Starting phenix.real_space_refine on Fri Jul 3 19:45:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byz_45049/07_2026/9byz_45049_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byz_45049/07_2026/9byz_45049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9byz_45049/07_2026/9byz_45049_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byz_45049/07_2026/9byz_45049_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9byz_45049/07_2026/9byz_45049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byz_45049/07_2026/9byz_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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.36, per 1000 atoms: 0.21 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: 1.29 Conformation dependent library (CDL) restraints added in 523.1 milliseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A 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: 2.37 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4770 1.34 - 1.46: 3070 1.46 - 1.58: 8365 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" O3B TTP B 801 " pdb=" PG TTP B 801 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" O3B TTP A 803 " pdb=" PG TTP A 803 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.060 1.25e-02 6.40e+03 2.33e+01 bond pdb=" O3A TTP A 803 " pdb=" PB TTP A 803 " ideal model delta sigma weight residual 1.675 1.606 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.15e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21527 2.09 - 4.18: 525 4.18 - 6.27: 64 6.27 - 8.36: 9 8.36 - 10.45: 9 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.62 -6.08 1.36e+00 5.41e-01 2.00e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.18 -4.47 1.15e+00 7.56e-01 1.51e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.83 -4.33 1.23e+00 6.61e-01 1.24e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.72 -4.01 1.15e+00 7.56e-01 1.21e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.53 3.66 1.06e+00 8.90e-01 1.19e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.05: 9092 25.05 - 50.10: 653 50.10 - 75.15: 125 75.15 - 100.20: 26 100.20 - 125.24: 2 Dihedral angle restraints: 9898 sinusoidal: 4140 harmonic: 5758 Sorted by residual: dihedral pdb=" O4' GDP A 802 " pdb=" C1' GDP A 802 " pdb=" N9 GDP A 802 " pdb=" C8 GDP A 802 " ideal model delta sinusoidal sigma weight residual 27.02 -98.22 125.24 1 2.00e+01 2.50e-03 3.78e+01 dihedral pdb=" O4' GDP B 804 " pdb=" C1' GDP B 804 " pdb=" N9 GDP B 804 " pdb=" C8 GDP B 804 " ideal model delta sinusoidal sigma weight residual 27.02 -95.53 122.55 1 2.00e+01 2.50e-03 3.69e+01 dihedral pdb=" C VAL C 125 " pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual -122.00 -134.31 12.31 0 2.50e+00 1.60e-01 2.42e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2141 0.093 - 0.186: 184 0.186 - 0.278: 30 0.278 - 0.371: 3 0.371 - 0.464: 2 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.38e+00 chirality pdb=" CA TYR C 169 " pdb=" N TYR C 169 " pdb=" C TYR C 169 " pdb=" CB TYR C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.63e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO D 75 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " 0.017 2.00e-02 2.50e+03 1.10e-02 2.11e+00 pdb=" CG PHE D 92 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 179 " -0.016 2.00e-02 2.50e+03 9.81e-03 1.93e+00 pdb=" CG TYR D 179 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR D 179 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 179 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR D 179 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 179 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR D 179 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 179 " -0.005 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 129 2.51 - 3.11: 11559 3.11 - 3.70: 27048 3.70 - 4.30: 41564 4.30 - 4.90: 65457 Nonbonded interactions: 145757 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 3.060 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 3.060 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 3.060 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.991 3.060 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.013 3.040 ... (remaining 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: 1.060 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.640 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.139 16386 Z= 0.334 Angle : 0.788 10.448 22134 Z= 0.471 Chirality : 0.058 0.464 2360 Planarity : 0.003 0.042 2818 Dihedral : 17.635 125.244 6202 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.40 % Allowed : 15.21 % Favored : 83.39 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.18), residues: 1932 helix: 0.58 (0.14), residues: 1151 sheet: 0.46 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 196 TYR 0.021 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.009 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.33 (16386) covalent geometry : angle 0.78750 / 0.47 (22134) hydrogen bonds : bond 0.15420 / 9.51 ( 871) hydrogen bonds : angle 6.51780 / 4.65 ( 2571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 878 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.8819 (mt) cc_final: 0.8554 (mt) REVERT: A 37 PHE cc_start: 0.7949 (m-80) cc_final: 0.7497 (m-10) REVERT: A 144 MET cc_start: 0.6905 (mtm) cc_final: 0.6687 (mtm) REVERT: A 157 LEU cc_start: 0.9004 (tp) cc_final: 0.8741 (tt) REVERT: A 183 SER cc_start: 0.8618 (p) cc_final: 0.8372 (p) REVERT: A 186 ILE cc_start: 0.9440 (mt) cc_final: 0.9089 (mt) REVERT: A 188 ILE cc_start: 0.8765 (mt) cc_final: 0.8517 (mt) REVERT: A 218 ASN cc_start: 0.7691 (t0) cc_final: 0.7274 (t0) REVERT: A 257 ASP cc_start: 0.8041 (m-30) cc_final: 0.7733 (m-30) REVERT: A 267 ILE cc_start: 0.7996 (mp) cc_final: 0.7482 (tp) REVERT: A 362 ASP cc_start: 0.6663 (m-30) cc_final: 0.5927 (m-30) REVERT: A 390 GLN cc_start: 0.7453 (mt0) cc_final: 0.7134 (mt0) REVERT: A 405 LEU cc_start: 0.8644 (mt) cc_final: 0.8389 (mt) REVERT: A 433 THR cc_start: 0.8995 (m) cc_final: 0.8786 (m) REVERT: A 502 ARG cc_start: 0.8204 (tpt170) cc_final: 0.7738 (tpt170) REVERT: A 640 MET cc_start: 0.8149 (tpp) cc_final: 0.7871 (tpp) REVERT: A 644 ILE cc_start: 0.8792 (mt) cc_final: 0.8438 (mt) REVERT: B 51 LEU cc_start: 0.8148 (tp) cc_final: 0.7902 (tp) REVERT: B 157 LEU cc_start: 0.8341 (tp) cc_final: 0.8034 (tp) REVERT: B 177 ASP cc_start: 0.8218 (t0) cc_final: 0.6646 (p0) REVERT: B 180 ASN cc_start: 0.7454 (m-40) cc_final: 0.7184 (m110) REVERT: B 184 ARG cc_start: 0.8306 (tpp-160) cc_final: 0.8094 (tpp-160) REVERT: B 322 MET cc_start: 0.7732 (mmm) cc_final: 0.7446 (mmm) REVERT: B 425 ILE cc_start: 0.8674 (mt) cc_final: 0.8112 (mt) REVERT: B 485 ARG cc_start: 0.8037 (mtm-85) cc_final: 0.7801 (mtm-85) REVERT: B 597 ILE cc_start: 0.9135 (pt) cc_final: 0.8856 (pt) REVERT: B 605 THR cc_start: 0.7858 (m) cc_final: 0.7568 (t) REVERT: B 645 GLN cc_start: 0.8532 (tp-100) cc_final: 0.8331 (tp40) REVERT: B 658 LEU cc_start: 0.8924 (mt) cc_final: 0.8383 (mt) REVERT: C 85 GLN cc_start: 0.4929 (mt0) cc_final: 0.4089 (pt0) REVERT: C 112 LEU cc_start: 0.3484 (mt) cc_final: 0.3053 (mp) REVERT: C 130 TYR cc_start: 0.3400 (m-80) cc_final: 0.3146 (m-80) REVERT: C 287 LEU cc_start: 0.2172 (OUTLIER) cc_final: 0.1826 (mp) REVERT: D 256 VAL cc_start: 0.6873 (t) cc_final: 0.6170 (t) REVERT: D 260 ILE cc_start: 0.6984 (mt) cc_final: 0.6360 (tp) outliers start: 24 outliers final: 8 residues processed: 885 average time/residue: 0.1278 time to fit residues: 165.1492 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 : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain D residue 59 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.0870 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.1980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN A 320 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 320 ASN B 329 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN C 263 ASN C 270 ASN D 23 ASN D 28 GLN D 71 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.138015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.099187 restraints weight = 34384.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.102784 restraints weight = 16326.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.105116 restraints weight = 9603.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.106663 restraints weight = 6502.