Starting phenix.real_space_refine on Fri Jul 3 19:48:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzd_45064/07_2026/9bzd_45064_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzd_45064/07_2026/9bzd_45064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bzd_45064/07_2026/9bzd_45064_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzd_45064/07_2026/9bzd_45064_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bzd_45064/07_2026/9bzd_45064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzd_45064/07_2026/9bzd_45064.map" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.49, per 1000 atoms: 0.22 Number of scatterers: 16038 At special positions: 0 Unit cell: (93.288, 128.778, 129.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 656.8 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: 0.49 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: 3.984A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.953A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.664A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.128A 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: 4.074A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.677A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.878A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.645A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.729A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.027A 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: 4.068A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.544A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.934A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.668A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.359A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.478A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.902A 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: 8.393A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.453A 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: 5.660A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.383A 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: 6.063A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.049A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.564A 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: 6.549A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 1.53 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: 4892 1.34 - 1.46: 3091 1.46 - 1.58: 8222 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" O3B TTP B 801 " pdb=" PG TTP B 801 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" O3B TTP A 803 " pdb=" PG TTP A 803 " ideal model delta sigma weight residual 1.748 1.610 0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.060 1.25e-02 6.40e+03 2.34e+01 bond pdb=" O3A TTP A 803 " pdb=" PB TTP A 803 " ideal model delta sigma weight residual 1.675 1.606 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 21530 2.10 - 4.19: 523 4.19 - 6.29: 64 6.29 - 8.38: 8 8.38 - 10.48: 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 110.54 116.60 -6.06 1.36e+00 5.41e-01 1.99e+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 SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.22 -3.94 1.09e+00 8.42e-01 1.31e+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 111.71 115.73 -4.02 1.15e+00 7.56e-01 1.22e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.05: 9090 25.05 - 50.10: 654 50.10 - 75.15: 126 75.15 - 100.19: 26 100.19 - 125.24: 2 Dihedral angle restraints: 9898 sinusoidal: 4140 harmonic: 5758 Sorted by residual: dihedral pdb=" O4' GDP A 802 " pdb=" C1' GDP A 802 " pdb=" N9 GDP A 802 " pdb=" C8 GDP A 802 " ideal model delta sinusoidal sigma weight residual 27.02 -98.22 125.24 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 -95.65 122.67 1 2.00e+01 2.50e-03 3.70e+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 -134.38 12.38 0 2.50e+00 1.60e-01 2.45e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2142 0.093 - 0.187: 185 0.187 - 0.280: 28 0.280 - 0.373: 3 0.373 - 0.467: 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 5.44e+00 chirality pdb=" CA TYR C 169 " pdb=" N TYR C 169 " pdb=" C TYR C 169 " pdb=" CB TYR C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " -0.017 2.00e-02 2.50e+03 1.10e-02 2.13e+00 pdb=" CG PHE D 92 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 169 " 0.017 2.00e-02 2.50e+03 1.01e-02 2.04e+00 pdb=" CG TYR C 169 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR C 169 " -0.000 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 " 0.008 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 131 2.51 - 3.11: 11547 3.11 - 3.70: 27037 3.70 - 4.30: 41565 4.30 - 4.90: 65447 Nonbonded interactions: 145727 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.911 3.060 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.962 3.060 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 3.060 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 3.060 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.012 3.040 ... (remaining 145722 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: 0.01 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.840 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 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 : 0.788 10.479 22134 Z= 0.472 Chirality : 0.058 0.467 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.675 125.244 6202 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.34 % Allowed : 15.33 % Favored : 83.33 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.18), residues: 1932 helix: 0.59 (0.14), residues: 1149 sheet: 0.46 (0.42), residues: 124 loop : 0.24 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 196 TYR 0.021 0.002 TYR D 179 PHE 0.021 0.002 PHE C 168 TRP 0.009 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.33 (16386) covalent geometry : angle 0.78784 / 0.47 (22134) hydrogen bonds : bond 0.15424 / 9.51 ( 871) hydrogen bonds : angle 6.51733 / 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 1098 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 1075 time to evaluate : 0.524 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: A 11 GLN cc_start: 0.8048 (mt0) cc_final: 0.7538 (mt0) REVERT: A 12 LEU cc_start: 0.7978 (mt) cc_final: 0.7774 (mp) REVERT: A 28 LYS cc_start: 0.8502 (mmtm) cc_final: 0.8296 (tppp) REVERT: A 76 ASP cc_start: 0.7984 (m-30) cc_final: 0.7351 (m-30) REVERT: A 127 LEU cc_start: 0.8535 (mt) cc_final: 0.8222 (mt) REVERT: A 179 LEU cc_start: 0.8733 (tp) cc_final: 0.8516 (tp) REVERT: A 181 ASP cc_start: 0.7596 (m-30) cc_final: 0.7211 (m-30) REVERT: A 204 SER cc_start: 0.8470 (m) cc_final: 0.8039 (t) REVERT: A 265 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8590 (mmmt) REVERT: A 280 ILE cc_start: 0.8960 (pt) cc_final: 0.8670 (pt) REVERT: A 348 MET cc_start: 0.7366 (tmm) cc_final: 0.6799 (tmm) REVERT: A 352 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6376 (mt-10) REVERT: A 362 ASP cc_start: 0.5957 (m-30) cc_final: 0.5559 (m-30) REVERT: A 598 MET cc_start: 0.7520 (mtm) cc_final: 0.6916 (mtp) REVERT: A 604 ARG cc_start: 0.7657 (mmp80) cc_final: 0.6307 (mmt90) REVERT: A 606 TYR cc_start: 0.6419 (m-80) cc_final: 0.5935 (m-80) REVERT: A 645 GLN cc_start: 0.8195 (tp40) cc_final: 0.7666 (tp40) REVERT: B 11 GLN cc_start: 0.7881 (mt0) cc_final: 0.7483 (mt0) REVERT: B 12 LEU cc_start: 0.8243 (mt) cc_final: 0.7944 (mt) REVERT: B 33 VAL cc_start: 0.9342 (OUTLIER) cc_final: 0.9138 (t) REVERT: B 109 ASN cc_start: 0.8024 (m-40) cc_final: 0.7577 (p0) REVERT: B 121 ARG cc_start: 0.8401 (tpm170) cc_final: 0.7984 (tpp-160) REVERT: B 187 ASP cc_start: 0.6443 (t70) cc_final: 0.6237 (t0) REVERT: B 286 ASP cc_start: 0.6756 (OUTLIER) cc_final: 0.6117 (m-30) REVERT: B 295 ASP cc_start: 0.8037 (t0) cc_final: 0.7783 (t0) REVERT: B 348 MET cc_start: 0.6874 (tmm) cc_final: 0.6617 (ttp) REVERT: B 350 ARG cc_start: 0.7566 (mtp85) cc_final: 0.7299 (mtp85) REVERT: B 362 ASP cc_start: 0.6613 (m-30) cc_final: 0.6351 (m-30) REVERT: B 366 LYS cc_start: 0.8398 (ptpp) cc_final: 0.8183 (ttmt) REVERT: B 381 LEU cc_start: 0.8713 (tp) cc_final: 0.8398 (tp) REVERT: B 458 MET cc_start: 0.8485 (mmm) cc_final: 0.8224 (mmm) REVERT: B 460 SER cc_start: 0.8996 (t) cc_final: 0.8648 (p) REVERT: B 471 TYR cc_start: 0.8414 (t80) cc_final: 0.7955 (t80) REVERT: B 485 ARG cc_start: 0.7856 (mtm-85) cc_final: 0.7315 (mtm-85) REVERT: B 493 MET cc_start: 0.8356 (tmm) cc_final: 0.8146 (tmm) REVERT: B 496 ASN cc_start: 0.8372 (t0) cc_final: 0.8076 (t0) REVERT: B 500 ILE cc_start: 0.8730 (mt) cc_final: 0.8328 (mt) REVERT: B 546 LEU cc_start: 0.9032 (mt) cc_final: 0.8740 (mt) REVERT: B 550 MET cc_start: 0.7893 (mtm) cc_final: 0.7345 (mtm) REVERT: B 601 ILE cc_start: 0.8457 (mt) cc_final: 0.8137 (mt) REVERT: B 604 ARG cc_start: 0.7109 (mmp80) cc_final: 0.6769 (tpp80) REVERT: B 612 TYR cc_start: 0.7795 (m-80) cc_final: 0.7493 (m-80) REVERT: B 664 THR cc_start: 0.8952 (p) cc_final: 0.8744 (p) REVERT: C 106 SER cc_start: 0.7759 (m) cc_final: 0.6430 (m) REVERT: C 212 ILE cc_start: 0.6000 (mt) cc_final: 0.5751 (mt) REVERT: D 178 PHE cc_start: 0.5471 (m-80) cc_final: 0.5088 (m-80) REVERT: D 193 LEU cc_start: 0.7895 (mt) cc_final: 0.7623 (mt) REVERT: D 260 ILE cc_start: 0.7126 (mt) cc_final: 0.6763 (mt) REVERT: D 315 LEU cc_start: 0.7097 (mt) cc_final: 0.6817 (mt) outliers start: 23 outliers final: 7 residues processed: 1082 average time/residue: 0.1317 time to fit residues: 206.6427 Evaluate side-chains 725 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 716 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 282 ILE 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: 0.0370 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 25 GLN B 320 ASN B 329 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN B 467 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN B 676 HIS C 24 GLN C 28 GLN C 80 HIS C 85 GLN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 HIS C 263 ASN C 270 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN D 80 HIS D 91 ASN D 128 ASN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.129303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.093394 restraints weight = 35371.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.097186 restraints weight = 16453.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.099467 restraints weight = 9735.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.101158 restraints weight = 6756.