Starting phenix.real_space_refine on Thu Aug 6 15:10:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byz_45049/08_2026/9byz_45049_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byz_45049/08_2026/9byz_45049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9byz_45049/08_2026/9byz_45049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byz_45049/08_2026/9byz_45049.map" model { file = "/net/cci-nas-00/data/ceres_data/9byz_45049/08_2026/9byz_45049_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byz_45049/08_2026/9byz_45049_neut.cif" } resolution = 3.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 2.57, per 1000 atoms: 0.16 Number of scatterers: 16038 At special positions: 0 Unit cell: (95.598, 134.244, 133.227, 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: 0.86 Conformation dependent library (CDL) restraints added in 580.3 milliseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 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: 4.095A 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: 3.985A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.954A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.665A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.126A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.694A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.628A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A 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: 3.579A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.677A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.646A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.730A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.026A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.069A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.669A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A 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: 6.604A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.478A 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: 7.184A 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: 6.709A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.049A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.906A 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: 8.344A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A 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: 1.89 Time building geometry restraints manager: 1.20 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: 4770 1.34 - 1.46: 3070 1.46 - 1.58: 8365 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" O3B TTP B 801 " pdb=" PG TTP B 801 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" O3B TTP A 803 " pdb=" PG TTP A 803 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.82e+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 2.33e+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 1.20e+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 1.15e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21527 2.09 - 4.18: 525 4.18 - 6.27: 64 6.27 - 8.36: 9 8.36 - 10.45: 9 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.62 -6.08 1.36e+00 5.41e-01 2.00e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.18 -4.47 1.15e+00 7.56e-01 1.51e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.83 -4.33 1.23e+00 6.61e-01 1.24e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.72 -4.01 1.15e+00 7.56e-01 1.21e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.53 3.66 1.06e+00 8.90e-01 1.19e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.05: 9092 25.05 - 50.10: 653 50.10 - 75.15: 125 75.15 - 100.20: 26 100.20 - 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 -95.53 122.55 1 2.00e+01 2.50e-03 3.69e+01 dihedral pdb=" C VAL C 125 " pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual -122.00 -134.31 12.31 0 2.50e+00 1.60e-01 2.42e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2141 0.093 - 0.186: 184 0.186 - 0.278: 30 0.278 - 0.371: 3 0.371 - 0.464: 2 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.38e+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 4.63e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+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 4.15e-02 2.76e+00 pdb=" N PRO D 75 " 0.072 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 2.11e+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 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " -0.001 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 D 179 " -0.016 2.00e-02 2.50e+03 9.81e-03 1.93e+00 pdb=" CG TYR D 179 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR D 179 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 179 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR D 179 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 179 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR D 179 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 179 " -0.005 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 129 2.51 - 3.11: 11559 3.11 - 3.70: 27048 3.70 - 4.30: 41564 4.30 - 4.90: 65457 Nonbonded interactions: 145757 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.991 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.013 3.040 ... (remaining 145752 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: 0.930 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.050 Find NCS groups from input model: 0.220 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 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 10.448 22134 Z= 0.471 Chirality : 0.058 0.464 2360 Planarity : 0.003 0.042 2818 Dihedral : 17.635 125.244 6202 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.40 % Allowed : 15.21 % Favored : 83.39 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.18), residues: 1932 helix: 0.58 (0.14), residues: 1151 sheet: 0.46 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 196 TYR 0.021 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.009 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.33 (16386) covalent geometry : angle 0.78750 / 0.47 (22134) hydrogen bonds : bond 0.15420 / 9.51 ( 871) hydrogen bonds : angle 6.51780 / 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 902 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 878 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.8819 (mt) cc_final: 0.8554 (mt) REVERT: A 37 PHE cc_start: 0.7949 (m-80) cc_final: 0.7497 (m-10) REVERT: A 144 MET cc_start: 0.6905 (mtm) cc_final: 0.6687 (mtm) REVERT: A 157 LEU cc_start: 0.9004 (tp) cc_final: 0.8741 (tt) REVERT: A 183 SER cc_start: 0.8618 (p) cc_final: 0.8372 (p) REVERT: A 186 ILE cc_start: 0.9440 (mt) cc_final: 0.9089 (mt) REVERT: A 188 ILE cc_start: 0.8765 (mt) cc_final: 0.8517 (mt) REVERT: A 218 ASN cc_start: 0.7691 (t0) cc_final: 0.7274 (t0) REVERT: A 257 ASP cc_start: 0.8041 (m-30) cc_final: 0.7733 (m-30) REVERT: A 267 ILE cc_start: 0.7996 (mp) cc_final: 0.7482 (tp) REVERT: A 362 ASP cc_start: 0.6663 (m-30) cc_final: 0.5927 (m-30) REVERT: A 390 GLN cc_start: 0.7453 (mt0) cc_final: 0.7134 (mt0) REVERT: A 405 LEU cc_start: 0.8644 (mt) cc_final: 0.8389 (mt) REVERT: A 433 THR cc_start: 0.8995 (m) cc_final: 0.8786 (m) REVERT: A 502 ARG cc_start: 0.8204 (tpt170) cc_final: 0.7738 (tpt170) REVERT: A 640 MET cc_start: 0.8149 (tpp) cc_final: 0.7871 (tpp) REVERT: A 644 ILE cc_start: 0.8792 (mt) cc_final: 0.8438 (mt) REVERT: B 51 LEU cc_start: 0.8148 (tp) cc_final: 0.7902 (tp) REVERT: B 157 LEU cc_start: 0.8341 (tp) cc_final: 0.8034 (tp) REVERT: B 177 ASP cc_start: 0.8218 (t0) cc_final: 0.6646 (p0) REVERT: B 180 ASN cc_start: 0.7454 (m-40) cc_final: 0.7184 (m110) REVERT: B 184 ARG cc_start: 0.8306 (tpp-160) cc_final: 0.8094 (tpp-160) REVERT: B 322 MET cc_start: 0.7732 (mmm) cc_final: 0.7446 (mmm) REVERT: B 425 ILE cc_start: 0.8674 (mt) cc_final: 0.8112 (mt) REVERT: B 485 ARG cc_start: 0.8037 (mtm-85) cc_final: 0.7801 (mtm-85) REVERT: B 597 ILE cc_start: 0.9135 (pt) cc_final: 0.8856 (pt) REVERT: B 605 THR cc_start: 0.7858 (m) cc_final: 0.7568 (t) REVERT: B 645 GLN cc_start: 0.8532 (tp-100) cc_final: 0.8331 (tp40) REVERT: B 658 LEU cc_start: 0.8924 (mt) cc_final: 0.8383 (mt) REVERT: C 85 GLN cc_start: 0.4929 (mt0) cc_final: 0.4089 (pt0) REVERT: C 112 LEU cc_start: 