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.107687 restraints weight = 4880.312| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16386 Z= 0.149 Angle : 0.673 14.559 22134 Z= 0.350 Chirality : 0.044 0.169 2360 Planarity : 0.004 0.038 2818 Dihedral : 10.006 127.044 2307 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.55 % Allowed : 19.87 % 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 are not related in a simple way. whole: 1.34 (0.19), residues: 1932 helix: 1.32 (0.15), residues: 1128 sheet: 0.22 (0.42), residues: 130 loop : 0.50 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 350 TYR 0.021 0.002 TYR D 177 PHE 0.037 0.002 PHE C 168 TRP 0.024 0.002 TRP C 30 HIS 0.007 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (16386) covalent geometry : angle 0.67302 / 0.35 (22134) hydrogen bonds : bond 0.04759 / 3.02 ( 871) hydrogen bonds : angle 5.20254 / 3.70 ( 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: 61 poor density : 639 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: A 12 LEU cc_start: 0.9219 (mt) cc_final: 0.8974 (mt) REVERT: A 87 LYS cc_start: 0.9049 (tptm) cc_final: 0.8818 (tptm) REVERT: A 99 LYS cc_start: 0.9196 (mmmm) cc_final: 0.8608 (mmmm) REVERT: A 103 ASP cc_start: 0.8723 (m-30) cc_final: 0.8497 (m-30) REVERT: A 161 ARG cc_start: 0.8043 (ttm170) cc_final: 0.7772 (mmm-85) REVERT: A 164 ARG cc_start: 0.8336 (ptt90) cc_final: 0.8105 (ptt90) REVERT: A 218 ASN cc_start: 0.8802 (t0) cc_final: 0.8238 (t0) REVERT: A 256 ARG cc_start: 0.9083 (ttp80) cc_final: 0.8649 (ttp80) REVERT: A 291 LEU cc_start: 0.9663 (mt) cc_final: 0.9412 (mp) REVERT: A 308 LYS cc_start: 0.9165 (mtmm) cc_final: 0.8908 (mtmt) REVERT: A 335 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7305 (mt-10) REVERT: A 384 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7432 (pm20) REVERT: A 385 VAL cc_start: 0.8879 (t) cc_final: 0.8429 (t) REVERT: A 483 GLU cc_start: 0.9046 (mp0) cc_final: 0.8237 (pm20) REVERT: A 505 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7617 (mt-10) REVERT: A 640 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8339 (tpp) REVERT: A 686 ARG cc_start: 0.7859 (mtp85) cc_final: 0.7652 (mtp85) REVERT: B 71 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8990 (mp) REVERT: B 95 MET cc_start: 0.8487 (tpp) cc_final: 0.8191 (tpp) REVERT: B 149 TYR cc_start: 0.9089 (t80) cc_final: 0.8459 (t80) REVERT: B 184 ARG cc_start: 0.9137 (tpp-160) cc_final: 0.8655 (tpp-160) REVERT: B 190 MET cc_start: 0.9130 (mtm) cc_final: 0.8811 (mtm) REVERT: B 202 ASN cc_start: 0.8836 (t0) cc_final: 0.8453 (t0) REVERT: B 235 ARG cc_start: 0.8447 (ttm110) cc_final: 0.7841 (mtm-85) REVERT: B 290 GLU cc_start: 0.8965 (tt0) cc_final: 0.8594 (tm-30) REVERT: B 322 MET cc_start: 0.8809 (mmm) cc_final: 0.8395 (mmm) REVERT: B 335 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8171 (mt-10) REVERT: B 348 MET cc_start: 0.8143 (tpp) cc_final: 0.7925 (tpp) REVERT: B 361 GLN cc_start: 0.8589 (tt0) cc_final: 0.8369 (tt0) REVERT: B 362 ASP cc_start: 0.7672 (m-30) cc_final: 0.7336 (m-30) REVERT: B 374 SER cc_start: 0.9383 (t) cc_final: 0.9129 (t) REVERT: B 375 LYS cc_start: 0.8824 (mtmm) cc_final: 0.8354 (mtpp) REVERT: B 384 GLU cc_start: 0.8227 (pm20) cc_final: 0.7607 (pm20) REVERT: B 467 ASN cc_start: 0.9108 (t0) cc_final: 0.8900 (m-40) REVERT: B 515 ASP cc_start: 0.8846 (m-30) cc_final: 0.8623 (m-30) REVERT: B 576 LEU cc_start: 0.9412 (mt) cc_final: 0.9132 (mt) REVERT: B 645 GLN cc_start: 0.9077 (tp-100) cc_final: 0.8781 (tp-100) REVERT: B 669 ARG cc_start: 0.8833 (mtp85) cc_final: 0.8619 (mmm-85) REVERT: B 683 TYR cc_start: 0.8528 (t80) cc_final: 0.8210 (t80) REVERT: C 56 MET cc_start: 0.5803 (mmm) cc_final: 0.5558 (ptp) REVERT: C 85 GLN cc_start: 0.4168 (mt0) cc_final: 0.3342 (pt0) REVERT: C 154 PHE cc_start: 0.8713 (t80) cc_final: 0.8369 (t80) REVERT: C 157 MET cc_start: 0.9000 (mtt) cc_final: 0.8714 (mtt) REVERT: C 158 VAL cc_start: 0.9517 (t) cc_final: 0.8857 (t) REVERT: C 162 TYR cc_start: 0.9288 (m-10) cc_final: 0.8815 (m-10) REVERT: C 201 HIS cc_start: 0.8131 (m90) cc_final: 0.7792 (m90) REVERT: C 233 ASN cc_start: 0.9115 (m-40) cc_final: 0.8764 (m-40) REVERT: C 266 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.9033 (mtmt) REVERT: C 271 LEU cc_start: 0.8560 (mm) cc_final: 0.7979 (mm) REVERT: C 317 ASP cc_start: 0.8276 (m-30) cc_final: 0.7901 (m-30) REVERT: C 320 PHE cc_start: 0.9302 (m-80) cc_final: 0.8979 (m-80) REVERT: D 71 ASN cc_start: 0.8479 (m-40) cc_final: 0.8173 (m110) REVERT: D 92 PHE cc_start: 0.7150 (t80) cc_final: 0.6812 (t80) REVERT: D 96 MET cc_start: 0.5987 (mmm) cc_final: 0.5683 (mmt) REVERT: D 137 MET cc_start: 0.5422 (mtp) cc_final: 0.5211 (ptp) REVERT: D 174 TYR cc_start: 0.7944 (OUTLIER) cc_final: 0.7125 (t80) REVERT: D 184 LEU cc_start: 0.8687 (mt) cc_final: 0.8421 (mt) REVERT: D 195 LEU cc_start: 0.8764 (tt) cc_final: 0.8532 (mm) REVERT: D 223 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8397 (tp30) REVERT: D 227 PHE cc_start: 0.8399 (m-10) cc_final: 0.8180 (m-10) outliers start: 61 outliers final: 25 residues processed: 666 average time/residue: 0.1273 time to fit residues: 127.5657 Evaluate side-chains 539 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 508 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 565 VAL Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 266 LYS Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 254 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 164 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 182 optimal weight: 0.9980 chunk 159 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN A 259 ASN A 320 ASN A 387 GLN A 410 ASN A 447 ASN ** B 11 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 645 GLN B 646 GLN B 676 HIS C 91 ASN C 234 GLN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.131408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.093572 restraints weight = 35127.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.096962 restraints weight = 16941.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.099097 restraints weight = 10124.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.100621 restraints weight = 6932.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.101539 restraints weight = 5220.914| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 11 (16 function evaluations) r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4591 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= 0.183 Angle : 0.632 14.336 22134 Z= 0.329 Chirality : 0.043 0.168 2360 Planarity : 0.003 0.033 2818 Dihedral : 9.112 128.112 2303 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.20 % Allowed : 20.63 % Favored : 75.17 % 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 are not related in a simple way. whole: 1.28 (0.19), residues: 1932 helix: 1.33 (0.15), residues: 1131 sheet: -0.15 (0.40), residues: 146 loop : 0.46 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 121 TYR 0.033 0.002 TYR A 498 PHE 0.032 0.002 PHE C 168 TRP 0.027 0.002 TRP D 30 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (16386) covalent geometry : angle 0.63215 / 0.33 (22134) hydrogen bonds : bond 0.04208 / 2.65 ( 871) hydrogen bonds : angle 5.05432 / 3.58 ( 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 621 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 549 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.9180 (mmmm) cc_final: 0.8447 (mmmm) REVERT: A 102 ASN cc_start: 0.9047 (OUTLIER) cc_final: 0.8810 (m-40) REVERT: A 103 ASP cc_start: 0.8901 (m-30) cc_final: 0.8556 (m-30) REVERT: A 214 LYS cc_start: 0.8482 (ttmm) cc_final: 0.8263 (mttm) REVERT: A 218 ASN cc_start: 0.8931 (t0) cc_final: 0.8399 (t0) REVERT: A 256 ARG cc_start: 0.9131 (ttp80) cc_final: 0.8706 (ttp80) REVERT: A 307 TYR cc_start: 0.9201 (t80) cc_final: 0.8913 (t80) REVERT: A 335 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7254 (mt-10) REVERT: A 344 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8652 (mt-10) REVERT: A 359 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7778 (ttp) REVERT: A 362 ASP cc_start: 0.8306 (m-30) cc_final: 0.7630 (m-30) REVERT: A 381 LEU cc_start: 0.9030 (tp) cc_final: 0.8490 (pt) REVERT: A 384 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7384 (pm20) REVERT: A 385 VAL cc_start: 0.8933 (t) cc_final: 0.8418 (t) REVERT: A 483 GLU cc_start: 0.9008 (mp0) cc_final: 0.8543 (pm20) REVERT: A 505 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7730 (mt-10) REVERT: A 548 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8310 (mm-30) REVERT: A 628 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8085 (mm-30) REVERT: A 640 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.8291 (tpp) REVERT: A 645 