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.102327 restraints weight = 5036.574| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (15 function evaluations) r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16386 Z= 0.173 Angle : 0.719 14.814 22134 Z= 0.376 Chirality : 0.046 0.194 2360 Planarity : 0.004 0.041 2818 Dihedral : 9.867 130.176 2305 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.67 % Allowed : 22.09 % Favored : 74.24 % 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: 1.34 (0.18), residues: 1932 helix: 1.34 (0.15), residues: 1128 sheet: 1.09 (0.48), residues: 100 loop : 0.28 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 243 TYR 0.020 0.002 TYR B 72 PHE 0.031 0.002 PHE D 172 TRP 0.027 0.003 TRP D 30 HIS 0.008 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (16386) covalent geometry : angle 0.71889 / 0.38 (22134) hydrogen bonds : bond 0.04927 / 3.13 ( 871) hydrogen bonds : angle 5.16663 / 3.69 ( 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 850 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 787 time to evaluate : 0.595 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 65 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8219 (mm-30) REVERT: A 66 GLU cc_start: 0.8558 (tp30) cc_final: 0.8352 (tp30) REVERT: A 144 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8760 (mtm) REVERT: A 181 ASP cc_start: 0.8745 (m-30) cc_final: 0.8416 (m-30) REVERT: A 218 ASN cc_start: 0.8896 (t0) cc_final: 0.8685 (t0) REVERT: A 221 LYS cc_start: 0.8899 (mmtp) cc_final: 0.8666 (mttp) REVERT: A 243 ARG cc_start: 0.7643 (ttp80) cc_final: 0.7372 (tmm-80) REVERT: A 274 ARG cc_start: 0.8166 (ttp80) cc_final: 0.7378 (mtm-85) REVERT: A 335 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8547 (mm-30) REVERT: A 348 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7228 (tmm) REVERT: A 352 GLU cc_start: 0.7827 (mt-10) cc_final: 0.6881 (mt-10) REVERT: A 384 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.7900 (pm20) REVERT: A 415 ASN cc_start: 0.9378 (t0) cc_final: 0.9115 (t0) REVERT: A 420 MET cc_start: 0.9277 (mmm) cc_final: 0.8969 (mmm) REVERT: A 444 ASP cc_start: 0.8590 (t70) cc_final: 0.8352 (t70) REVERT: A 492 PHE cc_start: 0.9174 (m-80) cc_final: 0.8955 (m-10) REVERT: A 493 MET cc_start: 0.8995 (tmm) cc_final: 0.8599 (tmm) REVERT: A 505 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8570 (mt-10) REVERT: A 528 PHE cc_start: 0.8982 (m-80) cc_final: 0.8664 (m-80) REVERT: A 586 TYR cc_start: 0.8626 (m-80) cc_final: 0.8399 (m-10) REVERT: A 598 MET cc_start: 0.8664 (mtm) cc_final: 0.8177 (mtp) REVERT: A 602 GLU cc_start: 0.7775 (pt0) cc_final: 0.7454 (pt0) REVERT: A 615 MET cc_start: 0.9322 (mmm) cc_final: 0.9122 (mmm) REVERT: A 630 TYR cc_start: 0.8399 (m-80) cc_final: 0.8198 (m-80) REVERT: A 640 MET cc_start: 0.9460 (tpp) cc_final: 0.9189 (tpp) REVERT: A 686 ARG cc_start: 0.8388 (mmm-85) cc_final: 0.7813 (mmm-85) REVERT: B 18 ILE cc_start: 0.9510 (mm) cc_final: 0.9155 (pt) REVERT: B 20 LYS cc_start: 0.9483 (OUTLIER) cc_final: 0.8933 (mmmm) REVERT: B 41 ILE cc_start: 0.9551 (mm) cc_final: 0.9310 (mm) REVERT: B 65 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8022 (mp0) REVERT: B 99 LYS cc_start: 0.9520 (mmmm) cc_final: 0.9257 (mmmm) REVERT: B 106 LEU cc_start: 0.9146 (tp) cc_final: 0.8727 (tt) REVERT: B 109 ASN cc_start: 0.9091 (m-40) cc_final: 0.8383 (p0) REVERT: B 147 GLN cc_start: 0.8758 (mt0) cc_final: 0.8031 (mm110) REVERT: B 184 ARG cc_start: 0.9221 (mmm-85) cc_final: 0.8947 (tpp80) REVERT: B 257 ASP cc_start: 0.8784 (m-30) cc_final: 0.8446 (m-30) REVERT: B 286 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7333 (m-30) REVERT: B 288 PHE cc_start: 0.9377 (t80) cc_final: 0.9122 (t80) REVERT: B 290 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8472 (tm-30) REVERT: B 312 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8594 (pm20) REVERT: B 317 MET cc_start: 0.8510 (ptp) cc_final: 0.8041 (pmm) REVERT: B 321 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8330 (tm-30) REVERT: B 322 MET cc_start: 0.9283 (mmm) cc_final: 0.8928 (mmm) REVERT: B 348 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8148 (tmm) REVERT: B 362 ASP cc_start: 0.8556 (m-30) cc_final: 0.7382 (m-30) REVERT: B 374 SER cc_start: 0.8896 (t) cc_final: 0.8518 (t) REVERT: B 408 SER cc_start: 0.9374 (OUTLIER) cc_final: 0.9169 (p) REVERT: B 447 ASN cc_start: 0.8479 (m-40) cc_final: 0.7866 (t0) REVERT: B 471 TYR cc_start: 0.9421 (t80) cc_final: 0.9187 (t80) REVERT: B 477 ILE cc_start: 0.9283 (mp) cc_final: 0.9035 (pt) REVERT: B 492 PHE cc_start: 0.9486 (m-80) cc_final: 0.9030 (m-10) REVERT: B 493 MET cc_start: 0.9698 (tmm) cc_final: 0.9089 (tmm) REVERT: B 515 ASP cc_start: 0.9144 (m-30) cc_final: 0.8770 (m-30) REVERT: B 610 LYS cc_start: 0.8768 (mmmt) cc_final: 0.8499 (mmmt) REVERT: B 612 TYR cc_start: 0.8735 (m-80) cc_final: 0.8215 (m-80) REVERT: B 640 MET cc_start: 0.9319 (tpp) cc_final: 0.9054 (tpp) REVERT: B 664 THR cc_start: 0.9338 (p) cc_final: 0.9027 (p) REVERT: B 668 ASN cc_start: 0.9239 (m-40) cc_final: 0.8858 (m110) REVERT: B 677 ARG cc_start: 0.9292 (mmm-85) cc_final: 0.9089 (mmm-85) REVERT: C 41 LEU cc_start: 0.8474 (mm) cc_final: 0.8241 (mm) REVERT: C 47 LEU cc_start: 0.8054 (mt) cc_final: 0.7626 (tp) REVERT: C 55 TYR cc_start: 0.8201 (t80) cc_final: 0.7439 (t80) REVERT: C 96 MET cc_start: 0.8797 (mmt) cc_final: 0.8460 (mmm) REVERT: C 130 TYR cc_start: 0.9432 (m-10) cc_final: 0.9216 (m-10) REVERT: C 164 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8794 (tp30) REVERT: C 168 PHE cc_start: 0.8870 (m-80) cc_final: 0.8554 (m-80) REVERT: C 178 PHE cc_start: 0.8985 (m-80) cc_final: 0.7716 (m-10) REVERT: C 185 MET cc_start: 0.8378 (pmm) cc_final: 0.7138 (pmm) REVERT: C 186 GLN cc_start: 0.9445 (mm110) cc_final: 0.8968 (mp10) REVERT: C 259 PHE cc_start: 0.8954 (t80) cc_final: 0.8687 (t80) REVERT: C 270 ASN cc_start: 0.7867 (m110) cc_final: 0.7497 (m110) REVERT: C 320 PHE cc_start: 0.8853 (m-80) cc_final: 0.8644 (m-10) REVERT: D 21 PHE cc_start: 0.9414 (m-80) cc_final: 0.9199 (m-80) REVERT: D 46 TYR cc_start: 0.9206 (m-80) cc_final: 0.8872 (m-80) REVERT: D 178 PHE cc_start: 0.9031 (m-10) cc_final: 0.8261 (m-80) REVERT: D 186 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8677 (mp10) REVERT: D 200 ILE cc_start: 0.8018 (tt) cc_final: 0.7528 (tt) REVERT: D 207 LEU cc_start: 0.9229 (mp) cc_final: 0.8966 (mp) REVERT: D 212 ILE cc_start: 0.9060 (mt) cc_final: 0.8665 (mt) REVERT: D 227 PHE cc_start: 0.8389 (t80) cc_final: 0.8119 (m-80) REVERT: D 247 TYR cc_start: 0.8682 (m-10) cc_final: 0.8476 (m-10) outliers start: 63 outliers final: 29 residues processed: 812 average time/residue: 0.1121 time to fit residues: 137.3284 Evaluate side-chains 740 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 703 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 281 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 10.0000 chunk 131 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 159 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 158 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 19 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 HIS B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN B 410 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.118846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.082989 restraints weight = 36761.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.086356 restraints weight = 17306.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.088601 restraints weight = 10294.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.090088 restraints weight = 7112.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.090994 restraints weight = 5456.864| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16386 Z= 0.254 Angle : 0.712 14.122 22134 Z= 0.374 Chirality : 0.046 0.234 2360 Planarity : 0.004 0.048 2818 Dihedral : 9.536 132.842 2295 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 5.13 % Allowed : 25.35 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.19), residues: 1932 helix: 1.25 (0.15), residues: 1137 sheet: 0.03 (0.42), residues: 136 loop : 0.33 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 243 TYR 0.030 0.002 TYR A 612 PHE 0.033 0.002 PHE D 172 TRP 0.024 0.003 TRP D 30 HIS 0.009 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.25 (16386) covalent geometry : angle 0.71202 / 0.37 (22134) hydrogen bonds : bond 0.04481 / 2.84 ( 871) hydrogen bonds : angle 5.15348 / 3.66 ( 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 821 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 733 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8653 (mm-30) cc_final: 0.7984 (mp0) REVERT: A 82 LYS cc_start: 0.9657 (mmmm) cc_final: 0.9347 (mmmm) REVERT: A 99 LYS cc_start: 0.9450 (mmtm) cc_final: 0.9244 (mmtm) REVERT: A 144 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8827 (mtm) REVERT: A 147 GLN cc_start: 0.9198 (mt0) cc_final: 0.8094 (mt0) REVERT: A 181 ASP cc_start: 0.8797 (m-30) cc_final: 0.8437 (m-30) REVERT: A 187 ASP cc_start: 0.9032 (t70) cc_final: 0.8707 (t70) REVERT: A 214 LYS cc_start: 0.8720 (tppt) cc_final: 0.8252 (mmtt) REVERT: A 218 ASN cc_start: 0.9253 (t0) cc_final: 0.8884 (t0) REVERT: A 221 LYS cc_start: 0.8969 (mmtp) cc_final: 0.8701 (mttp) REVERT: A 257 ASP cc_start: 0.9420 (m-30) cc_final: 0.8912 (m-30) REVERT: A 261 PHE cc_start: 0.9358 (t80) cc_final: 0.9100 (t80) REVERT: A 270 ASP cc_start: 0.9085 (p0) cc_final: 0.8780 (p0) REVERT: A 321 GLU cc_start: 0.8760 (tp30) cc_final: 0.8372 (tp30) REVERT: A 359 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8259 (ttp) REVERT: A 370 ASN cc_start: 0.9234 (m-40) cc_final: 0.8915 (m-40) REVERT: A 384 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.7349 (pm20) REVERT: A 415 ASN cc_start: 0.9261 (t0) cc_final: 0.8971 (t0) REVERT: A 420 MET cc_start: 0.9432 (mmm) cc_final: 0.9153 (mmm) REVERT: A 466 MET cc_start: 0.9247 (ptt) cc_final: 0.8960 (ptt) REVERT: A 493 MET cc_start: 0.9058 (tmm) cc_final: 0.8621 (tmm) REVERT: A 505 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8776 (mt-10) REVERT: A 599 GLU cc_start: 0.8352 (mp0) cc_final: 0.8137 (mp0) REVERT: A 604 ARG cc_start: 0.8864 (mmp80) cc_final: 0.8423 (mmt-90) REVERT: A 632 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8044 (mtp) REVERT: A 634 MET cc_start: 0.8985 (mmm) cc_final: 0.8673 (mmt) REVERT: A 640 MET cc_start: 0.9596 (tpp) cc_final: 0.9001 (tpp) REVERT: A 659 LYS cc_start: 0.8936 (mmmt) cc_final: 0.8444 (mmmt) REVERT: B 27 ASP cc_start: 0.9037 (p0) cc_final: 0.8621 (p0) REVERT: B 65 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8018 (mp0) REVERT: B 89 PHE cc_start: 