0.3484 (mt) cc_final: 0.3053 (mp) REVERT: C 130 TYR cc_start: 0.3400 (m-80) cc_final: 0.3146 (m-80) REVERT: C 287 LEU cc_start: 0.2172 (OUTLIER) cc_final: 0.1826 (mp) REVERT: D 256 VAL cc_start: 0.6873 (t) cc_final: 0.6170 (t) REVERT: D 260 ILE cc_start: 0.6984 (mt) cc_final: 0.6360 (tp) outliers start: 24 outliers final: 8 residues processed: 885 average time/residue: 0.1172 time to fit residues: 151.5525 Evaluate side-chains 577 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 568 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN 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 C residue 220 LYS Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain D residue 59 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.0870 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.1980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN A 320 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN B 11 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 320 ASN B 329 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN C 263 ASN C 270 ASN D 23 ASN D 28 GLN D 71 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.139312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.100233 restraints weight = 34433.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.103810 restraints weight = 16517.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.106181 restraints weight = 9701.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.107715 restraints weight = 6545.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.108826 restraints weight = 4897.405| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 10 (15 function evaluations) r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16386 Z= 0.151 Angle : 0.660 14.320 22134 Z= 0.343 Chirality : 0.044 0.188 2360 Planarity : 0.004 0.033 2818 Dihedral : 9.927 127.031 2307 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.26 % Allowed : 20.22 % Favored : 76.52 % 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: 1.36 (0.19), residues: 1932 helix: 1.33 (0.15), residues: 1129 sheet: 0.22 (0.41), residues: 130 loop : 0.51 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 350 TYR 0.022 0.002 TYR B 626 PHE 0.037 0.002 PHE C 168 TRP 0.024 0.002 TRP C 30 HIS 0.006 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (16386) covalent geometry : angle 0.65953 / 0.34 (22134) hydrogen bonds : bond 0.04714 / 2.99 ( 871) hydrogen bonds : angle 5.18131 / 3.68 ( 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 695 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 639 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.9218 (mt) cc_final: 0.8971 (mt) REVERT: A 87 LYS cc_start: 0.9016 (tptm) cc_final: 0.8796 (tptm) REVERT: A 99 LYS cc_start: 0.9197 (mmmm) cc_final: 0.8609 (mmmm) REVERT: A 103 ASP cc_start: 0.8718 (m-30) cc_final: 0.8506 (m-30) REVERT: A 161 ARG cc_start: 0.7998 (ttm170) cc_final: 0.7736 (mmm-85) REVERT: A 164 ARG cc_start: 0.8304 (ptt90) cc_final: 0.8093 (ptt90) REVERT: A 194 LYS cc_start: 0.9268 (tttp) cc_final: 0.8796 (tttt) REVERT: A 218 ASN cc_start: 0.8729 (t0) cc_final: 0.8164 (t0) REVERT: A 256 ARG cc_start: 0.9072 (ttp80) cc_final: 0.8674 (ttp80) REVERT: A 291 LEU cc_start: 0.9663 (mt) cc_final: 0.9416 (mp) REVERT: A 308 LYS cc_start: 0.9166 (mtmm) cc_final: 0.8933 (mtmt) REVERT: A 335 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7291 (mt-10) REVERT: A 384 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7454 (pm20) REVERT: A 385 VAL cc_start: 0.8901 (t) cc_final: 0.8465 (t) REVERT: A 483 GLU cc_start: 0.9043 (mp0) cc_final: 0.8226 (pm20) REVERT: A 505 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7649 (mt-10) REVERT: A 548 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8305 (mm-30) REVERT: A 640 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8306 (tpp) REVERT: A 644 ILE cc_start: 0.9497 (mt) cc_final: 0.9277 (mt) REVERT: A 686 ARG cc_start: 0.7868 (mtp85) cc_final: 0.7624 (mtp85) REVERT: B 71 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9005 (mp) REVERT: B 95 MET cc_start: 0.8455 (tpp) cc_final: 0.8156 (tpp) REVERT: B 149 TYR cc_start: 0.9091 (t80) cc_final: 0.8451 (t80) REVERT: B 184 ARG cc_start: 0.9128 (tpp-160) cc_final: 0.8648 (tpp-160) REVERT: B 190 MET cc_start: 0.9094 (mtm) cc_final: 0.8771 (mtm) REVERT: B 202 ASN cc_start: 0.8823 (t0) cc_final: 0.8451 (t0) REVERT: B 235 ARG cc_start: 0.8470 (ttm110) cc_final: 0.7845 (mtm-85) REVERT: B 286 ASP cc_start: 0.7698 (m-30) cc_final: 0.7492 (m-30) REVERT: B 290 GLU cc_start: 0.8930 (tt0) cc_final: 0.8581 (tm-30) REVERT: B 322 MET cc_start: 0.8788 (mmm) cc_final: 0.8439 (mmm) REVERT: B 335 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8194 (mt-10) REVERT: B 348 MET cc_start: 0.8086 (tpp) cc_final: 0.7870 (tpp) REVERT: B 361 GLN cc_start: 0.8612 (tt0) cc_final: 0.8395 (tt0) REVERT: B 362 ASP cc_start: 0.7658 (m-30) cc_final: 0.7292 (m-30) REVERT: B 374 SER cc_start: 0.9402 (t) cc_final: 0.9158 (t) REVERT: B 375 LYS cc_start: 0.8820 (mtmm) cc_final: 0.8367 (mtpp) REVERT: B 384 GLU cc_start: 0.8322 (pm20) cc_final: 0.7775 (pm20) REVERT: B 467 ASN cc_start: 0.9098 (t0) cc_final: 0.8893 (m-40) REVERT: B 576 LEU cc_start: 0.9420 (mt) cc_final: 0.9126 (mt) REVERT: B 645 GLN cc_start: 0.9081 (tp-100) cc_final: 0.8797 (tp-100) REVERT: B 669 ARG cc_start: 0.8834 (mtp85) cc_final: 0.8613 (mmm-85) REVERT: B 683 TYR cc_start: 0.8554 (t80) cc_final: 0.8216 (t80) REVERT: C 56 MET cc_start: 0.5856 (mmm) cc_final: 0.5604 (ptp) REVERT: C 68 GLU cc_start: 0.9377 (mm-30) cc_final: 0.9122 (mm-30) REVERT: C 85 GLN cc_start: 0.4247 (mt0) cc_final: 0.3413 (pt0) REVERT: C 93 MET cc_start: 0.8447 (mtt) cc_final: 0.8233 (mtt) REVERT: C 137 MET cc_start: 0.6888 (mtp) cc_final: 0.6627 (mtp) REVERT: C 154 PHE cc_start: 0.8681 (t80) cc_final: 0.8360 (t80) REVERT: C 157 MET cc_start: 0.8948 (mtt) cc_final: 0.8673 (mtt) REVERT: C 158 VAL cc_start: 0.9516 (t) cc_final: 0.8909 (t) REVERT: C 162 TYR cc_start: 0.9301 (m-10) cc_final: 0.8854 (m-10) REVERT: C 233 ASN cc_start: 0.9110 (m-40) cc_final: 0.8751 (m-40) REVERT: C 271 LEU cc_start: 0.8516 (mm) cc_final: 0.7920 (mm) REVERT: C 317 ASP cc_start: 0.8252 (m-30) cc_final: 0.7878 (m-30) REVERT: C 320 PHE cc_start: 0.9302 (m-80) cc_final: 0.8987 (m-80) REVERT: D 92 PHE cc_start: 0.7110 (t80) cc_final: 0.6768 (t80) REVERT: D 96 MET cc_start: 0.5966 (mmm) cc_final: 0.5633 (mmm) REVERT: D 137 MET cc_start: 0.5413 (mtp) cc_final: 0.5207 (ptp) REVERT: D 174 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7155 (t80) REVERT: D 179 TYR cc_start: 0.8050 (t80) cc_final: 0.7532 (t80) REVERT: D 184 LEU cc_start: 0.8713 (mt) cc_final: 0.8351 (mt) REVERT: D 185 MET cc_start: 0.7157 (mmp) cc_final: 0.6543 (mmp) REVERT: D 189 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7422 (tm-30) REVERT: D 195 LEU cc_start: 0.8780 (tt) cc_final: 0.8496 (mm) REVERT: D 223 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8349 (tp30) REVERT: D 227 PHE cc_start: 0.8412 (m-10) cc_final: 0.8185 (m-10) outliers start: 56 outliers final: 25 residues processed: 664 average time/residue: 0.1015 time to fit residues: 102.6947 Evaluate side-chains 540 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 509 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 646 GLN Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 254 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 182 optimal weight: 0.9980 chunk 159 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 42 ASN A 259 ASN A 320 ASN A 387 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS A 447 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 191 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN B 646 GLN B 676 HIS C 69 GLN C 91 ASN C 234 GLN D 25 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.134966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.096686 restraints weight = 35065.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.100031 restraints weight = 16767.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.102299 restraints weight = 10119.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.103881 restraints weight = 6812.