Starting phenix.real_space_refine on Sun Aug 24 01:07:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byz_45049/08_2025/9byz_45049_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byz_45049/08_2025/9byz_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 { model { file = "/net/cci-nas-00/data/ceres_data/9byz_45049/08_2025/9byz_45049_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byz_45049/08_2025/9byz_45049_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9byz_45049/08_2025/9byz_45049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byz_45049/08_2025/9byz_45049.map" } 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-2.0-5787/lib/python3.9/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: 4.30, per 1000 atoms: 0.27 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: 1.55 Conformation dependent library (CDL) restraints added in 705.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.60 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: 3.16 Time building geometry restraints manager: 2.00 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=" 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=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.039 1.20e-02 6.94e+03 1.04e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.032 1.08e-02 8.57e+03 9.05e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.569 -0.032 1.17e-02 7.31e+03 7.41e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.573 -0.033 1.25e-02 6.40e+03 6.86e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21576 2.09 - 4.18: 515 4.18 - 6.27: 37 6.27 - 8.36: 2 8.36 - 10.45: 4 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 - 35.81: 9470 35.81 - 71.61: 337 71.61 - 107.42: 37 107.42 - 143.22: 3 143.22 - 179.03: 3 Dihedral angle restraints: 9850 sinusoidal: 4092 harmonic: 5758 Sorted by residual: dihedral pdb=" C2 TTP A 803 " pdb=" C1' TTP A 803 " pdb=" N1 TTP A 803 " pdb=" O4' TTP A 803 " ideal model delta sinusoidal sigma weight residual -58.32 120.71 -179.03 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 TTP B 801 " pdb=" C1' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " ideal model delta sinusoidal sigma weight residual 301.68 151.10 150.58 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" C5' TTP A 803 " pdb=" O5' TTP A 803 " pdb=" PA TTP A 803 " pdb=" O3A TTP A 803 " ideal model delta sinusoidal sigma weight residual 179.97 31.91 148.06 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 9847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2146 0.093 - 0.186: 179 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 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: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.200 Find NCS groups from input model: 0.320 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: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 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 0.060 16386 Z= 0.315 Angle : 0.740 10.448 22134 Z= 0.463 Chirality : 0.057 0.464 2360 Planarity : 0.003 0.042 2818 Dihedral : 17.908 179.029 6154 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 aren 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 covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.74014 (22134) hydrogen bonds : bond 0.15420 ( 871) hydrogen bonds : angle 6.51780 ( 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 : 0.696 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: 0.8740 (tt) REVERT: A 183 SER cc_start: 0.8618 (p) cc_final: 0.8373 (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: 0.7273 (t0) REVERT: A 257 ASP cc_start: 0.8040 (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: 0.8787 (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: 0.8149 (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: 0.8219 (t0) cc_final: 0.6646 (p0) REVERT: B 180 ASN cc_start: 0.7454 (m-40) cc_final: 0.7185 (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: 0.3147 (m-80) REVERT: C 287 LEU cc_start: 0.2172 (OUTLIER) cc_final: 0.1826 (mp) REVERT: D 256 VAL cc_start: 0.6874 (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: 0.1505 time to fit residues: 192.0986 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 : 0.641 ------------------------------------------------------------------------------- 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: 5.9990 chunk 149 optimal weight: 0.1980 overall best weight: 1.3760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 320 ASN A 387 GLN ** 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** B 645 GLN C 24 GLN ** 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 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.135648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.097169 restraints weight = 34598.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.100564 restraints weight = 16646.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102822 restraints weight = 9820.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.104256 restraints weight = 6694.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.105343 restraints weight = 5085.533| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16386 Z= 0.173 Angle : 0.677 14.925 22134 Z= 0.351 Chirality : 0.044 0.171 2360 Planarity : 0.004 0.040 2818 Dihedral : 11.512 172.487 2259 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 4.02 % Allowed : 19.41 % Favored : 76.57 % 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 aren not related in a simple way. whole: 1.40 (0.19), residues: 1932 helix: 1.36 (0.15), residues: 1129 sheet: 0.28 (0.42), residues: 130 loop : 0.53 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 235 TYR 0.022 0.002 TYR D 177 PHE 0.037 0.002 PHE C 168 TRP 0.021 0.002 TRP C 30 HIS 0.006 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00384 (16386) covalent geometry : angle 0.67667 (22134) hydrogen bonds : bond 0.04712 ( 871) hydrogen bonds : angle 5.19615 ( 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 700 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 631 time to evaluate : 0.629 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: 0.9279 (mt) cc_final: 0.9066 (mt) REVERT: A 99 LYS cc_start: 0.9196 (mmmm) cc_final: 0.8677 (mmmm) REVERT: A 103 ASP cc_start: 0.8737 (m-30) cc_final: 0.8504 (m-30) REVERT: A 194 LYS cc_start: 0.9306 (tttp) cc_final: 0.8960 (tttt) REVERT: A 214 LYS cc_start: 0.8415 (ttmm) cc_final: 0.8171 (mttm) REVERT: A 218 ASN cc_start: 0.8871 (t0) cc_final: 0.8341 (t0) REVERT: A 256 ARG cc_start: 0.9101 (ttp80) cc_final: 0.8852 (ttp80) REVERT: A 291 LEU cc_start: 0.9670 (mt) cc_final: 0.9424 (mp) REVERT: A 335 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7591 (mt-10) REVERT: A 358 ILE cc_start: 0.9362 (mm) cc_final: 0.9142 (mm) REVERT: A 384 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7574 (pm20) REVERT: A 385 VAL cc_start: 0.8889 (t) cc_final: 0.8313 (t) REVERT: A 467 ASN cc_start: 0.9156 (t0) cc_final: 0.8953 (m-40) REVERT: A 477 ILE cc_start: 0.9612 (mt) cc_final: 0.9411 (mp) REVERT: A 483 GLU cc_start: 0.9026 (mp0) cc_final: 0.8264 (pm20) REVERT: A 505 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7707 (mt-10) REVERT: A 548 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8357 (mm-30) REVERT: A 640 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8393 (tpp) REVERT: A 644 ILE cc_start: 0.9541 (mt) cc_final: 0.9302 (mt) REVERT: B 71 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9051 (mp) REVERT: B 95 MET cc_start: 0.8530 (tpp) cc_final: 0.8236 (tpp) REVERT: B 177 ASP cc_start: 0.7910 (t0) cc_final: 0.7546 (t70) REVERT: B 184 ARG cc_start: 0.9160 (tpp-160) cc_final: 0.8646 (tpp-160) REVERT: B 190 MET cc_start: 0.9158 (mtm) cc_final: 0.8828 (mtm) REVERT: B 235 ARG cc_start: 0.8411 (ttm110) cc_final: 0.7801 (mtm-85) REVERT: B 256 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7650 (ttp80) REVERT: B 290 GLU cc_start: 0.8941 (tt0) cc_final: 0.8605 (tm-30) REVERT: B 322 MET cc_start: 0.8873 (mmm) cc_final: 0.8276 (mmm) REVERT: B 335 GLU cc_start: 0.8458 (mt-10) cc_final: 0.7878 (mt-10) REVERT: B 362 ASP cc_start: 0.7707 (m-30) cc_final: 0.7425 (m-30) REVERT: B 374 SER cc_start: 0.9439 (t) cc_final: 0.9193 (t) REVERT: B 375 LYS cc_start: 0.8855 (mtmm) cc_final: 0.8392 (mtpp) REVERT: B 384 GLU cc_start: 0.8286 (pm20) cc_final: 0.7584 (pm20) REVERT: B 425 ILE cc_start: 0.9162 (mt) cc_final: 