Starting phenix.real_space_refine on Fri Jul 3 19:43:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz6_45054/07_2026/9bz6_45054_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz6_45054/07_2026/9bz6_45054.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bz6_45054/07_2026/9bz6_45054_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz6_45054/07_2026/9bz6_45054_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bz6_45054/07_2026/9bz6_45054.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz6_45054/07_2026/9bz6_45054.map" } resolution = 3.87 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): 0.01s 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: 3.28, per 1000 atoms: 0.20 Number of scatterers: 16038 At special positions: 0 Unit cell: (94.302, 137.904, 130.806, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 721.3 milliseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.516A 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: 3.569A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.954A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.665A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.948A 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: 4.850A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.627A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.074A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.579A 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: 3.676A 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: 3.872A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.645A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.729A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.027A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.068A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.544A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A 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: 3.567A 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: 6.453A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.479A 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: 5.661A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.048A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.308A 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: 6.751A 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: 2.27 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4683 1.33 - 1.46: 3123 1.46 - 1.58: 8399 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 4.86e+01 bond pdb=" O3B TTP A 803 " pdb=" PG TTP A 803 " ideal model delta sigma weight residual 1.748 1.610 0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.061 1.25e-02 6.40e+03 2.37e+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 1.608 0.067 2.00e-02 2.50e+03 1.14e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21528 2.09 - 4.19: 524 4.19 - 6.28: 63 6.28 - 8.37: 10 8.37 - 10.46: 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 110.54 116.61 -6.07 1.36e+00 5.41e-01 1.99e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.16 -4.45 1.15e+00 7.56e-01 1.50e+01 angle pdb=" N SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.21 -3.93 1.09e+00 8.42e-01 1.30e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.85 -4.35 1.23e+00 6.61e-01 1.25e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.48 3.71 1.06e+00 8.90e-01 1.22e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.04: 9092 25.04 - 50.07: 652 50.07 - 75.11: 126 75.11 - 100.15: 26 100.15 - 125.18: 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 -98.16 125.18 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 -95.62 122.65 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 -134.36 12.36 0 2.50e+00 1.60e-01 2.44e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2142 0.093 - 0.187: 186 0.187 - 0.280: 27 0.280 - 0.374: 3 0.374 - 0.467: 2 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.45e+00 chirality pdb=" CA TYR C 169 " pdb=" N TYR C 169 " pdb=" C TYR C 169 " pdb=" CB TYR C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " 0.017 2.00e-02 2.50e+03 1.10e-02 2.13e+00 pdb=" CG PHE D 92 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 169 " 0.017 2.00e-02 2.50e+03 9.80e-03 1.92e+00 pdb=" CG TYR C 169 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 169 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 169 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 169 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 169 " 0.008 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 130 2.51 - 3.11: 11571 3.11 - 3.70: 27063 3.70 - 4.30: 41557 4.30 - 4.90: 65468 Nonbonded interactions: 145789 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 1.965 3.060 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 3.060 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.013 3.040 ... (remaining 145784 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.100 Find NCS groups from input model: 0.240 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 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= 0.335 Angle : 0.788 10.463 22134 Z= 0.472 Chirality : 0.058 0.467 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.634 125.184 6202 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.34 % Allowed : 15.27 % 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: 0.56 (0.18), residues: 1932 helix: 0.59 (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 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE C 168 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.33 (16386) covalent geometry : angle 0.78776 / 0.47 (22134) hydrogen bonds : bond 0.15421 / 9.51 ( 