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.104862 restraints weight = 5070.019| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (13 function evaluations) r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16386 Z= 0.151 Angle : 0.618 13.784 22134 Z= 0.320 Chirality : 0.043 0.181 2360 Planarity : 0.003 0.031 2818 Dihedral : 9.034 127.368 2303 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.90 % Allowed : 20.57 % Favored : 75.52 % 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: 1.29 (0.19), residues: 1932 helix: 1.34 (0.15), residues: 1132 sheet: 0.09 (0.42), residues: 134 loop : 0.38 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 235 TYR 0.036 0.002 TYR A 498 PHE 0.035 0.002 PHE C 172 TRP 0.028 0.002 TRP D 30 HIS 0.008 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (16386) covalent geometry : angle 0.61798 / 0.32 (22134) hydrogen bonds : bond 0.04132 / 2.60 ( 871) hydrogen bonds : angle 5.01801 / 3.56 ( 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 628 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 561 time to evaluate : 0.523 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 87 LYS cc_start: 0.8977 (tptm) cc_final: 0.8745 (tptm) REVERT: A 99 LYS cc_start: 0.9180 (mmmm) cc_final: 0.8749 (mmmm) REVERT: A 103 ASP cc_start: 0.8813 (m-30) cc_final: 0.8568 (m-30) REVERT: A 139 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8193 (mp0) REVERT: A 161 ARG cc_start: 0.8054 (ttm170) cc_final: 0.7747 (mmm-85) REVERT: A 214 LYS cc_start: 0.8405 (ttmm) cc_final: 0.8201 (mttm) REVERT: A 218 ASN cc_start: 0.8864 (t0) cc_final: 0.8337 (t0) REVERT: A 256 ARG cc_start: 0.9132 (ttp80) cc_final: 0.8756 (ttp80) REVERT: A 307 TYR cc_start: 0.9223 (t80) cc_final: 0.8997 (t80) REVERT: A 335 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7272 (mt-10) REVERT: A 344 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8686 (mt-10) REVERT: A 359 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7764 (ttp) REVERT: A 362 ASP cc_start: 0.8199 (m-30) cc_final: 0.7573 (m-30) REVERT: A 367 VAL cc_start: 0.9431 (m) cc_final: 0.9218 (p) REVERT: A 381 LEU cc_start: 0.8940 (tp) cc_final: 0.8484 (pt) REVERT: A 384 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7481 (pm20) REVERT: A 385 VAL cc_start: 0.8875 (t) cc_final: 0.8314 (t) REVERT: A 483 GLU cc_start: 0.9014 (mp0) cc_final: 0.8555 (pm20) REVERT: A 505 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7682 (mt-10) REVERT: A 548 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8411 (mm-30) REVERT: A 628 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8622 (mt-10) REVERT: A 640 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8286 (tpp) REVERT: B 95 MET cc_start: 0.8584 (tpp) cc_final: 0.8186 (tpp) REVERT: B 128 PHE cc_start: 0.9258 (t80) cc_final: 0.9039 (t80) REVERT: B 181 ASP cc_start: 0.8349 (m-30) cc_final: 0.7948 (m-30) REVERT: B 184 ARG cc_start: 0.9150 (tpp-160) cc_final: 0.8662 (tpp-160) REVERT: B 190 MET cc_start: 0.9121 (mtm) cc_final: 0.8882 (mtm) REVERT: B 202 ASN cc_start: 0.8873 (t0) cc_final: 0.8615 (t0) REVERT: B 267 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8886 (pt) REVERT: B 322 MET cc_start: 0.8933 (mmm) cc_final: 0.8321 (mmm) REVERT: B 335 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8058 (mt-10) REVERT: B 348 MET cc_start: 0.8088 (tpp) cc_final: 0.7860 (tpp) REVERT: B 361 GLN cc_start: 0.8551 (tt0) cc_final: 0.8223 (tt0) REVERT: B 374 SER cc_start: 0.9415 (t) cc_final: 0.9189 (t) REVERT: B 375 LYS cc_start: 0.8763 (mtmm) cc_final: 0.8339 (mtpp) REVERT: B 398 ASP cc_start: 0.8113 (t0) cc_final: 0.7715 (t0) REVERT: B 425 ILE cc_start: 0.9200 (mt) cc_final: 0.8898 (mt) REVERT: B 467 ASN cc_start: 0.9158 (t0) cc_final: 0.8843 (m-40) REVERT: B 493 MET cc_start: 0.9414 (tmm) cc_final: 0.9059 (tmm) REVERT: B 550 MET cc_start: 0.7926 (mtm) cc_final: 0.7644 (mtm) REVERT: B 602 GLU cc_start: 0.7939 (tp30) cc_final: 0.7421 (tp30) REVERT: B 645 GLN cc_start: 0.9132 (tp40) cc_final: 0.8833 (tp-100) REVERT: B 668 ASN cc_start: 0.8810 (m-40) cc_final: 0.8590 (m110) REVERT: B 669 ARG cc_start: 0.8846 (mtp85) cc_final: 0.8625 (mmm-85) REVERT: B 683 TYR cc_start: 0.8790 (t80) cc_final: 0.8267 (t80) REVERT: C 72 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8720 (p) REVERT: C 76 ILE cc_start: 0.8303 (mm) cc_final: 0.7732 (tp) REVERT: C 85 GLN cc_start: 0.4255 (mt0) cc_final: 0.3533 (pt0) REVERT: C 93 MET cc_start: 0.8959 (mtt) cc_final: 0.8534 (mtt) REVERT: C 95 MET cc_start: 0.8530 (tmm) cc_final: 0.8296 (tmm) REVERT: C 155 LYS cc_start: 0.8421 (mttm) cc_final: 0.8133 (mmtt) REVERT: C 157 MET cc_start: 0.9125 (mtt) cc_final: 0.8648 (mtt) REVERT: C 158 VAL cc_start: 0.9673 (t) cc_final: 0.9065 (t) REVERT: C 162 TYR cc_start: 0.9342 (m-10) cc_final: 0.8772 (m-10) REVERT: C 174 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7974 (t80) REVERT: C 196 ARG cc_start: 0.9155 (mmm-85) cc_final: 0.8943 (mmm-85) REVERT: C 200 ILE cc_start: 0.9247 (mp) cc_final: 0.8782 (tp) REVERT: C 201 HIS cc_start: 0.8788 (m90) cc_final: 0.8327 (m90) REVERT: C 212 ILE cc_start: 0.8412 (mm) cc_final: 0.7255 (mm) REVERT: C 254 HIS cc_start: 0.9184 (t70) cc_final: 0.8959 (t70) REVERT: C 271 LEU cc_start: 0.8408 (mm) cc_final: 0.7701 (mm) REVERT: C 317 ASP cc_start: 0.8340 (m-30) cc_final: 0.7977 (m-30) REVERT: D 96 MET cc_start: 0.5999 (mmm) cc_final: 0.5738 (mmm) REVERT: D 137 MET cc_start: 0.5448 (mtp) cc_final: 0.5067 (ptp) REVERT: D 138 ILE cc_start: 0.9029 (mm) cc_final: 0.8785 (mm) REVERT: D 174 TYR cc_start: 0.8067 (OUTLIER) cc_final: 0.7248 (t80) REVERT: D 195 LEU cc_start: 0.8894 (tt) cc_final: 0.8636 (mm) REVERT: D 197 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8624 (t0) outliers start: 67 outliers final: 37 residues processed: 597 average time/residue: 0.0980 time to fit residues: 89.3891 Evaluate side-chains 552 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 506 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 381 LEU 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 561 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 6.9990 chunk 157 optimal weight: 9.9990 chunk 168 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 60 optimal weight: 0.1980 chunk 185 optimal weight: 9.9990 chunk 191 optimal weight: 0.0770 chunk 159 optimal weight: 0.7980 chunk 182 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 overall best weight: 1.2140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN A 25 GLN A 365 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 191 GLN B 304 HIS ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.134300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.096017 restraints weight = 34964.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.099490 restraints weight = 16619.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.101739 restraints weight = 9734.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.103091 restraints weight = 6633.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.104097 restraints weight = 5065.866| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16386 Z= 0.148 Angle : 0.607 13.316 22134 Z= 0.315 Chirality : 0.042 0.175 2360 Planarity : 0.003 0.035 2818 Dihedral : 8.755 129.209 2302 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.96 % Allowed : 21.50 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.19), residues: 1932 helix: 1.25 (0.15), residues: 1135 sheet: -0.02 (0.42), residues: 134 loop : 0.37 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 164 TYR 0.022 0.001 TYR B 626 PHE 0.032 0.002 PHE C 172 TRP 0.031 0.002 TRP D 30 HIS 0.008 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (16386) covalent geometry : angle 0.60671 / 0.31 (22134) hydrogen bonds : bond 0.03904 / 2.48 ( 871) hydrogen bonds : angle 4.96779 / 3.52 ( 2571) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 543 time to evaluate : 0.627 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 56 ASP cc_start: 0.8772 (m-30) cc_final: 0.8436 (m-30) REVERT: A 99 LYS cc_start: 0.9108 (mmmm) cc_final: 0.8488 (mmmm) REVERT: A 103 ASP cc_start: 0.8895 (m-30) cc_final: 0.8565 (m-30) REVERT: A 161 ARG cc_start: 0.8019 (ttm170) cc_final: 0.7494 (mtp85) REVERT: A 214 LYS cc_start: 0.8353 (ttmm) cc_final: 0.8141 (mttm) REVERT: A 