0.8961 (mt) REVERT: B 467 ASN cc_start: 0.9184 (t0) cc_final: 0.8897 (m-40) REVERT: B 493 MET cc_start: 0.9432 (tmm) cc_final: 0.9090 (tmm) REVERT: B 515 ASP cc_start: 0.8825 (m-30) cc_final: 0.8624 (m-30) REVERT: B 620 SER cc_start: 0.9137 (OUTLIER) cc_final: 0.8932 (p) REVERT: B 645 GLN cc_start: 0.9126 (tp40) cc_final: 0.8840 (tp-100) REVERT: B 669 ARG cc_start: 0.8872 (mtp85) cc_final: 0.8642 (mmm-85) REVERT: B 683 TYR cc_start: 0.8757 (t80) cc_final: 0.8245 (t80) REVERT: C 68 GLU cc_start: 0.9371 (mm-30) cc_final: 0.9098 (mm-30) REVERT: C 85 GLN cc_start: 0.4136 (mt0) cc_final: 0.3342 (pt0) REVERT: C 93 MET cc_start: 0.8479 (mtt) cc_final: 0.8217 (mtt) REVERT: C 137 MET cc_start: 0.6922 (mtp) cc_final: 0.6644 (mtp) REVERT: C 154 PHE cc_start: 0.8691 (t80) cc_final: 0.8365 (t80) REVERT: C 157 MET cc_start: 0.9014 (mtt) cc_final: 0.8734 (mtt) REVERT: C 158 VAL cc_start: 0.9532 (t) cc_final: 0.8896 (t) REVERT: C 162 TYR cc_start: 0.9288 (m-10) cc_final: 0.8840 (m-10) REVERT: C 266 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.9082 (tppt) REVERT: C 271 LEU cc_start: 0.8603 (mm) cc_final: 0.8025 (mm) REVERT: C 317 ASP cc_start: 0.8274 (m-30) cc_final: 0.7872 (m-30) REVERT: C 320 PHE cc_start: 0.9403 (m-80) cc_final: 0.9044 (m-80) REVERT: D 44 TRP cc_start: 0.7800 (t-100) cc_final: 0.7524 (t-100) REVERT: D 71 ASN cc_start: 0.8459 (m-40) cc_final: 0.8114 (m110) REVERT: D 92 PHE cc_start: 0.7193 (t80) cc_final: 0.6834 (t80) REVERT: D 96 MET cc_start: 0.5997 (mmm) cc_final: 0.5776 (mmt) REVERT: D 137 MET cc_start: 0.5407 (mtp) cc_final: 0.5164 (ptp) REVERT: D 174 TYR cc_start: 0.8030 (OUTLIER) cc_final: 0.7192 (t80) REVERT: D 184 LEU cc_start: 0.8674 (mt) cc_final: 0.8386 (mt) REVERT: D 195 LEU cc_start: 0.8800 (tt) cc_final: 0.8490 (mm) REVERT: D 223 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8358 (tp30) REVERT: D 227 PHE cc_start: 0.8359 (m-10) cc_final: 0.8073 (m-10) outliers start: 69 outliers final: 31 residues processed: 665 average time/residue: 0.1299 time to fit residues: 129.8574 Evaluate side-chains 554 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 514 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE 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 621 ASN Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 646 GLN 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 96 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 256 ARG Chi-restraints excluded: chain B residue 260 ASP 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 583 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 43 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 266 LYS 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 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: 1.9990 chunk 131 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 182 optimal weight: 0.9990 chunk 159 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 158 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 42 ASN A 259 ASN A 320 ASN ** 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 361 GLN B 646 GLN B 676 HIS C 24 GLN C 69 GLN C 91 ASN C 234 GLN C 249 GLN D 25 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.132157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.093845 restraints weight = 35343.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.097199 restraints weight = 17146.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.099375 restraints weight = 10249.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.100740 restraints weight = 7033.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.101758 restraints weight = 5376.562| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16386 Z= 0.192 Angle : 0.649 14.040 22134 Z= 0.335 Chirality : 0.044 0.172 2360 Planarity : 0.003 0.031 2818 Dihedral : 11.220 171.191 2255 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.60 % Allowed : 20.69 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.19), residues: 1932 helix: 1.31 (0.15), residues: 1132 sheet: -0.12 (0.41), residues: 146 loop : 0.37 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 117 TYR 0.038 0.002 TYR A 498 PHE 0.033 0.002 PHE C 172 TRP 0.029 0.002 TRP D 30 HIS 0.006 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00428 (16386) covalent geometry : angle 0.64890 (22134) hydrogen bonds : bond 0.04246 ( 871) hydrogen bonds : angle 5.11443 ( 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 630 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 551 time to evaluate : 0.652 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 99 LYS cc_start: 0.9167 (mmmm) cc_final: 0.8446 (mmmm) REVERT: A 102 ASN cc_start: 0.9056 (OUTLIER) cc_final: 0.8806 (m-40) REVERT: A 103 ASP cc_start: 0.8899 (m-30) cc_final: 0.8548 (m-30) REVERT: A 117 ARG cc_start: 0.7853 (mtt-85) cc_final: 0.7370 (mtt-85) REVERT: A 158 ASN cc_start: 0.8933 (m-40) cc_final: 0.8536 (m-40) REVERT: A 161 ARG cc_start: 0.8030 (ttm110) cc_final: 0.7796 (mmm-85) REVERT: A 218 ASN cc_start: 0.8880 (t0) cc_final: 0.8294 (t0) REVERT: A 335 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7497 (mt-10) REVERT: A 344 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8628 (mt-10) REVERT: A 359 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7940 (ttp) REVERT: A 362 ASP cc_start: 0.8317 (m-30) cc_final: 0.7589 (m-30) REVERT: A 381 LEU cc_start: 0.9053 (tp) cc_final: 0.8484 (pt) REVERT: A 384 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7521 (pm20) REVERT: A 385 VAL cc_start: 0.8961 (t) cc_final: 0.8508 (t) REVERT: A 453 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8631 (ttp80) REVERT: A 483 GLU cc_start: 0.9033 (mp0) cc_final: 0.8596 (pm20) REVERT: A 505 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7749 (mt-10) REVERT: A 548 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8407 (mm-30) REVERT: A 628 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8118 (mm-30) REVERT: A 640 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.8316 (tpp) REVERT: B 95 MET cc_start: 0.8553 (tpp) cc_final: 0.8176 (tpp) REVERT: B 178 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.7691 (p) REVERT: B 181 ASP cc_start: 0.8427 (m-30) cc_final: 0.8062 (m-30) REVERT: B 184 ARG cc_start: 0.9146 (tpp-160) cc_final: 0.8666 (tpp-160) REVERT: B 190 MET cc_start: 0.9176 (mtm) cc_final: 0.8914 (mtm) REVERT: B 202 ASN cc_start: 0.8808 (t0) cc_final: 0.8402 (t0) REVERT: B 252 ASN cc_start: 0.9014 (t0) cc_final: 0.8711 (t0) REVERT: B 286 ASP cc_start: 0.7736 (m-30) cc_final: 0.7505 (m-30) REVERT: B 322 MET cc_start: 0.9015 (mmm) cc_final: 0.8432 (mmm) REVERT: B 335 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8019 (mt-10) REVERT: B 362 ASP cc_start: 0.7645 (m-30) cc_final: 0.7304 (m-30) REVERT: B 374 SER cc_start: 0.9420 (t) cc_final: 0.9195 (t) REVERT: B 375 LYS cc_start: 0.8883 (mtmm) cc_final: 0.8457 (mtpp) REVERT: B 467 ASN cc_start: 0.9211 (t0) cc_final: 0.8853 (m-40) REVERT: B 493 MET cc_start: 0.9432 (tmm) cc_final: 0.9023 (tmm) REVERT: B 515 ASP cc_start: 0.8876 (m-30) cc_final: 0.8466 (m-30) REVERT: B 602 GLU cc_start: 0.7838 (tp30) cc_final: 0.7362 (tp30) REVERT: B 668 ASN cc_start: 0.8823 (m-40) cc_final: 0.8618 (m110) REVERT: B 669 ARG cc_start: 0.8809 (mtp85) cc_final: 0.8551 (mmm-85) REVERT: B 683 TYR cc_start: 0.8811 (t80) cc_final: 0.8446 (t80) REVERT: C 72 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8681 (p) REVERT: C 76 ILE cc_start: 0.8332 (mm) cc_final: 0.7823 (tp) REVERT: C 85 GLN cc_start: 0.4232 (mt0) cc_final: 0.3511 (pt0) REVERT: C 93 MET cc_start: 0.8711 (mtt) cc_final: 0.8502 (mtt) REVERT: C 95 MET cc_start: 0.8583 (tmm) cc_final: 0.8377 (tmm) REVERT: C 127 GLN cc_start: 0.8953 (mm-40) cc_final: 0.8587 (pp30) REVERT: C 154 PHE cc_start: 0.8752 (t80) cc_final: 0.8537 (t80) REVERT: C 155 LYS cc_start: 0.8468 (mttm) cc_final: 0.8170 (mmtt) REVERT: C 157 MET cc_start: 0.9144 (mtt) cc_final: 0.8772 (mtt) REVERT: C 158 VAL cc_start: 0.9710 (t) cc_final: 0.9069 (t) REVERT: C 162 TYR cc_start: 0.9364 (m-10) cc_final: 0.8845 (m-10) REVERT: C 174 TYR cc_start: 0.8338 (OUTLIER) cc_final: 0.7945 (t80) REVERT: C 200 ILE cc_start: 0.9127 (mp) cc_final: 0.8839 (tp) REVERT: C 201 HIS cc_start: 0.8719 (m90) cc_final: 0.8268 (m90) REVERT: C 212 ILE cc_start: 0.8481 (mm) cc_final: 0.7562 (mm) REVERT: C 240 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8945 (mt) REVERT: C 254 HIS cc_start: 0.9184 (t70) cc_final: 0.8940 (t70) REVERT: C 271 LEU cc_start: 0.8608 (mm) cc_final: 0.7901 (mm) REVERT: C 317 ASP cc_start: 0.8384 (m-30) cc_final: 0.8011 (m-30) REVERT: D 96 MET cc_start: 0.6070 (mmm) cc_final: 0.5774 (mmm) REVERT: D 137 MET cc_start: 0.5323 (mtp) cc_final: 0.4975 (ptp) REVERT: D 138 ILE cc_start: 0.9043 (mm) cc_final: 0.8792 (mm) REVERT: D 174 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.7315 (t80) REVERT: D 197 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8666 (t0) outliers start: 79 outliers final: 41 residues processed: 593 average time/residue: 0.1306 time to fit residues: 116.4718 Evaluate side-chains 556 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 503 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 33 VAL 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 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 443 THR Chi-restraints excluded: chain A residue 453 ARG 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 590 SER 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 99 LYS 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 218 ASN Chi-restraints excluded: chain B residue 223 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 443 THR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 644 ILE 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 72 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 240 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 182 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN A 259 ASN A 410 ASN B 180 ASN B 191 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 263 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.127835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.090181 restraints weight = 35454.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.093375 restraints weight = 17113.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.095483 restraints weight = 10264.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.096799 restraints weight = 7084.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.097529 restraints weight = 5460.318| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 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 = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16386 Z= 0.235 Angle : 0.647 10.648 22134 Z= 0.338 Chirality : 0.044 0.161 2360 Planarity : 0.004 0.035 2818 Dihedral : 11.200 174.295 2254 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 5.42 % Allowed : 21.33 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.19), residues: 1932 helix: 1.20 (0.15), residues: 1135 sheet: -0.29 (0.41), residues: 146 loop : 0.39 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 117 TYR 0.023 0.002 TYR B 394 PHE 0.029 0.002 PHE C 168 TRP 0.031 0.003 TRP D 30 HIS 0.009 0.001 HIS A 568 Details of bonding type rmsd covalent geometry : bond 0.00514 (16386) covalent geometry : angle 0.64670 (22134) hydrogen bonds : bond 0.04130 ( 871) hydrogen bonds : angle 5.16438 ( 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 632 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 539 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8359 (mm-30) REVERT: A 99 LYS cc_start: 0.9152 (mmmm) cc_final: 0.8809 (mmmm) REVERT: A 102 ASN cc_start: 0.9058 (OUTLIER) cc_final: 0.8776 (m-40) REVERT: A 161 ARG cc_start: 0.8089 (ttm170) cc_final: 0.7839 (mmm-85) REVERT: A 172 LEU cc_start: 0.9144 (mp) cc_final: 0.8808 (mp) REVERT: A 188 ILE cc_start: 0.9424 (mt) cc_final: 0.9175 (mm) REVERT: A 218 ASN cc_start: 0.8978 (t0) cc_final: 0.8478 (t0) REVERT: A 256 ARG cc_start: 0.9272 (ttp80) cc_final: 0.7803 (ttp80) REVERT: A 335 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7575 (mt-10) REVERT: A 344 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8541 (mt-10) REVERT: A 359 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7935 (ttp) REVERT: A 381 LEU cc_start: 0.9114 (tp) cc_final: 0.8488 (pt) REVERT: A 384 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7574 (pm20) REVERT: A 385 VAL cc_start: 0.8882 (t) cc_final: 0.8589 (t) REVERT: A 390 GLN cc_start: 0.8503 (mt0) cc_final: 0.8143 (mt0) REVERT: A 393 SER cc_start: 0.9135 (m) cc_final: 0.8739 (p) REVERT: A 505 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7805 (mt-10) REVERT: A 548 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8423 (mm-30) REVERT: A 628 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8452 (mm-30) REVERT: A 640 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.8310 (tpp) REVERT: A 662 MET cc_start: 0.8472 (ptp) cc_final: 0.8074 (ptp) REVERT: B 95 MET cc_start: 0.8686 (tpp) cc_final: 0.8236 (tpp) REVERT: B 178 SER cc_start: 0.8402 (OUTLIER) cc_final: 0.7574 (p) REVERT: B 181 ASP cc_start: 0.8450 (m-30) cc_final: 0.8085 (m-30) REVERT: B 184 ARG cc_start: 0.9145 (tpp-160) cc_final: 0.8925 (tpp-160) REVERT: B 190 MET cc_start: 0.9197 (mtm) cc_final: 0.8902 (mtm) REVERT: B 252 ASN cc_start: 0.9240 (t0) cc_final: 0.8878 (t0) REVERT: B 257 ASP cc_start: 0.8741 (m-30) cc_final: 0.8458 (m-30) REVERT: B 312 GLN cc_start: 0.8576 (tt0) cc_final: 0.7903 (tt0) REVERT: B 335 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8017 (mt-10) REVERT: B 350 ARG cc_start: 0.8859 (mtp-110) cc_final: 0.8647 (mtp-110) REVERT: B 361 GLN cc_start: 0.8593 (tt0) cc_final: 0.8357 (tt0) REVERT: B 362 ASP cc_start: 0.7709 (m-30) cc_final: 0.7347 (m-30) REVERT: B 467 ASN cc_start: 0.9262 (t0) cc_final: 0.8890 (m-40) REVERT: B 493 MET cc_start: 0.9424 (tmm) cc_final: 0.8993 (tmm) REVERT: B 515 ASP cc_start: 0.8907 (m-30) cc_final: 0.8581 (m-30) REVERT: B 550 MET cc_start: 0.7964 (mtp) cc_final: 0.7620 (mtp) REVERT: B 632 MET cc_start: 0.8549 (mtt) cc_final: 0.8287 (mtt) REVERT: B 669 ARG cc_start: 0.8866 (mtp85) cc_final: 0.8607 (mmm-85) REVERT: C 69 GLN cc_start: 0.8886 (tm-30) cc_final: 0.8632 (tm-30) REVERT: C 76 ILE cc_start: 0.8495 (mm) cc_final: 0.8111 (tp) REVERT: C 85 GLN cc_start: 0.4113 (mt0) cc_final: 0.3363 (pt0) REVERT: C 93 MET cc_start: 0.8979 (mtt) cc_final: 0.8717 (mtt) REVERT: C 127 GLN cc_start: 0.8983 (mm-40) cc_final: 0.8620 (pp30) REVERT: C 155 LYS cc_start: 0.8602 (mttm) cc_final: 0.8239 (mmtt) REVERT: C 157 MET cc_start: 0.9118 (mtt) cc_final: 0.8776 (mtt) REVERT: C 158 VAL cc_start: 0.9741 (t) cc_final: 0.9131 (t) REVERT: C 162 TYR cc_start: 0.9376 (m-10) cc_final: 0.8789 (m-10) REVERT: C 174 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.7916 (t80) REVERT: C 177 TYR cc_start: 0.8445 (t80) cc_final: 0.8086 (t80) REVERT: C 201 HIS cc_start: 0.8700 (m90) cc_final: 0.8250 (m90) REVERT: C 212 ILE cc_start: 0.8561 (mm) cc_final: 0.7679 (mm) REVERT: C 243 THR cc_start: 0.7663 (m) cc_final: 0.7408 (m) REVERT: C 271 LEU cc_start: 0.8696 (mm) cc_final: 0.8051 (mm) REVERT: D 96 MET cc_start: 0.6271 (mmm) cc_final: 0.5910 (mmm) REVERT: D 137 MET cc_start: 0.5297 (mtp) cc_final: 0.4936 (ptp) REVERT: D 174 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7342 (t80) REVERT: D 235 LEU cc_start: 0.8941 (mm) cc_final: 0.8715 (mp) outliers start: 93 outliers final: 58 residues processed: 588 average time/residue: 0.1342 time to fit residues: 118.8628 Evaluate side-chains 546 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 480 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 33 VAL 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 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 443 THR 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 A residue 667 LEU Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 143 LEU 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 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 367 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 495 VAL 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 605 THR Chi-restraints excluded: chain B residue 624 PHE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 115 THR 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 285 ILE 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 195 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 129 optimal weight: 0.0060 chunk 32 optimal weight: 0.9980 chunk 122 optimal weight: 0.0770 chunk 115 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 158 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 312 GLN A 365 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 191 GLN B 312 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN B 668 ASN C 263 ASN D 25 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.133836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.096264 restraints weight = 35303.