871) hydrogen bonds : angle 6.51761 / 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 1091 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 1068 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8399 (mt) cc_final: 0.7102 (mp) REVERT: A 76 ASP cc_start: 0.8141 (m-30) cc_final: 0.7768 (m-30) REVERT: A 172 LEU cc_start: 0.9016 (mp) cc_final: 0.8790 (mp) REVERT: A 188 ILE cc_start: 0.8484 (mt) cc_final: 0.8199 (mt) REVERT: A 258 ILE cc_start: 0.8967 (tp) cc_final: 0.8687 (tp) REVERT: A 267 ILE cc_start: 0.8497 (mp) cc_final: 0.7407 (mm) REVERT: A 345 LYS cc_start: 0.8631 (tttt) cc_final: 0.8419 (ttmm) REVERT: A 378 PHE cc_start: 0.8737 (p90) cc_final: 0.8535 (p90) REVERT: A 447 ASN cc_start: 0.7436 (m-40) cc_final: 0.6479 (m-40) REVERT: A 501 GLN cc_start: 0.8010 (tt0) cc_final: 0.7771 (tt0) REVERT: A 550 MET cc_start: 0.7374 (mtm) cc_final: 0.7104 (mtm) REVERT: A 597 ILE cc_start: 0.8819 (pt) cc_final: 0.8570 (pt) REVERT: A 618 LEU cc_start: 0.9315 (tp) cc_final: 0.9090 (tt) REVERT: A 624 PHE cc_start: 0.6889 (t80) cc_final: 0.6470 (t80) REVERT: A 630 TYR cc_start: 0.7985 (m-80) cc_final: 0.7422 (m-80) REVERT: B 11 GLN cc_start: 0.7869 (mt0) cc_final: 0.7570 (mt0) REVERT: B 27 ASP cc_start: 0.8050 (p0) cc_final: 0.7847 (p0) REVERT: B 157 LEU cc_start: 0.8567 (tp) cc_final: 0.8311 (tp) REVERT: B 172 LEU cc_start: 0.9171 (mp) cc_final: 0.8957 (mp) REVERT: B 177 ASP cc_start: 0.8070 (t0) cc_final: 0.7364 (t0) REVERT: B 204 SER cc_start: 0.8823 (m) cc_final: 0.8307 (t) REVERT: B 288 PHE cc_start: 0.8348 (t80) cc_final: 0.7494 (t80) REVERT: B 294 GLU cc_start: 0.6937 (mt-10) cc_final: 0.5187 (mt-10) REVERT: B 295 ASP cc_start: 0.7755 (t0) cc_final: 0.7390 (t0) REVERT: B 366 LYS cc_start: 0.8551 (ptpp) cc_final: 0.8316 (ptmt) REVERT: B 376 VAL cc_start: 0.9423 (t) cc_final: 0.9180 (m) REVERT: B 384 GLU cc_start: 0.8925 (pm20) cc_final: 0.8285 (pm20) REVERT: B 387 GLN cc_start: 0.7499 (mt0) cc_final: 0.7208 (mt0) REVERT: B 435 SER cc_start: 0.9153 (p) cc_final: 0.8911 (p) REVERT: B 480 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6877 (mt-10) REVERT: B 543 ILE cc_start: 0.8870 (mm) cc_final: 0.8653 (mm) REVERT: B 550 MET cc_start: 0.7979 (mtm) cc_final: 0.7718 (mtp) REVERT: B 597 ILE cc_start: 0.9119 (pt) cc_final: 0.8876 (pt) REVERT: C 24 GLN cc_start: 0.6658 (tp40) cc_final: 0.6392 (tp40) REVERT: C 112 LEU cc_start: 0.3588 (mt) cc_final: 0.3255 (mt) REVERT: C 118 ILE cc_start: 0.6611 (mt) cc_final: 0.6398 (mt) REVERT: C 163 LEU cc_start: 0.6487 (tt) cc_final: 0.6195 (tt) REVERT: D 80 HIS cc_start: 0.7053 (m-70) cc_final: 0.6704 (m170) REVERT: D 104 SER cc_start: 0.7255 (m) cc_final: 0.6975 (m) REVERT: D 119 ASN cc_start: 0.5382 (m-40) cc_final: 0.5118 (m-40) REVERT: D 125 VAL cc_start: 0.6417 (t) cc_final: 0.6128 (p) REVERT: D 131 LEU cc_start: 0.5783 (tp) cc_final: 0.5205 (tt) REVERT: D 195 LEU cc_start: 0.7591 (tt) cc_final: 0.7242 (tt) outliers start: 23 outliers final: 7 residues processed: 1072 average time/residue: 0.1242 time to fit residues: 195.6915 Evaluate side-chains 743 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 736 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 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 D residue 59 LEU Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.0670 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN A 312 GLN A 370 ASN A 410 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 320 ASN B 329 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN B 676 HIS C 24 GLN C 28 GLN C 127 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN C 263 ASN D 28 GLN D 71 ASN D 80 HIS D 201 HIS ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.131008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.096502 restraints weight = 36572.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.100489 restraints weight = 17418.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.103127 restraints weight = 10380.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.104850 restraints weight = 7099.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.106125 restraints weight = 5383.983| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16386 Z= 0.174 Angle : 0.718 12.133 22134 Z= 0.376 Chirality : 0.046 0.264 2360 Planarity : 0.004 0.036 2818 Dihedral : 10.031 127.325 2301 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.31 % Allowed : 21.04 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.18), residues: 1932 helix: 1.17 (0.15), residues: 1138 sheet: 1.02 (0.46), residues: 96 loop : 0.31 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 243 TYR 0.050 0.002 TYR D 262 PHE 0.041 0.003 PHE C 168 TRP 0.024 0.002 TRP D 30 HIS 0.010 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (16386) covalent geometry : angle 0.71799 / 0.38 (22134) hydrogen bonds : bond 0.05103 / 3.21 ( 871) hydrogen bonds : angle 5.38620 / 3.82 ( 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 861 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 787 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8909 (m-30) cc_final: 0.8644 (m-30) REVERT: A 51 LEU cc_start: 0.9254 (tp) cc_final: 0.9008 (tp) REVERT: A 75 GLU cc_start: 0.8525 (tm-30) cc_final: 0.7569 (pp20) REVERT: A 76 ASP cc_start: 0.9132 (m-30) cc_final: 0.8365 (m-30) REVERT: A 172 LEU cc_start: 0.9433 (mp) cc_final: 0.9198 (mp) REVERT: A 202 ASN cc_start: 0.9552 (t0) cc_final: 0.8876 (t0) REVERT: A 221 LYS cc_start: 0.9324 (mmtp) cc_final: 0.9023 (mttp) REVERT: A 290 GLU cc_start: 0.9311 (tt0) cc_final: 0.8985 (tm-30) REVERT: A 322 MET cc_start: 0.8596 (mmt) cc_final: 0.8250 (mmm) REVERT: A 335 