218 ASN cc_start: 0.8849 (t0) cc_final: 0.8306 (t0) REVERT: A 256 ARG cc_start: 0.9157 (ttp80) cc_final: 0.8850 (ttp80) REVERT: A 307 TYR cc_start: 0.9205 (t80) cc_final: 0.8943 (t80) REVERT: A 335 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7254 (mt-10) REVERT: A 344 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8593 (mt-10) REVERT: A 359 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7632 (ttp) REVERT: A 381 LEU cc_start: 0.8984 (tp) cc_final: 0.8467 (pt) REVERT: A 384 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7443 (pm20) REVERT: A 385 VAL cc_start: 0.8816 (t) cc_final: 0.8368 (t) REVERT: A 393 SER cc_start: 0.9090 (m) cc_final: 0.8776 (p) REVERT: A 453 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8608 (ttp80) REVERT: A 483 GLU cc_start: 0.8995 (mp0) cc_final: 0.8487 (pm20) REVERT: A 505 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7846 (mt-10) REVERT: A 590 SER cc_start: 0.9266 (p) cc_final: 0.8953 (p) REVERT: A 640 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8179 (tpp) REVERT: B 95 MET cc_start: 0.8605 (tpp) cc_final: 0.8225 (tpp) REVERT: B 99 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8578 (tptp) REVERT: B 108 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.8042 (p) REVERT: B 128 PHE cc_start: 0.9294 (t80) cc_final: 0.9012 (t80) REVERT: B 143 LEU cc_start: 0.9388 (tt) cc_final: 0.9057 (tt) REVERT: B 184 ARG cc_start: 0.9175 (tpp-160) cc_final: 0.8905 (tpp-160) REVERT: B 190 MET cc_start: 0.9149 (mtm) cc_final: 0.8900 (mtm) REVERT: B 202 ASN cc_start: 0.8889 (t0) cc_final: 0.8649 (t0) REVERT: B 252 ASN cc_start: 0.8942 (t0) cc_final: 0.8721 (t0) REVERT: B 322 MET cc_start: 0.8978 (mmm) cc_final: 0.8503 (mmm) REVERT: B 348 MET cc_start: 0.8132 (tpp) cc_final: 0.7884 (tpp) REVERT: B 361 GLN cc_start: 0.8636 (tt0) cc_final: 0.8214 (tt0) REVERT: B 362 ASP cc_start: 0.7695 (m-30) cc_final: 0.7418 (m-30) REVERT: B 374 SER cc_start: 0.9398 (t) cc_final: 0.9195 (t) REVERT: B 398 ASP cc_start: 0.8194 (t0) cc_final: 0.7830 (t0) REVERT: B 467 ASN cc_start: 0.9120 (t0) cc_final: 0.8837 (m-40) REVERT: B 493 MET cc_start: 0.9421 (tmm) cc_final: 0.9201 (tmm) REVERT: B 550 MET cc_start: 0.7756 (mtm) cc_final: 0.7502 (mtp) REVERT: B 632 MET cc_start: 0.8455 (mtp) cc_final: 0.7703 (mtt) REVERT: B 645 GLN cc_start: 0.9117 (tp40) cc_final: 0.8859 (tp40) REVERT: B 668 ASN cc_start: 0.8766 (m-40) cc_final: 0.8178 (m110) REVERT: B 669 ARG cc_start: 0.8853 (mtp85) cc_final: 0.8617 (mmm-85) REVERT: C 69 GLN cc_start: 0.8886 (tm-30) cc_final: 0.8553 (tm-30) REVERT: C 76 ILE cc_start: 0.8321 (mm) cc_final: 0.7807 (tp) REVERT: C 85 GLN cc_start: 0.4293 (mt0) cc_final: 0.3569 (pt0) REVERT: C 93 MET cc_start: 0.8989 (mtt) cc_final: 0.8682 (mtt) REVERT: C 155 LYS cc_start: 0.8566 (mttm) cc_final: 0.8175 (mmtt) REVERT: C 157 MET cc_start: 0.9281 (mtt) cc_final: 0.8987 (mtt) REVERT: C 158 VAL cc_start: 0.9676 (t) cc_final: 0.9014 (t) REVERT: C 162 TYR cc_start: 0.9360 (m-10) cc_final: 0.8762 (m-10) REVERT: C 177 TYR cc_start: 0.8449 (t80) cc_final: 0.8151 (t80) REVERT: C 200 ILE cc_start: 0.9243 (mp) cc_final: 0.8784 (tp) REVERT: C 201 HIS cc_start: 0.8733 (m90) cc_final: 0.8349 (m90) REVERT: C 212 ILE cc_start: 0.8556 (mm) cc_final: 0.7772 (mm) REVERT: C 243 THR cc_start: 0.7851 (m) cc_final: 0.7575 (m) REVERT: C 271 LEU cc_start: 0.8394 (mm) cc_final: 0.7672 (mm) REVERT: C 317 ASP cc_start: 0.8351 (m-30) cc_final: 0.8058 (m-30) REVERT: D 96 MET cc_start: 0.6112 (mmm) cc_final: 0.5768 (mmm) REVERT: D 137 MET cc_start: 0.5177 (mtp) cc_final: 0.4861 (ptp) REVERT: D 174 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.7214 (t80) REVERT: D 195 LEU cc_start: 0.8954 (tt) cc_final: 0.8701 (mm) REVERT: D 197 ASP cc_start: 0.8793 (OUTLIER) cc_final: 0.8585 (t0) REVERT: D 231 LEU cc_start: 0.9183 (tp) cc_final: 0.8973 (tp) REVERT: D 240 LEU cc_start: 0.7510 (mt) cc_final: 0.7117 (mt) outliers start: 68 outliers final: 40 residues processed: 580 average time/residue: 0.1196 time to fit residues: 105.6745 Evaluate side-chains 546 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 498 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 381 LEU 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 495 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 197 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 168 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 312 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 312 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 84 HIS C 238 ASN C 249 GLN D 25 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.126988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.089792 restraints weight = 35632.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.092889 restraints weight = 17358.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.094875 restraints weight = 10503.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.096348 restraints weight = 7339.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.097186 restraints weight = 5599.796| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 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 = 0.3146 r_free = 0.3146 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: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 16386 Z= 0.259 Angle : 0.665 10.482 22134 Z= 0.348 Chirality : 0.045 0.247 2360 Planarity : 0.004 0.037 2818 Dihedral : 8.808 133.246 2297 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.90 % Allowed : 22.20 % Favored : 72.90 % 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: 1.13 (0.15), residues: 1133 sheet: -0.36 (0.41), residues: 146 loop : 0.39 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 164 TYR 0.023 0.002 TYR B 394 PHE 0.027 0.002 PHE C 172 TRP 0.037 0.003 TRP D 30 HIS 0.006 0.001 HIS A 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.26 (16386) covalent geometry : angle 0.66502 / 0.35 (22134) hydrogen bonds : bond 0.04092 / 2.62 ( 871) hydrogen bonds : angle 5.10770 / 3.62 ( 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 592 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 508 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8393 (mm-30) REVERT: A 99 LYS cc_start: 0.9116 (mmmm) cc_final: 0.8775 (mmmm) REVERT: A 102 ASN cc_start: 0.9074 (OUTLIER) cc_final: 0.8761 (m-40) REVERT: A 117 ARG cc_start: 0.8159 (mtt-85) cc_final: 0.7551 (mtt90) REVERT: A 161 ARG cc_start: 0.8085 (ttm170) cc_final: 0.7546 (mmm-85) REVERT: A 172 LEU cc_start: 0.9149 (mp) cc_final: 0.8932 (mp) REVERT: A 214 LYS cc_start: 0.8403 (ttmm) cc_final: 0.8152 (mttm) REVERT: A 218 ASN cc_start: 0.8975 (t0) cc_final: 0.8480 (t0) REVERT: A 291 LEU cc_start: 0.9685 (mt) cc_final: 0.9386 (mp) REVERT: A 344 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8583 (mt-10) REVERT: A 359 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.7964 (ttp) REVERT: A 384 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7519 (pm20) REVERT: A 385 VAL cc_start: 0.8820 (t) cc_final: 0.8451 (t) REVERT: A 393 SER cc_start: 0.9152 (m) cc_final: 0.8538 (p) REVERT: A 402 GLU cc_start: 0.8106 (mp0) cc_final: 0.7328 (mp0) REVERT: A 505 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7846 (mt-10) REVERT: A 527 TYR cc_start: 0.8576 (t80) cc_final: 0.8359 (t80) REVERT: A 548 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8300 (mm-30) REVERT: A 595 MET cc_start: 0.9074 (mmm) cc_final: 0.8784 (mmp) REVERT: A 640 MET cc_start: 0.9300 (OUTLIER) cc_final: 0.8134 (tpp) REVERT: A 662 MET cc_start: 0.8375 (ptp) cc_final: 0.7839 (ptp) REVERT: B 95 MET cc_start: 0.8692 (tpp) cc_final: 0.8252 (tpp) REVERT: B 108 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8500 (p) REVERT: B 128 PHE cc_start: 0.9329 (t80) cc_final: 0.9090 (t80) REVERT: B 190 MET cc_start: 0.9184 (mtm) cc_final: 0.8902 (mtm) REVERT: B 257 ASP cc_start: 0.8651 (m-30) cc_final: 0.8417 (m-30) REVERT: B 312 GLN cc_start: 0.8704 (tt0) cc_final: 0.8344 (tt0) REVERT: B 348 MET cc_start: 0.8102 (tpp) cc_final: 0.7856 (tpp) REVERT: B 425 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9112 (mp) REVERT: B 441 GLU cc_start: 0.8626 (pt0) cc_final: 0.8391 (pt0) REVERT: B 467 ASN cc_start: 0.9221 (t0) cc_final: 0.8869 (m-40) REVERT: B 493 