0.9019 (t80) cc_final: 0.8807 (t80) REVERT: B 99 LYS cc_start: 0.9594 (mmmm) cc_final: 0.9350 (mmmm) REVERT: B 106 LEU cc_start: 0.9225 (tp) cc_final: 0.8922 (tt) REVERT: B 109 ASN cc_start: 0.9134 (m-40) cc_final: 0.8613 (p0) REVERT: B 184 ARG cc_start: 0.9260 (mmm-85) cc_final: 0.8975 (tpp80) REVERT: B 202 ASN cc_start: 0.9333 (t0) cc_final: 0.8377 (t0) REVERT: B 286 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.7519 (m-30) REVERT: B 290 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8509 (tm-30) REVERT: B 312 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8668 (pm20) REVERT: B 316 GLU cc_start: 0.8624 (tm-30) cc_final: 0.7787 (tm-30) REVERT: B 317 MET cc_start: 0.8776 (ptp) cc_final: 0.7824 (pmm) REVERT: B 322 MET cc_start: 0.9305 (mmm) cc_final: 0.9078 (mmm) REVERT: B 362 ASP cc_start: 0.8686 (m-30) cc_final: 0.7465 (m-30) REVERT: B 374 SER cc_start: 0.9152 (t) cc_final: 0.8782 (t) REVERT: B 393 SER cc_start: 0.9430 (m) cc_final: 0.9118 (t) REVERT: B 399 GLU cc_start: 0.8401 (mp0) cc_final: 0.8122 (mp0) REVERT: B 403 ILE cc_start: 0.9500 (mm) cc_final: 0.9269 (tp) REVERT: B 434 ASP cc_start: 0.9033 (m-30) cc_final: 0.8774 (m-30) REVERT: B 447 ASN cc_start: 0.8621 (m-40) cc_final: 0.8076 (t0) REVERT: B 467 ASN cc_start: 0.9468 (t0) cc_final: 0.8931 (t0) REVERT: B 471 TYR cc_start: 0.9448 (t80) cc_final: 0.9207 (t80) REVERT: B 477 ILE cc_start: 0.9356 (mp) cc_final: 0.9132 (pt) REVERT: B 493 MET cc_start: 0.9724 (tmm) cc_final: 0.8930 (tmm) REVERT: B 515 ASP cc_start: 0.9105 (m-30) cc_final: 0.8839 (m-30) REVERT: B 550 MET cc_start: 0.8340 (mtm) cc_final: 0.8018 (ttm) REVERT: B 602 GLU cc_start: 0.8672 (tt0) cc_final: 0.8437 (tt0) REVERT: B 610 LYS cc_start: 0.8714 (mmmt) cc_final: 0.8410 (mmmt) REVERT: B 612 TYR cc_start: 0.8750 (m-80) cc_final: 0.8099 (m-80) REVERT: B 640 MET cc_start: 0.9263 (tpp) cc_final: 0.8929 (tpp) REVERT: C 19 GLN cc_start: 0.7809 (mp10) cc_final: 0.7359 (pm20) REVERT: C 55 TYR cc_start: 0.8372 (t80) cc_final: 0.7981 (t80) REVERT: C 80 HIS cc_start: 0.8564 (m90) cc_final: 0.8073 (m90) REVERT: C 86 ARG cc_start: 0.6716 (mmt-90) cc_final: 0.6512 (mmt180) REVERT: C 131 LEU cc_start: 0.9491 (mt) cc_final: 0.9141 (mt) REVERT: C 164 GLU cc_start: 0.9407 (mm-30) cc_final: 0.8615 (tp30) REVERT: C 168 PHE cc_start: 0.9334 (m-80) cc_final: 0.8514 (m-80) REVERT: C 169 TYR cc_start: 0.8506 (m-80) cc_final: 0.8250 (m-80) REVERT: C 178 PHE cc_start: 0.9296 (m-80) cc_final: 0.8345 (m-80) REVERT: C 185 MET cc_start: 0.8446 (pmm) cc_final: 0.7449 (pmm) REVERT: C 186 GLN cc_start: 0.9391 (mm110) cc_final: 0.8928 (mp10) REVERT: C 216 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.6644 (mp10) REVERT: C 223 GLU cc_start: 0.8970 (tm-30) cc_final: 0.7764 (pt0) REVERT: C 259 PHE cc_start: 0.8866 (t80) cc_final: 0.8441 (t80) REVERT: C 268 LEU cc_start: 0.9076 (tp) cc_final: 0.8516 (pp) REVERT: C 270 ASN cc_start: 0.8112 (m110) cc_final: 0.7839 (m110) REVERT: D 28 GLN cc_start: 0.8522 (mt0) cc_final: 0.8008 (tm-30) REVERT: D 30 TRP cc_start: 0.8932 (p-90) cc_final: 0.8665 (p-90) REVERT: D 46 TYR cc_start: 0.9257 (m-80) cc_final: 0.8837 (m-80) REVERT: D 172 PHE cc_start: 0.8744 (m-80) cc_final: 0.8453 (m-80) REVERT: D 174 TYR cc_start: 0.8687 (t80) cc_final: 0.8468 (t80) REVERT: D 186 GLN cc_start: 0.9235 (mm-40) cc_final: 0.8836 (mp10) REVERT: D 196 ARG cc_start: 0.9181 (ttp-110) cc_final: 0.8527 (mtm110) REVERT: D 212 ILE cc_start: 0.9368 (mt) cc_final: 0.9090 (mm) outliers start: 88 outliers final: 61 residues processed: 760 average time/residue: 0.1228 time to fit residues: 141.6060 Evaluate side-chains 752 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 684 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 281 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 0.6980 chunk 157 optimal weight: 8.9990 chunk 168 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 185 optimal weight: 10.0000 chunk 191 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 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 = 0.3593 r_free = 0.3593 target = 0.122213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.085803 restraints weight = 36503.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.089253 restraints weight = 17055.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.091540 restraints weight = 10145.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.093008 restraints weight = 6994.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.093948 restraints weight = 5325.611| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 10 (19 function evaluations) r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.5981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16386 Z= 0.157 Angle : 0.696 14.685 22134 Z= 0.354 Chirality : 0.045 0.255 2360 Planarity : 0.004 0.050 2818 Dihedral : 9.164 131.469 2295 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.67 % Allowed : 28.09 % Favored : 68.24 % 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: 1.13 (0.19), residues: 1932 helix: 1.20 (0.15), residues: 1140 sheet: 0.89 (0.50), residues: 104 loop : 0.14 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 225 TYR 0.019 0.001 TYR A 612 PHE 0.031 0.002 PHE D 172 TRP 0.017 0.002 TRP D 44 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (16386) covalent geometry : angle 0.69553 / 0.35 (22134) hydrogen bonds : bond 0.04165 / 2.63 ( 871) hydrogen bonds : angle 5.05703 / 3.61 ( 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 799 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 736 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.8674 (mmm) cc_final: 0.8090 (mmm) REVERT: A 64 TYR cc_start: 0.9097 (m-10) cc_final: 0.8467 (m-10) REVERT: A 65 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8018 (mp0) REVERT: A 66 GLU cc_start: 0.8481 (tp30) cc_final: 0.8178 (tp30) REVERT: A 82 LYS cc_start: 0.9650 (mmmm) cc_final: 0.9352 (mmmm) REVERT: A 144 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8667 (mtm) REVERT: A 147 GLN cc_start: 0.9180 (mt0) cc_final: 0.8117 (mt0) REVERT: A 181 ASP cc_start: 0.8788 (m-30) cc_final: 0.8529 (m-30) REVERT: A 187 ASP cc_start: 0.9076 (t70) cc_final: 0.8732 (t70) REVERT: A 202 ASN cc_start: 0.9500 (t0) cc_final: 0.9170 (t0) REVERT: A 218 ASN cc_start: 0.9233 (t0) cc_final: 0.8898 (t0) REVERT: A 221 LYS cc_start: 0.8969 (mmtp) cc_final: 0.8735 (mttp) REVERT: A 257 ASP cc_start: 0.9385 (m-30) cc_final: 0.9095 (m-30) REVERT: A 286 ASP cc_start: 0.8509 (m-30) cc_final: 0.8176 (m-30) REVERT: A 296 LYS cc_start: 0.8154 (mmmt) cc_final: 0.7910 (mtmm) REVERT: A 321 GLU cc_start: 0.8767 (tp30) cc_final: 0.8374 (tp30) REVERT: A 341 LYS cc_start: 0.9186 (mmtt) cc_final: 0.8942 (mmtt) REVERT: A 362 ASP cc_start: 0.8531 (m-30) cc_final: 0.7984 (m-30) REVERT: A 370 ASN cc_start: 0.9201 (m-40) cc_final: 0.8885 (m-40) REVERT: A 384 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.7439 (pm20) REVERT: A 415 ASN cc_start: 0.9236 (t0) cc_final: 0.8945 (t0) REVERT: A 420 MET cc_start: 0.9425 (mmm) cc_final: 0.9155 (mmm) REVERT: A 435 SER cc_start: 0.9531 (OUTLIER) cc_final: 0.9146 (t) REVERT: A 447 ASN cc_start: 0.8776 (m-40) cc_final: 0.8277 (t0) REVERT: A 466 MET cc_start: 0.9210 (ptt) cc_final: 0.9001 (ptt) REVERT: A 493 MET cc_start: 0.9085 (tmm) cc_final: 0.8510 (tmm) REVERT: A 505 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8590 (mt-10) REVERT: A 550 MET cc_start: 0.7738 (mtm) cc_final: 0.7256 (mtm) REVERT: A 570 MET cc_start: 0.8821 (mtp) cc_final: 0.8482 (mtp) REVERT: A 588 GLN cc_start: 0.9089 (mm-40) cc_final: 0.8730 (mm-40) REVERT: A 612 TYR cc_start: 0.8997 (m-80) cc_final: 0.8762 (m-80) REVERT: A 632 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8076 (mtp) REVERT: A 634 MET cc_start: 0.8974 (mmm) cc_final: 0.8705 (mmt) REVERT: A 640 MET cc_start: 0.9600 (tpp) cc_final: 0.8962 (tpp) REVERT: A 686 ARG cc_start: 0.8714 (mmm-85) cc_final: 0.8313 (ttm-80) REVERT: B 8 LYS cc_start: 0.9061 (tppt) cc_final: 0.8769 (tppt) REVERT: B 15 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8619 (tm-30) REVERT: B 17 MET cc_start: 0.8652 (mmm) cc_final: 0.8206 (mmm) REVERT: B 65 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8012 (mp0) REVERT: B 99 LYS cc_start: 0.9551 (mmmm) cc_final: 0.9290 (mmmm) REVERT: B 109 ASN cc_start: 0.9245 (m-40) cc_final: 0.8747 (p0) REVERT: B 174 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8395 (mm-30) REVERT: B 202 ASN cc_start: 0.9456 (t0) cc_final: 0.9013 (t0) REVERT: B 257 ASP cc_start: 0.8933 (m-30) cc_final: 0.8431 (m-30) REVERT: B 286 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.7600 (m-30) REVERT: B 290 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8456 (tm-30) REVERT: B 312 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8745 (pm20) REVERT: B 317 MET cc_start: 0.8634 (ptp) cc_final: 0.8257 (pmm) REVERT: B 344 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8745 (mt-10) REVERT: B 362 ASP cc_start: 0.8685 (m-30) cc_final: 0.7454 (m-30) REVERT: B 374 SER cc_start: 0.9184 (t) cc_final: 0.8815 (t) REVERT: B 393 SER cc_start: 0.9402 (m) cc_final: 0.9116 (t) REVERT: B 403 ILE cc_start: 0.9525 (mm) cc_final: 0.9297 (tp) REVERT: B 415 ASN cc_start: 0.9262 (t0) cc_final: 0.9007 (t0) REVERT: B 434 ASP cc_start: 0.9040 (m-30) cc_final: 0.8809 (m-30) REVERT: B 447 ASN cc_start: 0.8582 (m-40) cc_final: 0.8084 (t0) REVERT: B 467 ASN cc_start: 0.9510 (t0) cc_final: 0.9246 (m-40) REVERT: B 471 TYR cc_start: 0.9310 (t80) cc_final: 0.8984 (t80) REVERT: B 483 GLU cc_start: 0.9463 (mp0) cc_final: 0.9258 (mp0) REVERT: B 493 MET cc_start: 0.9685 (tmm) cc_final: 0.8873 (tmm) REVERT: B 515 ASP cc_start: 0.9043 (m-30) cc_final: 0.8769 (m-30) REVERT: B 602 GLU cc_start: 0.8648 (tt0) cc_final: 0.8366 (tt0) REVERT: B 610 LYS cc_start: 0.8842 (mmmt) cc_final: 0.8569 (mmmt) REVERT: B 612 TYR cc_start: 0.8681 (m-80) cc_final: 0.8193 (m-80) REVERT: B 628 GLU cc_start: 0.8482 (mm-30) cc_final: 0.7984 (mm-30) REVERT: C 19 GLN cc_start: 0.7686 (mp10) cc_final: 0.7248 (pm20) REVERT: C 55 TYR cc_start: 0.8278 (t80) cc_final: 0.7441 (t80) REVERT: C 80 HIS cc_start: 0.8725 (m90) cc_final: 0.8184 (m90) REVERT: C 96 MET cc_start: 0.8801 (mmt) cc_final: 0.8513 (mmm) REVERT: C 163 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9053 (tt) REVERT: C 164 GLU cc_start: 0.9475 (mm-30) cc_final: 0.8669 (tp30) REVERT: C 168 PHE cc_start: 0.9247 (m-80) cc_final: 0.8637 (m-80) REVERT: C 178 PHE cc_start: 0.9354 (m-80) cc_final: 0.8390 (m-10) REVERT: C 185 MET cc_start: 0.8565 (pmm) cc_final: 0.7554 (pmm) REVERT: C 186 GLN cc_start: 0.9309 (mm110) cc_final: 0.8826 (mp10) REVERT: C 242 TYR cc_start: 0.9437 (t80) cc_final: 0.9021 (t80) REVERT: C 259 PHE cc_start: 0.8864 (t80) cc_final: 0.8391 (t80) REVERT: C 268 LEU cc_start: 0.9083 (tp) cc_final: 0.8823 (tp) REVERT: C 270 ASN cc_start: 0.8190 (m110) cc_final: 0.7895 (m110) REVERT: D 30 TRP cc_start: 0.8648 (p-90) cc_final: 0.8133 (p-90) REVERT: D 34 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8415 (mm-30) REVERT: D 46 TYR cc_start: 0.9250 (m-80) cc_final: 0.8886 (m-80) REVERT: D 178 PHE cc_start: 0.9134 (m-10) cc_final: 0.8383 (m-80) REVERT: D 186 GLN cc_start: 0.9236 (mm-40) cc_final: 0.8823 (mp10) REVERT: D 210 GLN cc_start: 0.9410 (tm-30) cc_final: 0.9189 (pt0) REVERT: D 246 LEU cc_start: 0.8043 (tp) cc_final: 0.7795 (mt) REVERT: D 247 TYR cc_start: 0.8795 (m-10) cc_final: 0.8431 (m-10) outliers start: 63 outliers final: 38 residues processed: 758 average time/residue: 0.1227 time to fit residues: 141.9003 Evaluate side-chains 729 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 684 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 168 optimal weight: 6.9990 chunk 157 optimal weight: 10.0000 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN C 84 HIS C 98 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.121589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.087251 restraints weight = 36193.