: 0.9015 (m-30) cc_final: 0.8553 (m-30) REVERT: B 266 LYS cc_start: 0.9391 (mtpp) cc_final: 0.9101 (mttm) REVERT: B 276 LYS cc_start: 0.9414 (mmtm) cc_final: 0.9099 (mmmt) REVERT: B 286 ASP cc_start: 0.8534 (m-30) cc_final: 0.7595 (m-30) REVERT: B 290 GLU cc_start: 0.9173 (tp30) cc_final: 0.8787 (tp30) REVERT: B 291 LEU cc_start: 0.9745 (mt) cc_final: 0.9436 (mt) REVERT: B 312 GLN cc_start: 0.8683 (pm20) cc_final: 0.8375 (pm20) REVERT: B 317 MET cc_start: 0.8791 (ptm) cc_final: 0.8543 (ptm) REVERT: B 318 ASP cc_start: 0.8954 (t0) cc_final: 0.8656 (t0) REVERT: B 322 MET cc_start: 0.9281 (tpt) cc_final: 0.8845 (mmm) REVERT: B 349 LEU cc_start: 0.9662 (mp) cc_final: 0.9439 (mp) REVERT: B 362 ASP cc_start: 0.8613 (m-30) cc_final: 0.7581 (m-30) REVERT: B 373 ILE cc_start: 0.9503 (mt) cc_final: 0.9175 (tp) REVERT: B 393 SER cc_start: 0.9567 (t) cc_final: 0.9254 (p) REVERT: B 398 ASP cc_start: 0.8577 (t0) cc_final: 0.8263 (t70) REVERT: B 413 SER cc_start: 0.9570 (m) cc_final: 0.9299 (t) REVERT: B 415 ASN cc_start: 0.9567 (t0) cc_final: 0.9059 (t0) REVERT: B 445 ILE cc_start: 0.9378 (mp) cc_final: 0.8613 (mp) REVERT: B 446 ARG cc_start: 0.7861 (mmp80) cc_final: 0.7567 (mmp80) REVERT: B 458 MET cc_start: 0.9325 (mmm) cc_final: 0.8563 (mmm) REVERT: B 467 ASN cc_start: 0.9063 (t0) cc_final: 0.8778 (t0) REVERT: B 493 MET cc_start: 0.9532 (tmm) cc_final: 0.9196 (tmm) REVERT: B 501 GLN cc_start: 0.9427 (tt0) cc_final: 0.9134 (tt0) REVERT: B 529 ASP cc_start: 0.8632 (m-30) cc_final: 0.8390 (m-30) REVERT: B 601 ILE cc_start: 0.9117 (mm) cc_final: 0.8856 (mm) REVERT: B 610 LYS cc_start: 0.9251 (tttm) cc_final: 0.9013 (tmtt) REVERT: B 615 MET cc_start: 0.9282 (mmp) cc_final: 0.9039 (mmm) REVERT: B 618 LEU cc_start: 0.9273 (mt) cc_final: 0.8929 (mt) REVERT: B 627 LYS cc_start: 0.9388 (tttp) cc_final: 0.8937 (tttp) REVERT: B 628 GLU cc_start: 0.8517 (mm-30) cc_final: 0.7899 (mm-30) REVERT: B 632 MET cc_start: 0.8878 (mtp) cc_final: 0.8643 (mtp) REVERT: B 633 ASP cc_start: 0.8651 (t0) cc_final: 0.7893 (t0) REVERT: B 636 LYS cc_start: 0.9616 (mmtp) cc_final: 0.9266 (mmtp) REVERT: B 640 MET cc_start: 0.9468 (tpp) cc_final: 0.9133 (tpp) REVERT: B 655 THR cc_start: 0.9772 (m) cc_final: 0.9353 (t) REVERT: B 667 LEU cc_start: 0.9581 (tp) cc_final: 0.9200 (tp) REVERT: B 668 ASN cc_start: 0.9425 (m-40) cc_final: 0.9125 (m110) REVERT: B 671 ASP cc_start: 0.8736 (m-30) cc_final: 0.8435 (m-30) REVERT: C 96 MET cc_start: 0.7774 (mmm) cc_final: 0.6579 (mmm) REVERT: C 118 ILE cc_start: 0.8322 (mm) cc_final: 0.8080 (mm) REVERT: C 233 ASN cc_start: 0.9191 (m110) cc_final: 0.8933 (m110) REVERT: D 74 MET cc_start: 0.4252 (tmm) cc_final: 0.4044 (tmm) REVERT: D 95 MET cc_start: 0.5152 (tmm) cc_final: 0.3953 (tmm) REVERT: D 109 PHE cc_start: 0.8205 (m-80) cc_final: 0.7991 (m-80) REVERT: D 137 MET cc_start: 0.8757 (mmp) cc_final: 0.8389 (ptp) REVERT: D 174 TYR cc_start: 0.8195 (t80) cc_final: 0.7759 (t80) REVERT: D 185 MET cc_start: 0.6086 (mmp) cc_final: 0.5678 (mmp) REVERT: D 212 ILE cc_start: 0.8306 (pt) cc_final: 0.7749 (pt) REVERT: D 233 ASN cc_start: 0.8943 (m110) cc_final: 0.8703 (m110) outliers start: 0 outliers final: 0 residues processed: 658 average time/residue: 0.1036 time to fit residues: 103.5728 Evaluate side-chains 588 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 588 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 48 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN A 158 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.136614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.098026 restraints weight = 40634.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.101718 restraints weight = 21710.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.104132 restraints weight = 13668.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.105704 restraints weight = 9692.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.106756 restraints weight = 7490.292| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.7878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16386 Z= 0.156 Angle : 0.632 8.107 22134 Z= 0.338 Chirality : 0.045 0.254 2360 Planarity : 0.004 0.054 2818 Dihedral : 8.194 147.303 2290 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.19), residues: 1932 helix: 1.03 (0.15), residues: 1127 sheet: -0.65 (0.40), residues: 146 loop : -0.01 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 243 TYR 0.031 0.001 TYR A 118 PHE 0.031 0.002 PHE D 109 TRP 0.013 0.001 TRP D 124 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (16386) covalent geometry : angle 0.63223 / 0.34 (22134) hydrogen bonds : bond 0.03803 / 2.45 ( 871) hydrogen bonds : angle 5.01584 / 3.60 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3084.88 seconds wall clock time: 54 minutes 12.97 seconds (3252.97 seconds total)