MET cc_start: 0.9430 (tmm) cc_final: 0.9012 (tmm) REVERT: B 599 GLU cc_start: 0.8362 (pt0) cc_final: 0.8105 (pt0) REVERT: B 668 ASN cc_start: 0.8817 (m-40) cc_final: 0.8586 (m110) REVERT: C 69 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8499 (tm-30) REVERT: C 76 ILE cc_start: 0.8466 (mm) cc_final: 0.8022 (tp) REVERT: C 85 GLN cc_start: 0.4275 (mt0) cc_final: 0.3521 (pt0) REVERT: C 90 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8923 (tp) REVERT: C 93 MET cc_start: 0.9033 (mtt) cc_final: 0.8625 (mtt) REVERT: C 137 MET cc_start: 0.7543 (mtt) cc_final: 0.7129 (mpp) REVERT: C 157 MET cc_start: 0.9364 (mtt) cc_final: 0.9135 (mtt) REVERT: C 158 VAL cc_start: 0.9697 (t) cc_final: 0.9179 (m) REVERT: C 162 TYR cc_start: 0.9368 (m-10) cc_final: 0.8861 (m-10) REVERT: C 201 HIS cc_start: 0.8643 (m90) cc_final: 0.8155 (m90) REVERT: C 211 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8223 (pp20) REVERT: C 271 LEU cc_start: 0.8640 (mm) cc_final: 0.8085 (mm) REVERT: D 56 MET cc_start: 0.7955 (mmt) cc_final: 0.7356 (ptt) REVERT: D 96 MET cc_start: 0.6133 (mmm) cc_final: 0.5909 (mmm) REVERT: D 137 MET cc_start: 0.5191 (mtp) cc_final: 0.4876 (ptp) REVERT: D 174 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.7316 (t80) REVERT: D 231 LEU cc_start: 0.9195 (tp) cc_final: 0.8949 (tp) REVERT: D 235 LEU cc_start: 0.9004 (mm) cc_final: 0.8794 (mp) outliers start: 84 outliers final: 55 residues processed: 551 average time/residue: 0.1145 time to fit residues: 95.9225 Evaluate side-chains 542 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 478 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 624 PHE Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 254 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 0.6980 chunk 183 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 172 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 136 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 312 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 191 GLN B 218 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN D 71 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.131803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.094507 restraints weight = 35072.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.097879 restraints weight = 16698.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.099998 restraints weight = 9830.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.101310 restraints weight = 6736.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.102275 restraints weight = 5178.777| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.5722 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= 0.136 Angle : 0.642 11.899 22134 Z= 0.328 Chirality : 0.043 0.221 2360 Planarity : 0.003 0.035 2818 Dihedral : 8.571 133.321 2297 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.21 % Allowed : 25.00 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.19), residues: 1932 helix: 1.14 (0.15), residues: 1126 sheet: -0.04 (0.44), residues: 130 loop : 0.26 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 686 TYR 0.025 0.001 TYR B 394 PHE 0.027 0.002 PHE C 172 TRP 0.035 0.002 TRP D 30 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (16386) covalent geometry : angle 0.64193 / 0.33 (22134) hydrogen bonds : bond 0.03866 / 2.50 ( 871) hydrogen bonds : angle 4.99131 / 3.54 ( 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 580 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 525 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ASP cc_start: 0.8797 (m-30) cc_final: 0.8362 (m-30) REVERT: A 65 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8239 (mm-30) REVERT: A 150 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8520 (tm-30) REVERT: A 161 ARG cc_start: 0.8087 (ttm170) cc_final: 0.7652 (mtp85) REVERT: A 172 LEU cc_start: 0.9090 (mp) cc_final: 0.8845 (mp) REVERT: A 214 LYS cc_start: 0.8258 (ttmm) cc_final: 0.7999 (mttm) REVERT: A 218 ASN cc_start: 0.8888 (t0) cc_final: 0.8263 (t0) REVERT: A 307 TYR cc_start: 0.9129 (t80) cc_final: 0.8899 (t80) REVERT: A 316 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8211 (mm-30) REVERT: A 341 LYS cc_start: 0.9347 (mmtm) cc_final: 0.8874 (mmpt) REVERT: A 344 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8646 (mt-10) REVERT: A 359 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7715 (ttp) REVERT: A 362 ASP cc_start: 0.8023 (m-30) cc_final: 0.7782 (m-30) REVERT: A 366 LYS cc_start: 0.9169 (mtmt) cc_final: 0.8825 (ptpp) REVERT: A 381 LEU cc_start: 0.9044 (tp) cc_final: 0.8425 (pt) REVERT: A 384 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7392 (pm20) REVERT: A 385 VAL cc_start: 0.8794 (t) cc_final: 0.8362 (t) REVERT: A 390 GLN cc_start: 0.8495 (mt0) cc_final: 0.8135 (mt0) REVERT: A 393 SER cc_start: 0.9141 (m) cc_final: 0.8512 (p) REVERT: A 402 GLU cc_start: 0.8089 (mp0) cc_final: 0.7252 (mp0) REVERT: A 483 GLU cc_start: 0.9065 (mp0) cc_final: 0.8463 (pm20) REVERT: A 505 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7779 (mt-10) REVERT: A 548 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8311 (mm-30) REVERT: A 588 GLN cc_start: 0.9323 (tp40) cc_final: 0.9078 (tp40) REVERT: A 595 MET cc_start: 0.8876 (mmm) cc_final: 0.8676 (mmp) REVERT: A 640 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.7981 (tpp) REVERT: A 666 ASP cc_start: 0.8603 (t0) cc_final: 0.8356 (t0) REVERT: B 95 MET cc_start: 0.8542 (tpp) cc_final: 0.8212 (tpp) REVERT: B 99 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8636 (tptp) REVERT: B 108 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8420 (p) REVERT: B 143 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9017 (tt) REVERT: B 184 ARG cc_start: 0.9075 (tpp-160) cc_final: 0.8676 (tpp-160) REVERT: B 190 MET cc_start: 0.9142 (mtm) cc_final: 0.8864 (mtm) REVERT: B 257 ASP cc_start: 0.8594 (m-30) cc_final: 0.8267 (m-30) REVERT: B 322 MET cc_start: 0.8955 (mmm) cc_final: 0.8216 (mmm) REVERT: B 348 MET cc_start: 0.8003 (tpp) cc_final: 0.7777 (tpp) REVERT: B 362 ASP cc_start: 0.7662 (m-30) cc_final: 0.7362 (m-30) REVERT: B 374 SER cc_start: 0.9458 (t) cc_final: 0.9251 (t) REVERT: B 398 ASP cc_start: 0.8279 (t0) cc_final: 0.7986 (t0) REVERT: B 441 GLU cc_start: 0.8609 (pt0) cc_final: 0.8353 (pt0) REVERT: B 467 ASN cc_start: 0.9037 (t0) cc_final: 0.8819 (m-40) REVERT: B 493 MET cc_start: 0.9415 (tmm) cc_final: 0.9001 (tmm) REVERT: B 576 LEU cc_start: 0.9439 (mt) cc_final: 0.9239 (mt) REVERT: B 599 GLU cc_start: 0.8303 (pt0) cc_final: 0.8049 (pt0) REVERT: C 76 ILE cc_start: 0.8485 (mm) cc_final: 0.8048 (tp) REVERT: C 85 GLN cc_start: 0.4479 (mt0) cc_final: 0.3596 (pt0) REVERT: C 93 MET cc_start: 0.9018 (mtt) cc_final: 0.8649 (mtt) REVERT: C 158 VAL cc_start: 0.9655 (t) cc_final: 0.9115 (m) REVERT: C 162 TYR cc_start: 0.9339 (m-10) cc_final: 0.8796 (m-10) REVERT: C 174 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.7819 (t80) REVERT: C 201 HIS cc_start: 0.8837 (m90) cc_final: 0.8274 (m90) REVERT: C 271 LEU cc_start: 0.8593 (mm) cc_final: 0.7969 (mm) REVERT: C 317 ASP cc_start: 0.8488 (m-30) cc_final: 0.8212 (m-30) REVERT: D 56 MET cc_start: 0.8218 (mmt) cc_final: 0.7643 (ptt) REVERT: D 96 MET cc_start: 0.5921 (mmm) cc_final: 0.5709 (mmm) REVERT: D 137 MET cc_start: 0.5211 (mtp) cc_final: 0.4893 (ptp) REVERT: D 157 MET cc_start: 0.6670 (ptp) cc_final: 0.6364 (ptt) REVERT: D 162 TYR cc_start: 0.6437 (m-10) cc_final: 0.6163 (m-10) REVERT: D 174 TYR cc_start: 0.8183 (OUTLIER) cc_final: 0.7289 (t80) outliers start: 55 outliers final: 32 residues processed: 551 average time/residue: 0.1067 time to fit residues: 90.2248 Evaluate side-chains 537 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 496 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 381 LEU 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 561 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 624 PHE Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 254 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 186 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 115 optimal weight: 0.0770 chunk 45 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 overall best weight: 1.