GLN cc_start: 0.8910 (tp40) cc_final: 0.8710 (tp-100) REVERT: B 95 MET cc_start: 0.8584 (tpp) cc_final: 0.8189 (tpp) REVERT: B 184 ARG cc_start: 0.9174 (tpp-160) cc_final: 0.8729 (tpp-160) REVERT: B 190 MET cc_start: 0.9177 (mtm) cc_final: 0.8913 (mtm) REVERT: B 202 ASN cc_start: 0.8912 (t0) cc_final: 0.8706 (t0) REVERT: B 231 ASP cc_start: 0.8587 (t70) cc_final: 0.8351 (t0) REVERT: B 235 ARG cc_start: 0.8341 (ttm110) cc_final: 0.7829 (ttm110) REVERT: B 252 ASN cc_start: 0.8929 (t0) cc_final: 0.8726 (t0) REVERT: B 322 MET cc_start: 0.8973 (mmm) cc_final: 0.8305 (mmm) REVERT: B 335 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8031 (mt-10) REVERT: B 348 MET cc_start: 0.8082 (tpp) cc_final: 0.7853 (tpp) REVERT: B 374 SER cc_start: 0.9384 (t) cc_final: 0.9138 (t) REVERT: B 375 LYS cc_start: 0.8844 (mtmm) cc_final: 0.8398 (mtpp) REVERT: B 384 GLU cc_start: 0.8397 (pm20) cc_final: 0.7658 (pm20) REVERT: B 398 ASP cc_start: 0.8235 (t0) cc_final: 0.7897 (t0) REVERT: B 467 ASN cc_start: 0.9145 (t0) cc_final: 0.8847 (m-40) REVERT: B 493 MET cc_start: 0.9402 (tmm) cc_final: 0.9061 (tmm) REVERT: B 515 ASP cc_start: 0.8886 (m-30) cc_final: 0.8461 (m-30) REVERT: B 550 MET cc_start: 0.7883 (mtm) cc_final: 0.7524 (mtp) REVERT: B 602 GLU cc_start: 0.7960 (tp30) cc_final: 0.7440 (tp30) REVERT: B 645 GLN cc_start: 0.9158 (tp40) cc_final: 0.8818 (tp-100) REVERT: B 668 ASN cc_start: 0.8815 (m-40) cc_final: 0.8596 (m110) REVERT: B 669 ARG cc_start: 0.8861 (mtp85) cc_final: 0.8614 (mmm-85) REVERT: B 683 TYR cc_start: 0.8858 (t80) cc_final: 0.8313 (t80) REVERT: C 76 ILE cc_start: 0.8177 (mm) cc_final: 0.7677 (tp) REVERT: C 85 GLN cc_start: 0.4079 (mt0) cc_final: 0.3339 (pt0) REVERT: C 93 MET cc_start: 0.8892 (mtt) cc_final: 0.8686 (mtt) REVERT: C 95 MET cc_start: 0.8523 (tmm) cc_final: 0.8296 (tmm) REVERT: C 155 LYS cc_start: 0.8441 (mttm) cc_final: 0.8097 (mmtt) REVERT: C 157 MET cc_start: 0.9133 (mtt) cc_final: 0.8735 (mtt) REVERT: C 158 VAL cc_start: 0.9684 (t) cc_final: 0.9090 (t) REVERT: C 162 TYR cc_start: 0.9349 (m-10) cc_final: 0.8811 (m-10) REVERT: C 174 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.7931 (t80) REVERT: C 200 ILE cc_start: 0.9295 (mp) cc_final: 0.8847 (tp) REVERT: C 201 HIS cc_start: 0.8810 (m90) cc_final: 0.8401 (m90) REVERT: C 212 ILE cc_start: 0.8419 (mm) cc_final: 0.7476 (mm) REVERT: C 254 HIS cc_start: 0.9173 (t70) cc_final: 0.8951 (t70) REVERT: C 271 LEU cc_start: 0.8609 (mm) cc_final: 0.7924 (mm) REVERT: C 317 ASP cc_start: 0.8350 (m-30) cc_final: 0.7960 (m-30) REVERT: D 96 MET cc_start: 0.5869 (mmm) cc_final: 0.5553 (mmm) REVERT: D 137 MET cc_start: 0.5482 (mtp) cc_final: 0.5263 (ptp) REVERT: D 174 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.7251 (t80) outliers start: 72 outliers final: 40 residues processed: 588 average time/residue: 0.1235 time to fit residues: 109.8585 Evaluate side-chains 554 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 507 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 102 ASN 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 425 ILE 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 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 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 587 VAL Chi-restraints excluded: chain B residue 598 MET 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 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 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 174 TYR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 6.9990 chunk 157 optimal weight: 9.9990 chunk 168 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 185 optimal weight: 8.9990 chunk 191 optimal weight: 0.1980 chunk 159 optimal weight: 6.9990 chunk 182 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN A 365 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 191 GLN B 304 HIS ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN B 646 GLN C 249 GLN C 263 ASN D 25 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.133624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.095475 restraints weight = 34974.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.098843 restraints weight = 16759.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.101054 restraints weight = 9965.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.102558 restraints weight = 6783.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.103487 restraints weight = 5140.559| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16386 Z= 0.158 Angle : 0.607 11.052 22134 Z= 0.316 Chirality : 0.043 0.164 2360 Planarity : 0.003 0.032 2818 Dihedral : 8.851 129.684 2302 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.79 % Allowed : 22.32 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.19), residues: 1932 helix: 1.25 (0.15), residues: 1136 sheet: -0.25 (0.41), residues: 146 loop : 0.47 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 164 TYR 0.021 0.001 TYR D 262 PHE 0.037 0.002 PHE C 168 TRP 0.030 0.002 TRP D 30 HIS 0.008 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (16386) covalent geometry : angle 0.60741 / 0.32 (22134) hydrogen bonds : bond 0.04017 / 2.56 ( 871) hydrogen bonds : angle 5.01068 / 3.56 ( 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 609 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 544 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.9102 (mmmm) cc_final: 0.8754 (mmmm) REVERT: A 103 ASP cc_start: 0.8910 (m-30) cc_final: 0.8645 (m-30) REVERT: A 157 LEU cc_start: 0.9069 (tp) cc_final: 0.8733 (tt) REVERT: A 161 ARG cc_start: 0.8077 (ttm170) cc_final: 0.7744 (mmm-85) REVERT: A 214 LYS cc_start: 0.8399 (ttmm) cc_final: 0.8156 (mttm) REVERT: A 218 ASN cc_start: 0.8863 (t0) cc_final: 0.8253 (t0) REVERT: A 307 TYR cc_start: 0.9182 (t80) cc_final: 0.8918 (t80) REVERT: A 344 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8582 (mt-10) REVERT: A 359 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7799 (ttp) REVERT: A 381 LEU cc_start: 0.9090 (tp) cc_final: 0.8476 (pt) REVERT: A 384 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7394 (pm20) REVERT: A 385 VAL cc_start: 0.8907 (t) cc_final: 0.8537 (t) REVERT: A 390 GLN cc_start: 0.8488 (mt0) cc_final: 0.8101 (mt0) REVERT: A 406 ASP cc_start: 0.8133 (m-30) cc_final: 0.7859 (t0) REVERT: A 453 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8589 (ttp80) REVERT: A 483 GLU cc_start: 0.8984 (mp0) cc_final: 0.8505 (pm20) REVERT: A 505 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7803 (mt-10) REVERT: A 548 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8325 (mm-30) REVERT: A 590 SER cc_start: 0.9295 (p) cc_final: 0.9066 (p) REVERT: A 628 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8386 (mm-30) REVERT: A 640 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.8153 (tpp) REVERT: A 645 GLN cc_start: 0.8880 (tp40) cc_final: 0.8637 (tp-100) REVERT: B 71 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9010 (mp) REVERT: B 95 MET cc_start: 0.8595 (tpp) cc_final: 0.8216 (tpp) REVERT: B 99 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8617 (tptp) REVERT: B 108 THR cc_start: 0.8388 (OUTLIER) cc_final: 0.8149 (p) REVERT: B 184 ARG cc_start: 0.9144 (tpp-160) cc_final: 0.8878 (tpp-160) REVERT: B 190 MET cc_start: 0.9156 (mtm) cc_final: 0.8885 (mtm) REVERT: B 257 ASP cc_start: 0.8683 (m-30) cc_final: 0.8387 (m-30) REVERT: B 322 MET cc_start: 0.8982 (mmm) cc_final: 0.8445 (mmm) REVERT: B 335 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8138 (mt-10) REVERT: B 348 MET cc_start: 0.8112 (tpp) cc_final: 0.7871 (tpp) REVERT: B 361 GLN cc_start: 0.8557 (tt0) cc_final: 0.8276 (tt0) REVERT: B 362 ASP cc_start: 0.7661 (m-30) cc_final: 0.7434 (m-30) REVERT: B 374 SER cc_start: 0.9415 (t) cc_final: 0.9215 (t) REVERT: B 375 LYS cc_start: 0.8792 (mtmm) cc_final: 0.8404 (mtpp) REVERT: B 398 ASP cc_start: 0.8164 (t0) cc_final: 0.7823 (t0) REVERT: B 467 ASN cc_start: 0.9163 (t0) cc_final: 0.8866 (m-40) REVERT: B 493 MET cc_start: 0.9416 (tmm) cc_final: 0.9039 (tmm) REVERT: B 515 ASP cc_start: 0.8852 (m-30) cc_final: 0.8436 (m-30) REVERT: B 632 MET cc_start: 0.8404 (mtt) cc_final: 0.8184 (mtt) REVERT: B 668 ASN cc_start: 0.8757 (m-40) cc_final: 0.8466 (m110) REVERT: B 669 ARG cc_start: 0.8872 (mtp85) cc_final: 0.8629 (mmm-85) REVERT: C 76 ILE cc_start: 0.8480 (mm) cc_final: 0.8011 (tp) REVERT: C 85 GLN cc_start: 0.4241 (mt0) cc_final: 0.3507 (pt0) REVERT: C 93 MET cc_start: 0.9000 (mtt) cc_final: 0.8715 (mtt) REVERT: C 155 LYS cc_start: 0.8475 (mttm) cc_final: 0.8071 (mmtt) REVERT: C 157 MET cc_start: 