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8115 (mt-10) REVERT: A 370 ASN cc_start: 0.9163 (m-40) cc_final: 0.8962 (m110) REVERT: A 377 LYS cc_start: 0.9063 (mttt) cc_final: 0.8844 (mttp) REVERT: A 378 PHE cc_start: 0.9256 (p90) cc_final: 0.8862 (p90) REVERT: A 384 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7371 (pm20) REVERT: A 386 LEU cc_start: 0.9237 (mt) cc_final: 0.9022 (mt) REVERT: A 447 ASN cc_start: 0.8388 (m-40) cc_final: 0.8115 (m-40) REVERT: A 561 LEU cc_start: 0.9157 (tp) cc_final: 0.8835 (tp) REVERT: A 618 LEU cc_start: 0.9525 (tp) cc_final: 0.9156 (tt) REVERT: A 639 ASP cc_start: 0.8459 (m-30) cc_final: 0.8078 (m-30) REVERT: A 640 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8615 (tpp) REVERT: A 668 ASN cc_start: 0.9461 (m-40) cc_final: 0.9151 (m-40) REVERT: A 684 TYR cc_start: 0.7919 (OUTLIER) cc_final: 0.7375 (m-10) REVERT: B 15 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8331 (tp30) REVERT: B 87 LYS cc_start: 0.9261 (tptm) cc_final: 0.9026 (tppt) REVERT: B 172 LEU cc_start: 0.9371 (mp) cc_final: 0.9035 (mp) REVERT: B 181 ASP cc_start: 0.8825 (m-30) cc_final: 0.8590 (m-30) REVERT: B 211 GLU cc_start: 0.8510 (mm-30) cc_final: 0.7961 (mm-30) REVERT: B 288 PHE cc_start: 0.9283 (t80) cc_final: 0.8889 (t80) REVERT: B 290 GLU cc_start: 0.8016 (tp30) cc_final: 0.7808 (tp30) REVERT: B 350 ARG cc_start: 0.8523 (mtp85) cc_final: 0.7934 (mtp85) REVERT: B 355 TYR cc_start: 0.8243 (m-80) cc_final: 0.7701 (m-80) REVERT: B 361 GLN cc_start: 0.9009 (tt0) cc_final: 0.8460 (tt0) REVERT: B 374 SER cc_start: 0.9064 (t) cc_final: 0.8770 (t) REVERT: B 378 PHE cc_start: 0.9349 (p90) cc_final: 0.9148 (p90) REVERT: B 399 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8208 (tp30) REVERT: B 425 ILE cc_start: 0.9444 (mt) cc_final: 0.9015 (mt) REVERT: B 493 MET cc_start: 0.9671 (tmm) cc_final: 0.9204 (tmm) REVERT: B 496 ASN cc_start: 0.9626 (t0) cc_final: 0.9412 (t0) REVERT: B 515 ASP cc_start: 0.9070 (m-30) cc_final: 0.8754 (m-30) REVERT: B 543 ILE cc_start: 0.9489 (mm) cc_final: 0.9166 (mm) REVERT: B 550 MET cc_start: 0.8013 (mtm) cc_final: 0.7748 (mtm) REVERT: B 558 TRP cc_start: 0.9505 (m100) cc_final: 0.8637 (m100) REVERT: B 588 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8935 (mm-40) REVERT: B 598 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7980 (mtm) REVERT: B 599 GLU cc_start: 0.8521 (pt0) cc_final: 0.8279 (pt0) REVERT: B 604 ARG cc_start: 0.8415 (mmp80) cc_final: 0.8129 (mmt-90) REVERT: B 621 ASN cc_start: 0.9501 (p0) cc_final: 0.9297 (p0) REVERT: B 632 MET cc_start: 0.8350 (mtp) cc_final: 0.5592 (mtp) REVERT: B 686 ARG cc_start: 0.8288 (mtp-110) cc_final: 0.7674 (mtp-110) REVERT: C 66 ASP cc_start: 0.8946 (OUTLIER) cc_final: 0.8509 (t70) REVERT: C 69 GLN cc_start: 0.8711 (tp40) cc_final: 0.8502 (tt0) REVERT: C 86 ARG cc_start: 0.8248 (mtt180) cc_final: 0.7879 (mpt180) REVERT: C 109 PHE cc_start: 0.8830 (m-80) cc_final: 0.8629 (m-80) REVERT: C 116 GLU cc_start: 0.9100 (pm20) cc_final: 0.8884 (pm20) REVERT: C 122 PHE cc_start: 0.8859 (m-80) cc_final: 0.8494 (m-80) REVERT: C 143 LYS cc_start: 0.9240 (tptp) cc_final: 0.9012 (pttp) REVERT: C 157 MET cc_start: 0.8993 (mtt) cc_final: 0.8526 (mtt) REVERT: C 163 LEU cc_start: 0.9490 (tt) cc_final: 0.9052 (tt) REVERT: C 168 PHE cc_start: 0.9253 (m-80) cc_final: 0.9001 (m-80) REVERT: C 185 MET cc_start: 0.7913 (mmm) cc_final: 0.7477 (mmm) REVERT: C 201 HIS cc_start: 0.8562 (m90) cc_final: 0.8159 (m90) REVERT: C 237 GLU cc_start: 0.9518 (pt0) cc_final: 0.9142 (pp20) REVERT: C 255 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8322 (m-30) REVERT: C 268 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9212 (mt) REVERT: C 269 MET cc_start: 0.9487 (tmm) cc_final: 0.9188 (tmm) REVERT: C 271 LEU cc_start: 0.9328 (mt) cc_final: 0.9025 (mt) REVERT: D 18 THR cc_start: 0.9018 (p) cc_final: 0.8291 (m) REVERT: D 24 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8416 (mp10) REVERT: D 33 GLU cc_start: 0.9214 (mp0) cc_final: 0.8901 (pp20) REVERT: D 92 PHE cc_start: 0.8205 (t80) cc_final: 0.7895 (t80) REVERT: D 131 LEU cc_start: 0.7694 (tp) cc_final: 0.7308 (tt) REVERT: D 137 MET cc_start: 0.9201 (mtt) cc_final: 0.8957 (mtp) REVERT: D 178 PHE cc_start: 0.8919 (m-80) cc_final: 0.8618 (m-80) REVERT: D 184 LEU cc_start: 0.8642 (mt) cc_final: 0.8324 (mt) REVERT: D 231 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9184 (mm) REVERT: D 233 ASN cc_start: 0.9018 (m110) cc_final: 0.8797 (p0) REVERT: D 241 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8404 (mp0) REVERT: D 242 TYR cc_start: 0.8176 (t80) cc_final: 0.7660 (t80) REVERT: D 259 PHE cc_start: 0.8270 (t80) cc_final: 0.7421 (t80) REVERT: D 261 ARG cc_start: 0.8033 (mtm-85) cc_final: 0.7813 (mtp-110) REVERT: D 262 TYR cc_start: 0.9005 (t80) cc_final: 0.8772 (t80) outliers start: 74 outliers final: 33 residues processed: 814 average time/residue: 0.1168 time to fit residues: 143.3678 Evaluate side-chains 756 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 715 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 231 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 182 optimal weight: 0.6980 chunk 159 optimal weight: 0.8980 chunk 91 optimal weight: 9.9990 chunk 150 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.132721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.099066 restraints weight = 36791.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.102891 restraints weight = 17059.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.105466 restraints weight = 9978.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.107197 restraints weight = 6772.