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.090661 restraints weight = 16891.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.092901 restraints weight = 9980.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.094398 restraints weight = 6844.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.095389 restraints weight = 5178.258| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (13 function evaluations) r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.6328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16386 Z= 0.160 Angle : 0.714 16.214 22134 Z= 0.358 Chirality : 0.046 0.393 2360 Planarity : 0.004 0.051 2818 Dihedral : 8.972 132.113 2295 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.14 % Allowed : 28.79 % Favored : 67.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.19), residues: 1932 helix: 1.18 (0.15), residues: 1134 sheet: -0.23 (0.41), residues: 148 loop : 0.25 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 86 TYR 0.023 0.001 TYR C 242 PHE 0.029 0.002 PHE A 261 TRP 0.017 0.002 TRP C 44 HIS 0.010 0.001 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (16386) covalent geometry : angle 0.71362 / 0.36 (22134) hydrogen bonds : bond 0.04071 / 2.59 ( 871) hydrogen bonds : angle 5.03940 / 3.58 ( 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 775 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 704 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.9207 (m-10) cc_final: 0.8654 (m-10) REVERT: A 65 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8064 (mp0) REVERT: A 66 GLU cc_start: 0.8482 (tp30) cc_final: 0.8176 (tp30) REVERT: A 82 LYS cc_start: 0.9651 (mmmm) cc_final: 0.9350 (mmmm) REVERT: A 144 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8652 (mtm) REVERT: A 147 GLN cc_start: 0.9221 (mt0) cc_final: 0.8977 (mt0) REVERT: A 163 ARG cc_start: 0.8379 (mmm-85) cc_final: 0.8151 (mmm160) REVERT: A 181 ASP cc_start: 0.8794 (m-30) cc_final: 0.8514 (m-30) REVERT: A 187 ASP cc_start: 0.9021 (t70) cc_final: 0.8642 (t70) REVERT: A 202 ASN cc_start: 0.9516 (t0) cc_final: 0.9166 (t0) REVERT: A 218 ASN cc_start: 0.9286 (t0) cc_final: 0.8947 (t0) REVERT: A 221 LYS cc_start: 0.8959 (mmtp) cc_final: 0.8734 (mttp) REVERT: A 252 ASN cc_start: 0.9152 (t0) cc_final: 0.8937 (t0) REVERT: A 257 ASP cc_start: 0.9332 (m-30) cc_final: 0.9126 (m-30) REVERT: A 286 ASP cc_start: 0.8472 (m-30) cc_final: 0.8163 (m-30) REVERT: A 321 GLU cc_start: 0.8778 (tp30) cc_final: 0.8299 (tp30) REVERT: A 335 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7550 (mm-30) REVERT: A 341 LYS cc_start: 0.9171 (mmtt) cc_final: 0.8912 (mmtt) REVERT: A 359 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8234 (ttp) REVERT: A 362 ASP cc_start: 0.8584 (m-30) cc_final: 0.7984 (m-30) REVERT: A 370 ASN cc_start: 0.9179 (m-40) cc_final: 0.8900 (m110) REVERT: A 384 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.7659 (pm20) REVERT: A 389 SER cc_start: 0.9437 (OUTLIER) cc_final: 0.9128 (p) REVERT: A 415 ASN cc_start: 0.9243 (t0) cc_final: 0.8969 (t0) REVERT: A 420 MET cc_start: 0.9462 (mmm) cc_final: 0.9158 (mmm) REVERT: A 435 SER cc_start: 0.9520 (OUTLIER) cc_final: 0.9145 (t) REVERT: A 447 ASN cc_start: 0.8750 (m-40) cc_final: 0.8405 (m-40) REVERT: A 466 MET cc_start: 0.9246 (ptt) cc_final: 0.8966 (ptt) REVERT: A 493 MET cc_start: 0.9052 (tmm) cc_final: 0.8287 (tmm) REVERT: A 505 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8727 (mt-10) REVERT: A 512 GLU cc_start: 0.8598 (pt0) cc_final: 0.8135 (pt0) REVERT: A 632 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8005 (mtp) REVERT: A 634 MET cc_start: 0.8941 (mmm) cc_final: 0.8728 (mmt) REVERT: A 640 MET cc_start: 0.9634 (tpp) cc_final: 0.8679 (tpp) REVERT: A 686 ARG cc_start: 0.8734 (mmm-85) cc_final: 0.8303 (ttm-80) REVERT: B 8 LYS cc_start: 0.9073 (tppt) cc_final: 0.8808 (tppt) REVERT: B 17 MET cc_start: 0.8715 (mmm) cc_final: 0.8273 (mmm) REVERT: B 31 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8198 (mt-10) REVERT: B 65 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8560 (mm-30) REVERT: B 99 LYS cc_start: 0.9540 (mmmm) cc_final: 0.9260 (mmmm) REVERT: B 109 ASN cc_start: 0.9280 (m-40) cc_final: 0.8596 (p0) REVERT: B 147 GLN cc_start: 0.9096 (mt0) cc_final: 0.8871 (mm-40) REVERT: B 174 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8329 (mm-30) REVERT: B 202 ASN cc_start: 0.9453 (t0) cc_final: 0.8902 (t0) REVERT: B 257 ASP cc_start: 0.8887 (m-30) cc_final: 0.8412 (m-30) REVERT: B 286 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.7649 (m-30) REVERT: B 290 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8385 (tm-30) REVERT: B 312 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8711 (pm20) REVERT: B 317 MET cc_start: 0.8604 (ptp) cc_final: 0.8217 (pmm) REVERT: B 362 ASP cc_start: 0.8672 (m-30) cc_final: 0.7466 (m-30) REVERT: B 374 SER cc_start: 0.9219 (t) cc_final: 0.8959 (t) REVERT: B 393 SER cc_start: 0.9339 (m) cc_final: 0.9113 (p) REVERT: B 394 TYR cc_start: 0.9069 (m-80) cc_final: 0.8753 (m-80) REVERT: B 415 ASN cc_start: 0.9279 (t0) cc_final: 0.8954 (t0) REVERT: B 434 ASP cc_start: 0.9093 (m-30) cc_final: 0.8847 (m-30) REVERT: B 447 ASN cc_start: 0.8549 (m-40) cc_final: 0.8076 (t0) REVERT: B 467 ASN cc_start: 0.9490 (t0) cc_final: 0.9184 (m-40) REVERT: B 471 TYR cc_start: 0.9439 (t80) cc_final: 0.9111 (t80) REVERT: B 483 GLU cc_start: 0.9456 (mp0) cc_final: 0.9249 (mp0) REVERT: B 493 MET cc_start: 0.9698 (tmm) cc_final: 0.8879 (tmm) REVERT: B 515 ASP cc_start: 0.9065 (m-30) cc_final: 0.8805 (m-30) REVERT: B 610 LYS cc_start: 0.8849 (mmmt) cc_final: 0.8543 (mmmt) REVERT: B 612 TYR cc_start: 0.8632 (m-80) cc_final: 0.8179 (m-80) REVERT: B 627 LYS cc_start: 0.8910 (ttpp) cc_final: 0.8443 (tttp) REVERT: B 628 GLU cc_start: 0.8549 (mm-30) cc_final: 0.7814 (mm-30) REVERT: C 19 GLN cc_start: 0.7683 (mp10) cc_final: 0.7295 (pm20) REVERT: C 55 TYR cc_start: 0.8247 (t80) cc_final: 0.7718 (t80) REVERT: C 69 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8818 (tm-30) REVERT: C 80 HIS cc_start: 0.8755 (m90) cc_final: 0.8387 (m90) REVERT: C 96 MET cc_start: 0.8695 (mmt) cc_final: 0.8404 (mmm) REVERT: C 98 ASN cc_start: 0.7934 (m-40) cc_final: 0.7711 (m-40) REVERT: C 130 TYR cc_start: 0.9237 (m-10) cc_final: 0.9020 (m-10) REVERT: C 134 LYS cc_start: 0.9661 (pttt) cc_final: 0.9242 (pttt) REVERT: C 164 GLU cc_start: 0.9448 (mm-30) cc_final: 0.9196 (tp30) REVERT: C 168 PHE cc_start: 0.9269 (m-80) cc_final: 0.8834 (m-80) REVERT: C 178 PHE cc_start: 0.9308 (m-80) cc_final: 0.8504 (m-10) REVERT: C 185 MET cc_start: 0.8595 (pmm) cc_final: 0.7751 (pmm) REVERT: C 186 GLN cc_start: 0.9279 (mm110) cc_final: 0.8837 (mp10) REVERT: C 189 GLU cc_start: 0.8640 (tp30) cc_final: 0.8374 (mm-30) REVERT: C 242 TYR cc_start: 0.9326 (t80) cc_final: 0.8885 (t80) REVERT: C 259 PHE cc_start: 0.8826 (t80) cc_final: 0.8270 (t80) REVERT: C 268 LEU cc_start: 0.8999 (tp) cc_final: 0.8757 (tp) REVERT: C 269 MET cc_start: 0.9214 (ppp) cc_final: 0.9007 (ppp) REVERT: C 270 ASN cc_start: 0.8286 (m110) cc_final: 0.7902 (m110) REVERT: C 313 GLU cc_start: 0.9007 (tt0) cc_final: 0.8758 (tt0) REVERT: D 21 PHE cc_start: 0.9506 (m-80) cc_final: 0.9198 (m-80) REVERT: D 28 GLN cc_start: 0.8588 (mt0) cc_final: 0.8323 (mt0) REVERT: D 30 TRP cc_start: 0.8676 (p-90) cc_final: 0.7961 (p-90) REVERT: D 34 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8389 (mm-30) REVERT: D 46 TYR cc_start: 0.9180 (m-80) cc_final: 0.8882 (m-10) REVERT: D 96 MET cc_start: 0.8475 (mmt) cc_final: 0.8012 (mmm) REVERT: D 136 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8288 (mt0) REVERT: D 178 PHE cc_start: 0.9250 (m-10) cc_final: 0.8522 (m-80) REVERT: D 186 GLN cc_start: 0.9268 (mm-40) cc_final: 0.8863 (mp10) REVERT: D 207 LEU cc_start: 0.9304 (mm) cc_final: 0.8899 (mp) REVERT: D 210 GLN cc_start: 0.9415 (tm-30) cc_final: 0.9169 (pt0) REVERT: D 247 TYR cc_start: 0.8759 (m-10) cc_final: 0.8406 (m-10) REVERT: D 252 LEU cc_start: 0.6930 (mt) cc_final: 0.6548 (mp) REVERT: D 269 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8250 (ppp) REVERT: D 287 LEU cc_start: 0.6987 (mt) cc_final: 0.6725 (mt) outliers start: 71 outliers final: 41 residues processed: 732 average time/residue: 0.1160 time to fit residues: 129.4563 Evaluate side-chains 714 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 662 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 52 optimal weight: 0.1980 chunk 28 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 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 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN ** D 216 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 = 0.3533 r_free = 0.3533 target = 0.118004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.083671 restraints weight = 36615.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.086890 restraints weight = 17597.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.089102 restraints weight = 10536.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.090565 restraints weight = 7237.