0.9240 (mtt) cc_final: 0.8952 (mtt) REVERT: C 158 VAL cc_start: 0.9703 (t) cc_final: 0.9051 (t) REVERT: C 162 TYR cc_start: 0.9357 (m-10) cc_final: 0.8741 (m-10) REVERT: C 201 HIS cc_start: 0.8807 (m90) cc_final: 0.8364 (m90) REVERT: C 212 ILE cc_start: 0.8615 (mm) cc_final: 0.7889 (mm) REVERT: C 240 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8771 (mt) REVERT: C 269 MET cc_start: 0.9447 (tpp) cc_final: 0.9228 (mmp) REVERT: C 271 LEU cc_start: 0.8630 (mm) cc_final: 0.7936 (mm) REVERT: D 71 ASN cc_start: 0.8385 (m-40) cc_final: 0.7911 (m110) REVERT: D 92 PHE cc_start: 0.7242 (t80) cc_final: 0.6717 (t80) REVERT: D 96 MET cc_start: 0.5878 (mmm) cc_final: 0.5215 (mmm) REVERT: D 137 MET cc_start: 0.5298 (mtp) cc_final: 0.5004 (ptp) REVERT: D 174 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.7183 (t80) REVERT: D 197 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8590 (t0) REVERT: D 231 LEU cc_start: 0.9167 (tp) cc_final: 0.8933 (tp) outliers start: 65 outliers final: 38 residues processed: 579 average time/residue: 0.1222 time to fit residues: 107.1076 Evaluate side-chains 544 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 495 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 195 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 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 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 71 LEU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 72 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 240 LEU Chi-restraints excluded: chain C residue 245 ASP 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 131 LEU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 197 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 126 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 157 optimal weight: 9.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 259 ASN A 312 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.128741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.090837 restraints weight = 35750.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.094009 restraints weight = 17363.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.096098 restraints weight = 10461.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.097164 restraints weight = 7237.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.098198 restraints weight = 5743.604| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16386 Z= 0.246 Angle : 0.655 11.488 22134 Z= 0.343 Chirality : 0.044 0.166 2360 Planarity : 0.004 0.034 2818 Dihedral : 8.832 133.503 2301 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.78 % Allowed : 23.72 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.19), residues: 1932 helix: 1.16 (0.15), residues: 1143 sheet: -0.29 (0.41), residues: 146 loop : 0.32 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 164 TYR 0.022 0.002 TYR B 394 PHE 0.034 0.002 PHE B 261 TRP 0.037 0.003 TRP D 30 HIS 0.005 0.001 HIS A 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.25 (16386) covalent geometry : angle 0.65535 / 0.34 (22134) hydrogen bonds : bond 0.04074 / 2.58 ( 871) hydrogen bonds : angle 5.13758 / 3.65 ( 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 591 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 509 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8324 (mm-30) REVERT: A 99 LYS cc_start: 0.9126 (mmmm) cc_final: 0.8783 (mmmm) REVERT: A 102 ASN cc_start: 0.9070 (OUTLIER) cc_final: 0.8801 (m-40) REVERT: A 117 ARG cc_start: 0.8188 (mtt-85) cc_final: 0.7621 (mtt90) REVERT: A 161 ARG cc_start: 0.8106 (ttm170) cc_final: 0.7542 (mmm-85) REVERT: A 172 LEU cc_start: 0.9144 (mp) cc_final: 0.8437 (mp) REVERT: A 214 LYS cc_start: 0.8381 (ttmm) cc_final: 0.8124 (mttm) REVERT: A 218 ASN cc_start: 0.8920 (t0) cc_final: 0.8444 (t0) REVERT: A 344 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8599 (mt-10) REVERT: A 359 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8021 (ttp) REVERT: A 381 LEU cc_start: 0.9115 (tp) cc_final: 0.8468 (pt) REVERT: A 384 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7617 (pm20) REVERT: A 385 VAL cc_start: 0.8923 (t) cc_final: 0.8668 (t) REVERT: A 390 GLN cc_start: 0.8524 (mt0) cc_final: 0.8102 (mt0) REVERT: A 393 SER cc_start: 0.9120 (m) cc_final: 0.8606 (p) REVERT: A 505 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7792 (mt-10) REVERT: A 527 TYR cc_start: 0.8570 (t80) cc_final: 0.8361 (t80) REVERT: A 548 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8367 (mm-30) REVERT: A 628 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8500 (mm-30) REVERT: A 640 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.8111 (tpp) REVERT: A 645 GLN cc_start: 0.9055 (tp40) cc_final: 0.8804 (tp-100) REVERT: B 95 MET cc_start: 0.8666 (tpp) cc_final: 0.8309 (tpp) REVERT: B 99 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.8659 (tptp) REVERT: B 108 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8514 (p) REVERT: B 184 ARG cc_start: 0.9139 (tpp-160) cc_final: 0.8939 (tpp-160) REVERT: B 190 MET cc_start: 0.9156 (mtm) cc_final: 0.8866 (mtm) REVERT: B 252 ASN cc_start: 0.9196 (t0) cc_final: 0.8960 (t0) REVERT: B 257 ASP cc_start: 0.8738 (m-30) cc_final: 0.8449 (m-30) REVERT: B 312 GLN cc_start: 0.8562 (tt0) cc_final: 0.8152 (tt0) REVERT: B 335 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8034 (mt-10) REVERT: B 348 MET cc_start: 0.8106 (tpp) cc_final: 0.7886 (tpp) REVERT: B 441 GLU cc_start: 0.8610 (pt0) cc_final: 0.8408 (pt0) REVERT: B 467 ASN cc_start: 0.9231 (t0) cc_final: 0.8880 (m-40) REVERT: B 493 MET cc_start: 0.9414 (tmm) cc_final: 0.9025 (tmm) REVERT: B 515 ASP cc_start: 0.8892 (m-30) cc_final: 0.8476 (m-30) REVERT: B 599 GLU cc_start: 0.8323 (pt0) cc_final: 0.8122 (pt0) REVERT: B 604 ARG cc_start: 0.9029 (mmm-85) cc_final: 0.8805 (mmm-85) REVERT: C 17 PHE cc_start: 0.8512 (p90) cc_final: 0.7782 (p90) REVERT: C 76 ILE cc_start: 0.8473 (mm) cc_final: 0.8060 (tp) REVERT: C 85 GLN cc_start: 0.4442 (mt0) cc_final: 0.3688 (pt0) REVERT: C 93 MET cc_start: 0.9052 (mtt) cc_final: 0.8748 (mtt) REVERT: C 137 MET cc_start: 0.7703 (mtt) cc_final: 0.7214 (mpp) REVERT: C 155 LYS cc_start: 0.8614 (mttm) cc_final: 0.7859 (pttp) REVERT: C 157 MET cc_start: 0.9358 (mtt) cc_final: 0.8897 (mtt) REVERT: C 158 VAL cc_start: 0.9711 (t) cc_final: 0.9120 (t) REVERT: C 162 TYR cc_start: 0.9345 (m-10) cc_final: 0.8779 (m-10) REVERT: C 174 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.8000 (t80) REVERT: C 201 HIS cc_start: 0.8828 (m90) cc_final: 0.8358 (m90) REVERT: C 211 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8158 (pp20) REVERT: C 212 ILE cc_start: 0.8818 (mm) cc_final: 0.8175 (mt) REVERT: C 271 LEU cc_start: 0.8781 (mm) cc_final: 0.8169 (mm) REVERT: D 56 MET cc_start: 0.8157 (mmt) cc_final: 0.7537 (ptt) REVERT: D 71 ASN cc_start: 0.8371 (m-40) cc_final: 0.7977 (m110) REVERT: D 92 PHE cc_start: 0.7337 (t80) cc_final: 0.7020 (t80) REVERT: D 96 MET cc_start: 0.5928 (mmm) cc_final: 0.5261 (mmm) REVERT: D 137 MET cc_start: 0.5244 (mtp) cc_final: 0.4976 (ptp) REVERT: D 162 TYR cc_start: 0.6508 (m-10) cc_final: 0.6213 (m-10) REVERT: D 172 PHE cc_start: 0.7129 (OUTLIER) cc_final: 0.6179 (m-80) REVERT: D 174 TYR cc_start: 0.8229 (OUTLIER) cc_final: 0.7352 (t80) REVERT: D 197 ASP cc_start: 0.8853 (OUTLIER) cc_final: 0.8602 (t0) REVERT: D 231 LEU cc_start: 0.9173 (tp) cc_final: 0.8963 (tp) outliers start: 82 outliers final: 52 residues processed: 555 average time/residue: 0.1224 time to fit residues: 103.1831 Evaluate side-chains 548 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 485 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 257 ASP 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 443 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 638 VAL 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 108 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 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 381 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 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 55 TYR 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 245 ASP 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 172 PHE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 203 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 387 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 191 GLN B 218 ASN B 312 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN C 263 ASN D 25 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.129573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.092718 restraints weight = 35223.