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.099628 restraints weight = 16959.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.101821 restraints weight = 9975.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.103172 restraints weight = 6838.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.104158 restraints weight = 5242.018| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.5567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16386 Z= 0.131 Angle : 0.633 10.131 22134 Z= 0.323 Chirality : 0.043 0.255 2360 Planarity : 0.003 0.035 2818 Dihedral : 10.843 172.020 2253 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.73 % Allowed : 24.01 % Favored : 72.26 % 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 aren not related in a simple way. whole: 1.07 (0.19), residues: 1932 helix: 1.16 (0.15), residues: 1128 sheet: -0.07 (0.44), residues: 134 loop : 0.32 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 117 TYR 0.024 0.001 TYR B 394 PHE 0.031 0.002 PHE C 172 TRP 0.031 0.002 TRP D 30 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00296 (16386) covalent geometry : angle 0.63316 (22134) hydrogen bonds : bond 0.03910 ( 871) hydrogen bonds : angle 5.02057 ( 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 618 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 554 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8783 (tptt) cc_final: 0.8518 (tppt) REVERT: A 56 ASP cc_start: 0.8794 (m-30) cc_final: 0.8364 (m-30) REVERT: A 65 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8258 (mm-30) REVERT: A 99 LYS cc_start: 0.9086 (mmmm) cc_final: 0.8824 (mmmm) REVERT: A 103 ASP cc_start: 0.8854 (m-30) cc_final: 0.8547 (m-30) REVERT: A 161 ARG cc_start: 0.8048 (ttm170) cc_final: 0.7711 (mtp85) REVERT: A 188 ILE cc_start: 0.9342 (mt) cc_final: 0.9076 (mm) REVERT: A 218 ASN cc_start: 0.8853 (t0) cc_final: 0.8238 (t0) REVERT: A 307 TYR cc_start: 0.9129 (t80) cc_final: 0.8905 (t80) REVERT: A 341 LYS cc_start: 0.9353 (mmtm) cc_final: 0.8867 (mmpt) REVERT: A 344 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8565 (mt-10) REVERT: A 359 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7814 (ttp) REVERT: A 381 LEU cc_start: 0.9121 (tp) cc_final: 0.8491 (pt) REVERT: A 384 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7502 (pm20) REVERT: A 385 VAL cc_start: 0.8953 (t) cc_final: 0.8595 (t) REVERT: A 390 GLN cc_start: 0.8419 (mt0) cc_final: 0.8028 (mt0) REVERT: A 483 GLU cc_start: 0.9095 (mp0) cc_final: 0.8486 (pm20) REVERT: A 505 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7800 (mt-10) REVERT: A 548 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8480 (mm-30) REVERT: A 628 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8501 (mm-30) REVERT: A 640 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.7963 (tpp) REVERT: B 95 MET cc_start: 0.8482 (tpp) cc_final: 0.8169 (tpp) REVERT: B 99 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8632 (tptp) REVERT: B 167 LEU cc_start: 0.8604 (mt) cc_final: 0.7925 (mt) REVERT: B 181 ASP cc_start: 0.8334 (m-30) cc_final: 0.7997 (m-30) REVERT: B 184 ARG cc_start: 0.9087 (tpp-160) cc_final: 0.8854 (tpp-160) REVERT: B 190 MET cc_start: 0.9121 (mtm) cc_final: 0.8829 (mtm) REVERT: B 252 ASN cc_start: 0.9239 (t0) cc_final: 0.8857 (t0) REVERT: B 257 ASP cc_start: 0.8589 (m-30) cc_final: 0.8145 (m-30) REVERT: B 322 MET cc_start: 0.8966 (mmm) cc_final: 0.8274 (mmm) REVERT: B 361 GLN cc_start: 0.8504 (tt0) cc_final: 0.8297 (tt0) REVERT: B 362 ASP cc_start: 0.7649 (m-30) cc_final: 0.7240 (m-30) REVERT: B 415 ASN cc_start: 0.9360 (t0) cc_final: 0.8983 (t0) REVERT: B 467 ASN cc_start: 0.9064 (t0) cc_final: 0.8842 (m-40) REVERT: B 493 MET cc_start: 0.9396 (tmm) cc_final: 0.9038 (tmm) REVERT: B 515 ASP cc_start: 0.8800 (m-30) cc_final: 0.8436 (m-30) REVERT: B 550 MET cc_start: 0.8026 (mtp) cc_final: 0.7641 (mtp) REVERT: B 576 LEU cc_start: 0.9442 (mt) cc_final: 0.9184 (mt) REVERT: B 646 GLN cc_start: 0.8903 (pt0) cc_final: 0.8475 (pm20) REVERT: B 668 ASN cc_start: 0.8414 (m-40) cc_final: 0.8041 (m110) REVERT: C 69 GLN cc_start: 0.8968 (tm-30) cc_final: 0.8652 (tm-30) REVERT: C 76 ILE cc_start: 0.8488 (mm) cc_final: 0.8070 (tp) REVERT: C 85 GLN cc_start: 0.4657 (mt0) cc_final: 0.3749 (pt0) REVERT: C 93 MET cc_start: 0.8959 (mtt) cc_final: 0.8695 (mtt) REVERT: C 96 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8602 (tpp) REVERT: C 127 GLN cc_start: 0.8938 (mm-40) cc_final: 0.8680 (pp30) REVERT: C 137 MET cc_start: 0.7823 (mtt) cc_final: 0.7564 (mtt) REVERT: C 153 LEU cc_start: 0.9494 (mt) cc_final: 0.9268 (pp) REVERT: C 155 LYS cc_start: 0.8663 (mttm) cc_final: 0.8312 (mmtt) REVERT: C 157 MET cc_start: 0.9262 (mtt) cc_final: 0.8936 (mtt) REVERT: C 158 VAL cc_start: 0.9746 (t) cc_final: 0.9083 (t) REVERT: C 162 TYR cc_start: 0.9361 (m-10) cc_final: 0.8700 (m-10) REVERT: C 201 HIS cc_start: 0.8771 (m90) cc_final: 0.8319 (m90) REVERT: C 212 ILE cc_start: 0.8675 (mm) cc_final: 0.7840 (mm) REVERT: C 220 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7652 (mptt) REVERT: C 243 THR cc_start: 0.7650 (m) cc_final: 0.7395 (p) REVERT: C 260 ILE cc_start: 0.8128 (pt) cc_final: 0.7878 (pt) REVERT: C 271 LEU cc_start: 0.8561 (mm) cc_final: 0.7850 (mm) REVERT: D 25 ASN cc_start: 0.9383 (OUTLIER) cc_final: 0.8837 (m110) REVERT: D 56 MET cc_start: 0.7604 (ptt) cc_final: 0.7238 (mmt) REVERT: D 74 MET cc_start: 0.6117 (tmm) cc_final: 0.5759 (tmm) REVERT: D 96 MET cc_start: 0.6209 (mmm) cc_final: 0.5976 (mmm) REVERT: D 137 MET cc_start: 0.4938 (mtp) cc_final: 0.4649 (ptp) REVERT: D 174 TYR cc_start: 0.8047 (OUTLIER) cc_final: 0.7238 (t80) REVERT: D 197 ASP cc_start: 0.8797 (t0) cc_final: 0.8444 (t0) REVERT: D 231 LEU cc_start: 0.9181 (tp) cc_final: 0.8841 (tp) REVERT: D 235 LEU cc_start: 0.8950 (mm) cc_final: 0.8732 (mp) outliers start: 64 outliers final: 29 residues processed: 588 average time/residue: 0.1331 time to fit residues: 117.3422 Evaluate side-chains 549 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 511 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 257 ASP 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 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 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 143 LEU 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 561 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 624 PHE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 96 MET 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 D residue 25 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 195 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 7.9990 chunk 183 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 27 optimal weight: 0.5980 chunk 136 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 191 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.135183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.096932 restraints weight = 35235.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.100270 restraints weight = 16774.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.102486 restraints weight = 9994.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.103921 restraints weight = 6833.