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.091484 restraints weight = 5524.556| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.6750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16386 Z= 0.217 Angle : 0.733 15.942 22134 Z= 0.373 Chirality : 0.046 0.201 2360 Planarity : 0.004 0.052 2818 Dihedral : 8.981 134.959 2294 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.72 % Allowed : 30.42 % Favored : 64.86 % 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: 1.07 (0.15), residues: 1143 sheet: -0.54 (0.40), residues: 148 loop : 0.10 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 196 TYR 0.017 0.002 TYR D 130 PHE 0.032 0.002 PHE A 261 TRP 0.016 0.002 TRP C 44 HIS 0.008 0.001 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.22 (16386) covalent geometry : angle 0.73312 / 0.37 (22134) hydrogen bonds : bond 0.04129 / 2.61 ( 871) hydrogen bonds : angle 5.07948 / 3.62 ( 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 759 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 678 time to evaluate : 0.628 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: A 64 TYR cc_start: 0.9253 (m-10) cc_final: 0.8606 (m-10) REVERT: A 65 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8128 (mp0) REVERT: A 66 GLU cc_start: 0.8478 (tp30) cc_final: 0.8192 (tp30) REVERT: A 82 LYS cc_start: 0.9665 (mmmm) cc_final: 0.9364 (mmmm) REVERT: A 144 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8719 (mtm) REVERT: A 150 GLN cc_start: 0.9106 (tp40) cc_final: 0.8139 (tm-30) REVERT: A 181 ASP cc_start: 0.8805 (m-30) cc_final: 0.8516 (m-30) REVERT: A 187 ASP cc_start: 0.9036 (OUTLIER) cc_final: 0.8652 (t70) REVERT: A 202 ASN cc_start: 0.9620 (t0) cc_final: 0.9337 (t0) REVERT: A 218 ASN cc_start: 0.9373 (t0) cc_final: 0.9117 (t0) REVERT: A 221 LYS cc_start: 0.9021 (mmtp) cc_final: 0.8699 (mttp) REVERT: A 321 GLU cc_start: 0.8880 (tp30) cc_final: 0.8492 (tp30) REVERT: A 322 MET cc_start: 0.9205 (mmp) cc_final: 0.8993 (mmm) REVERT: A 335 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7677 (mm-30) REVERT: A 341 LYS cc_start: 0.9201 (mmtt) cc_final: 0.8931 (mmtt) REVERT: A 359 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8280 (ttp) REVERT: A 384 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.7672 (pm20) REVERT: A 389 SER cc_start: 0.9472 (OUTLIER) cc_final: 0.9153 (p) REVERT: A 415 ASN cc_start: 0.9285 (t0) cc_final: 0.9038 (t0) REVERT: A 420 MET cc_start: 0.9438 (mmm) cc_final: 0.9172 (mmm) REVERT: A 453 ARG cc_start: 0.9228 (OUTLIER) cc_final: 0.9005 (ttp80) REVERT: A 466 MET cc_start: 0.9304 (ptt) cc_final: 0.8972 (ptt) REVERT: A 493 MET cc_start: 0.9001 (tmm) cc_final: 0.8226 (tmm) REVERT: A 505 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8493 (mt-10) REVERT: A 512 GLU cc_start: 0.8661 (pt0) cc_final: 0.8218 (pt0) REVERT: A 550 MET cc_start: 0.8435 (ptm) cc_final: 0.8209 (ptp) REVERT: A 583 SER cc_start: 0.9341 (m) cc_final: 0.8767 (t) REVERT: A 586 TYR cc_start: 0.8960 (m-80) cc_final: 0.8756 (m-10) REVERT: A 599 GLU cc_start: 0.8478 (mp0) cc_final: 0.8259 (mp0) REVERT: A 604 ARG cc_start: 0.8666 (mmt-90) cc_final: 0.8419 (mmt-90) REVERT: A 632 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.7976 (mtp) REVERT: A 640 MET cc_start: 0.9565 (tpp) cc_final: 0.8713 (tpp) REVERT: B 8 LYS cc_start: 0.9101 (tppt) cc_final: 0.8862 (tppt) REVERT: B 17 MET cc_start: 0.8923 (mmm) cc_final: 0.8509 (mmm) REVERT: B 31 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8155 (mt-10) REVERT: B 65 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8452 (mm-30) REVERT: B 99 LYS cc_start: 0.9553 (mmmm) cc_final: 0.9328 (mmmm) REVERT: B 108 THR cc_start: 0.8710 (OUTLIER) cc_final: 0.8475 (p) REVERT: B 109 ASN cc_start: 0.9288 (m-40) cc_final: 0.8863 (p0) REVERT: B 112 LYS cc_start: 0.9067 (pttm) cc_final: 0.8824 (pttm) REVERT: B 174 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8242 (mm-30) REVERT: B 202 ASN cc_start: 0.9439 (t0) cc_final: 0.8923 (t0) REVERT: B 214 LYS cc_start: 0.8934 (mtmm) cc_final: 0.8220 (mmtt) REVERT: B 215 ASP cc_start: 0.8674 (m-30) cc_final: 0.8320 (p0) REVERT: B 257 ASP cc_start: 0.8873 (m-30) cc_final: 0.8382 (m-30) REVERT: B 263 ASP cc_start: 0.9152 (m-30) cc_final: 0.8794 (p0) REVERT: B 286 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.7776 (m-30) REVERT: B 290 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8341 (tm-30) REVERT: B 317 MET cc_start: 0.8669 (ptp) cc_final: 0.8253 (pmm) REVERT: B 362 ASP cc_start: 0.8712 (m-30) cc_final: 0.7385 (m-30) REVERT: B 370 ASN cc_start: 0.9575 (m110) cc_final: 0.9352 (m-40) REVERT: B 393 SER cc_start: 0.9290 (m) cc_final: 0.9067 (p) REVERT: B 394 TYR cc_start: 0.9274 (m-80) cc_final: 0.9040 (m-80) REVERT: B 415 ASN cc_start: 0.9250 (t0) cc_final: 0.8848 (t0) REVERT: B 434 ASP cc_start: 0.9100 (m-30) cc_final: 0.8879 (m-30) REVERT: B 447 ASN cc_start: 0.8590 (m-40) cc_final: 0.8360 (m-40) REVERT: B 467 ASN cc_start: 0.9496 (t0) cc_final: 0.9248 (m-40) REVERT: B 471 TYR cc_start: 0.9363 (t80) cc_final: 0.8768 (t80) REVERT: B 483 GLU cc_start: 0.9482 (mp0) cc_final: 0.9254 (mp0) REVERT: B 493 MET cc_start: 0.9710 (tmm) cc_final: 0.8877 (tmm) REVERT: B 515 ASP cc_start: 0.9076 (m-30) cc_final: 0.8840 (m-30) REVERT: B 546 LEU cc_start: 0.9668 (mt) cc_final: 0.9405 (mt) REVERT: B 588 GLN cc_start: 0.9600 (mm110) cc_final: 0.9355 (mm110) REVERT: B 610 LYS cc_start: 0.8927 (mmmt) cc_final: 0.8620 (mmmt) REVERT: B 612 TYR cc_start: 0.8614 (m-80) cc_final: 0.8191 (m-80) REVERT: B 628 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8328 (mm-30) REVERT: B 632 MET cc_start: 0.8927 (mtp) cc_final: 0.8389 (mpp) REVERT: C 19 GLN cc_start: 0.7659 (mp10) cc_final: 0.7276 (pm20) REVERT: C 29 PHE cc_start: 0.8120 (t80) cc_final: 0.7891 (t80) REVERT: C 55 TYR cc_start: 0.8233 (t80) cc_final: 0.7669 (t80) REVERT: C 68 GLU cc_start: 0.9424 (tm-30) cc_final: 0.9157 (tm-30) REVERT: C 69 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8773 (tm-30) REVERT: C 80 HIS cc_start: 0.8837 (m90) cc_final: 0.8510 (m90) REVERT: C 96 MET cc_start: 0.8682 (mmt) cc_final: 0.7981 (mmm) REVERT: C 134 LYS cc_start: 0.9652 (pttt) cc_final: 0.9177 (pttt) REVERT: C 164 GLU cc_start: 0.9395 (mm-30) cc_final: 0.9074 (tp30) REVERT: C 168 PHE cc_start: 0.9277 (m-80) cc_final: 0.8652 (m-80) REVERT: C 169 TYR cc_start: 0.8557 (m-80) cc_final: 0.8342 (m-80) REVERT: C 174 TYR cc_start: 0.9227 (OUTLIER) cc_final: 0.8658 (t80) REVERT: C 189 GLU cc_start: 0.8645 (tp30) cc_final: 0.7949 (mp0) REVERT: C 242 TYR cc_start: 0.9375 (t80) cc_final: 0.8916 (t80) REVERT: C 259 PHE cc_start: 0.8861 (t80) cc_final: 0.8323 (t80) REVERT: C 268 LEU cc_start: 0.8910 (tp) cc_final: 0.8641 (tp) REVERT: C 269 MET cc_start: 0.9154 (ppp) cc_final: 0.8945 (ppp) REVERT: C 270 ASN cc_start: 0.8425 (m110) cc_final: 0.8064 (m110) REVERT: C 313 GLU cc_start: 0.9052 (tt0) cc_final: 0.8749 (tt0) REVERT: D 21 PHE cc_start: 0.9423 (m-80) cc_final: 0.8955 (m-80) REVERT: D 25 ASN cc_start: 0.9272 (p0) cc_final: 0.8988 (p0) REVERT: D 46 TYR cc_start: 0.9134 (m-80) cc_final: 0.8838 (m-10) REVERT: D 96 MET cc_start: 0.8938 (mmt) cc_final: 0.8557 (mmm) REVERT: D 136 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8393 (mt0) REVERT: D 153 LEU cc_start: 0.9144 (tp) cc_final: 0.8780 (mt) REVERT: D 178 PHE cc_start: 0.9405 (m-10) cc_final: 0.8731 (m-80) REVERT: D 186 GLN cc_start: 0.9220 (mm-40) cc_final: 0.8754 (mp10) REVERT: D 207 LEU cc_start: 0.9284 (mm) cc_final: 0.8889 (mm) REVERT: D 210 GLN cc_start: 0.9404 (tm-30) cc_final: 0.9131 (pt0) REVERT: D 252 LEU cc_start: 0.6810 (mt) cc_final: 0.6406 (mp) REVERT: D 269 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8264 (ppp) outliers start: 81 outliers final: 59 residues processed: 704 average time/residue: 0.1196 time to fit residues: 128.4231 Evaluate side-chains 710 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 638 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 186 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 chunk 115 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 GLN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN D 249 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.123073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.088104 restraints weight = 35528.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.091404 restraints weight = 16672.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.093701 restraints weight = 10236.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.095183 restraints weight = 7019.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.096249 restraints weight = 5350.007| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.7025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16386 Z= 0.153 Angle : 0.744 16.266 22134 Z= 0.370 Chirality : 0.045 0.215 2360 Planarity : 0.004 0.052 2818 Dihedral : 8.786 134.414 2294 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.20 % Allowed : 32.46 % Favored : 63.34 % 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: 0.76 (0.19), residues: 1932 helix: 1.00 (0.15), residues: 1131 sheet: -0.54 (0.41), residues: 148 loop : 0.10 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 243 TYR 0.031 0.001 TYR A 612 PHE 0.034 0.002 PHE C 172 TRP 0.019 0.001 TRP C 44 HIS 0.009 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (16386) covalent geometry : angle 0.74356 / 0.37 (22134) hydrogen bonds : bond 0.04038 / 2.58 ( 871) hydrogen bonds : angle 5.05944 / 3.62 ( 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 750 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 678 time to evaluate : 0.691 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: A 64 TYR cc_start: 0.9225 (m-10) cc_final: 0.8808 (m-10) REVERT: A 65 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8171 (mp0) REVERT: A 66 GLU cc_start: 0.8467 (tp30) cc_final: 0.8157 (tp30) REVERT: A 82 LYS cc_start: 0.9656 (mmmm) cc_final: 0.9348 (mmmm) REVERT: A 99 LYS cc_start: 0.9338 (tppt) cc_final: 0.9063 (tppt) REVERT: A 149 TYR cc_start: 0.9316 (t80) cc_final: 0.8854 (t80) REVERT: A 181 ASP cc_start: 0.8825 (m-30) cc_final: 0.8518 (m-30) REVERT: A 187 ASP cc_start: 0.8970 (OUTLIER) cc_final: 0.8676 (t70) REVERT: A 202 ASN cc_start: 0.9573 (t0) cc_final: 0.9234 (t0) REVERT: A 218 ASN cc_start: 0.9319 (t0) cc_final: 0.9058 (t0) REVERT: A 221 LYS cc_start: 0.8950 (mmtp) cc_final: 0.8598 (mttt) REVERT: A 227 MET cc_start: 0.9129 (mtp) cc_final: 0.8917 (mtp) REVERT: A 228 LYS cc_start: 0.9460 (mmmm) cc_final: 0.8971 (mmtt) REVERT: A 286 ASP cc_start: 0.8489 (m-30) cc_final: 0.8062 (m-30) REVERT: A 314 MET cc_start: 0.8921 (ptm) cc_final: 0.8693 (ttp) REVERT: A 321 GLU cc_start: 0.8856 (tp30) cc_final: 0.8424 (tp30) REVERT: A 