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.095930 restraints weight = 17003.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.098097 restraints weight = 10144.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.099405 restraints weight = 6950.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.100401 restraints weight = 5299.575| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16386 Z= 0.162 Angle : 0.637 11.589 22134 Z= 0.328 Chirality : 0.043 0.220 2360 Planarity : 0.003 0.034 2818 Dihedral : 8.641 133.646 2301 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.79 % Allowed : 25.70 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.19), residues: 1932 helix: 1.14 (0.15), residues: 1139 sheet: -0.18 (0.43), residues: 142 loop : 0.26 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 243 TYR 0.022 0.001 TYR B 394 PHE 0.029 0.002 PHE B 261 TRP 0.034 0.002 TRP D 30 HIS 0.004 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (16386) covalent geometry : angle 0.63749 / 0.33 (22134) hydrogen bonds : bond 0.03918 / 2.48 ( 871) hydrogen bonds : angle 5.06604 / 3.60 ( 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 577 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 512 time to evaluate : 0.641 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: 0.8575 (mm-30) cc_final: 0.8228 (mm-30) REVERT: A 99 LYS cc_start: 0.9049 (mmmm) cc_final: 0.8845 (mmmm) REVERT: A 161 ARG cc_start: 0.8085 (ttm170) cc_final: 0.7814 (mmm-85) REVERT: A 214 LYS cc_start: 0.8341 (ttmm) cc_final: 0.8053 (mttm) REVERT: A 218 ASN cc_start: 0.8974 (t0) cc_final: 0.8516 (t0) REVERT: A 341 LYS cc_start: 0.9369 (mmtm) cc_final: 0.8855 (mmpt) REVERT: A 344 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8582 (mt-10) REVERT: A 359 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7833 (ttp) REVERT: A 362 ASP cc_start: 0.8094 (m-30) cc_final: 0.7855 (m-30) REVERT: A 381 LEU cc_start: 0.9076 (tp) cc_final: 0.8422 (pt) REVERT: A 384 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7413 (pm20) REVERT: A 385 VAL cc_start: 0.8871 (t) cc_final: 0.8494 (t) REVERT: A 390 GLN cc_start: 0.8517 (mt0) cc_final: 0.8099 (mt0) REVERT: A 393 SER cc_start: 0.9041 (m) cc_final: 0.8660 (p) REVERT: A 483 GLU cc_start: 0.9053 (mp0) cc_final: 0.8546 (pm20) REVERT: A 505 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7783 (mt-10) REVERT: A 527 TYR cc_start: 0.8602 (t80) cc_final: 0.8399 (t80) REVERT: A 548 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8412 (mm-30) REVERT: A 628 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8515 (mm-30) REVERT: A 640 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.8034 (tpp) REVERT: A 645 GLN cc_start: 0.9014 (tp40) cc_final: 0.8736 (tp-100) REVERT: B 95 MET cc_start: 0.8606 (tpp) cc_final: 0.8252 (tpp) REVERT: B 99 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8629 (tptp) REVERT: B 108 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8521 (p) REVERT: B 184 ARG cc_start: 0.9120 (tpp-160) cc_final: 0.8706 (tpp-160) REVERT: B 190 MET cc_start: 0.9172 (mtm) cc_final: 0.8881 (mtm) REVERT: B 235 ARG cc_start: 0.8567 (ttm110) cc_final: 0.8300 (ttm110) REVERT: B 252 ASN cc_start: 0.9254 (t0) cc_final: 0.8932 (t0) REVERT: B 257 ASP cc_start: 0.8663 (m-30) cc_final: 0.8322 (m-30) REVERT: B 322 MET cc_start: 0.9008 (mmm) cc_final: 0.8286 (mmm) REVERT: B 348 MET cc_start: 0.8027 (tpp) cc_final: 0.7768 (tpp) REVERT: B 415 ASN cc_start: 0.9409 (t0) cc_final: 0.8943 (t0) REVERT: B 420 MET cc_start: 0.8937 (mmm) cc_final: 0.8633 (mmm) REVERT: B 467 ASN cc_start: 0.9088 (t0) cc_final: 0.8816 (m-40) REVERT: B 493 MET cc_start: 0.9407 (tmm) cc_final: 0.9042 (tmm) REVERT: B 515 ASP cc_start: 0.8893 (m-30) cc_final: 0.8518 (m-30) REVERT: B 546 LEU cc_start: 0.9434 (mt) cc_final: 0.9172 (mt) REVERT: B 576 LEU cc_start: 0.9468 (mt) cc_final: 0.9250 (mt) REVERT: B 599 GLU cc_start: 0.8300 (pt0) cc_final: 0.7946 (pt0) REVERT: B 668 ASN cc_start: 0.8645 (m-40) cc_final: 0.8204 (m110) REVERT: C 17 PHE cc_start: 0.8439 (p90) cc_final: 0.7647 (p90) REVERT: C 76 ILE cc_start: 0.8548 (mm) cc_final: 0.8148 (tp) REVERT: C 85 GLN cc_start: 0.4756 (mt0) cc_final: 0.3911 (pt0) REVERT: C 93 MET cc_start: 0.9032 (mtt) cc_final: 0.8818 (mtt) REVERT: C 137 MET cc_start: 0.7727 (mtt) cc_final: 0.7518 (mtt) REVERT: C 153 LEU cc_start: 0.9478 (mt) cc_final: 0.9232 (pp) REVERT: C 157 MET cc_start: 0.9427 (mtt) cc_final: 0.9163 (mtt) REVERT: C 158 VAL cc_start: 0.9687 (t) cc_final: 0.9190 (m) REVERT: C 162 TYR cc_start: 0.9316 (m-10) cc_final: 0.8753 (m-10) REVERT: C 201 HIS cc_start: 0.8881 (m90) cc_final: 0.8407 (m90) REVERT: C 211 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8120 (pp20) REVERT: C 220 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7600 (mptt) REVERT: C 271 LEU cc_start: 0.8805 (mm) cc_final: 0.7998 (mm) REVERT: D 18 THR cc_start: 0.7714 (m) cc_final: 0.7434 (m) REVERT: D 25 ASN cc_start: 0.9373 (OUTLIER) cc_final: 0.9034 (m110) REVERT: D 56 MET cc_start: 0.8124 (mmt) cc_final: 0.7618 (ptt) REVERT: D 71 ASN cc_start: 0.8328 (m-40) cc_final: 0.7911 (m-40) REVERT: D 92 PHE cc_start: 0.7399 (t80) cc_final: 0.6998 (t80) REVERT: D 96 MET cc_start: 0.5749 (mmm) cc_final: 0.5255 (mmm) REVERT: D 137 MET cc_start: 0.5200 (mtp) cc_final: 0.4831 (ptp) REVERT: D 172 PHE cc_start: 0.6978 (OUTLIER) cc_final: 0.5944 (m-80) REVERT: D 174 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.7279 (t80) REVERT: D 195 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8871 (tp) REVERT: D 197 ASP cc_start: 0.8971 (OUTLIER) cc_final: 0.8720 (t0) REVERT: D 212 ILE cc_start: 0.7818 (mt) cc_final: 0.7401 (tt) REVERT: D 231 LEU cc_start: 0.9179 (tp) cc_final: 0.8957 (tp) REVERT: D 270 ASN cc_start: 0.7708 (m-40) cc_final: 0.7350 (m110) outliers start: 65 outliers final: 43 residues processed: 540 average time/residue: 0.1247 time to fit residues: 102.3165 Evaluate side-chains 541 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 486 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 143 LEU 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 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 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 638 VAL 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 108 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 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 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 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 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 172 PHE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 203 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 74 optimal weight: 0.0670 chunk 105 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 186 optimal weight: 20.0000 chunk 140 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 0.9990 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 387 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.135491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.097658 restraints weight = 35109.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.101087 restraints weight = 16841.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.103271 restraints weight = 9933.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.104687 restraints weight = 6805.