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.108386 restraints weight = 5105.144| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16386 Z= 0.154 Angle : 0.680 13.341 22134 Z= 0.350 Chirality : 0.045 0.186 2360 Planarity : 0.004 0.042 2818 Dihedral : 9.266 130.454 2295 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.50 % Allowed : 23.37 % Favored : 73.14 % 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: 1.09 (0.15), residues: 1152 sheet: 0.91 (0.45), residues: 98 loop : 0.16 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 243 TYR 0.039 0.002 TYR D 262 PHE 0.053 0.002 PHE D 172 TRP 0.017 0.002 TRP D 30 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (16386) covalent geometry : angle 0.68003 / 0.35 (22134) hydrogen bonds : bond 0.04503 / 2.85 ( 871) hydrogen bonds : angle 5.24199 / 3.74 ( 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 810 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 750 time to evaluate : 0.600 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 39 ASP cc_start: 0.8955 (m-30) cc_final: 0.8676 (m-30) REVERT: A 76 ASP cc_start: 0.9125 (m-30) cc_final: 0.8597 (m-30) REVERT: A 123 SER cc_start: 0.9590 (OUTLIER) cc_final: 0.9219 (p) REVERT: A 163 ARG cc_start: 0.7910 (tpp80) cc_final: 0.7681 (mmm-85) REVERT: A 178 SER cc_start: 0.8946 (OUTLIER) cc_final: 0.8049 (t) REVERT: A 221 LYS cc_start: 0.9273 (mmtp) cc_final: 0.8968 (mttp) REVERT: A 243 ARG cc_start: 0.8037 (ptm-80) cc_final: 0.7778 (ppt170) REVERT: A 252 ASN cc_start: 0.9137 (t0) cc_final: 0.8918 (t0) REVERT: A 290 GLU cc_start: 0.9308 (tt0) cc_final: 0.8962 (tm-30) REVERT: A 335 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8028 (mt-10) REVERT: A 390 GLN cc_start: 0.8703 (mt0) cc_final: 0.8334 (mt0) REVERT: A 393 SER cc_start: 0.9644 (m) cc_final: 0.9379 (t) REVERT: A 444 ASP cc_start: 0.8582 (t0) cc_final: 0.7196 (t0) REVERT: A 446 ARG cc_start: 0.7500 (mtp85) cc_final: 0.7047 (mmm160) REVERT: A 447 ASN cc_start: 0.8424 (m-40) cc_final: 0.8061 (m-40) REVERT: A 459 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.8887 (mtmm) REVERT: A 469 HIS cc_start: 0.8681 (t-170) cc_final: 0.8477 (t70) REVERT: A 491 PHE cc_start: 0.9527 (t80) cc_final: 0.9288 (t80) REVERT: A 512 GLU cc_start: 0.8386 (pt0) cc_final: 0.8112 (pm20) REVERT: A 515 ASP cc_start: 0.9035 (m-30) cc_final: 0.8780 (m-30) REVERT: A 550 MET cc_start: 0.7740 (mtm) cc_final: 0.7478 (mtm) REVERT: A 561 LEU cc_start: 0.9254 (tp) cc_final: 0.9016 (tp) REVERT: A 588 GLN cc_start: 0.8978 (mm-40) cc_final: 0.8646 (tp40) REVERT: A 639 ASP cc_start: 0.8622 (m-30) cc_final: 0.8204 (m-30) REVERT: A 640 MET cc_start: 0.9450 (OUTLIER) cc_final: 0.8548 (tpp) REVERT: A 645 GLN cc_start: 0.9249 (tp40) cc_final: 0.9041 (tp-100) REVERT: A 654 PHE cc_start: 0.9324 (t80) cc_final: 0.8754 (t80) REVERT: A 662 MET cc_start: 0.8699 (ptp) cc_final: 0.8064 (ptp) REVERT: A 663 THR cc_start: 0.9524 (OUTLIER) cc_final: 0.9270 (t) REVERT: A 668 ASN cc_start: 0.9543 (m-40) cc_final: 0.9315 (m-40) REVERT: A 684 TYR cc_start: 0.7843 (OUTLIER) cc_final: 0.7171 (m-10) REVERT: B 65 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8123 (mm-30) REVERT: B 150 GLN cc_start: 0.9117 (tp40) cc_final: 0.8802 (tp40) REVERT: B 152 SER cc_start: 0.9699 (p) cc_final: 0.9429 (p) REVERT: B 172 LEU cc_start: 0.9378 (mp) cc_final: 0.9034 (mp) REVERT: B 211 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8060 (mm-30) REVERT: B 235 ARG cc_start: 0.8815 (mtm110) cc_final: 0.8309 (mtm110) REVERT: B 274 ARG cc_start: 0.8651 (ttm-80) cc_final: 0.8379 (ttm-80) REVERT: B 288 PHE cc_start: 0.9233 (t80) cc_final: 0.8975 (t80) REVERT: B 290 GLU cc_start: 0.8038 (tp30) cc_final: 0.7762 (tp30) REVERT: B 322 MET cc_start: 0.9196 (tpp) cc_final: 0.8967 (mmt) REVERT: B 350 ARG cc_start: 0.8617 (mtp85) cc_final: 0.7667 (mtp85) REVERT: B 355 TYR cc_start: 0.8372 (m-80) cc_final: 0.7797 (m-80) REVERT: B 361 GLN cc_start: 0.9067 (tt0) cc_final: 0.8502 (tt0) REVERT: B 374 SER cc_start: 0.8964 (t) cc_final: 0.8445 (p) REVERT: B 399 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8190 (tp30) REVERT: B 407 ILE cc_start: 0.8777 (mt) cc_final: 0.8547 (mt) REVERT: B 446 ARG cc_start: 0.7766 (ttm-80) cc_final: 0.7469 (mmm-85) REVERT: B 458 MET cc_start: 0.9346 (mmm) cc_final: 0.9103 (mmp) REVERT: B 493 MET cc_start: 0.9666 (tmm) cc_final: 0.9383 (tmm) REVERT: B 515 ASP cc_start: 0.9065 (m-30) cc_final: 0.8666 (m-30) REVERT: B 550 MET cc_start: 0.8225 (mtm) cc_final: 0.7854 (mtm) REVERT: B 558 TRP cc_start: 0.9561 (m100) cc_final: 0.8670 (m100) REVERT: B 588 GLN cc_start: 0.9324 (mm-40) cc_final: 0.8743 (mm-40) REVERT: B 598 MET cc_start: 0.8441 (mtm) cc_final: 0.8199 (mtm) REVERT: B 599 GLU cc_start: 0.8485 (pt0) cc_final: 0.8225 (pt0) REVERT: B 604 ARG cc_start: 0.8573 (mmp80) cc_final: 0.8227 (mmt-90) REVERT: B 610 LYS cc_start: 0.8820 (mtpp) cc_final: 0.8580 (mtpp) REVERT: B 686 ARG cc_start: 0.8315 (mtp-110) cc_final: 0.7566 (mtp85) REVERT: C 29 PHE cc_start: 0.7837 (t80) cc_final: 0.7415 (t80) REVERT: C 86 ARG cc_start: 0.8416 (mtt180) cc_final: 0.7964 (mpt180) REVERT: C 122 PHE cc_start: 0.8783 (m-80) cc_final: 0.8389 (m-80) REVERT: C 154 PHE cc_start: 0.9205 (t80) cc_final: 0.8932 (t80) REVERT: C 163 LEU cc_start: 0.9519 (tt) cc_final: 0.8977 (tt) REVERT: C 168 PHE cc_start: 0.9196 (m-80) cc_final: 0.8978 (m-80) REVERT: C 174 TYR cc_start: 0.8744 (OUTLIER) cc_final: 0.7394 (t80) REVERT: C 179 TYR cc_start: 0.8751 (t80) cc_final: 0.8551 (t80) REVERT: C 212 ILE cc_start: 0.9067 (mt) cc_final: 0.8637 (mp) REVERT: C 242 TYR cc_start: 0.9337 (t80) cc_final: 0.8866 (t80) REVERT: C 268 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9214 (mt) REVERT: C 269 MET cc_start: 0.9530 (tmm) cc_final: 0.9287 (tmm) REVERT: D 18 THR cc_start: 0.8992 (p) cc_final: 0.8600 (m) REVERT: D 24 GLN cc_start: 0.8901 (mm-40) cc_final: 0.8394 (mp10) REVERT: D 74 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.7101 (tpt) REVERT: D 92 PHE cc_start: 0.8326 (t80) cc_final: 0.8024 (t80) REVERT: D 109 PHE cc_start: 0.8476 (m-80) cc_final: 0.8219 (m-80) REVERT: D 137 MET cc_start: 0.9292 (mtt) cc_final: 0.8960 (mtp) REVERT: D 178 PHE cc_start: 0.8791 (m-80) cc_final: 0.7835 (m-80) REVERT: D 184 LEU cc_start: 0.8789 (mt) cc_final: 0.8574 (mt) REVERT: D 231 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9147 (mm) REVERT: D 259 PHE cc_start: 0.8398 (t80) cc_final: 0.7463 (t80) REVERT: D 266 LYS cc_start: 0.8753 (mtmm) cc_final: 0.8480 (mtmm) outliers start: 60 outliers final: 33 residues processed: 776 average time/residue: 0.1192 time to fit residues: 140.0034 Evaluate side-chains 727 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 684 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 615 MET 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 A residue 684 TYR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 309 LYS Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 287 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 0.8980 chunk 157 optimal weight: 9.9990 chunk 168 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 191 optimal weight: 8.9990 chunk 159 optimal weight: 0.0870 chunk 182 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN D 28 GLN D 233 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.124818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.091144 restraints weight = 37665.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.094776 restraints weight = 17737.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.097198 restraints weight = 10549.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.098803 restraints weight = 7277.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.099906 restraints weight = 5573.806| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.5818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16386 Z= 0.209 Angle : 0.708 13.398 22134 Z= 0.368 Chirality : 0.046 0.194 2360 Planarity : 0.004 0.044 2818 Dihedral : 8.991 134.913 2292 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.66 % Allowed : 25.58 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.19), residues: 1932 helix: 0.95 (0.15), residues: 1147 sheet: -0.44 (0.37), residues: 160 loop : 0.23 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 686 TYR 0.048 0.002 TYR D 142 PHE 0.050 0.002 PHE C 109 TRP 0.029 0.002 TRP D 30 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.21 (16386) covalent geometry : angle 0.70758 / 0.37 (22134) hydrogen bonds : bond 0.04410 / 2.80 ( 871) hydrogen bonds : angle 5.25614 / 3.74 ( 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 796 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 716 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9088 (mmm) cc_final: 0.8807 (tpp) REVERT: A 162 LYS cc_start: 0.9135 (tmmt) cc_final: 0.8899 (ttpt) REVERT: A 163 ARG cc_start: 0.8134 (tpp80) cc_final: 0.7875 (mmm-85) REVERT: A 178 SER cc_start: 0.8892 (OUTLIER) cc_final: 0.8325 (t) REVERT: A 194 LYS cc_start: 0.9583 (ttpp) cc_final: 0.9338 (ttpp) REVERT: A 220 THR cc_start: 0.9395 (m) cc_final: 0.9063 (p) REVERT: A 221 LYS cc_start: 0.9230 (mmtp) cc_final: 0.8909 (mttp) REVERT: A 243 ARG cc_start: 0.7971 (ptm-80) cc_final: 0.7717 (ppt170) REVERT: A 290 GLU cc_start: 0.9305 (tt0) cc_final: 0.8923 (tm-30) REVERT: A 335 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8082 (mt-10) REVERT: A 384 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.7825 (pm20) REVERT: A 390 GLN cc_start: 0.8752 (mt0) cc_final: 0.8395 (mt0) REVERT: A 444 ASP cc_start: 0.8645 (t0) cc_final: 0.7526 (t0) REVERT: A 446 ARG cc_start: 0.7449 (mtp85) cc_final: 0.7166 (mmm160) REVERT: A 459 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.8900 (mtmm) REVERT: A 515 ASP cc_start: 0.9106 (m-30) cc_final: 0.8863 (m-30) REVERT: A 588 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8791 (mm-40) REVERT: A 590 SER cc_start: 0.9519 (t) cc_final: 0.9008 (p) REVERT: A 595 MET cc_start: 0.9109 (mmp) cc_final: 0.8846 (mmm) REVERT: A 639 ASP cc_start: 0.8778 (m-30) cc_final: 0.8253 (m-30) REVERT: A 640 MET cc_start: 0.9476 (OUTLIER) cc_final: 0.8581 (tpp) REVERT: A 645 GLN cc_start: 0.9419 (tp40) cc_final: 0.9174 (tp-100) REVERT: A 668 ASN cc_start: 0.9568 (m-40) cc_final: 0.9353 (m-40) REVERT: A 684 TYR cc_start: 0.8101 (OUTLIER) cc_final: 0.7272 (m-10) REVERT: B 87 LYS cc_start: 0.9413 (tptt) cc_final: 0.9155 (tppt) REVERT: B 99 LYS cc_start: 0.9267 (mmtt) cc_final: 0.8720 (mmmm) REVERT: B 112 LYS cc_start: 0.9476 (mmmt) cc_final: 0.9184 (mmmt) REVERT: B 168 VAL cc_start: 0.9319 (t) cc_final: 0.9106 (t) REVERT: B 172 LEU cc_start: 0.9435 (mp) cc_final: 0.9109 (mp) REVERT: B 181 ASP cc_start: 0.8714 (m-30) cc_final: 0.8274 (m-30) REVERT: B 202 ASN cc_start: 0.9350 (t0) cc_final: 0.9014 (t0) REVERT: B 235 ARG cc_start: 0.8921 (mtm110) cc_final: 0.8541 (mtm110) REVERT: B 238 ASP cc_start: 0.8043 (t0) cc_final: 0.7763 (t0) REVERT: B 257 ASP cc_start: 0.8942 (m-30) cc_final: 0.8664 (m-30) REVERT: B 288 PHE cc_start: 0.9221 (t80) cc_final: 0.8836 (t80) REVERT: B 290 GLU cc_start: 0.8293 (tp30) cc_final: 0.8002 (tp30) REVERT: B 308 LYS cc_start: 0.9499 (mtpp) cc_final: 0.9194 (mtmm) REVERT: B 352 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8162 (mm-30) REVERT: B 374 SER cc_start: 0.9214 (t) cc_final: 0.8723 (p) REVERT: B 423 LYS cc_start: 0.9510 (mtmm) cc_final: 0.9148 (mmtp) REVERT: B 434 ASP cc_start: 0.8661 (m-30) cc_final: 0.8381 (m-30) REVERT: B 446 ARG cc_start: 0.7823 (ttm-80) cc_final: 0.7548 (mmm-85) REVERT: B 458 MET cc_start: 0.9303 (mmm) cc_final: 0.9030 (mmp) REVERT: B 493 MET cc_start: 0.9643 (tmm) cc_final: 0.9269 (tmm) REVERT: B 515 ASP cc_start: 0.9065 (m-30) cc_final: 0.8717 (m-30) REVERT: B 599 GLU cc_start: 0.8487 (pt0) cc_final: 0.8250 (pt0) REVERT: B 604 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8215 (mmt-90) REVERT: B 610 LYS cc_start: 0.8924 (mtpp) cc_final: 0.8600 (mtpp) REVERT: B 631 ASP cc_start: 0.8792 (t0) cc_final: 0.8414 (t0) REVERT: B 686 ARG cc_start: 0.8367 (mtp-110) cc_final: 0.7782 (mtp85) REVERT: C 55 TYR cc_start: 0.9091 (t80) cc_final: 0.8804 (t80) REVERT: C 66 ASP cc_start: 0.8791 (OUTLIER) cc_final: 0.8201 (t70) REVERT: C 86 ARG cc_start: 0.8589 (mtt180) cc_final: 0.8090 (mpt180) REVERT: C 143 LYS cc_start: 0.9483 (tptp) cc_final: 0.9170 (pttt) REVERT: C 163 LEU cc_start: 0.9518 (tt) cc_final: 0.9077 (tt) REVERT: C 168 PHE cc_start: 0.9177 (m-80) cc_final: 0.8861 (m-80) REVERT: C 174 TYR cc_start: 0.8899 (OUTLIER) cc_final: 0.7236 (t80) REVERT: C 179 TYR cc_start: 0.8781 (t80) cc_final: 0.8459 (t80) REVERT: C 242 TYR cc_start: 0.9403 (t80) cc_final: 0.9078 (t80) REVERT: C 259 PHE cc_start: 0.8464 (t80) cc_final: 0.7524 (t80) REVERT: C 260 ILE cc_start: 0.8204 (pp) cc_final: 0.7924 (pp) REVERT: C 268 LEU cc_start: 0.9227 (mm) cc_final: 0.8967 (mt) REVERT: C 269 MET cc_start: 0.9570 (tmm) cc_final: 0.9295 (tmm) REVERT: D 18 THR cc_start: 0.9030 (p) cc_final: 0.8686 (m) REVERT: D 20 MET cc_start: 0.8645 (ttt) cc_final: 0.8070 (ptm) REVERT: D 24 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8412 (mp10) REVERT: D 74 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7278 (tpt) REVERT: D 109 PHE cc_start: 0.8518 (m-80) cc_final: 0.8174 (m-80) REVERT: D 129 LYS cc_start: 0.9510 (mmmt) cc_final: 0.9214 (tptp) REVERT: D 137 MET cc_start: 0.9480 (mtt) cc_final: 0.9216 (mtp) REVERT: D 168 PHE cc_start: 0.8670 (m-80) cc_final: 0.8340 (m-80) REVERT: D 224 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8280 (mm) REVERT: D 259 PHE cc_start: 0.8503 (t80) cc_final: 0.7602 (t80) REVERT: D 270 ASN cc_start: 0.8840 (m-40) cc_final: 0.8631 (m-40) outliers start: 80 outliers final: 49 residues processed: 751 average time/residue: 0.1133 time to fit residues: 128.9281 Evaluate side-chains 720 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 661 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 0.0030 chunk 46 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 168 optimal weight: 0.9990 chunk 157 optimal weight: 8.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 GLN A 259 ASN ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.121847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.089426 restraints weight = 37007.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.092763 restraints weight = 17804.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.094843 restraints weight = 10790.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.096181 restraints weight = 7679.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.097451 restraints weight = 6005.684| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (22 function evaluations) r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.6279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16386 Z= 0.154 Angle : 0.715 13.858 22134 Z= 0.367 Chirality : 0.045 0.199 2360 Planarity : 0.004 0.047 2818 Dihedral : 8.748 135.145 2291 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.31 % Allowed : 28.96 % Favored : 66.72 % 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: 0.61 (0.19), residues: 1932 helix: 0.82 (0.15), residues: 1150 sheet: -0.45 (0.38), residues: 160 loop : 0.10 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 686 TYR 0.054 0.002 TYR D 142 PHE 0.049 0.002 PHE C 109 TRP 0.031 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 0.71505 / 0.37 (22134) hydrogen bonds : bond 0.04333 / 2.78 ( 871) hydrogen bonds : angle 5.24251 / 3.74 ( 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 789 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 715 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ASP cc_start: 0.9058 (m-30) cc_final: 0.8777 (m-30) REVERT: A 123 SER cc_start: 0.9623 (OUTLIER) cc_final: 0.9222 (p) REVERT: A 128 PHE cc_start: 0.9374 (t80) cc_final: 0.9160 (t80) REVERT: A 163 ARG cc_start: 0.8088 (tpp80) cc_final: 0.7853 (mmm-85) REVERT: A 178 SER cc_start: 0.8897 (OUTLIER) cc_final: 0.8357 (t) REVERT: A 190 MET cc_start: 0.9193 (mtp) cc_final: 0.8976 (mtp) REVERT: A 220 THR cc_start: 0.9368 (m) cc_final: 0.8981 (p) REVERT: A 221 LYS cc_start: 0.9163 (mmtp) cc_final: 0.8805 (mttp) REVERT: A 232 ASN cc_start: 0.9493 (m-40) cc_final: 0.9180 (m110) REVERT: A 243 ARG cc_start: 0.8003 (ptm-80) cc_final: 0.7725 (ppt170) REVERT: A 290 GLU cc_start: 0.9300 (tt0) cc_final: 0.8927 (tm-30) REVERT: A 335 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8163 (mt-10) REVERT: A 362 ASP cc_start: 0.8228 (m-30) cc_final: 0.7690 (m-30) REVERT: A 390 GLN cc_start: 0.8811 (mt0) cc_final: 0.8453 (mt0) REVERT: A 420 MET cc_start: 0.8956 (mmm) cc_final: 0.8360 (mmm) REVERT: A 444 ASP cc_start: 0.8783 (t0) cc_final: 0.8221 (t0) REVERT: A 446 ARG cc_start: 0.7497 (mtp85) cc_final: 0.7064 (mmm160) REVERT: A 459 LYS cc_start: 0.9346 (OUTLIER) cc_final: 0.8929 (mtmm) REVERT: A 493 MET cc_start: 0.8963 (tmm) cc_final: 0.8588 (tmm) REVERT: A 498 TYR cc_start: 0.8749 (m-80) cc_final: 0.8327 (m-80) REVERT: A 515 ASP cc_start: 0.9114 (m-30) cc_final: 0.8902 (m-30) REVERT: A 588 GLN cc_start: 0.9131 (mm-40) cc_final: 0.8799 (tp40) REVERT: A 599 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8396 (pt0) REVERT: A 639 ASP cc_start: 0.8774 (m-30) cc_final: 0.8177 (m-30) REVERT: A 640 MET cc_start: 0.9500 (OUTLIER) cc_final: 0.8555 (tpp) REVERT: A 645 GLN cc_start: 0.9388 (tp40) cc_final: 0.8993 (tp-100) REVERT: A 668 ASN cc_start: 0.9617 (m-40) cc_final: 0.9410 (m-40) REVERT: A 684 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.7139 (m-10) REVERT: B 15 GLU cc_start: 0.8743 (tp30) cc_final: 0.8465 (tp30) REVERT: B 87 LYS cc_start: 0.9387 (tptt) cc_final: 0.9101 (tppt) REVERT: B 99 LYS cc_start: 0.9280 (mmtt) cc_final: 0.8720 (mmmm) REVERT: B 112 LYS cc_start: 0.9444 (mmmt) cc_final: 0.9206 (mmmt) REVERT: B 152 SER cc_start: 0.9739 (p) cc_final: 0.9523 (p) REVERT: B 172 LEU cc_start: 0.9464 (mp) cc_final: 0.9215 (mp) REVERT: B 181 ASP cc_start: 0.8680 (m-30) cc_final: 0.8182 (m-30) REVERT: B 238 ASP cc_start: 0.8059 (t0) cc_final: 0.7698 (t0) REVERT: B 257 ASP cc_start: 0.9013 (m-30) cc_final: 0.8774 (m-30) REVERT: B 290 GLU cc_start: 0.8375 (tp30) cc_final: 0.8051 (tp30) REVERT: B 308 LYS cc_start: 0.9466 (mtpp) cc_final: 0.9128 (mtmm) REVERT: B 352 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8102 (mm-30) REVERT: B 374 SER cc_start: 0.9212 (t) cc_final: 0.8763 (p) REVERT: B 423 LYS cc_start: 0.9561 (mtmm) cc_final: 0.9270 (mmtp) REVERT: B 434 ASP cc_start: 0.8740 (m-30) cc_final: 0.8535 (m-30) REVERT: B 458 MET cc_start: 0.9244 (mmm) cc_final: 0.8924 (mmp) REVERT: B 493 MET cc_start: 0.9619 (tmm) cc_final: 0.9211 (tmm) REVERT: B 515 ASP cc_start: 0.9054 (m-30) cc_final: 0.8687 (m-30) REVERT: B 599 GLU cc_start: 0.8438 (pt0) cc_final: 0.8181 (pt0) REVERT: B 610 LYS cc_start: 0.9053 (mtpp) cc_final: 0.8765 (mtpp) REVERT: B 631 ASP cc_start: 0.8803 (t0) cc_final: 0.8437 (t0) REVERT: B 686 ARG cc_start: 0.8433 (mtp-110) cc_final: 0.8052 (mtp-110) REVERT: C 55 TYR cc_start: 0.9104 (t80) cc_final: 0.8593 (t80) REVERT: C 86 ARG cc_start: 0.8549 (mtt180) cc_final: 0.8091 (mpt180) REVERT: C 92 PHE cc_start: 0.8916 (t80) cc_final: 0.8511 (t80) REVERT: C 143 LYS cc_start: 0.9423 (tptp) cc_final: 0.9084 (pttt) REVERT: C 163 LEU cc_start: 0.9514 (tt) cc_final: 0.9177 (tt) REVERT: C 174 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.7193 (t80) REVERT: C 178 PHE cc_start: 0.8808 (t80) cc_final: 0.8502 (t80) REVERT: C 242 TYR cc_start: 0.9467 (t80) cc_final: 0.9036 (t80) REVERT: C 259 PHE cc_start: 0.8191 (t80) cc_final: 0.7173 (t80) REVERT: C 260 ILE cc_start: 0.8098 (pp) cc_final: 0.7804 (pp) REVERT: C 268 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8446 (mt) REVERT: C 269 MET cc_start: 0.9535 (tmm) cc_final: 0.9095 (mmp) REVERT: D 17 PHE cc_start: 0.8282 (p90) cc_final: 0.8056 (p90) REVERT: D 18 THR cc_start: 0.9034 (p) cc_final: 0.8820 (m) REVERT: D 20 MET cc_start: 0.8763 (ttt) cc_final: 0.8505 (ptm) REVERT: D 28 GLN cc_start: 0.8943 (mt0) cc_final: 0.8705 (tt0) REVERT: D 74 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7345 (tpt) REVERT: D 109 PHE cc_start: 0.8545 (m-80) cc_final: 0.8157 (m-80) REVERT: D 120 GLU cc_start: 0.9181 (tm-30) cc_final: 0.8951 (tm-30) REVERT: D 123 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8299 (tm-30) REVERT: D 129 LYS cc_start: 0.9508 (mmmt) cc_final: 0.9250 (tptp) REVERT: D 137 MET cc_start: 0.9561 (mtt) cc_final: 0.9291 (mtp) REVERT: D 153 LEU cc_start: 0.7087 (tt) cc_final: 0.6835 (tt) REVERT: D 168 PHE cc_start: 0.8597 (m-80) cc_final: 0.8254 (m-80) REVERT: D 231 LEU cc_start: 0.9497 (mm) cc_final: 0.9230 (mm) REVERT: D 259 PHE cc_start: 0.8570 (t80) cc_final: 0.7886 (t80) REVERT: D 262 TYR cc_start: 0.8857 (t80) cc_final: 0.8621 (t80) REVERT: D 266 LYS cc_start: 0.8657 (ptpp) cc_final: 0.8385 (mtmm) REVERT: D 270 ASN cc_start: 0.8902 (m-40) cc_final: 0.8693 (m-40) outliers start: 74 outliers final: 49 residues processed: 744 average time/residue: 0.1147 time to fit residues: 129.7901 Evaluate side-chains 719 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 662 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 314 MET 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 417 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 0.0570 chunk 183 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN A 313 HIS ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN D 91 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.121697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.089683 restraints weight = 37161.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.092963 restraints weight = 18003.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.095230 restraints weight = 10934.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.096785 restraints weight = 7563.