335 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7633 (mm-30) REVERT: A 341 LYS cc_start: 0.9172 (mmtt) cc_final: 0.8904 (mmtt) REVERT: A 350 ARG cc_start: 0.9249 (mtp85) cc_final: 0.8967 (mtp180) REVERT: A 359 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8186 (ttp) REVERT: A 362 ASP cc_start: 0.8574 (m-30) cc_final: 0.8203 (m-30) REVERT: A 370 ASN cc_start: 0.9279 (m-40) cc_final: 0.8908 (m110) REVERT: A 384 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8165 (pm20) REVERT: A 415 ASN cc_start: 0.9299 (t0) cc_final: 0.9094 (t0) REVERT: A 420 MET cc_start: 0.9334 (mmm) cc_final: 0.9111 (tpt) REVERT: A 435 SER cc_start: 0.9486 (OUTLIER) cc_final: 0.9222 (t) REVERT: A 453 ARG cc_start: 0.9218 (OUTLIER) cc_final: 0.8990 (ttp80) REVERT: A 466 MET cc_start: 0.9135 (ptt) cc_final: 0.8867 (ptt) REVERT: A 493 MET cc_start: 0.8967 (tmm) cc_final: 0.8215 (tmm) REVERT: A 505 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8687 (mt-10) REVERT: A 512 GLU cc_start: 0.8650 (pt0) cc_final: 0.8343 (pt0) REVERT: A 570 MET cc_start: 0.8936 (mtp) cc_final: 0.8673 (mtm) REVERT: A 583 SER cc_start: 0.9335 (m) cc_final: 0.8781 (t) REVERT: A 586 TYR cc_start: 0.8910 (m-80) cc_final: 0.8650 (m-10) REVERT: A 598 MET cc_start: 0.8602 (mtp) cc_final: 0.8311 (mmm) REVERT: A 599 GLU cc_start: 0.8537 (mp0) cc_final: 0.8291 (mp0) REVERT: A 604 ARG cc_start: 0.8690 (mmt-90) cc_final: 0.8485 (mmt-90) REVERT: A 632 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8063 (mtp) REVERT: A 640 MET cc_start: 0.9633 (tpp) cc_final: 0.8815 (tpp) REVERT: A 645 GLN cc_start: 0.8891 (tp40) cc_final: 0.8689 (tp40) REVERT: B 8 LYS cc_start: 0.9089 (tppt) cc_final: 0.8875 (tppt) REVERT: B 17 MET cc_start: 0.8893 (mmm) cc_final: 0.8592 (mmm) REVERT: B 28 LYS cc_start: 0.9272 (mmtt) cc_final: 0.8968 (mmmm) REVERT: B 31 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8076 (mt-10) REVERT: B 65 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8415 (mm-30) REVERT: B 99 LYS cc_start: 0.9526 (mmmm) cc_final: 0.9289 (mmmm) REVERT: B 172 LEU cc_start: 0.9183 (mt) cc_final: 0.8976 (mt) REVERT: B 202 ASN cc_start: 0.9427 (t0) cc_final: 0.9022 (t0) REVERT: B 218 ASN cc_start: 0.9539 (m110) cc_final: 0.9326 (m-40) REVERT: B 257 ASP cc_start: 0.8886 (m-30) cc_final: 0.8388 (m-30) REVERT: B 286 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.7906 (m-30) REVERT: B 290 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8219 (tm-30) REVERT: B 294 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8721 (mm-30) REVERT: B 317 MET cc_start: 0.8529 (ptp) cc_final: 0.8287 (pmm) REVERT: B 362 ASP cc_start: 0.8685 (m-30) cc_final: 0.7460 (m-30) REVERT: B 394 TYR cc_start: 0.9032 (m-80) cc_final: 0.8665 (m-80) REVERT: B 415 ASN cc_start: 0.9218 (t0) cc_final: 0.8814 (t0) REVERT: B 447 ASN cc_start: 0.8450 (m-40) cc_final: 0.8237 (m-40) REVERT: B 467 ASN cc_start: 0.9471 (t0) cc_final: 0.9197 (m-40) REVERT: B 471 TYR cc_start: 0.9333 (t80) cc_final: 0.8660 (t80) REVERT: B 493 MET cc_start: 0.9697 (tmm) cc_final: 0.8873 (tmm) REVERT: B 515 ASP cc_start: 0.9051 (m-30) cc_final: 0.8815 (m-30) REVERT: B 546 LEU cc_start: 0.9627 (mt) cc_final: 0.9384 (mt) REVERT: B 610 LYS cc_start: 0.8996 (mmmt) cc_final: 0.8736 (mmmt) REVERT: B 612 TYR cc_start: 0.8586 (m-80) cc_final: 0.8194 (m-80) REVERT: B 628 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8176 (mm-30) REVERT: B 632 MET cc_start: 0.8870 (mtp) cc_final: 0.8361 (mpp) REVERT: B 668 ASN cc_start: 0.9283 (m-40) cc_final: 0.8918 (m110) REVERT: C 19 GLN cc_start: 0.7594 (mp10) cc_final: 0.7164 (pm20) REVERT: C 25 ASN cc_start: 0.9293 (t0) cc_final: 0.8860 (p0) REVERT: C 29 PHE cc_start: 0.8060 (t80) cc_final: 0.7830 (t80) REVERT: C 55 TYR cc_start: 0.8054 (t80) cc_final: 0.7026 (t80) REVERT: C 64 LEU cc_start: 0.4432 (OUTLIER) cc_final: 0.4216 (mm) REVERT: C 69 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8804 (tm-30) REVERT: C 80 HIS cc_start: 0.8818 (m90) cc_final: 0.8483 (m90) REVERT: C 96 MET cc_start: 0.8695 (mmt) cc_final: 0.8000 (mmm) REVERT: C 134 LYS cc_start: 0.9629 (pttt) cc_final: 0.9199 (pttt) REVERT: C 145 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7902 (tp) REVERT: C 168 PHE cc_start: 0.9166 (m-80) cc_final: 0.8648 (m-80) REVERT: C 169 TYR cc_start: 0.8562 (m-80) cc_final: 0.8342 (m-80) REVERT: C 178 PHE cc_start: 0.9307 (m-80) cc_final: 0.8333 (m-10) REVERT: C 186 GLN cc_start: 0.9215 (mm110) cc_final: 0.8763 (mp10) REVERT: C 242 TYR cc_start: 0.9390 (t80) cc_final: 0.8992 (t80) REVERT: C 259 PHE cc_start: 0.8947 (t80) cc_final: 0.8450 (t80) REVERT: C 268 LEU cc_start: 0.8849 (tp) cc_final: 0.8580 (tp) REVERT: C 269 MET cc_start: 0.9079 (ppp) cc_final: 0.8852 (ppp) REVERT: C 270 ASN cc_start: 0.8473 (m110) cc_final: 0.8137 (m110) REVERT: D 21 PHE cc_start: 0.9435 (m-80) cc_final: 0.8910 (m-80) REVERT: D 34 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8450 (mm-30) REVERT: D 46 TYR cc_start: 0.9057 (m-80) cc_final: 0.8792 (m-10) REVERT: D 130 TYR cc_start: 0.6480 (m-10) cc_final: 0.6207 (m-10) REVERT: D 178 PHE cc_start: 0.9379 (m-10) cc_final: 0.8747 (m-80) REVERT: D 186 GLN cc_start: 0.9215 (mm-40) cc_final: 0.8749 (mp10) REVERT: D 207 LEU cc_start: 0.9272 (mm) cc_final: 0.8840 (mm) REVERT: D 210 GLN cc_start: 0.9376 (tm-30) cc_final: 0.9093 (pt0) REVERT: D 240 LEU cc_start: 0.8840 (mt) cc_final: 0.8357 (pp) REVERT: D 247 TYR cc_start: 0.8781 (m-10) cc_final: 0.8398 (m-10) REVERT: D 269 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8227 (ppp) outliers start: 72 outliers final: 49 residues processed: 707 average time/residue: 0.1179 time to fit residues: 126.1764 Evaluate side-chains 697 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 637 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 61 optimal weight: 0.0040 chunk 19 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 GLN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN D 50 ASN ** D 101 HIS ** 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 = 0.3561 r_free = 0.3561 target = 0.120699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.085486 restraints weight = 36233.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.088841 restraints weight = 17306.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.091133 restraints weight = 10529.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.092642 restraints weight = 7330.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.093615 restraints weight = 5663.401| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.7285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16386 Z= 0.194 Angle : 0.778 16.315 22134 Z= 0.387 Chirality : 0.047 0.190 2360 Planarity : 0.004 0.053 2818 Dihedral : 8.812 136.494 2294 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.25 % Allowed : 32.46 % Favored : 63.29 % 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: 0.55 (0.19), residues: 1932 helix: 0.85 (0.15), residues: 1153 sheet: -0.52 (0.42), residues: 148 loop : -0.11 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 261 TYR 0.024 0.002 TYR A 522 PHE 0.032 0.002 PHE C 172 TRP 0.028 0.002 TRP D 124 HIS 0.010 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (16386) covalent geometry : angle 0.77838 / 0.39 (22134) hydrogen bonds : bond 0.04104 / 2.60 ( 871) hydrogen bonds : angle 5.14414 / 3.67 ( 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 736 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 663 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.9788 (mt) cc_final: 0.9507 (pp) REVERT: A 64 TYR cc_start: 0.9222 (m-10) cc_final: 0.8655 (m-10) REVERT: A 65 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8196 (mp0) REVERT: A 66 GLU cc_start: 0.8457 (tp30) cc_final: 0.8157 (tp30) REVERT: A 82 LYS cc_start: 0.9642 (mmmm) cc_final: 0.9302 (mmmm) REVERT: A 102 ASN cc_start: 0.9249 (m110) cc_final: 0.8715 (m110) REVERT: A 144 MET cc_start: 0.9118 (mtm) cc_final: 0.8739 (mtm) REVERT: A 149 TYR cc_start: 0.9307 (t80) cc_final: 0.8656 (t80) REVERT: A 180 ASN cc_start: 0.8740 (m-40) cc_final: 0.8465 (m-40) REVERT: A 181 ASP cc_start: 0.8788 (m-30) cc_final: 0.8481 (m-30) REVERT: A 187 ASP cc_start: 0.9012 (t70) cc_final: 0.8646 (t70) REVERT: A 202 ASN cc_start: 0.9604 (t0) cc_final: 0.9269 (t0) REVERT: A 218 ASN cc_start: 0.9365 (t0) cc_final: 0.9094 (t0) REVERT: A 221 LYS cc_start: 0.9004 (mmtp) cc_final: 0.8693 (mttp) REVERT: A 227 MET cc_start: 0.9138 (mtp) cc_final: 0.8903 (mtp) REVERT: A 228 LYS cc_start: 0.9495 (mmmm) cc_final: 0.8787 (mmtt) REVERT: A 232 ASN cc_start: 0.9135 (m-40) cc_final: 0.8673 (m-40) REVERT: A 286 ASP cc_start: 0.8539 (m-30) cc_final: 0.8191 (m-30) REVERT: A 321 GLU cc_start: 0.8868 (tp30) cc_final: 0.8443 (tp30) REVERT: A 335 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7584 (mm-30) REVERT: A 359 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8227 (ttp) REVERT: A 362 ASP cc_start: 0.8616 (m-30) cc_final: 0.8031 (m-30) REVERT: A 384 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8161 (pm20) REVERT: A 389 SER cc_start: 0.9422 (OUTLIER) cc_final: 0.9135 (p) REVERT: A 415 ASN cc_start: 0.9281 (t0) cc_final: 0.9003 (t0) REVERT: A 420 MET cc_start: 0.9304 (mmm) cc_final: 0.8994 (tpt) REVERT: A 435 SER cc_start: 0.9519 (OUTLIER) cc_final: 0.9280 (t) REVERT: A 493 MET cc_start: 0.8979 (tmm) cc_final: 0.8179 (tmm) REVERT: A 505 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8489 (mt-10) REVERT: A 512 GLU cc_start: 0.8663 (pt0) cc_final: 0.8393 (pt0) REVERT: A 526 GLU cc_start: 0.7991 (mp0) cc_final: 0.7789 (mp0) REVERT: A 583 SER cc_start: 0.9379 (m) cc_final: 0.8804 (t) REVERT: A 598 MET cc_start: 0.8546 (mtp) cc_final: 0.8197 (mmm) REVERT: A 599 GLU cc_start: 0.8526 (mp0) cc_final: 0.8294 (mp0) REVERT: A 632 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8003 (mtp) REVERT: A 640 MET cc_start: 0.9614 (tpp) cc_final: 0.8711 (tpp) REVERT: B 8 LYS cc_start: 0.9061 (tppt) cc_final: 0.8859 (tppt) REVERT: B 17 MET cc_start: 0.9007 (mmm) cc_final: 0.8696 (mmm) REVERT: B 28 LYS cc_start: 0.9288 (mmtt) cc_final: 0.8985 (mmmm) REVERT: B 31 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8107 (mt-10) REVERT: B 65 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8466 (mm-30) REVERT: B 71 LEU cc_start: 0.9714 (mm) cc_final: 0.9482 (mp) REVERT: B 99 LYS cc_start: 0.9537 (mmmm) cc_final: 0.9301 (mmmm) REVERT: B 172 LEU cc_start: 0.9241 (mt) cc_final: 0.9026 (mt) REVERT: B 174 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8279 (mm-30) REVERT: B 202 ASN cc_start: 0.9467 (t0) cc_final: 0.8893 (t0) REVERT: B 218 ASN cc_start: 0.9538 (m110) cc_final: 0.9314 (m110) REVERT: B 257 ASP cc_start: 0.8822 (m-30) cc_final: 0.8328 (m-30) REVERT: B 263 ASP cc_start: 0.9161 (m-30) cc_final: 0.8738 (p0) REVERT: B 286 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.7800 (m-30) REVERT: B 290 GLU cc_start: 0.8755 (tm-30) cc_final: 0.7423 (tm-30) REVERT: B 294 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8749 (mt-10) REVERT: B 316 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8384 (tt0) REVERT: B 362 ASP cc_start: 0.8710 (m-30) cc_final: 0.7380 (m-30) REVERT: B 394 TYR cc_start: 0.9241 (m-80) cc_final: 0.8946 (m-80) REVERT: B 415 ASN cc_start: 0.9208 (t0) cc_final: 0.8795 (t0) REVERT: B 447 ASN cc_start: 0.8388 (m-40) cc_final: 0.7880 (m-40) REVERT: B 467 ASN cc_start: 0.9478 (t0) cc_final: 0.9234 (m-40) REVERT: B 471 TYR cc_start: 0.9352 (t80) cc_final: 0.8716 (t80) REVERT: B 493 MET cc_start: 0.9692 (tmm) cc_final: 0.8854 (tmm) REVERT: B 515 ASP cc_start: 0.9068 (m-30) cc_final: 0.8849 (m-30) REVERT: B 546 LEU cc_start: 0.9614 (mt) cc_final: 0.9379 (mt) REVERT: B 548 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8273 (mm-30) REVERT: B 606 TYR cc_start: 0.8623 (m-80) cc_final: 0.8209 (m-80) REVERT: B 610 LYS cc_start: 0.9015 (mmmt) cc_final: 0.8718 (mmmt) REVERT: B 612 TYR cc_start: 0.8570 (m-80) cc_final: 0.8290 (m-80) REVERT: B 628 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8247 (mm-30) REVERT: B 668 ASN cc_start: 0.9374 (m-40) cc_final: 0.9101 (m110) REVERT: C 19 GLN cc_start: 0.7587 (mp10) cc_final: 0.7205 (pm20) REVERT: C 56 MET cc_start: 0.5404 (ttt) cc_final: 0.4542 (mtt) REVERT: C 64 LEU cc_start: 0.4367 (OUTLIER) cc_final: 0.4165 (mm) REVERT: C 69 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8829 (tm-30) REVERT: C 80 HIS cc_start: 0.8834 (m90) cc_final: 0.8512 (m90) REVERT: C 96 MET cc_start: 0.8865 (mmt) cc_final: 0.8331 (mmm) REVERT: C 134 LYS cc_start: 0.9634 (pttt) cc_final: 0.9351 (pttp) REVERT: C 145 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7948 (tp) REVERT: C 164 GLU cc_start: 0.9360 (tp30) cc_final: 0.9108 (tp30) REVERT: C 169 TYR cc_start: 0.8689 (m-80) cc_final: 0.8458 (m-80) REVERT: C 178 PHE cc_start: 0.9332 (m-80) cc_final: 0.8748 (m-10) REVERT: C 259 PHE cc_start: 0.8985 (t80) cc_final: 0.8490 (t80) REVERT: C 268 LEU cc_start: 0.8814 (tp) cc_final: 0.8546 (tp) REVERT: C 269 MET cc_start: 0.9050 (ppp) cc_final: 0.8847 (ppp) REVERT: C 270 ASN cc_start: 0.8574 (m110) cc_final: 0.8215 (m110) REVERT: D 21 PHE cc_start: 0.9346 (m-80) cc_final: 0.9091 (m-80) REVERT: D 34 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8212 (mm-30) REVERT: D 46 TYR cc_start: 0.9083 (m-80) cc_final: 0.8809 (m-10) REVERT: D 96 MET cc_start: 0.8977 (mmt) cc_final: 0.8591 (mmm) REVERT: D 130 TYR cc_start: 0.7049 (m-10) cc_final: 0.6792 (m-10) REVERT: D 153 LEU cc_start: 0.9171 (tp) cc_final: 0.8951 (mt) REVERT: D 178 PHE cc_start: 0.9431 (m-10) cc_final: 0.8811 (m-80) REVERT: D 186 GLN cc_start: 0.9221 (mm-40) cc_final: 0.8749 (mp10) REVERT: D 207 LEU cc_start: 0.9237 (mm) cc_final: 0.8779 (mm) REVERT: D 210 GLN cc_start: 0.9369 (tm-30) cc_final: 0.9068 (pt0) REVERT: D 240 LEU cc_start: 0.8861 (mt) cc_final: 0.8394 (pp) REVERT: D 269 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8010 (ppp) outliers start: 73 outliers final: 52 residues processed: 690 average time/residue: 0.1166 time to fit residues: 122.2120 Evaluate side-chains 709 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 647 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 149 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN B 232 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN C 98 ASN D 50 ASN D 101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.122789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.087836 restraints weight = 36016.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.091192 restraints weight = 16881.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.093500 restraints weight = 10308.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.095052 restraints weight = 7035.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.096022 restraints weight = 5351.847| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.7570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16386 Z= 0.164 Angle : 0.812 16.177 22134 Z= 0.401 Chirality : 0.047 0.207 2360 Planarity : 0.004 0.047 2818 Dihedral : 8.749 137.781 2294 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.96 % Allowed : 33.28 % Favored : 62.76 % 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: 0.49 (0.19), residues: 1932 helix: 0.81 (0.15), residues: 1152 sheet: -0.49 (0.42), residues: 148 loop : -0.17 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG C 261 TYR 0.028 0.001 TYR A 522 PHE 0.036 0.002 PHE C 172 TRP 0.039 0.002 TRP C 44 HIS 0.010 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (16386) covalent geometry : angle 0.81175 / 0.40 (22134) hydrogen bonds : bond 0.04165 / 2.63 ( 871) hydrogen bonds : angle 5.16909 / 3.70 ( 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 742 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 674 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.9790 (mt) cc_final: 0.9507 (pp) REVERT: A 64 TYR cc_start: 0.9247 (m-10) cc_final: 0.8886 (m-10) REVERT: A 65 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8240 (mp0) REVERT: A 66 GLU cc_start: 0.8392 (tp30) cc_final: 0.8096 (tp30) REVERT: A 82 LYS cc_start: 0.9624 (mmmm) cc_final: 0.9267 (mmmm) REVERT: A 102 ASN cc_start: 0.9261 (m110) cc_final: 0.8754 (m110) REVERT: A 144 MET cc_start: 0.9100 (mtm) cc_final: 0.8625 (mtm) REVERT: A 181 ASP cc_start: 0.8759 (m-30) cc_final: 0.8497 (m-30) REVERT: A 187 ASP cc_start: 0.8997 (t70) cc_final: 0.8676 (t70) REVERT: A 202 ASN cc_start: 0.9559 (t0) cc_final: 0.9198 (t0) REVERT: A 218 ASN cc_start: 0.9336 (t0) cc_final: 0.9027 (t0) REVERT: A 221 LYS cc_start: 0.8963 (mmtp) cc_final: 0.8590 (mttt) REVERT: A 227 MET cc_start: 0.9076 (mtp) cc_final: 0.8813 (mtp) REVERT: A 228 LYS cc_start: 0.9474 (mmmm) cc_final: 0.8780 (mmtt) REVERT: A 232 ASN cc_start: 0.9040 (m-40) cc_final: 0.8638 (m-40) REVERT: A 286 ASP cc_start: 0.8471 (m-30) cc_final: 0.8176 (m-30) REVERT: A 321 GLU cc_start: 0.8838 (tp30) cc_final: 0.8370 (tp30) REVERT: A 335 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7567 (mm-30) REVERT: A 350 ARG cc_start: 0.9211 (mtp85) cc_final: 0.8928 (mtp180) REVERT: A 359 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8195 (ttp) REVERT: A 362 ASP cc_start: 0.8633 (m-30) cc_final: 0.8059 (m-30) REVERT: A 370 ASN cc_start: 0.9214 (m-40) cc_final: 0.8793 (m-40) REVERT: A 384 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.7713 (pm20) REVERT: A 389 SER cc_start: 0.9404 (OUTLIER) cc_final: 0.9120 (p) REVERT: A 415 ASN cc_start: 0.9202 (t0) cc_final: 0.8979 (t0) REVERT: A 420 MET cc_start: 0.9358 (mmm) cc_final: 0.9000 (tpt) REVERT: A 435 SER cc_start: 0.9506 (OUTLIER) cc_final: 0.9258 (t) REVERT: A 447 ASN cc_start: 0.8619 (m-40) cc_final: 0.8147 (t0) REVERT: A 493 MET cc_start: 0.8929 (tmm) cc_final: 0.8079 (tmm) REVERT: A 505 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8720 (mt-10) REVERT: A 512 GLU cc_start: 0.8624 (pt0) cc_final: 0.8357 (pt0) REVERT: A 583 SER cc_start: 0.9366 (m) cc_final: 0.8780 (t) REVERT: A 598 MET cc_start: 0.8874 (mtp) cc_final: 0.8458 (mmt) REVERT: A 599 GLU cc_start: 0.8710 (mp0) cc_final: 0.8499 (mp0) REVERT: A 604 ARG cc_start: 0.8747 (mmt-90) cc_final: 0.8417 (mmt-90) REVERT: A 632 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8083 (mtp) REVERT: A 640 MET cc_start: 0.9654 (tpp) cc_final: 0.8757 (tpp) REVERT: B 8 LYS cc_start: 0.9078 (tppt) cc_final: 0.8824 (tppt) REVERT: B 65 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8117 (mp0) REVERT: B 99 LYS cc_start: 0.9519 (mmmm) cc_final: 0.9285 (mmmm) REVERT: B 172 LEU cc_start: 0.9220 (mt) cc_final: 0.8862 (mt) REVERT: B 202 ASN cc_start: 0.9454 (t0) cc_final: 0.9021 (t0) REVERT: B 218 ASN cc_start: 0.9545 (m110) cc_final: 0.9309 (m-40) REVERT: B 257 ASP cc_start: 0.8890 (m-30) cc_final: 0.8380 (m-30) REVERT: B 274 ARG cc_start: 0.8871 (ttm-80) cc_final: 0.8651 (ttm-80) REVERT: B 286 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.7777 (m-30) REVERT: B 290 GLU cc_start: 0.8766 (tm-30) cc_final: 0.7383 (tm-30) REVERT: B 294 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8781 (mt-10) REVERT: B 362 ASP cc_start: 0.8632 (m-30) cc_final: 0.7344 (m-30) REVERT: B 378 PHE cc_start: 0.9386 (p90) cc_final: 0.9080 (p90) REVERT: B 394 TYR cc_start: 0.9140 (m-80) cc_final: 0.8842 (m-80) REVERT: B 415 ASN cc_start: 0.9192 (t0) cc_final: 0.8855 (t0) REVERT: B 452 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8748 (ttm-80) REVERT: B 471 TYR cc_start: 0.9288 (t80) cc_final: 0.8675 (t80) REVERT: B 493 MET cc_start: 0.9681 (tmm) cc_final: 0.9089 (tmm) REVERT: B 515 ASP cc_start: 0.9025 (m-30) cc_final: 0.8802 (m-30) REVERT: B 546 LEU cc_start: 0.9597 (mt) cc_final: 0.9386 (mt) REVERT: B 548 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8164 (mm-30) REVERT: B 606 TYR cc_start: 0.8596 (m-80) cc_final: 0.8200 (m-80) REVERT: B 610 LYS cc_start: 0.9073 (mmmt) cc_final: 0.8815 (mmmt) REVERT: B 628 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8339 (mm-30) REVERT: B 688 LYS cc_start: 0.8253 (tppt) cc_final: 0.7990 (ttpp) REVERT: C 17 PHE cc_start: 0.8536 (p90) cc_final: 0.8267 (p90) REVERT: C 69 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8756 (tm-30) REVERT: C 80 HIS cc_start: 0.8768 (m90) cc_final: 0.8432 (m90) REVERT: C 134 LYS cc_start: 0.9634 (pttt) cc_final: 0.9369 (pttp) REVERT: C 145 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7882 (tp) REVERT: C 178 PHE cc_start: 0.9439 (m-80) cc_final: 0.8601 (m-80) REVERT: C 186 GLN cc_start: 0.9244 (mm110) cc_final: 0.8805 (mp10) REVERT: C 189 GLU cc_start: 0.8630 (tp30) cc_final: 0.8306 (mm-30) REVERT: C 212 ILE cc_start: 0.9240 (mm) cc_final: 0.8919 (tt) REVERT: C 229 ILE cc_start: 0.8561 (mm) cc_final: 0.8229 (mm) REVERT: C 259 PHE cc_start: 0.8985 (t80) cc_final: 0.8467 (t80) REVERT: C 268 LEU cc_start: 0.8745 (tp) cc_final: 0.8483 (tp) REVERT: C 270 ASN cc_start: 0.8591 (m110) cc_final: 0.8236 (m110) REVERT: D 21 PHE cc_start: 0.9373 (m-80) cc_final: 0.8857 (m-80) REVERT: D 34 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8251 (mm-30) REVERT: D 46 TYR cc_start: 0.9042 (m-80) cc_final: 0.8824 (m-10) REVERT: D 96 MET cc_start: 0.8980 (mmt) cc_final: 0.8581 (mmm) REVERT: D 178 PHE cc_start: 0.9390 (m-10) cc_final: 0.8802 (m-80) REVERT: D 186 GLN cc_start: 0.9169 (mm-40) cc_final: 0.8643 (mp10) REVERT: D 207 LEU cc_start: 0.9166 (mm) cc_final: 0.8815 (mm) REVERT: D 210 GLN cc_start: 0.9267 (tm-30) cc_final: 0.8999 (pt0) REVERT: D 240 LEU cc_start: 0.8850 (mt) cc_final: 0.8403 (pp) REVERT: D 269 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7980 (ppp) outliers start: 68 outliers final: 53 residues processed: 704 average time/residue: 0.1175 time to fit residues: 126.3350 Evaluate side-chains 701 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 638 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 189 optimal weight: 10.0000 chunk 181 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 54 optimal weight: 0.0060 chunk 132 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN B 668 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN D 50 ASN D 127 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.124898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.090003 restraints weight = 35847.