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.105570 restraints weight = 5183.481| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | 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 | |-----------------------------------------------------------------------------| |-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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.6039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16386 Z= 0.132 Angle : 0.637 11.367 22134 Z= 0.326 Chirality : 0.043 0.201 2360 Planarity : 0.003 0.036 2818 Dihedral : 8.456 133.540 2299 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.38 % Allowed : 27.10 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.19), residues: 1932 helix: 1.12 (0.15), residues: 1133 sheet: 0.01 (0.45), residues: 130 loop : 0.15 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 686 TYR 0.021 0.001 TYR D 142 PHE 0.032 0.002 PHE B 128 TRP 0.039 0.002 TRP D 30 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (16386) covalent geometry : angle 0.63710 / 0.33 (22134) hydrogen bonds : bond 0.03818 / 2.45 ( 871) hydrogen bonds : angle 5.04851 / 3.58 ( 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 578 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 520 time to evaluate : 0.633 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 30 LYS cc_start: 0.8749 (tptt) cc_final: 0.8446 (tppt) REVERT: A 56 ASP cc_start: 0.8766 (m-30) cc_final: 0.8430 (m-30) REVERT: A 65 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8305 (mm-30) REVERT: A 214 LYS cc_start: 0.8211 (ttmm) cc_final: 0.7926 (mttm) REVERT: A 218 ASN cc_start: 0.8867 (t0) cc_final: 0.8245 (t0) REVERT: A 341 LYS cc_start: 0.9345 (mmtm) cc_final: 0.8845 (mmpt) REVERT: A 344 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8635 (mt-10) REVERT: A 359 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7787 (ttp) REVERT: A 366 LYS cc_start: 0.9061 (mtmt) cc_final: 0.8761 (ptpp) REVERT: A 381 LEU cc_start: 0.9108 (tp) cc_final: 0.8475 (pt) REVERT: A 384 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7376 (pm20) REVERT: A 385 VAL cc_start: 0.8871 (t) cc_final: 0.8474 (t) REVERT: A 390 GLN cc_start: 0.8472 (mt0) cc_final: 0.8191 (mt0) REVERT: A 393 SER cc_start: 0.8977 (m) cc_final: 0.8736 (p) REVERT: A 427 LYS cc_start: 0.8973 (ttpp) cc_final: 0.8642 (ttpp) REVERT: A 483 GLU cc_start: 0.9072 (mp0) cc_final: 0.8366 (pm20) REVERT: A 505 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7733 (mt-10) REVERT: A 548 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8370 (mm-30) REVERT: A 628 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8483 (mm-30) REVERT: A 640 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.7942 (tpp) REVERT: A 645 GLN cc_start: 0.8946 (tp40) cc_final: 0.8594 (tp-100) REVERT: B 95 MET cc_start: 0.8529 (tpp) cc_final: 0.8184 (tpp) REVERT: B 99 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8657 (tptp) REVERT: B 108 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8530 (p) REVERT: B 143 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8914 (tt) REVERT: B 190 MET cc_start: 0.9138 (mtm) cc_final: 0.8883 (mtm) REVERT: B 252 ASN cc_start: 0.9244 (t0) cc_final: 0.8911 (t0) REVERT: B 257 ASP cc_start: 0.8556 (m-30) cc_final: 0.8204 (m-30) REVERT: B 322 MET cc_start: 0.8972 (mmm) cc_final: 0.8248 (mmm) REVERT: B 348 MET cc_start: 0.8073 (tpp) cc_final: 0.7826 (tpp) REVERT: B 384 GLU cc_start: 0.8661 (pm20) cc_final: 0.7926 (pp20) REVERT: B 415 ASN cc_start: 0.9321 (t0) cc_final: 0.8939 (t0) REVERT: B 467 ASN cc_start: 0.9047 (t0) cc_final: 0.8778 (m-40) REVERT: B 493 MET cc_start: 0.9414 (tmm) cc_final: 0.9047 (tmm) REVERT: B 515 ASP cc_start: 0.8833 (m-30) cc_final: 0.8611 (m-30) REVERT: B 576 LEU cc_start: 0.9432 (mt) cc_final: 0.9204 (mt) REVERT: B 599 GLU cc_start: 0.8155 (pt0) cc_final: 0.7905 (pt0) REVERT: B 646 GLN cc_start: 0.8889 (pt0) cc_final: 0.8463 (pm20) REVERT: B 668 ASN cc_start: 0.8618 (m-40) cc_final: 0.8169 (m110) REVERT: C 17 PHE cc_start: 0.8461 (p90) cc_final: 0.7674 (p90) REVERT: C 76 ILE cc_start: 0.8567 (mm) cc_final: 0.8135 (tp) REVERT: C 85 GLN cc_start: 0.5158 (mt0) cc_final: 0.4360 (pt0) REVERT: C 153 LEU cc_start: 0.9447 (mt) cc_final: 0.9239 (pp) REVERT: C 157 MET cc_start: 0.9493 (mtt) cc_final: 0.9243 (mtt) REVERT: C 158 VAL cc_start: 0.9691 (t) cc_final: 0.9252 (m) REVERT: C 162 TYR cc_start: 0.9333 (OUTLIER) cc_final: 0.8833 (m-10) REVERT: C 271 LEU cc_start: 0.8690 (mm) cc_final: 0.8051 (mm) REVERT: D 24 GLN cc_start: 0.8731 (tp-100) cc_final: 0.8237 (tm-30) REVERT: D 25 ASN cc_start: 0.9391 (m-40) cc_final: 0.8829 (m110) REVERT: D 27 LYS cc_start: 0.9451 (pttm) cc_final: 0.9215 (pttm) REVERT: D 56 MET cc_start: 0.8227 (mmt) cc_final: 0.7757 (ptt) REVERT: D 71 ASN cc_start: 0.8281 (m-40) cc_final: 0.7884 (m110) REVERT: D 74 MET cc_start: 0.5809 (tpt) cc_final: 0.5185 (tpt) REVERT: D 92 PHE cc_start: 0.7304 (t80) cc_final: 0.6797 (t80) REVERT: D 96 MET cc_start: 0.5865 (mmm) cc_final: 0.5343 (mmm) REVERT: D 162 TYR cc_start: 0.6513 (m-10) cc_final: 0.6196 (m-10) REVERT: D 174 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.7352 (t80) REVERT: D 197 ASP cc_start: 0.8951 (OUTLIER) cc_final: 0.8423 (t0) REVERT: D 212 ILE cc_start: 0.7894 (mt) cc_final: 0.7500 (tt) REVERT: D 270 ASN cc_start: 0.7730 (m-40) cc_final: 0.7338 (m110) outliers start: 58 outliers final: 37 residues processed: 543 average time/residue: 0.1225 time to fit residues: 101.1197 Evaluate side-chains 541 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 494 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 143 LEU 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 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 403 ILE Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU 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 638 VAL 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 108 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 587 VAL 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 162 TYR 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 245 ASP Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 203 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 153 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 158 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN A 410 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 218 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN C 214 ASN D 25 ASN D 186 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.130069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.092644 restraints weight = 35761.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.095944 restraints weight = 16975.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.097987 restraints weight = 10018.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.099495 restraints weight = 6884.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.100482 restraints weight = 5180.683| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 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 = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.6228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16386 Z= 0.223 Angle : 0.696 11.042 22134 Z= 0.360 Chirality : 0.046 0.211 2360 Planarity : 0.004 0.041 2818 Dihedral : 8.483 134.480 2299 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.96 % Allowed : 26.92 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.19), residues: 1932 helix: 1.14 (0.15), residues: 1121 sheet: -0.38 (0.43), residues: 142 loop : 0.27 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 686 TYR 0.023 0.002 TYR B 357 PHE 0.030 0.002 PHE D 227 TRP 0.033 0.002 TRP D 30 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.22 (16386) covalent geometry : angle 0.69585 / 0.36 (22134) hydrogen bonds : bond 0.03992 / 2.54 ( 871) hydrogen bonds : angle 5.17892 / 3.68 ( 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 554 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 486 time to evaluate : 0.622 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 65 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8381 (mm-30) REVERT: A 116 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7678 (mt-10) REVERT: A 119 GLU cc_start: 0.8552 (mp0) cc_final: 0.8316 (mp0) REVERT: A 139 GLU cc_start: 0.8444 (mp0) cc_final: 0.8117 (mp0) REVERT: A 214 LYS cc_start: 0.8289 (ttmm) cc_final: 0.7992 (mttm) REVERT: A 218 ASN cc_start: 0.8981 (t0) cc_final: 0.8486 (t0) REVERT: A 341 LYS cc_start: 0.9392 (mmtm) cc_final: 0.9100 (mmpt) REVERT: A 344 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8518 (mt-10) REVERT: A 359 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8006 (ttp) REVERT: A 366 LYS cc_start: 0.9144 (mtmt) cc_final: 0.8814 (ptpp) REVERT: A 381 LEU cc_start: 0.9131 (tp) cc_final: 0.8438 (pt) REVERT: A 384 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7511 (pm20) REVERT: A 385 VAL cc_start: 0.8856 (t) cc_final: 0.8534 (t) REVERT: A 390 GLN cc_start: 0.8549 (mt0) cc_final: 0.8114 (mt0) REVERT: A 427 LYS cc_start: 0.9068 (ttpp) cc_final: 0.8812 (ttmm) REVERT: A 483 GLU cc_start: 0.9073 (mp0) cc_final: 0.8351 (pm20) REVERT: A 527 TYR cc_start: 0.8788 (t80) cc_final: 0.8504 (t80) REVERT: A 548 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8360 (mm-30) REVERT: A 628 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8519 (mm-30) REVERT: A 640 MET cc_start: 0.9276 (OUTLIER) cc_final: 0.7921 (tpp) REVERT: A 645 GLN cc_start: 0.8980 (tp40) cc_final: 0.8659 (tp-100) REVERT: B 95 MET cc_start: 0.8651 (tpp) cc_final: 0.8263 (tpp) REVERT: B 99 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8457 (tptp) REVERT: B 108 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8596 (p) REVERT: B 178 