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 218 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN C 214 ASN D 25 ASN D 71 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.131428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.093957 restraints weight = 35106.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.097190 restraints weight = 16960.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.099302 restraints weight = 10065.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.100609 restraints weight = 6946.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.101507 restraints weight = 5375.711| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16386 Z= 0.179 Angle : 0.662 11.094 22134 Z= 0.342 Chirality : 0.044 0.225 2360 Planarity : 0.004 0.064 2818 Dihedral : 8.466 134.259 2295 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.61 % Allowed : 25.41 % Favored : 70.98 % 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: 0.93 (0.19), residues: 1932 helix: 1.07 (0.15), residues: 1138 sheet: -0.12 (0.44), residues: 130 loop : 0.18 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 261 TYR 0.030 0.002 TYR D 142 PHE 0.025 0.002 PHE C 172 TRP 0.028 0.002 TRP D 30 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (16386) covalent geometry : angle 0.66178 / 0.34 (22134) hydrogen bonds : bond 0.03946 / 2.53 ( 871) hydrogen bonds : angle 5.06121 / 3.61 ( 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 562 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 500 time to evaluate : 0.493 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 56 ASP cc_start: 0.8787 (m-30) cc_final: 0.8418 (m-30) REVERT: A 65 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8294 (mm-30) REVERT: A 161 ARG cc_start: 0.8021 (ttm170) cc_final: 0.7794 (mmm-85) REVERT: A 209 LYS cc_start: 0.8752 (tptt) cc_final: 0.8548 (tptt) REVERT: A 214 LYS cc_start: 0.8250 (ttmm) cc_final: 0.7973 (mttm) REVERT: A 218 ASN cc_start: 0.8909 (t0) cc_final: 0.8312 (t0) REVERT: A 307 TYR cc_start: 0.9141 (t80) cc_final: 0.8902 (t80) REVERT: A 341 LYS cc_start: 0.9361 (mmtm) cc_final: 0.9076 (mmpt) REVERT: A 344 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8555 (mt-10) REVERT: A 359 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.7785 (ttp) REVERT: A 366 LYS cc_start: 0.9152 (mtmt) cc_final: 0.8817 (ptpp) REVERT: A 381 LEU cc_start: 0.9101 (tp) cc_final: 0.8435 (pt) REVERT: A 384 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7544 (pm20) REVERT: A 385 VAL cc_start: 0.8812 (t) cc_final: 0.8406 (t) REVERT: A 390 GLN cc_start: 0.8525 (mt0) cc_final: 0.8136 (mt0) REVERT: A 393 SER cc_start: 0.9172 (m) cc_final: 0.8506 (p) REVERT: A 402 GLU cc_start: 0.8156 (mp0) cc_final: 0.7279 (mp0) REVERT: A 505 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7735 (mt-10) REVERT: A 548 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8353 (mm-30) REVERT: A 640 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.7979 (tpp) REVERT: B 95 MET cc_start: 0.8591 (tpp) cc_final: 0.8233 (tpp) REVERT: B 99 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8654 (tptp) REVERT: B 108 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8546 (p) REVERT: B 128 PHE cc_start: 0.9333 (t80) cc_final: 0.9106 (t80) REVERT: B 184 ARG cc_start: 0.9088 (tpp-160) cc_final: 0.8692 (tpp-160) REVERT: B 190 MET cc_start: 0.9149 (mtm) cc_final: 0.8865 (mtm) REVERT: B 257 ASP cc_start: 0.8597 (m-30) cc_final: 0.8259 (m-30) REVERT: B 322 MET cc_start: 0.8998 (mmm) cc_final: 0.8319 (mmm) REVERT: B 348 MET cc_start: 0.8049 (tpp) cc_final: 0.7819 (tpp) REVERT: B 357 TYR cc_start: 0.8361 (m-80) cc_final: 0.8016 (m-10) REVERT: B 362 ASP cc_start: 0.7551 (m-30) cc_final: 0.7285 (m-30) REVERT: B 384 GLU cc_start: 0.8638 (pm20) cc_final: 0.7961 (pp20) REVERT: B 415 ASN cc_start: 0.9350 (t0) cc_final: 0.8760 (t0) REVERT: B 467 ASN cc_start: 0.9082 (t0) cc_final: 0.8816 (m-40) REVERT: B 493 MET cc_start: 0.9439 (tmm) cc_final: 0.8994 (tmm) REVERT: B 599 GLU cc_start: 0.8218 (pt0) cc_final: 0.7982 (pt0) REVERT: B 668 ASN cc_start: 0.8709 (m-40) cc_final: 0.8201 (m110) REVERT: C 17 PHE cc_start: 0.8581 (p90) cc_final: 0.7835 (p90) REVERT: C 69 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8296 (pp30) REVERT: C 74 MET cc_start: 0.7049 (mtm) cc_final: 0.6514 (ptp) REVERT: C 76 ILE cc_start: 0.8560 (mm) cc_final: 0.8136 (tp) REVERT: C 85 GLN cc_start: 0.4743 (mt0) cc_final: 0.3901 (pt0) REVERT: C 93 MET cc_start: 0.8920 (mtt) cc_final: 0.8624 (mtt) REVERT: C 158 VAL cc_start: 0.9557 (t) cc_final: 0.8924 (t) REVERT: C 162 TYR cc_start: 0.9342 (OUTLIER) cc_final: 0.8711 (m-10) REVERT: C 201 HIS cc_start: 0.8796 (m90) cc_final: 0.8206 (m90) REVERT: C 271 LEU cc_start: 0.8663 (mm) cc_final: 0.7966 (mm) REVERT: D 18 THR cc_start: 0.7749 (m) cc_final: 0.7413 (m) REVERT: D 25 ASN cc_start: 0.9397 (OUTLIER) cc_final: 0.8968 (m110) REVERT: D 28 GLN cc_start: 0.8656 (tt0) cc_final: 0.8387 (tt0) REVERT: D 56 MET cc_start: 0.8341 (mmt) cc_final: 0.7773 (ptt) REVERT: D 137 MET cc_start: 0.5281 (mtp) cc_final: 0.4962 (ptp) REVERT: D 174 TYR cc_start: 0.8160 (OUTLIER) cc_final: 0.7328 (t80) REVERT: D 270 ASN cc_start: 0.7662 (m-40) cc_final: 0.7295 (m110) outliers start: 62 outliers final: 40 residues processed: 524 average time/residue: 0.1051 time to fit residues: 84.2280 Evaluate side-chains 527 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 478 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 381 LEU 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 561 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 624 PHE Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 254 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 153 optimal weight: 20.0000 chunk 11 optimal weight: 0.7980 chunk 158 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 151 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 646 GLN D 25 ASN D 28 GLN D 71 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.134099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.096519 restraints weight = 35356.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.099749 restraints weight = 16645.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.101932 restraints weight = 9990.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.103257 restraints weight = 6760.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.104146 restraints weight = 5158.987| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.6153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16386 Z= 0.149 Angle : 0.677 10.119 22134 Z= 0.345 Chirality : 0.044 0.176 2360 Planarity : 0.004 0.069 2818 Dihedral : 8.298 134.072 2293 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.26 % Allowed : 26.63 % Favored : 70.10 % 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: 0.83 (0.19), residues: 1932 helix: 1.01 (0.15), residues: 1138 sheet: -0.34 (0.44), residues: 136 loop : 0.14 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 235 TYR 0.035 0.001 TYR D 142 PHE 0.039 0.002 PHE C 154 TRP 0.039 0.002 TRP D 30 HIS 0.004 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (16386) covalent geometry : angle 0.67656 / 0.34 (22134) hydrogen bonds : bond 0.03937 / 2.53 ( 871) hydrogen bonds : angle 5.03266 / 3.58 ( 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 568 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 512 time to evaluate : 0.389 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: A 56 ASP cc_start: 0.8782 (m-30) cc_final: 0.8417 (m-30) REVERT: A 65 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8240 (mm-30) REVERT: A 116 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7475 (mt-10) REVERT: A 119 GLU cc_start: 0.8501 (mp0) cc_final: 0.8265 (mp0) REVERT: A 214 LYS cc_start: 0.8141 (ttmm) cc_final: 0.7873 (mttm) REVERT: A 218 ASN cc_start: 0.8865 (t0) cc_final: 0.8253 (t0) REVERT: A 307 TYR cc_start: 0.9100 (t80) cc_final: 0.8845 (t80) REVERT: A 341 LYS cc_start: 0.9352 (mmtm) cc_final: 0.9063 (mmpt) REVERT: A 344 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8528 (mt-10) REVERT: A 359 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7709 (ttp) REVERT: A 366 LYS cc_start: 0.9099 (mtmt) cc_final: 0.8780 (ptpp) REVERT: A 381 LEU cc_start: 0.9032 (tp) cc_final: 