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.093384 restraints weight = 17056.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.095666 restraints weight = 10410.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.097116 restraints weight = 7153.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.098123 restraints weight = 5446.874| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.7783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16386 Z= 0.164 Angle : 0.879 17.041 22134 Z= 0.428 Chirality : 0.049 0.277 2360 Planarity : 0.004 0.050 2818 Dihedral : 8.758 140.381 2294 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.44 % Allowed : 34.91 % Favored : 61.66 % 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: 0.45 (0.19), residues: 1932 helix: 0.79 (0.15), residues: 1135 sheet: -0.35 (0.43), residues: 148 loop : -0.21 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 261 TYR 0.040 0.002 TYR C 242 PHE 0.041 0.002 PHE B 74 TRP 0.019 0.002 TRP C 44 HIS 0.010 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (16386) covalent geometry : angle 0.87938 / 0.43 (22134) hydrogen bonds : bond 0.04313 / 2.73 ( 871) hydrogen bonds : angle 5.22258 / 3.73 ( 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 723 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 664 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.9085 (p0) cc_final: 0.8747 (p0) REVERT: A 55 LEU cc_start: 0.9792 (mt) cc_final: 0.9517 (pp) REVERT: A 64 TYR cc_start: 0.9194 (m-10) cc_final: 0.8908 (m-10) REVERT: A 65 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8311 (mp0) REVERT: A 66 GLU cc_start: 0.8324 (tp30) cc_final: 0.7996 (tp30) REVERT: A 82 LYS cc_start: 0.9604 (mmmm) cc_final: 0.9243 (mmmm) REVERT: A 102 ASN cc_start: 0.9247 (m110) cc_final: 0.8826 (m110) REVERT: A 187 ASP cc_start: 0.8960 (t70) cc_final: 0.8663 (t70) REVERT: A 202 ASN cc_start: 0.9519 (t0) cc_final: 0.9138 (t0) REVERT: A 218 ASN cc_start: 0.9300 (t0) cc_final: 0.8948 (t0) REVERT: A 221 LYS cc_start: 0.8933 (mmtp) cc_final: 0.8664 (mttp) REVERT: A 227 MET cc_start: 0.9092 (mtp) cc_final: 0.8821 (mtp) REVERT: A 228 LYS cc_start: 0.9479 (mmmm) cc_final: 0.8802 (mmtt) REVERT: A 232 ASN cc_start: 0.8979 (m-40) cc_final: 0.8717 (m-40) REVERT: A 286 ASP cc_start: 0.8437 (m-30) cc_final: 0.8181 (m-30) REVERT: A 321 GLU cc_start: 0.8803 (tp30) cc_final: 0.8044 (tp30) REVERT: A 335 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7538 (mm-30) REVERT: A 350 ARG cc_start: 0.9156 (mtp85) cc_final: 0.8889 (mtp180) REVERT: A 362 ASP cc_start: 0.8577 (m-30) cc_final: 0.8036 (m-30) REVERT: A 370 ASN cc_start: 0.9187 (m-40) cc_final: 0.8805 (m-40) REVERT: A 384 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.7599 (pm20) REVERT: A 389 SER cc_start: 0.9378 (OUTLIER) cc_final: 0.9034 (p) REVERT: A 390 GLN cc_start: 0.8847 (mt0) cc_final: 0.8517 (mt0) REVERT: A 415 ASN cc_start: 0.9187 (t0) cc_final: 0.8981 (t0) REVERT: A 435 SER cc_start: 0.9505 (OUTLIER) cc_final: 0.9262 (t) REVERT: A 447 ASN cc_start: 0.8575 (m-40) cc_final: 0.8111 (t0) REVERT: A 493 MET cc_start: 0.8907 (tmm) cc_final: 0.8081 (tmm) REVERT: A 494 MET cc_start: 0.9050 (mtm) cc_final: 0.8579 (mtt) REVERT: A 505 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8733 (mt-10) REVERT: A 512 GLU cc_start: 0.8566 (pt0) cc_final: 0.8175 (pt0) REVERT: A 583 SER cc_start: 0.9348 (m) cc_final: 0.8786 (t) REVERT: A 598 MET cc_start: 0.8839 (mtp) cc_final: 0.8478 (mmt) REVERT: A 599 GLU cc_start: 0.8733 (mp0) cc_final: 0.8526 (mp0) REVERT: A 604 ARG cc_start: 0.8684 (mmt-90) cc_final: 0.8360 (mmt-90) REVERT: A 632 MET cc_start: 0.8621 (mtm) cc_final: 0.8076 (mtp) REVERT: A 640 MET cc_start: 0.9633 (tpp) cc_final: 0.8700 (tpp) REVERT: B 8 LYS cc_start: 0.9059 (tppt) cc_final: 0.8834 (tppt) REVERT: B 31 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8110 (mt-10) REVERT: B 65 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8476 (mm-30) REVERT: B 95 MET cc_start: 0.9109 (tpp) cc_final: 0.8784 (mmm) REVERT: B 99 LYS cc_start: 0.9513 (mmmm) cc_final: 0.9214 (mmmm) REVERT: B 119 GLU cc_start: 0.8714 (mp0) cc_final: 0.8395 (mp0) REVERT: B 147 GLN cc_start: 0.9493 (mt0) cc_final: 0.8824 (mm110) REVERT: B 172 LEU cc_start: 0.9201 (mt) cc_final: 0.8879 (mt) REVERT: B 202 ASN cc_start: 0.9426 (t0) cc_final: 0.9020 (t0) REVERT: B 218 ASN cc_start: 0.9527 (m110) cc_final: 0.9267 (m-40) REVERT: B 252 ASN cc_start: 0.9046 (t0) cc_final: 0.8668 (t0) REVERT: B 257 ASP cc_start: 0.8799 (m-30) cc_final: 0.8285 (m-30) REVERT: B 274 ARG cc_start: 0.8897 (ttm-80) cc_final: 0.8677 (ttm-80) REVERT: B 286 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.7856 (m-30) REVERT: B 290 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8091 (tm-30) REVERT: B 294 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8706 (mm-30) REVERT: B 335 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7893 (mt-10) REVERT: B 362 ASP cc_start: 0.8664 (m-30) cc_final: 0.7438 (m-30) REVERT: B 378 PHE cc_start: 0.9396 (p90) cc_final: 0.9008 (p90) REVERT: B 394 TYR cc_start: 0.9075 (m-80) cc_final: 0.8794 (m-80) REVERT: B 399 GLU cc_start: 0.8461 (mp0) cc_final: 0.8166 (mp0) REVERT: B 415 ASN cc_start: 0.9157 (t0) cc_final: 0.8933 (t0) REVERT: B 471 TYR cc_start: 0.9324 (t80) cc_final: 0.8629 (t80) REVERT: B 493 MET cc_start: 0.9663 (tmm) cc_final: 0.9092 (tmm) REVERT: B 546 LEU cc_start: 0.9572 (mt) cc_final: 0.9321 (mt) REVERT: B 548 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8059 (mm-30) REVERT: B 610 LYS cc_start: 0.9060 (mmmt) cc_final: 0.8761 (mmmt) REVERT: C 20 MET cc_start: 0.8845 (tpp) cc_final: 0.8326 (tmm) REVERT: C 25 ASN cc_start: 0.9287 (t0) cc_final: 0.8826 (p0) REVERT: C 54 THR cc_start: 0.8066 (p) cc_final: 0.7703 (t) REVERT: C 56 MET cc_start: 0.5535 (ttt) cc_final: 0.4732 (mtt) REVERT: C 69 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8788 (tm-30) REVERT: C 80 HIS cc_start: 0.8689 (m90) cc_final: 0.8362 (m90) REVERT: C 134 LYS cc_start: 0.9620 (pttt) cc_final: 0.9151 (pttm) REVERT: C 145 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7903 (tp) REVERT: C 168 PHE cc_start: 0.8977 (m-80) cc_final: 0.8628 (m-80) REVERT: C 178 PHE cc_start: 0.9379 (m-80) cc_final: 0.8541 (m-10) REVERT: C 186 GLN cc_start: 0.9185 (mm110) cc_final: 0.8738 (mp10) REVERT: C 189 GLU cc_start: 0.8569 (tp30) cc_final: 0.8212 (mm-30) REVERT: C 229 ILE cc_start: 0.8539 (mm) cc_final: 0.8192 (mm) REVERT: C 242 TYR cc_start: 0.9242 (t80) cc_final: 0.8609 (m-80) REVERT: C 259 PHE cc_start: 0.8954 (t80) cc_final: 0.8382 (t80) REVERT: C 268 LEU cc_start: 0.8697 (tp) cc_final: 0.8447 (tp) REVERT: C 270 ASN cc_start: 0.8592 (m110) cc_final: 0.8344 (m110) REVERT: D 21 PHE cc_start: 0.9372 (m-80) cc_final: 0.8950 (m-80) REVERT: D 34 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8304 (mm-30) REVERT: D 42 LEU cc_start: 0.9408 (mp) cc_final: 0.9147 (mm) REVERT: D 96 MET cc_start: 0.8965 (mmt) cc_final: 0.8605 (mmm) REVERT: D 174 TYR cc_start: 0.9008 (t80) cc_final: 0.8791 (t80) REVERT: D 178 PHE cc_start: 0.9377 (m-10) cc_final: 0.8743 (m-80) REVERT: D 186 GLN cc_start: 0.9118 (mm-40) cc_final: 0.8570 (mp10) REVERT: D 207 LEU cc_start: 0.9152 (mm) cc_final: 0.8693 (mm) REVERT: D 210 GLN cc_start: 0.9265 (tm-30) cc_final: 0.8929 (pt0) REVERT: D 269 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7978 (ppp) outliers start: 59 outliers final: 49 residues processed: 689 average time/residue: 0.1087 time to fit residues: 114.5403 Evaluate side-chains 700 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 644 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 148 optimal weight: 9.9990 chunk 125 optimal weight: 0.6980 chunk 28 optimal weight: 0.0670 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN C 98 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN D 50 ASN D 127 GLN ** D 210 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 = 0.3608 r_free = 0.3608 target = 0.123956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.088916 restraints weight = 35399.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.092358 restraints weight = 17092.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.094607 restraints weight = 10305.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.096071 restraints weight = 7145.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.096970 restraints weight = 5486.002| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 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 = 0.3151 r_free = 0.3151 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: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.7933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16386 Z= 0.166 Angle : 0.871 17.132 22134 Z= 0.426 Chirality : 0.048 0.278 2360 Planarity : 0.004 0.049 2818 Dihedral : 8.763 141.022 2294 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.32 % Allowed : 35.43 % Favored : 61.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.19), residues: 1932 helix: 0.76 (0.15), residues: 1133 sheet: -0.25 (0.44), residues: 146 loop : -0.39 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 243 TYR 0.039 0.001 TYR C 242 PHE 0.043 0.002 PHE C 172 TRP 0.023 0.002 TRP C 44 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (16386) covalent geometry : angle 0.87082 / 0.43 (22134) hydrogen bonds : bond 0.04218 / 2.68 ( 871) hydrogen bonds : angle 5.20165 / 3.73 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3363.49 seconds wall clock time: 59 minutes 4.15 seconds (3544.15 seconds total)