SER cc_start: 0.8327 (OUTLIER) cc_final: 0.8126 (p) REVERT: B 184 ARG cc_start: 0.9069 (tpp-160) cc_final: 0.8751 (tpp-160) REVERT: B 190 MET cc_start: 0.9191 (mtm) cc_final: 0.8882 (mtm) REVERT: B 252 ASN cc_start: 0.9262 (t0) cc_final: 0.8935 (t0) REVERT: B 257 ASP cc_start: 0.8661 (m-30) cc_final: 0.8356 (m-30) REVERT: B 322 MET cc_start: 0.9110 (mmm) cc_final: 0.8414 (mmm) REVERT: B 348 MET cc_start: 0.8145 (tpp) cc_final: 0.7924 (tpp) REVERT: B 415 ASN cc_start: 0.9322 (t0) cc_final: 0.8741 (t0) REVERT: B 467 ASN cc_start: 0.9219 (t0) cc_final: 0.8871 (m-40) REVERT: B 493 MET cc_start: 0.9411 (tmm) cc_final: 0.8989 (tmm) REVERT: B 515 ASP cc_start: 0.8927 (m-30) cc_final: 0.8561 (m-30) REVERT: B 583 SER cc_start: 0.8135 (p) cc_final: 0.7717 (t) REVERT: B 599 GLU cc_start: 0.8070 (pt0) cc_final: 0.7787 (pt0) REVERT: B 668 ASN cc_start: 0.8722 (m-40) cc_final: 0.8256 (m110) REVERT: C 76 ILE cc_start: 0.8672 (mm) cc_final: 0.8349 (tp) REVERT: C 85 GLN cc_start: 0.5234 (mt0) cc_final: 0.4417 (pt0) REVERT: C 137 MET cc_start: 0.7199 (mtt) cc_final: 0.6908 (mpp) REVERT: C 158 VAL cc_start: 0.9631 (t) cc_final: 0.9211 (m) REVERT: C 162 TYR cc_start: 0.9326 (OUTLIER) cc_final: 0.8867 (m-10) REVERT: C 271 LEU cc_start: 0.8767 (mm) cc_final: 0.8168 (mm) REVERT: D 18 THR cc_start: 0.7865 (m) cc_final: 0.7524 (m) REVERT: D 25 ASN cc_start: 0.9221 (OUTLIER) cc_final: 0.8759 (m110) REVERT: D 56 MET cc_start: 0.8252 (mmt) cc_final: 0.7776 (ptt) REVERT: D 71 ASN cc_start: 0.8259 (m-40) cc_final: 0.7840 (m110) REVERT: D 74 MET cc_start: 0.6039 (tpt) cc_final: 0.5720 (tpt) REVERT: D 117 THR cc_start: 0.9357 (m) cc_final: 0.9062 (t) REVERT: D 172 PHE cc_start: 0.6939 (OUTLIER) cc_final: 0.6616 (m-10) REVERT: D 174 TYR cc_start: 0.8156 (OUTLIER) cc_final: 0.7452 (t80) REVERT: D 185 MET cc_start: 0.7065 (mmp) cc_final: 0.6245 (ttt) REVERT: D 197 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8334 (t0) REVERT: D 210 GLN cc_start: 0.8230 (mt0) cc_final: 0.8023 (mt0) REVERT: D 270 ASN cc_start: 0.7764 (m-40) cc_final: 0.7277 (m110) outliers start: 68 outliers final: 44 residues processed: 520 average time/residue: 0.1217 time to fit residues: 96.6077 Evaluate side-chains 526 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 469 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 143 LEU 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 275 VAL 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 403 ILE 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 425 ILE 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 599 GLU Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 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 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 624 PHE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 162 TYR 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 43 THR Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 203 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 chunk 149 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN C 263 ASN D 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.132673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.094573 restraints weight = 35455.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.097953 restraints weight = 16694.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.100201 restraints weight = 9718.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.101522 restraints weight = 6594.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.102474 restraints weight = 5044.262| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.6413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16386 Z= 0.154 Angle : 0.683 11.391 22134 Z= 0.350 Chirality : 0.045 0.200 2360 Planarity : 0.004 0.036 2818 Dihedral : 8.380 133.799 2299 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.26 % Allowed : 27.45 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.19), residues: 1932 helix: 1.03 (0.15), residues: 1132 sheet: -0.38 (0.44), residues: 142 loop : 0.14 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 261 TYR 0.022 0.001 TYR B 394 PHE 0.050 0.002 PHE C 154 TRP 0.028 0.002 TRP D 30 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (16386) covalent geometry : angle 0.68296 / 0.35 (22134) hydrogen bonds : bond 0.03900 / 2.51 ( 871) hydrogen bonds : angle 5.11253 / 3.63 ( 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 554 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 498 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8252 (mm-30) REVERT: A 116 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7586 (mt-10) REVERT: A 214 LYS cc_start: 0.8221 (ttmm) cc_final: 0.7988 (mttm) REVERT: A 218 ASN cc_start: 0.8911 (t0) cc_final: 0.8305 (t0) REVERT: A 232 ASN cc_start: 0.9157 (m110) cc_final: 0.8920 (m110) REVERT: A 250 TYR cc_start: 0.8547 (m-80) cc_final: 0.8339 (m-80) REVERT: A 341 LYS cc_start: 0.9360 (mmtm) cc_final: 0.9037 (mmpt) REVERT: A 344 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8448 (mt-10) REVERT: A 359 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7774 (ttp) REVERT: A 366 LYS cc_start: 0.9113 (mtmt) cc_final: 0.8795 (ptpp) REVERT: A 381 LEU cc_start: 0.9130 (tp) cc_final: 0.8467 (pt) REVERT: A 384 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7373 (pm20) REVERT: A 385 VAL cc_start: 0.8883 (t) cc_final: 0.8451 (t) REVERT: A 390 GLN cc_start: 0.8521 (mt0) cc_final: 0.8161 (mt0) REVERT: A 483 GLU cc_start: 0.9072 (mp0) cc_final: 0.8432 (pm20) REVERT: A 527 TYR cc_start: 0.8693 (t80) cc_final: 0.8453 (t80) REVERT: A 548 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8410 (mm-30) REVERT: A 628 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8477 (mm-30) REVERT: A 640 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.7944 (tpp) REVERT: A 645 GLN cc_start: 0.8951 (tp40) cc_final: 0.8613 (tp-100) REVERT: B 95 MET cc_start: 0.8532 (tpp) cc_final: 0.8195 (tpp) REVERT: B 99 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8481 (tptp) REVERT: B 108 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8511 (p) REVERT: B 184 ARG cc_start: 0.9084 (tpp-160) cc_final: 0.8715 (tpp-160) REVERT: B 190 MET cc_start: 0.9171 (mtm) cc_final: 0.8866 (mtm) REVERT: B 252 ASN cc_start: 0.9256 (t0) cc_final: 0.8937 (t0) REVERT: B 257 ASP cc_start: 0.8603 (m-30) cc_final: 0.8297 (m-30) REVERT: B 322 MET cc_start: 0.9069 (mmm) cc_final: 0.8381 (mmm) REVERT: B 357 TYR cc_start: 0.8216 (m-10) cc_final: 0.7341 (m-10) REVERT: B 415 ASN cc_start: 0.9301 (t0) cc_final: 0.8800 (t0) REVERT: B 467 ASN cc_start: 0.9121 (t0) cc_final: 0.8854 (m-40) REVERT: B 493 MET cc_start: 0.9406 (tmm) cc_final: 0.9022 (tmm) REVERT: B 515 ASP cc_start: 0.8865 (m-30) cc_final: 0.8607 (m-30) REVERT: B 583 SER cc_start: 0.8281 (p) cc_final: 0.7812 (t) REVERT: B 657 PHE cc_start: 0.9117 (m-80) cc_final: 0.8781 (m-80) REVERT: B 668 ASN cc_start: 0.8624 (m-40) cc_final: 0.8170 (m110) REVERT: C 17 PHE cc_start: 0.8656 (p90) cc_final: 0.7814 (p90) REVERT: C 85 GLN cc_start: 0.5423 (mt0) cc_final: 0.4739 (pt0) REVERT: C 93 MET cc_start: 0.9297 (ptp) cc_final: 0.8998 (ptp) REVERT: C 154 PHE cc_start: 0.9231 (m-80) cc_final: 0.8949 (m-80) REVERT: C 158 VAL cc_start: 0.9600 (t) cc_final: 0.9256 (m) REVERT: C 162 TYR cc_start: 0.9361 (OUTLIER) cc_final: 0.8920 (m-10) REVERT: C 201 HIS cc_start: 0.8898 (m90) cc_final: 0.8461 (m90) REVERT: C 271 LEU cc_start: 0.8763 (mm) cc_final: 0.8138 (mm) REVERT: D 25 ASN cc_start: 0.9183 (OUTLIER) cc_final: 0.8763 (m110) REVERT: D 56 MET cc_start: 0.8286 (mmt) cc_final: 0.7821 (ptt) REVERT: D 92 PHE cc_start: 0.7138 (t80) cc_final: 0.6796 (t80) REVERT: D 96 MET cc_start: 0.5932 (mmm) cc_final: 0.5128 (mmm) REVERT: D 117 THR cc_start: 0.9360 (m) cc_final: 0.9057 (t) REVERT: D 174 TYR cc_start: 0.8093 (OUTLIER) cc_final: 0.7451 (t80) REVERT: D 197 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8226 (t0) REVERT: D 210 GLN cc_start: 0.8252 (mt0) cc_final: 0.8043 (mt0) REVERT: D 269 MET cc_start: 0.8311 (tmm) cc_final: 0.7595 (ppp) REVERT: D 270 ASN cc_start: 0.7873 (m-40) cc_final: 0.7256 (m110) REVERT: D 287 LEU cc_start: 0.7048 (mt) cc_final: 0.6418 (pp) outliers start: 56 outliers final: 36 residues processed: 524 average time/residue: 0.1242 time to fit residues: 98.8606 Evaluate side-chains 528 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 481 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 143 LEU 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 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 403 ILE Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 108 THR 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 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 624 PHE Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 162 TYR 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 43 THR Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 189 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 chunk 165 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 668 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.130364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.092391 restraints weight = 35345.