0.8519 (pt) REVERT: A 384 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7462 (pm20) REVERT: A 385 VAL cc_start: 0.8720 (t) cc_final: 0.8211 (t) REVERT: A 390 GLN cc_start: 0.8526 (mt0) cc_final: 0.8154 (mt0) REVERT: A 393 SER cc_start: 0.9206 (m) cc_final: 0.8498 (p) REVERT: A 402 GLU cc_start: 0.8152 (mp0) cc_final: 0.7267 (mp0) REVERT: A 548 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8387 (mm-30) REVERT: A 640 MET cc_start: 0.9233 (OUTLIER) cc_final: 0.7895 (tpp) REVERT: B 95 MET cc_start: 0.8553 (tpp) cc_final: 0.8213 (tpp) REVERT: B 99 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8642 (tptp) REVERT: B 108 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8558 (p) REVERT: B 128 PHE cc_start: 0.9308 (t80) cc_final: 0.9024 (t80) REVERT: B 178 SER cc_start: 0.8265 (OUTLIER) cc_final: 0.8054 (p) REVERT: B 184 ARG cc_start: 0.9099 (tpp-160) cc_final: 0.8660 (tpp-160) REVERT: B 190 MET cc_start: 0.9128 (mtm) cc_final: 0.8837 (mtm) REVERT: B 257 ASP cc_start: 0.8552 (m-30) cc_final: 0.8222 (m-30) REVERT: B 322 MET cc_start: 0.9000 (mmm) cc_final: 0.8288 (mmm) REVERT: B 348 MET cc_start: 0.8030 (tpp) cc_final: 0.7797 (tpp) REVERT: B 361 GLN cc_start: 0.8636 (tt0) cc_final: 0.8301 (tt0) REVERT: B 415 ASN cc_start: 0.9308 (t0) cc_final: 0.8691 (t0) REVERT: B 467 ASN cc_start: 0.9054 (t0) cc_final: 0.8800 (m-40) REVERT: B 493 MET cc_start: 0.9429 (tmm) cc_final: 0.8995 (tmm) REVERT: B 576 LEU cc_start: 0.9430 (mt) cc_final: 0.9200 (mt) REVERT: B 646 GLN cc_start: 0.8878 (pt0) cc_final: 0.8467 (pm20) REVERT: B 668 ASN cc_start: 0.8702 (m-40) cc_final: 0.8224 (m110) REVERT: C 17 PHE cc_start: 0.8597 (p90) cc_final: 0.7789 (p90) REVERT: C 76 ILE cc_start: 0.8587 (mm) cc_final: 0.8143 (tp) REVERT: C 85 GLN cc_start: 0.5231 (mt0) cc_final: 0.4384 (pt0) REVERT: C 93 MET cc_start: 0.8970 (mtt) cc_final: 0.8706 (mtt) REVERT: C 154 PHE cc_start: 0.9132 (m-80) cc_final: 0.8685 (m-80) REVERT: C 158 VAL cc_start: 0.9543 (t) cc_final: 0.8588 (p) REVERT: C 162 TYR cc_start: 0.9290 (m-10) cc_final: 0.8665 (m-10) REVERT: C 201 HIS cc_start: 0.8912 (m90) cc_final: 0.8333 (m90) REVERT: C 271 LEU cc_start: 0.8669 (mm) cc_final: 0.8049 (mm) REVERT: D 18 THR cc_start: 0.7910 (m) cc_final: 0.7596 (m) REVERT: D 25 ASN cc_start: 0.9318 (OUTLIER) cc_final: 0.8584 (m110) REVERT: D 28 GLN cc_start: 0.8558 (tt0) cc_final: 0.8285 (tm-30) REVERT: D 56 MET cc_start: 0.8333 (mmt) cc_final: 0.7738 (ptt) REVERT: D 174 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.7239 (t80) REVERT: D 210 GLN cc_start: 0.8265 (mt0) cc_final: 0.8022 (mt0) REVERT: D 235 LEU cc_start: 0.8924 (mm) cc_final: 0.8693 (mp) REVERT: D 270 ASN cc_start: 0.7694 (m-40) cc_final: 0.7241 (m110) outliers start: 56 outliers final: 38 residues processed: 533 average time/residue: 0.0997 time to fit residues: 81.7445 Evaluate side-chains 527 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 479 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 381 LEU 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 561 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 624 PHE Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 254 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.133902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.096117 restraints weight = 35109.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.099486 restraints weight = 16722.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.101675 restraints weight = 9817.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.102953 restraints weight = 6713.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.103962 restraints weight = 5165.931| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.6326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16386 Z= 0.143 Angle : 0.699 10.315 22134 Z= 0.359 Chirality : 0.045 0.212 2360 Planarity : 0.004 0.065 2818 Dihedral : 8.223 134.283 2293 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.86 % Allowed : 27.39 % Favored : 69.76 % 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: 0.74 (0.19), residues: 1932 helix: 0.95 (0.15), residues: 1137 sheet: -0.25 (0.46), residues: 124 loop : 0.04 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 235 TYR 0.020 0.001 TYR D 142 PHE 0.032 0.002 PHE C 154 TRP 0.033 0.002 TRP D 30 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (16386) covalent geometry : angle 0.69864 / 0.36 (22134) hydrogen bonds : bond 0.03965 / 2.57 ( 871) hydrogen bonds : angle 5.08393 / 3.61 ( 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 553 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 504 time to evaluate : 0.574 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: A 56 ASP cc_start: 0.8788 (m-30) cc_final: 0.8441 (m-30) REVERT: A 65 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8249 (mm-30) REVERT: A 119 GLU cc_start: 0.8515 (mp0) cc_final: 0.8269 (mp0) REVERT: A 150 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8643 (tm-30) REVERT: A 214 LYS cc_start: 0.8135 (ttmm) cc_final: 0.7913 (mttm) REVERT: A 218 ASN cc_start: 0.8842 (t0) cc_final: 0.8215 (t0) REVERT: A 232 ASN cc_start: 0.9161 (m110) cc_final: 0.8927 (m110) REVERT: A 307 TYR cc_start: 0.9102 (t80) cc_final: 0.8851 (t80) REVERT: A 341 LYS cc_start: 0.9348 (mmtm) cc_final: 0.9058 (mmpt) REVERT: A 344 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8529 (mt-10) REVERT: A 359 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7522 (ttp) REVERT: A 361 GLN cc_start: 0.8525 (tp40) cc_final: 0.7952 (tp40) REVERT: A 366 LYS cc_start: 0.9077 (mtmt) cc_final: 0.8783 (ptpp) REVERT: A 381 LEU cc_start: 0.9026 (tp) cc_final: 0.8549 (pt) REVERT: A 384 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7539 (pm20) REVERT: A 385 VAL cc_start: 0.8739 (t) cc_final: 0.8220 (t) REVERT: A 390 GLN cc_start: 0.8537 (mt0) cc_final: 0.8171 (mt0) REVERT: A 393 SER cc_start: 0.9188 (m) cc_final: 0.8902 (m) REVERT: A 402 GLU cc_start: 0.8136 (mp0) cc_final: 0.7917 (mp0) REVERT: A 483 GLU cc_start: 0.9084 (mp0) cc_final: 0.8753 (mp0) REVERT: A 548 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8376 (mm-30) REVERT: A 640 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.7774 (tpp) REVERT: B 95 MET cc_start: 0.8521 (tpp) cc_final: 0.8208 (tpp) REVERT: B 99 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8651 (tptp) REVERT: B 128 PHE cc_start: 0.9295 (t80) cc_final: 0.8994 (t80) REVERT: B 184 ARG cc_start: 0.9106 (tpp-160) cc_final: 0.8709 (tpp-160) REVERT: B 190 MET cc_start: 0.9144 (mtm) cc_final: 0.8861 (mtm) REVERT: B 257 ASP cc_start: 0.8535 (m-30) cc_final: 0.8185 (m-30) REVERT: B 301 PHE cc_start: 0.9119 (m-80) cc_final: 0.8819 (m-80) REVERT: B 322 MET cc_start: 0.9042 (mmm) cc_final: 0.8335 (mmm) REVERT: B 348 MET cc_start: 0.8009 (tpp) cc_final: 0.7771 (tpp) REVERT: B 357 TYR cc_start: 0.8044 (m-10) cc_final: 0.7662 (m-10) REVERT: B 361 GLN cc_start: 0.8665 (tt0) cc_final: 0.8361 (tt0) REVERT: B 384 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.7903 (pp20) REVERT: B 415 ASN cc_start: 0.9185 (t0) cc_final: 0.8768 (t0) REVERT: B 467 ASN cc_start: 0.9006 (t0) cc_final: 0.8751 (m-40) REVERT: B 493 MET cc_start: 0.9418 (tmm) cc_final: 0.8984 (tmm) REVERT: B 576 LEU cc_start: 0.9421 (mt) cc_final: 0.9197 (mt) REVERT: B 657 PHE cc_start: 0.8790 (m-80) cc_final: 0.8494 (m-80) REVERT: B 668 ASN cc_start: 0.8704 (m-40) cc_final: 0.8221 (m110) REVERT: C 17 PHE cc_start: 0.8613 (p90) cc_final: 0.7793 (p90) REVERT: C 76 ILE cc_start: 0.8586 (mm) cc_final: 0.8134 (tp) REVERT: C 85 GLN cc_start: 0.5180 (mt0) cc_final: 0.4377 (pt0) REVERT: C 93 MET cc_start: 0.9052 (mtt) cc_final: 0.8792 (mtt) REVERT: C 154 PHE cc_start: 0.9167 (m-80) cc_final: 0.8836 (m-80) REVERT: C 158 VAL cc_start: 0.9557 (t) cc_final: 0.8612 (p) REVERT: C 162 TYR cc_start: 0.9313 (OUTLIER) cc_final: 0.8672 (m-10) REVERT: C 201 HIS cc_start: 0.8879 (m90) cc_final: 0.8271 (m90) REVERT: C 271 LEU cc_start: 0.8735 (mm) cc_final: 0.8074 (mm) REVERT: D 18 THR cc_start: 0.7821 (m) cc_final: 0.7460 (m) REVERT: D 24 GLN cc_start: 0.8687 (tp-100) cc_final: 0.8021 (tm-30) REVERT: D 25 ASN cc_start: 0.9362 (m-40) cc_final: 0.8803 (m110) REVERT: D 56 MET cc_start: 0.8355 (mmt) cc_final: 0.7802 (ptt) REVERT: D 174 TYR cc_start: 0.8034 (OUTLIER) cc_final: 0.7278 (t80) outliers start: 49 outliers final: 33 residues processed: 522 average time/residue: 0.0992 time to fit residues: 78.8614 Evaluate side-chains 520 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 479 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 GLU 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 561 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 624 PHE Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 174 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 181 optimal weight: 10.0000 chunk 165 optimal weight: 0.0670 chunk 16 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN C 71 ASN D 25 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.135080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.097207 restraints weight = 35214.