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.104826 restraints weight = 5230.775| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.5825 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= 0.139 Angle : 0.646 12.024 22134 Z= 0.329 Chirality : 0.044 0.259 2360 Planarity : 0.003 0.038 2818 Dihedral : 10.592 172.149 2251 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.73 % Allowed : 25.29 % 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 aren not related in a simple way. whole: 1.05 (0.19), residues: 1932 helix: 1.14 (0.15), residues: 1140 sheet: 0.14 (0.45), residues: 130 loop : 0.25 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 117 TYR 0.020 0.001 TYR B 394 PHE 0.033 0.002 PHE C 172 TRP 0.033 0.002 TRP D 30 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00316 (16386) covalent geometry : angle 0.64553 (22134) hydrogen bonds : bond 0.03848 ( 871) hydrogen bonds : angle 4.98604 ( 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 583 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 519 time to evaluate : 0.649 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 30 LYS cc_start: 0.8748 (tptt) cc_final: 0.8486 (tppt) REVERT: A 56 ASP cc_start: 0.8797 (m-30) cc_final: 0.8446 (m-30) REVERT: A 65 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8244 (mm-30) REVERT: A 87 LYS cc_start: 0.8936 (tptm) cc_final: 0.8666 (tptm) REVERT: A 99 LYS cc_start: 0.9047 (mmmm) cc_final: 0.8845 (mmmm) REVERT: A 161 ARG cc_start: 0.7987 (ttm170) cc_final: 0.7662 (mtp85) REVERT: A 188 ILE cc_start: 0.9361 (mt) cc_final: 0.9114 (mm) REVERT: A 218 ASN cc_start: 0.8857 (t0) cc_final: 0.8210 (t0) REVERT: A 256 ARG cc_start: 0.9145 (ttp80) cc_final: 0.8736 (ttp80) REVERT: A 307 TYR cc_start: 0.9137 (t80) cc_final: 0.8876 (t80) REVERT: A 335 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7375 (mt-10) REVERT: A 341 LYS cc_start: 0.9346 (mmtm) cc_final: 0.9112 (mmpt) REVERT: A 344 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8592 (mt-10) REVERT: A 359 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7887 (ttp) REVERT: A 379 SER cc_start: 0.9244 (t) cc_final: 0.8991 (t) REVERT: A 381 LEU cc_start: 0.9095 (tp) cc_final: 0.8526 (pt) REVERT: A 384 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7376 (pm20) REVERT: A 385 VAL cc_start: 0.8977 (t) cc_final: 0.8627 (t) REVERT: A 390 GLN cc_start: 0.8384 (mt0) cc_final: 0.7954 (mt0) REVERT: A 427 LYS cc_start: 0.8987 (ttpp) cc_final: 0.8711 (ttpp) REVERT: A 467 ASN cc_start: 0.9054 (m-40) cc_final: 0.8839 (m-40) REVERT: A 483 GLU cc_start: 0.9099 (mp0) cc_final: 0.8354 (pm20) REVERT: A 548 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8507 (mm-30) REVERT: A 628 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8483 (mm-30) REVERT: A 640 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.7721 (tpp) REVERT: A 666 ASP cc_start: 0.8702 (t0) cc_final: 0.8501 (m-30) REVERT: B 95 MET cc_start: 0.8469 (tpp) cc_final: 0.8161 (tpp) REVERT: B 99 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8663 (tptp) REVERT: B 190 MET cc_start: 0.9125 (mtm) cc_final: 0.8851 (mtm) REVERT: B 252 ASN cc_start: 0.9247 (t0) cc_final: 0.8857 (t0) REVERT: B 257 ASP cc_start: 0.8560 (m-30) cc_final: 0.8183 (m-30) REVERT: B 322 MET cc_start: 0.8956 (mmm) cc_final: 0.8280 (mmm) REVERT: B 362 ASP cc_start: 0.7521 (m-30) cc_final: 0.7131 (m-30) REVERT: B 384 GLU cc_start: 0.8617 (pm20) cc_final: 0.7917 (pp20) REVERT: B 398 ASP cc_start: 0.8170 (t0) cc_final: 0.7794 (t0) REVERT: B 415 ASN cc_start: 0.9311 (t0) cc_final: 0.8931 (t0) REVERT: B 467 ASN cc_start: 0.9051 (t0) cc_final: 0.8824 (m-40) REVERT: B 493 MET cc_start: 0.9400 (tmm) cc_final: 0.9011 (tmm) REVERT: B 515 ASP cc_start: 0.8766 (m-30) cc_final: 0.8462 (m-30) REVERT: B 550 MET cc_start: 0.7994 (mtp) cc_final: 0.7652 (mtp) REVERT: B 576 LEU cc_start: 0.9422 (mt) cc_final: 0.9160 (mt) REVERT: B 668 ASN cc_start: 0.8411 (m-40) cc_final: 0.8093 (m-40) REVERT: C 17 PHE cc_start: 0.8467 (p90) cc_final: 0.7706 (p90) REVERT: C 69 GLN cc_start: 0.8920 (tm-30) cc_final: 0.8601 (tm-30) REVERT: C 76 ILE cc_start: 0.8486 (mm) cc_final: 0.8050 (tp) REVERT: C 85 GLN cc_start: 0.4954 (mt0) cc_final: 0.4109 (pt0) REVERT: C 93 MET cc_start: 0.8923 (mtt) cc_final: 0.8667 (mtt) REVERT: C 127 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8690 (pp30) REVERT: C 137 MET cc_start: 0.7809 (mtt) cc_final: 0.7313 (mpp) REVERT: C 157 MET cc_start: 0.9389 (mtt) cc_final: 0.9137 (mtt) REVERT: C 158 VAL cc_start: 0.9710 (t) cc_final: 0.9243 (m) REVERT: C 162 TYR cc_start: 0.9334 (OUTLIER) cc_final: 0.8770 (m-10) REVERT: C 201 HIS cc_start: 0.8793 (m90) cc_final: 0.8361 (m90) REVERT: C 211 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8117 (pp20) REVERT: C 212 ILE cc_start: 0.8754 (mm) cc_final: 0.8254 (mm) REVERT: C 271 LEU cc_start: 0.8544 (mm) cc_final: 0.7925 (mm) REVERT: D 25 ASN cc_start: 0.9347 (m-40) cc_final: 0.8798 (m110) REVERT: D 28 GLN cc_start: 0.8608 (tt0) cc_final: 0.8330 (tt0) REVERT: D 56 MET cc_start: 0.7544 (ptt) cc_final: 0.7258 (mmt) REVERT: D 96 MET cc_start: 0.6133 (mmm) cc_final: 0.5929 (mmm) REVERT: D 137 MET cc_start: 0.4985 (mtp) cc_final: 0.4683 (ptp) REVERT: D 162 TYR cc_start: 0.6345 (m-10) cc_final: 0.6054 (m-10) REVERT: D 174 TYR cc_start: 0.8139 (OUTLIER) cc_final: 0.7265 (t80) REVERT: D 195 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8820 (mm) REVERT: D 231 LEU cc_start: 0.9039 (tp) cc_final: 0.8814 (tp) REVERT: D 266 LYS cc_start: 0.8225 (tptt) cc_final: 0.7905 (tptp) outliers start: 64 outliers final: 40 residues processed: 547 average time/residue: 0.1331 time to fit residues: 109.1292 Evaluate side-chains 535 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 487 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL 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 213 ILE 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 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 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 A residue 667 LEU Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 374 SER 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 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 71 ASN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 227 PHE 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 195 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 140 optimal weight: 20.0000 chunk 115 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 312 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 191 GLN B 202 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN B 646 GLN C 71 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.125626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.088514 restraints weight = 35408.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.091627 restraints weight = 17354.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.093595 restraints weight = 10439.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.095039 restraints weight = 7305.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.095969 restraints weight = 5561.062| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 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 = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.6029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 16386 Z= 0.261 Angle : 0.707 9.888 22134 Z= 0.366 Chirality : 0.045 0.213 2360 Planarity : 0.004 0.042 2818 Dihedral : 10.823 176.363 2247 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.96 % Allowed : 25.82 % Favored : 70.22 % 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 aren not related in a simple way. whole: 0.90 (0.19), residues: 1932 helix: 1.06 (0.15), residues: 1142 sheet: -0.39 (0.44), residues: 140 loop : 0.20 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 235 TYR 0.033 0.002 TYR D 142 PHE 0.025 0.002 PHE C 172 TRP 0.038 0.003 TRP D 30 HIS 0.005 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00574 (16386) covalent geometry : angle 0.70695 (22134) hydrogen bonds : bond 0.04118 ( 871) hydrogen bonds : angle 5.17464 ( 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 555 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 487 time to evaluate : 0.631 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 65 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8275 (mm-30) REVERT: A 87 LYS cc_start: 0.9141 (tptm) cc_final: 0.8937 (tptm) REVERT: A 99 LYS cc_start: 0.9039 (mmmm) cc_final: 0.8817 (mmmm) REVERT: A 116 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7666 (mt-10) REVERT: A 209 LYS cc_start: 0.8625 (tptt) cc_final: 0.8414 (tptt) REVERT: A 218 ASN cc_start: 0.9033 (t0) cc_final: 0.8541 (t0) REVERT: A 256 ARG cc_start: 0.9198 (ttp80) cc_final: 0.8540 (ttp80) REVERT: A 335 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7247 (mt-10) REVERT: A 341 LYS cc_start: 0.9383 (mmtm) cc_final: 0.9093 (mmpt) REVERT: A 344 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8523 (mt-10) REVERT: A 359 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8096 (ttp) REVERT: A 366 LYS cc_start: 0.9179 (mtmt) cc_final: 0.8843 (ptpp) REVERT: A 381 LEU cc_start: 0.9128 (tp) cc_final: 0.8483 (pt) REVERT: A 384 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7578 (pm20) REVERT: A 385 VAL cc_start: 0.8955 (t) cc_final: 0.8679 (t) REVERT: A 390 GLN cc_start: 0.8514 (mt0) cc_final: 0.8070 (mt0) REVERT: A 548 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8550 (mm-30) REVERT: A 628 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8513 (mm-30) REVERT: A 640 MET cc_start: 0.9271 (OUTLIER) cc_final: 0.7948 (tpp) REVERT: B 95 MET cc_start: 0.8677 (tpp) cc_final: 0.8304 (tpp) REVERT: B 99 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8429 (tptp) REVERT: B 184 ARG cc_start: 0.9073 (tpp-160) cc_final: 0.8741 (tpp-160) REVERT: B 190 MET cc_start: 0.9195 (mtm) cc_final: 0.8867 (mtm) REVERT: B 202 ASN cc_start: 0.8772 (t0) cc_final: 0.8309 (t0) REVERT: B 243 ARG cc_start: 0.7418 (tmm160) cc_final: 0.7196 (tmm160) REVERT: B 257 ASP cc_start: 0.8649 (m-30) cc_final: 0.8369 (m-30) REVERT: B 322 MET cc_start: 0.9070 (mmm) cc_final: 0.8428 (mmm) REVERT: B 384 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.6931 (pm20) REVERT: B 398 ASP cc_start: 0.8318 (t0) cc_final: 0.7984 (t0) REVERT: B 415 ASN cc_start: 0.9322 (t0) cc_final: 0.8753 (t0) REVERT: B 467 ASN cc_start: 0.9271 (t0) cc_final: 0.8893 (m-40) REVERT: B 493 MET cc_start: 0.9416 (tmm) cc_final: 0.8929 (tmm) REVERT: B 494 MET cc_start: 0.9207 (mtm) cc_final: 0.8982 (mtp) REVERT: B 515 ASP cc_start: 0.8989 (m-30) cc_final: 0.8586 (m-30) REVERT: B 583 SER cc_start: 0.8107 (p) cc_final: 0.7467 (t) REVERT: B 668 ASN cc_start: 0.8608 (m-40) cc_final: 0.8171 (m110) REVERT: C 69 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8639 (tm-30) REVERT: C 76 ILE cc_start: 0.8644 (mm) cc_final: 0.8243 (tp) REVERT: C 85 GLN cc_start: 0.4979 (mt0) cc_final: 0.4171 (pt0) REVERT: C 93 MET cc_start: 0.8913 (mtt) cc_final: 0.8533 (mtt) REVERT: C 127 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8688 (pp30) REVERT: C 157 MET cc_start: 0.9422 (mtt) cc_final: 0.9209 (mtt) REVERT: C 158 VAL cc_start: 0.9702 (t) cc_final: 0.9228 (m) REVERT: C 162 TYR cc_start: 0.9338 (OUTLIER) cc_final: 0.8855 (m-10) REVERT: C 201 HIS cc_start: 0.8759 (m90) cc_final: 0.8169 (m90) REVERT: C 211 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8153 (pp20) REVERT: C 271 LEU cc_start: 0.8728 (mm) cc_final: 0.8128 (mm) REVERT: D 18 THR cc_start: 0.7916 (m) cc_final: 0.7648 (m) REVERT: D 25 ASN cc_start: 0.9403 (m-40) cc_final: 0.8774 (m110) REVERT: D 56 MET cc_start: 0.7514 (ptt) cc_final: 0.7245 (mmt) REVERT: D 96 MET cc_start: 0.6433 (mmm) cc_final: 0.6031 (mmm) REVERT: D 137 MET cc_start: 0.5301 (mtp) cc_final: 0.4922 (ptp) REVERT: D 143 LYS cc_start: 0.8399 (mmmt) cc_final: 0.8160 (mmmt) REVERT: D 162 TYR cc_start: 0.6462 (m-10) cc_final: 0.6171 (m-10) REVERT: D 172 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.6489 (m-80) REVERT: D 174 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.7429 (t80) REVERT: D 195 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8870 (mm) REVERT: D 197 ASP cc_start: 0.8902 (t0) cc_final: 0.8634 (t0) REVERT: D 210 GLN cc_start: 0.8286 (mt0) cc_final: 0.8053 (mt0) outliers start: 68 outliers final: 47 residues processed: 519 average time/residue: 0.1321 time to fit residues: 103.1633 Evaluate side-chains 527 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 469 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 213 ILE 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 406 ASP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 421 GLU 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 A residue 667 LEU Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 99 LYS 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 260 ASP Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 374 SER 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 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 644 ILE 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 174 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 172 PHE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 239 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 153 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 418 ASN ** D 91 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 = 0.3704 r_free = 0.3704 target = 0.129942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.092655 restraints weight = 35277.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.095999 restraints weight = 17043.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.098072 restraints weight = 10092.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.099480 restraints weight = 6975.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.100457 restraints weight = 5329.093| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.6215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16386 Z= 0.149 Angle : 0.677 11.598 22134 Z= 0.345 Chirality : 0.045 0.222 2360 Planarity : 0.004 0.054 2818 Dihedral : 10.640 174.564 2247 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.50 % Allowed : 27.10 % 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 aren not related in a simple way. whole: 0.77 (0.19), residues: 1932 helix: 0.99 (0.15), residues: 1140 sheet: -0.47 (0.43), residues: 146 loop : 0.10 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 686 TYR 0.052 0.002 TYR D 142 PHE 0.031 0.002 PHE B 128 TRP 0.037 0.002 TRP D 30 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00339 (16386) covalent geometry : angle 0.67656 (22134) hydrogen bonds : bond 0.03938 ( 871) hydrogen bonds : angle 5.08510 ( 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 555 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 495 time to evaluate : 0.621 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: A 65 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8204 (mm-30) REVERT: A 131 ASN cc_start: 0.9506 (OUTLIER) cc_final: 0.9270 (p0) REVERT: A 139 GLU cc_start: 0.8402 (mp0) cc_final: 0.8079 (mp0) REVERT: A 161 ARG cc_start: 0.8374 (mmm-85) cc_final: 0.8087 (mtp85) REVERT: A 218 ASN cc_start: 0.8934 (t0) cc_final: 0.8232 (t0) REVERT: A 232 ASN cc_start: 0.9257 (m110) cc_final: 0.8978 (m110) REVERT: A 250 TYR cc_start: 0.8510 (m-80) cc_final: 0.8286 (m-80) REVERT: A 256 ARG cc_start: 0.9148 (ttp80) cc_final: 0.8436 (ttp80) REVERT: A 335 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7145 (mt-10) REVERT: A 341 LYS cc_start: 0.9356 (mmtm) cc_final: 0.8841 (mmpt) REVERT: A 344 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8536 (mt-10) REVERT: A 359 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.7947 (ttp) REVERT: A 366 LYS cc_start: 0.9109 (mtmt) cc_final: 0.8811 (ptpp) REVERT: A 381 LEU cc_start: 0.9079 (tp) cc_final: 0.8479 (pt) REVERT: A 384 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7460 (pm20) REVERT: A 385 VAL cc_start: 0.8973 (t) cc_final: 0.8659 (t) REVERT: A 390 GLN cc_start: 0.8491 (mt0) cc_final: 0.8048 (mt0) REVERT: A 483 GLU cc_start: 0.9096 (mp0) cc_final: 0.8629 (pm20) REVERT: A 548 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8536 (mm-30) REVERT: A 628 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8529 (mm-30) REVERT: A 640 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.7928 (tpp) REVERT: B 95 MET cc_start: 0.8562 (tpp) cc_final: 0.8232 (tpp) REVERT: B 99 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8677 (tptp) REVERT: B 184 ARG cc_start: 0.9073 (tpp-160) cc_final: 0.8683 (tpp-160) REVERT: B 190 MET cc_start: 0.9195 (mtm) cc_final: 0.8874 (mtm) REVERT: B 217 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7420 (tm-30) REVERT: B 218 ASN cc_start: 0.8838 (OUTLIER) cc_final: 0.8537 (m110) REVERT: B 243 ARG cc_start: 0.7415 (tmm160) cc_final: 0.7163 (tmm160) REVERT: B 257 ASP cc_start: 0.8558 (m-30) cc_final: 0.8227 (m-30) REVERT: B 274 ARG cc_start: 0.7187 (tpp-160) cc_final: 0.6973 (tpp-160) REVERT: B 322 MET cc_start: 0.9032 (mmm) cc_final: 0.8391 (mmm) REVERT: B 357 TYR cc_start: 0.8387 (m-10) cc_final: 0.8175 (m-80) REVERT: B 398 ASP cc_start: 0.8265 (t0) cc_final: 0.7824 (t0) REVERT: B 415 ASN cc_start: 0.9287 (t0) cc_final: 0.8783 (t0) REVERT: B 441 GLU cc_start: 0.8625 (pt0) cc_final: 0.8246 (pt0) REVERT: B 467 ASN cc_start: 0.9039 (t0) cc_final: 0.8764 (m-40) REVERT: B 493 MET cc_start: 0.9403 (tmm) cc_final: 0.9037 (tmm) REVERT: B 494 MET cc_start: 0.9211 (mtm) cc_final: 0.8940 (mtp) REVERT: B 515 ASP cc_start: 0.8911 (m-30) cc_final: 0.8513 (m-30) REVERT: B 576 LEU cc_start: 0.9430 (mt) cc_final: 0.9195 (mt) REVERT: B 668 ASN cc_start: 0.8485 (m-40) cc_final: 0.8203 (m-40) REVERT: C 17 PHE cc_start: 0.8625 (p90) cc_final: 0.7764 (p90) REVERT: C 56 MET cc_start: 0.4830 (ptp) cc_final: 0.4535 (mtm) REVERT: C 76 ILE cc_start: 0.8608 (mm) cc_final: 0.8180 (tp) REVERT: C 85 GLN cc_start: 0.4959 (mt0) cc_final: 0.4220 (pt0) REVERT: C 93 MET cc_start: 0.8926 (mtt) cc_final: 0.8640 (mtt) REVERT: C 127 GLN cc_start: 0.8989 (mm-40) cc_final: 0.8704 (pp30) REVERT: C 153 LEU cc_start: 0.9501 (mt) cc_final: 0.9260 (pp) REVERT: C 157 MET cc_start: 0.9511 (mtt) cc_final: 0.9305 (mtt) REVERT: C 158 VAL cc_start: 0.9648 (t) cc_final: 0.9262 (m) REVERT: C 162 TYR cc_start: 0.9343 (OUTLIER) cc_final: 0.8832 (m-10) REVERT: C 178 PHE cc_start: 0.7378 (m-10) cc_final: 0.7080 (m-10) REVERT: C 201 HIS cc_start: 0.8890 (m90) cc_final: 0.8254 (m90) REVERT: C 271 LEU cc_start: 0.8731 (mm) cc_final: 0.8076 (mm) REVERT: D 18 THR cc_start: 0.7702 (m) cc_final: 0.7370 (m) REVERT: D 25 ASN cc_start: 0.9392 (m-40) cc_final: 0.8702 (m110) REVERT: D 28 GLN cc_start: 0.8655 (tt0) cc_final: 0.8193 (pp30) REVERT: D 51 GLU cc_start: 0.8482 (pt0) cc_final: 0.8079 (pm20) REVERT: D 96 MET cc_start: 0.6186 (mmm) cc_final: 0.5961 (mmm) REVERT: D 174 TYR cc_start: 0.8088 (OUTLIER) cc_final: 0.7384 (t80) REVERT: D 195 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8828 (mm) REVERT: D 197 ASP cc_start: 0.8864 (t0) cc_final: 0.8246 (t0) outliers start: 60 outliers final: 43 residues processed: 523 average time/residue: 0.1302 time to fit residues: 102.6781 Evaluate side-chains 519 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 466 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 131 ASN 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 213 ILE 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 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 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 143 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 374 SER 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 475 ASN 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 624 PHE Chi-restraints excluded: chain B residue 644 ILE 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 174 TYR Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 239 GLU 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: 8.9990 chunk 149 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 312 GLN A 668 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 646 GLN C 214 ASN C 263 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.130295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.093254 restraints weight = 35417.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.096454 restraints weight = 17225.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.098448 restraints weight = 10223.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.099907 restraints weight = 7119.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.100845 restraints weight = 5399.689| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.6363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16386 Z= 0.196 Angle : 0.716 11.246 22134 Z= 0.366 Chirality : 0.046 0.212 2360 Planarity : 0.004 0.042 2818 Dihedral : 10.662 175.953 2247 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.90 % Allowed : 26.86 % Favored : 69.23 % 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 aren not related in a simple way. whole: 0.73 (0.19), residues: 1932 helix: 0.92 (0.15), residues: 1142 sheet: -0.57 (0.43), residues: 140 loop : 0.18 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 686 TYR 0.024 0.002 TYR D 142 PHE 0.050 0.002 PHE C 154 TRP 0.036 0.002 TRP D 30 HIS 0.006 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00439 (16386) covalent geometry : angle 0.71612 (22134) hydrogen bonds : bond 0.03976 ( 871) hydrogen bonds : angle 5.16357 ( 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 550 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 483 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8399 (mm-30) REVERT: A 131 ASN cc_start: 0.9535 (OUTLIER) cc_final: 0.9270 (p0) REVERT: A 209 LYS cc_start: 0.8533 (tptt) cc_final: 0.8270 (tptp) REVERT: A 218 ASN cc_start: 0.8976 (t0) cc_final: 0.8324 (t0) REVERT: A 232 ASN cc_start: 0.9264 (OUTLIER) cc_final: 0.8990 (m110) REVERT: A 250 TYR cc_start: 0.8549 (m-80) cc_final: 0.8337 (m-80) REVERT: A 341 LYS cc_start: 0.9356 (mmtm) cc_final: 0.9090 (mmpt) REVERT: A 344 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8546 (mt-10) REVERT: A 359 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7986 (ttp) REVERT: A 366 LYS cc_start: 0.9131 (mtmt) cc_final: 0.8819 (ptpp) REVERT: A 381 LEU cc_start: 0.9118 (tp) cc_final: 0.8501 (pt) REVERT: A 384 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7497 (pm20) REVERT: A 385 VAL cc_start: 0.8985 (t) cc_final: 0.8644 (t) REVERT: A 390 GLN cc_start: 0.8494 (mt0) cc_final: 0.8068 (mt0) REVERT: A 483 GLU cc_start: 0.9113 (mp0) cc_final: 0.8541 (pm20) REVERT: A 548 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8551 (mm-30) REVERT: A 628 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8301 (mp0) REVERT: A 640 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.7838 (tpp) REVERT: B 95 MET cc_start: 0.8579 (tpp) cc_final: 0.8210 (tpp) REVERT: B 99 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8692 (tptp) REVERT: B 184 ARG cc_start: 0.9082 (tpp-160) cc_final: 0.8698 (tpp-160) REVERT: B 190 MET cc_start: 0.9179 (mtm) cc_final: 0.8846 (mtm) REVERT: B 217 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7493 (tm-30) REVERT: B 218 ASN cc_start: 0.8869 (OUTLIER) cc_final: 0.8543 (m110) REVERT: B 257 ASP cc_start: 0.8594 (m-30) cc_final: 0.8264 (m-30) REVERT: B 274 ARG cc_start: 0.7338 (tpp-160) cc_final: 0.7094 (tpp-160) REVERT: B 322 MET cc_start: 0.9053 (mmm) cc_final: 0.8449 (mmm) REVERT: B 362 ASP cc_start: 0.7356 (m-30) cc_final: 0.7134 (m-30) REVERT: B 398 ASP cc_start: 0.8247 (t0) cc_final: 0.7854 (t0) REVERT: B 415 ASN cc_start: 0.9275 (t0) cc_final: 0.8728 (t0) REVERT: B 441 GLU cc_start: 0.8640 (pt0) cc_final: 0.8234 (pt0) REVERT: B 467 ASN cc_start: 0.9090 (t0) cc_final: 0.8828 (m-40) REVERT: B 493 MET cc_start: 0.9403 (tmm) cc_final: 0.8998 (tmm) REVERT: B 494 MET cc_start: 0.9236 (mtm) cc_final: 0.8973 (mtp) REVERT: B 515 ASP cc_start: 0.8860 (m-30) cc_final: 0.8564 (m-30) REVERT: B 668 ASN cc_start: 0.8594 (m-40) cc_final: 0.8253 (m110) REVERT: C 21 PHE cc_start: 0.9416 (m-80) cc_final: 0.9090 (m-80) REVERT: C 76 ILE cc_start: 0.8673 (mm) cc_final: 0.8246 (tp) REVERT: C 85 GLN cc_start: 0.5075 (mt0) cc_final: 0.4310 (pt0) REVERT: C 93 MET cc_start: 0.8861 (mtt) cc_final: 0.8579 (mtt) REVERT: C 127 GLN cc_start: 0.9033 (mm-40) cc_final: 0.8700 (pp30) REVERT: C 158 VAL cc_start: 0.9631 (t) cc_final: 0.9227 (m) REVERT: C 162 TYR cc_start: 0.9335 (OUTLIER) cc_final: 0.8845 (m-10) REVERT: C 201 HIS cc_start: 0.8954 (m90) cc_final: 0.8281 (m90) REVERT: C 271 LEU cc_start: 0.8723 (mm) cc_final: 0.8122 (mm) REVERT: D 18 THR cc_start: 0.7901 (m) cc_final: 0.7564 (m) REVERT: D 25 ASN cc_start: 0.9399 (m-40) cc_final: 0.8786 (m110) REVERT: D 28 GLN cc_start: 0.8632 (tt0) cc_final: 0.8248 (pp30) REVERT: D 96 MET cc_start: 0.6368 (mmm) cc_final: 0.6162 (mmm) REVERT: D 153 LEU cc_start: 0.6355 (mt) cc_final: 0.6051 (mt) REVERT: D 172 PHE cc_start: 0.6953 (OUTLIER) cc_final: 0.6484 (m-10) REVERT: D 174 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.7436 (t80) REVERT: D 197 ASP cc_start: 0.8881 (t0) cc_final: 0.8272 (t0) outliers start: 67 outliers final: 48 residues processed: 517 average time/residue: 0.1354 time to fit residues: 104.1264 Evaluate side-chains 518 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 459 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 131 ASN 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 213 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 232 ASN 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 349 LEU Chi-restraints excluded: chain A residue 352 GLU 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 A residue 667 LEU Chi-restraints excluded: chain B residue 49 HIS 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 218 ASN Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 374 SER 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 475 ASN 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 624 PHE Chi-restraints excluded: chain B residue 644 ILE 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 174 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 172 PHE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 239 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 3.9990 chunk 62 optimal weight: 0.0670 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 189 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 191 GLN B 202 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN C 238 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.134938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.097014 restraints weight = 35319.