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.095678 restraints weight = 17135.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.097851 restraints weight = 10220.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.099182 restraints weight = 6998.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.100148 restraints weight = 5345.806| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.6561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16386 Z= 0.151 Angle : 0.703 11.274 22134 Z= 0.359 Chirality : 0.045 0.278 2360 Planarity : 0.004 0.038 2818 Dihedral : 8.292 134.017 2299 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.97 % Allowed : 28.26 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.19), residues: 1932 helix: 0.97 (0.15), residues: 1134 sheet: -0.33 (0.45), residues: 142 loop : 0.06 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 235 TYR 0.021 0.001 TYR B 394 PHE 0.048 0.002 PHE C 154 TRP 0.028 0.002 TRP D 30 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (16386) covalent geometry : angle 0.70305 / 0.36 (22134) hydrogen bonds : bond 0.03910 / 2.51 ( 871) hydrogen bonds : angle 5.13362 / 3.64 ( 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 548 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 497 time to evaluate : 0.571 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: 0.8747 (tptt) cc_final: 0.8451 (tppt) REVERT: A 65 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8319 (mm-30) REVERT: A 119 GLU cc_start: 0.8525 (mp0) cc_final: 0.8302 (mp0) REVERT: A 139 GLU cc_start: 0.8407 (mp0) cc_final: 0.8188 (mp0) REVERT: A 161 ARG cc_start: 0.8325 (mmm-85) cc_final: 0.7915 (mtt180) REVERT: A 166 GLU cc_start: 0.8268 (tp30) cc_final: 0.7833 (tp30) REVERT: A 218 ASN cc_start: 0.8949 (t0) cc_final: 0.8272 (t0) REVERT: A 232 ASN cc_start: 0.9142 (m110) cc_final: 0.8911 (m110) REVERT: A 250 TYR cc_start: 0.8535 (m-80) cc_final: 0.8331 (m-80) REVERT: A 341 LYS cc_start: 0.9344 (mmtm) cc_final: 0.9121 (mmpt) REVERT: A 344 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8635 (mt-10) REVERT: A 359 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7715 (ttp) REVERT: A 366 LYS cc_start: 0.9080 (mtmt) cc_final: 0.8804 (ptpp) REVERT: A 381 LEU cc_start: 0.9109 (tp) cc_final: 0.8447 (pt) REVERT: A 384 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7382 (pm20) REVERT: A 385 VAL cc_start: 0.8852 (t) cc_final: 0.8409 (t) REVERT: A 390 GLN cc_start: 0.8568 (mt0) cc_final: 0.8316 (mt0) REVERT: A 483 GLU cc_start: 0.9074 (mp0) cc_final: 0.8449 (pm20) REVERT: A 527 TYR cc_start: 0.8690 (t80) cc_final: 0.8447 (t80) REVERT: A 548 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8399 (mm-30) REVERT: A 628 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8464 (mm-30) REVERT: A 640 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.7811 (tpp) REVERT: A 645 GLN cc_start: 0.8947 (tp40) cc_final: 0.8524 (tp-100) REVERT: B 95 MET cc_start: 0.8555 (tpp) cc_final: 0.8216 (tpp) REVERT: B 99 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8405 (tptp) REVERT: B 143 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8940 (tt) REVERT: B 184 ARG cc_start: 0.9098 (tpp-160) cc_final: 0.8780 (tpp-160) REVERT: B 190 MET cc_start: 0.9192 (mtm) cc_final: 0.8882 (mtm) REVERT: B 252 ASN cc_start: 0.9259 (t0) cc_final: 0.8949 (t0) REVERT: B 257 ASP cc_start: 0.8572 (m-30) cc_final: 0.8237 (m-30) REVERT: B 301 PHE cc_start: 0.9117 (m-80) cc_final: 0.8844 (m-80) REVERT: B 322 MET cc_start: 0.9064 (mmm) cc_final: 0.8340 (mmm) REVERT: B 357 TYR cc_start: 0.8203 (m-10) cc_final: 0.7467 (m-10) REVERT: B 415 ASN cc_start: 0.9268 (t0) cc_final: 0.8783 (t0) REVERT: B 467 ASN cc_start: 0.9076 (t0) cc_final: 0.8833 (m-40) REVERT: B 493 MET cc_start: 0.9407 (tmm) cc_final: 0.9007 (tmm) REVERT: B 515 ASP cc_start: 0.8801 (m-30) cc_final: 0.8587 (m-30) REVERT: B 583 SER cc_start: 0.8429 (p) cc_final: 0.7846 (t) REVERT: B 657 PHE cc_start: 0.8994 (m-80) cc_final: 0.8590 (m-80) REVERT: B 664 THR cc_start: 0.8892 (p) cc_final: 0.8245 (t) REVERT: B 668 ASN cc_start: 0.8678 (m-40) cc_final: 0.8188 (m110) REVERT: B 686 ARG cc_start: 0.7930 (ttm-80) cc_final: 0.7603 (mmt90) REVERT: C 21 PHE cc_start: 0.9381 (m-80) cc_final: 0.9087 (m-80) REVERT: C 85 GLN cc_start: 0.5805 (mt0) cc_final: 0.5090 (pt0) REVERT: C 93 MET cc_start: 0.9329 (ptp) cc_final: 0.9123 (ptp) REVERT: C 154 PHE cc_start: 0.9208 (m-80) cc_final: 0.8998 (m-80) REVERT: C 158 VAL cc_start: 0.9614 (t) cc_final: 0.9257 (m) REVERT: C 162 TYR cc_start: 0.9342 (OUTLIER) cc_final: 0.8907 (m-10) REVERT: C 201 HIS cc_start: 0.8896 (m90) cc_final: 0.8413 (m90) REVERT: C 271 LEU cc_start: 0.8718 (mm) cc_final: 0.8070 (mm) REVERT: D 18 THR cc_start: 0.7786 (m) cc_final: 0.7435 (m) REVERT: D 25 ASN cc_start: 0.9240 (m-40) cc_final: 0.8846 (m110) REVERT: D 56 MET cc_start: 0.8315 (mmt) cc_final: 0.7871 (ptt) REVERT: D 96 MET cc_start: 0.5922 (mmm) cc_final: 0.5341 (mmm) REVERT: D 174 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.7702 (t80) REVERT: D 176 LEU cc_start: 0.9399 (mm) cc_final: 0.9128 (pp) REVERT: D 197 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8212 (t0) REVERT: D 269 MET cc_start: 0.8355 (tmm) cc_final: 0.7730 (ppp) REVERT: D 270 ASN cc_start: 0.7945 (m-40) cc_final: 0.7283 (m110) REVERT: D 287 LEU cc_start: 0.7046 (mt) cc_final: 0.6411 (pp) outliers start: 51 outliers final: 37 residues processed: 520 average time/residue: 0.1148 time to fit residues: 91.3903 Evaluate side-chains 526 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 480 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 231 ASP 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 403 ILE 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 425 ILE 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 599 GLU Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 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 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 624 PHE Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 162 TYR 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 43 THR Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 223 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 5.9990 chunk 1 optimal weight: 0.0970 chunk 48 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 191 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN B 646 GLN C 238 ASN C 249 GLN D 25 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.135663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.097349 restraints weight = 35014.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.100714 restraints weight = 16838.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.102914 restraints weight = 9918.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.104252 restraints weight = 6791.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.105219 restraints weight = 5196.355| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 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 = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.6763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16386 Z= 0.137 Angle : 0.706 13.048 22134 Z= 0.359 Chirality : 0.045 0.270 2360 Planarity : 0.004 0.055 2818 Dihedral : 8.168 134.107 2299 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.91 % Allowed : 28.61 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.19), residues: 1932 helix: 0.93 (0.15), residues: 1133 sheet: -0.16 (0.47), residues: 134 loop : -0.15 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 261 TYR 0.020 0.001 TYR B 394 PHE 0.045 0.002 PHE C 154 TRP 0.027 0.002 TRP D 30 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (16386) covalent geometry : angle 0.70595 / 0.36 (22134) hydrogen bonds : bond 0.03877 / 2.51 ( 871) hydrogen bonds : angle 5.12318 / 3.63 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3162.15 seconds wall clock time: 55 minutes 49.85 seconds (3349.85 seconds total)