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.100584 restraints weight = 16872.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.102739 restraints weight = 9963.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.104066 restraints weight = 6838.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.105007 restraints weight = 5271.734| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.6518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16386 Z= 0.140 Angle : 0.722 14.706 22134 Z= 0.368 Chirality : 0.045 0.199 2360 Planarity : 0.004 0.080 2818 Dihedral : 8.150 134.490 2293 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.51 % Allowed : 28.09 % Favored : 69.41 % 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: 0.65 (0.19), residues: 1932 helix: 0.88 (0.15), residues: 1136 sheet: -0.30 (0.46), residues: 128 loop : 0.01 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 235 TYR 0.030 0.001 TYR C 55 PHE 0.032 0.002 PHE C 178 TRP 0.032 0.002 TRP D 30 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (16386) covalent geometry : angle 0.72199 / 0.37 (22134) hydrogen bonds : bond 0.03970 / 2.57 ( 871) hydrogen bonds : angle 5.07708 / 3.61 ( 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 535 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 492 time to evaluate : 0.395 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 56 ASP cc_start: 0.8781 (m-30) cc_final: 0.8430 (m-30) REVERT: A 65 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8283 (mm-30) REVERT: A 119 GLU cc_start: 0.8494 (mp0) cc_final: 0.8213 (mp0) REVERT: A 150 GLN cc_start: 0.8998 (tm-30) cc_final: 0.8620 (tm-30) REVERT: A 188 ILE cc_start: 0.9293 (mt) cc_final: 0.9062 (mm) REVERT: A 209 LYS cc_start: 0.8662 (tptt) cc_final: 0.8443 (tptt) REVERT: A 214 LYS cc_start: 0.8065 (ttmm) cc_final: 0.7851 (mttm) REVERT: A 218 ASN cc_start: 0.8834 (t0) cc_final: 0.8089 (t0) REVERT: A 232 ASN cc_start: 0.9128 (m110) cc_final: 0.8883 (m110) REVERT: A 307 TYR cc_start: 0.9108 (t80) cc_final: 0.8859 (t80) REVERT: A 341 LYS cc_start: 0.9347 (mmtm) cc_final: 0.8815 (mmpt) REVERT: A 344 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8557 (mt-10) REVERT: A 359 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7398 (ttp) REVERT: A 361 GLN cc_start: 0.8531 (tp40) cc_final: 0.7975 (tp40) REVERT: A 366 LYS cc_start: 0.9070 (mtmt) cc_final: 0.8764 (ptpp) REVERT: A 381 LEU cc_start: 0.8898 (tp) cc_final: 0.8535 (pt) REVERT: A 384 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7552 (pm20) REVERT: A 385 VAL cc_start: 0.8716 (t) cc_final: 0.8153 (t) REVERT: A 390 GLN cc_start: 0.8486 (mt0) cc_final: 0.8198 (mt0) REVERT: A 393 SER cc_start: 0.9181 (m) cc_final: 0.8214 (p) REVERT: A 402 GLU cc_start: 0.8094 (mp0) cc_final: 0.7206 (mp0) REVERT: A 427 LYS cc_start: 0.8924 (ttpp) cc_final: 0.8678 (ttpp) REVERT: A 483 GLU cc_start: 0.9071 (mp0) cc_final: 0.8755 (mp0) REVERT: A 640 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.7728 (tpp) REVERT: B 95 MET cc_start: 0.8512 (tpp) cc_final: 0.8183 (tpp) REVERT: B 99 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8643 (tptp) REVERT: B 128 PHE cc_start: 0.9269 (t80) cc_final: 0.9006 (t80) REVERT: B 184 ARG cc_start: 0.9098 (tpp-160) cc_final: 0.8697 (tpp-160) REVERT: B 190 MET cc_start: 0.9117 (mtm) cc_final: 0.8830 (mtm) REVERT: B 257 ASP cc_start: 0.8478 (m-30) cc_final: 0.8095 (m-30) REVERT: B 274 ARG cc_start: 0.7086 (tpp-160) cc_final: 0.6877 (tpp-160) REVERT: B 301 PHE cc_start: 0.9051 (m-80) cc_final: 0.8773 (m-80) REVERT: B 322 MET cc_start: 0.9007 (mmm) cc_final: 0.8341 (mmm) REVERT: B 348 MET cc_start: 0.7961 (tpp) cc_final: 0.7751 (tpp) REVERT: B 357 TYR cc_start: 0.7962 (m-10) cc_final: 0.7589 (m-10) REVERT: B 361 GLN cc_start: 0.8688 (tt0) cc_final: 0.8362 (tt0) REVERT: B 384 GLU cc_start: 0.8700 (pm20) cc_final: 0.7923 (pp20) REVERT: B 415 ASN cc_start: 0.9222 (t0) cc_final: 0.8856 (t0) REVERT: B 467 ASN cc_start: 0.8980 (t0) cc_final: 0.8727 (m-40) REVERT: B 474 GLN cc_start: 0.8261 (mt0) cc_final: 0.7897 (mt0) REVERT: B 493 MET cc_start: 0.9398 (tmm) cc_final: 0.8974 (tmm) REVERT: B 576 LEU cc_start: 0.9413 (mt) cc_final: 0.9195 (mt) REVERT: B 668 ASN cc_start: 0.8675 (m-40) cc_final: 0.8199 (m110) REVERT: C 17 PHE cc_start: 0.8609 (p90) cc_final: 0.7797 (p90) REVERT: C 67 THR cc_start: 0.9201 (t) cc_final: 0.8946 (p) REVERT: C 85 GLN cc_start: 0.5194 (mt0) cc_final: 0.4428 (pt0) REVERT: C 93 MET cc_start: 0.9034 (mtt) cc_final: 0.8820 (mtt) REVERT: C 154 PHE cc_start: 0.9187 (m-80) cc_final: 0.8979 (m-80) REVERT: C 158 VAL cc_start: 0.9570 (t) cc_final: 0.9038 (t) REVERT: C 162 TYR cc_start: 0.9310 (OUTLIER) cc_final: 0.8685 (m-10) REVERT: C 201 HIS cc_start: 0.8877 (m90) cc_final: 0.8282 (m90) REVERT: C 233 ASN cc_start: 0.9112 (m-40) cc_final: 0.8725 (m-40) REVERT: C 271 LEU cc_start: 0.8737 (mm) cc_final: 0.8099 (mm) REVERT: D 24 GLN cc_start: 0.8989 (tp-100) cc_final: 0.8466 (tm-30) REVERT: D 25 ASN cc_start: 0.9233 (OUTLIER) cc_final: 0.8455 (m110) REVERT: D 56 MET cc_start: 0.8390 (mmt) cc_final: 0.7817 (ptt) REVERT: D 174 TYR cc_start: 0.8077 (OUTLIER) cc_final: 0.7319 (t80) REVERT: D 189 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7702 (pt0) REVERT: D 269 MET cc_start: 0.8401 (tmm) cc_final: 0.7708 (ppp) REVERT: D 270 ASN cc_start: 0.7902 (m-40) cc_final: 0.7217 (m110) outliers start: 43 outliers final: 33 residues processed: 504 average time/residue: 0.0997 time to fit residues: 76.7049 Evaluate side-chains 516 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 476 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 381 LEU 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 561 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 624 PHE Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 174 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 148 optimal weight: 20.0000 chunk 125 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.135129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.097609 restraints weight = 34991.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.100951 restraints weight = 16697.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.103107 restraints weight = 9845.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.104520 restraints weight = 6754.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.105332 restraints weight = 5142.387| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.6542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 16386 Z= 0.207 Angle : 0.895 59.174 22134 Z= 0.501 Chirality : 0.045 0.363 2360 Planarity : 0.004 0.072 2818 Dihedral : 8.162 134.505 2293 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.56 % Allowed : 28.32 % Favored : 69.11 % Cbeta Deviations : 0.05 % 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: 0.64 (0.19), residues: 1932 helix: 0.87 (0.15), residues: 1136 sheet: -0.30 (0.46), residues: 128 loop : 0.00 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 256 TYR 0.026 0.002 TYR C 174 PHE 0.038 0.002 PHE C 178 TRP 0.029 0.002 TRP D 30 HIS 0.004 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.21 (16386) covalent geometry : angle 0.89525 / 0.50 (22134) hydrogen bonds : bond 0.04050 / 2.61 ( 871) hydrogen bonds : angle 5.11512 / 3.63 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2707.05 seconds wall clock time: 47 minutes 47.84 seconds (2867.84 seconds total)