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.100382 restraints weight = 16979.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.102585 restraints weight = 10063.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.103986 restraints weight = 6846.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.104873 restraints weight = 5245.978| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 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 = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.6589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16386 Z= 0.140 Angle : 0.732 11.767 22134 Z= 0.371 Chirality : 0.045 0.213 2360 Planarity : 0.004 0.124 2818 Dihedral : 10.480 174.673 2247 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.80 % Allowed : 28.03 % Favored : 69.17 % 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 aren not related in a simple way. whole: 0.75 (0.19), residues: 1932 helix: 0.94 (0.15), residues: 1127 sheet: -0.08 (0.46), residues: 134 loop : 0.06 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 686 TYR 0.034 0.001 TYR D 142 PHE 0.027 0.002 PHE C 154 TRP 0.031 0.002 TRP D 30 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00316 (16386) covalent geometry : angle 0.73215 (22134) hydrogen bonds : bond 0.03936 ( 871) hydrogen bonds : angle 5.12888 ( 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 542 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 494 time to evaluate : 0.694 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: A 56 ASP cc_start: 0.8805 (m-30) cc_final: 0.8456 (m-30) REVERT: A 65 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8192 (mm-30) REVERT: A 150 GLN cc_start: 0.8903 (tm-30) cc_final: 0.8564 (tm-30) REVERT: A 170 CYS cc_start: 0.8100 (p) cc_final: 0.7763 (m) REVERT: A 209 LYS cc_start: 0.8359 (tptt) cc_final: 0.8157 (tptp) REVERT: A 218 ASN cc_start: 0.8818 (t0) cc_final: 0.8045 (t0) REVERT: A 232 ASN cc_start: 0.9204 (m110) cc_final: 0.8804 (m110) REVERT: A 341 LYS cc_start: 0.9334 (mmtm) cc_final: 0.9078 (mmpt) REVERT: A 344 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8551 (mt-10) REVERT: A 359 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7946 (ttp) REVERT: A 361 GLN cc_start: 0.8513 (tp40) cc_final: 0.7859 (tp40) REVERT: A 381 LEU cc_start: 0.9069 (tp) cc_final: 0.8562 (pt) REVERT: A 384 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7419 (pm20) REVERT: A 385 VAL cc_start: 0.8984 (t) cc_final: 0.8576 (t) REVERT: A 390 GLN cc_start: 0.8457 (mt0) cc_final: 0.8058 (mt0) REVERT: A 483 GLU cc_start: 0.9091 (mp0) cc_final: 0.8493 (pm20) REVERT: A 576 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8464 (mt) REVERT: A 628 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8273 (mp0) REVERT: A 640 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.7818 (tpp) REVERT: B 95 MET cc_start: 0.8511 (tpp) cc_final: 0.8211 (tpp) REVERT: B 99 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8678 (tptp) REVERT: B 184 ARG cc_start: 0.9093 (tpp-160) cc_final: 0.8694 (tpp-160) REVERT: B 190 MET cc_start: 0.9162 (mtm) cc_final: 0.8841 (mtm) REVERT: B 243 ARG cc_start: 0.7447 (tmm160) cc_final: 0.7150 (tmm160) REVERT: B 257 ASP cc_start: 0.8544 (m-30) cc_final: 0.8177 (m-30) REVERT: B 274 ARG cc_start: 0.7191 (tpp-160) cc_final: 0.6922 (tpp-160) REVERT: B 301 PHE cc_start: 0.9062 (m-80) cc_final: 0.8712 (m-80) REVERT: B 322 MET cc_start: 0.9028 (mmm) cc_final: 0.8389 (mmm) REVERT: B 357 TYR cc_start: 0.7993 (m-80) cc_final: 0.7743 (m-10) REVERT: B 384 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.7951 (pp20) REVERT: B 398 ASP cc_start: 0.8213 (t0) cc_final: 0.7776 (t0) REVERT: B 415 ASN cc_start: 0.9273 (t0) cc_final: 0.8779 (t0) REVERT: B 467 ASN cc_start: 0.8989 (t0) cc_final: 0.8748 (m-40) REVERT: B 474 GLN cc_start: 0.8493 (mt0) cc_final: 0.8101 (mt0) REVERT: B 493 MET cc_start: 0.9375 (tmm) cc_final: 0.9040 (tmm) REVERT: B 494 MET cc_start: 0.9188 (mtm) cc_final: 0.8907 (mtp) REVERT: B 526 GLU cc_start: 0.8239 (mt-10) cc_final: 0.8014 (mp0) REVERT: B 576 LEU cc_start: 0.9408 (mt) cc_final: 0.9163 (mt) REVERT: B 668 ASN cc_start: 0.8466 (m-40) cc_final: 0.8228 (m-40) REVERT: C 21 PHE cc_start: 0.9389 (m-80) cc_final: 0.9158 (m-80) REVERT: C 76 ILE cc_start: 0.8652 (mm) cc_final: 0.8275 (tp) REVERT: C 85 GLN cc_start: 0.5039 (mt0) cc_final: 0.4361 (pt0) REVERT: C 93 MET cc_start: 0.8960 (mtt) cc_final: 0.8684 (mtt) REVERT: C 127 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8728 (pp30) REVERT: C 137 MET cc_start: 0.7150 (mtt) cc_final: 0.6513 (ptp) REVERT: C 154 PHE cc_start: 0.9158 (m-80) cc_final: 0.8870 (m-80) REVERT: C 158 VAL cc_start: 0.9622 (t) cc_final: 0.9284 (m) REVERT: C 162 TYR cc_start: 0.9332 (OUTLIER) cc_final: 0.8750 (m-10) REVERT: C 174 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.7129 (t80) REVERT: C 201 HIS cc_start: 0.8981 (m90) cc_final: 0.8293 (m90) REVERT: C 271 LEU cc_start: 0.8705 (mm) cc_final: 0.7755 (mm) REVERT: D 18 THR cc_start: 0.7912 (m) cc_final: 0.7555 (m) REVERT: D 25 ASN cc_start: 0.9293 (m-40) cc_final: 0.8679 (m110) REVERT: D 28 GLN cc_start: 0.8596 (tt0) cc_final: 0.8280 (pp30) REVERT: D 51 GLU cc_start: 0.8474 (pt0) cc_final: 0.8150 (pm20) REVERT: D 74 MET cc_start: 0.6120 (tmm) cc_final: 0.5830 (tmm) REVERT: D 153 LEU cc_start: 0.6217 (mt) cc_final: 0.5810 (mt) REVERT: D 174 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.7488 (t80) REVERT: D 189 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7745 (pt0) REVERT: D 197 ASP cc_start: 0.8890 (t0) cc_final: 0.8251 (t0) outliers start: 48 outliers final: 33 residues processed: 511 average time/residue: 0.1328 time to fit residues: 101.8920 Evaluate side-chains 510 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 468 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 33 VAL 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 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 576 LEU 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 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 475 ASN 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 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 174 TYR Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 239 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.135025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.097135 restraints weight = 35096.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.100470 restraints weight = 16792.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.102643 restraints weight = 9889.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.103950 restraints weight = 6763.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.104906 restraints weight = 5196.551| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- 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 = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.6755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16386 Z= 0.147 Angle : 0.737 12.582 22134 Z= 0.372 Chirality : 0.046 0.351 2360 Planarity : 0.004 0.050 2818 Dihedral : 10.367 172.876 2246 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.03 % Allowed : 28.03 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.19), residues: 1932 helix: 0.84 (0.15), residues: 1136 sheet: 0.02 (0.48), residues: 118 loop : 0.04 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 261 TYR 0.026 0.001 TYR D 142 PHE 0.027 0.002 PHE C 172 TRP 0.032 0.002 TRP D 30 HIS 0.004 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00335 (16386) covalent geometry : angle 0.73652 (22134) hydrogen bonds : bond 0.03983 ( 871) hydrogen bonds : angle 5.15342 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3374.69 seconds wall clock time: 59 minutes 34.74 seconds (3574.74 seconds total)