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.097865 restraints weight = 5719.229| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (17 function evaluations) r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.6659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 16386 Z= 0.169 Angle : 0.714 13.125 22134 Z= 0.368 Chirality : 0.046 0.175 2360 Planarity : 0.004 0.050 2818 Dihedral : 8.669 136.911 2291 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.31 % Allowed : 30.42 % Favored : 65.27 % 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: 0.46 (0.19), residues: 1932 helix: 0.73 (0.15), residues: 1158 sheet: -0.58 (0.38), residues: 160 loop : -0.01 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 686 TYR 0.047 0.002 TYR D 142 PHE 0.053 0.002 PHE C 109 TRP 0.032 0.002 TRP D 30 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (16386) covalent geometry : angle 0.71364 / 0.37 (22134) hydrogen bonds : bond 0.04276 / 2.74 ( 871) hydrogen bonds : angle 5.30603 / 3.79 ( 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 776 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 702 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: A 56 ASP cc_start: 0.9032 (m-30) cc_final: 0.8721 (m-30) REVERT: A 128 PHE cc_start: 0.9419 (t80) cc_final: 0.9202 (t80) REVERT: A 178 SER cc_start: 0.8826 (OUTLIER) cc_final: 0.8380 (t) REVERT: A 190 MET cc_start: 0.9214 (mtp) cc_final: 0.8991 (mtp) REVERT: A 194 LYS cc_start: 0.9533 (ttpp) cc_final: 0.9225 (ttpp) REVERT: A 221 LYS cc_start: 0.9192 (mmtp) cc_final: 0.8854 (mttp) REVERT: A 232 ASN cc_start: 0.9462 (m-40) cc_final: 0.9149 (m110) REVERT: A 243 ARG cc_start: 0.7919 (ptm-80) cc_final: 0.7644 (ppt170) REVERT: A 290 GLU cc_start: 0.9259 (tt0) cc_final: 0.8883 (tm-30) REVERT: A 335 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8058 (mt-10) REVERT: A 362 ASP cc_start: 0.8118 (m-30) cc_final: 0.7646 (m-30) REVERT: A 384 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.7776 (pm20) REVERT: A 390 GLN cc_start: 0.8869 (mt0) cc_final: 0.8520 (mt0) REVERT: A 444 ASP cc_start: 0.8739 (t0) cc_final: 0.8158 (t0) REVERT: A 446 ARG cc_start: 0.7509 (mtp85) cc_final: 0.7109 (mmm160) REVERT: A 459 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.8880 (mtmm) REVERT: A 498 TYR cc_start: 0.8859 (m-80) cc_final: 0.8444 (m-10) REVERT: A 515 ASP cc_start: 0.9085 (m-30) cc_final: 0.8879 (m-30) REVERT: A 588 GLN cc_start: 0.9082 (mm-40) cc_final: 0.8727 (tp40) REVERT: A 599 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8290 (pt0) REVERT: A 602 GLU cc_start: 0.7795 (pt0) cc_final: 0.7042 (pt0) REVERT: A 618 LEU cc_start: 0.9474 (tp) cc_final: 0.9230 (tt) REVERT: A 639 ASP cc_start: 0.8780 (m-30) cc_final: 0.8183 (m-30) REVERT: A 640 MET cc_start: 0.9472 (OUTLIER) cc_final: 0.8542 (tpp) REVERT: A 645 GLN cc_start: 0.9437 (tp40) cc_final: 0.9213 (tp-100) REVERT: A 684 TYR cc_start: 0.8064 (OUTLIER) cc_final: 0.7130 (m-10) REVERT: B 15 GLU cc_start: 0.8839 (tp30) cc_final: 0.8534 (tp30) REVERT: B 112 LYS cc_start: 0.9471 (mmmt) cc_final: 0.9204 (mmmt) REVERT: B 128 PHE cc_start: 0.9771 (t80) cc_final: 0.9452 (t80) REVERT: B 152 SER cc_start: 0.9712 (p) cc_final: 0.9485 (p) REVERT: B 172 LEU cc_start: 0.9514 (mp) cc_final: 0.9280 (mp) REVERT: B 181 ASP cc_start: 0.8682 (m-30) cc_final: 0.8170 (m-30) REVERT: B 238 ASP cc_start: 0.8036 (t0) cc_final: 0.7541 (t0) REVERT: B 257 ASP cc_start: 0.8935 (m-30) cc_final: 0.8630 (m-30) REVERT: B 290 GLU cc_start: 0.8316 (tp30) cc_final: 0.7998 (tp30) REVERT: B 352 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8029 (mm-30) REVERT: B 374 SER cc_start: 0.9187 (t) cc_final: 0.8746 (p) REVERT: B 423 LYS cc_start: 0.9581 (mtmm) cc_final: 0.9304 (mmtp) REVERT: B 446 ARG cc_start: 0.8009 (mmm-85) cc_final: 0.7773 (mmm-85) REVERT: B 458 MET cc_start: 0.9179 (mmm) cc_final: 0.8856 (mmp) REVERT: B 493 MET cc_start: 0.9609 (tmm) cc_final: 0.9215 (tmm) REVERT: B 515 ASP cc_start: 0.9014 (m-30) cc_final: 0.8678 (m-30) REVERT: B 598 MET cc_start: 0.8388 (mtm) cc_final: 0.8177 (mtm) REVERT: B 599 GLU cc_start: 0.8425 (pt0) cc_final: 0.8132 (pt0) REVERT: B 610 LYS cc_start: 0.9082 (mtpp) cc_final: 0.8714 (mtpp) REVERT: B 631 ASP cc_start: 0.8833 (t0) cc_final: 0.8462 (t0) REVERT: C 21 PHE cc_start: 0.9409 (m-80) cc_final: 0.9123 (m-80) REVERT: C 86 ARG cc_start: 0.8607 (mtt180) cc_final: 0.8265 (mpt180) REVERT: C 96 MET cc_start: 0.8518 (mmt) cc_final: 0.7717 (mmt) REVERT: C 122 PHE cc_start: 0.8837 (m-80) cc_final: 0.8415 (m-80) REVERT: C 143 LYS cc_start: 0.9302 (tptp) cc_final: 0.8951 (pttt) REVERT: C 154 PHE cc_start: 0.9356 (t80) cc_final: 0.9154 (t80) REVERT: C 242 TYR cc_start: 0.9450 (t80) cc_final: 0.8998 (t80) REVERT: C 259 PHE cc_start: 0.8172 (t80) cc_final: 0.7480 (t80) REVERT: C 268 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8676 (mp) REVERT: C 269 MET cc_start: 0.9498 (tmm) cc_final: 0.9101 (mmp) REVERT: D 17 PHE cc_start: 0.8533 (p90) cc_final: 0.8183 (p90) REVERT: D 20 MET cc_start: 0.8766 (ttt) cc_final: 0.8504 (ppp) REVERT: D 28 GLN cc_start: 0.8972 (mt0) cc_final: 0.8751 (tt0) REVERT: D 47 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7066 (mt) REVERT: D 74 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7698 (tpt) REVERT: D 109 PHE cc_start: 0.8560 (m-80) cc_final: 0.8174 (m-80) REVERT: D 120 GLU cc_start: 0.9193 (tm-30) cc_final: 0.8895 (tm-30) REVERT: D 123 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8312 (tm-30) REVERT: D 130 TYR cc_start: 0.8483 (m-10) cc_final: 0.8140 (m-10) REVERT: D 137 MET cc_start: 0.9586 (mtt) cc_final: 0.9296 (mtp) REVERT: D 174 TYR cc_start: 0.8977 (t80) cc_final: 0.8608 (t80) REVERT: D 178 PHE cc_start: 0.8954 (m-80) cc_final: 0.8505 (t80) REVERT: D 196 ARG cc_start: 0.9243 (ptm-80) cc_final: 0.8976 (ptm-80) REVERT: D 259 PHE cc_start: 0.8566 (t80) cc_final: 0.7826 (t80) REVERT: D 287 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7066 (pp) outliers start: 74 outliers final: 49 residues processed: 735 average time/residue: 0.1140 time to fit residues: 127.4561 Evaluate side-chains 725 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 667 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 SER 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 459 LYS Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 314 MET 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 611 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 216 GLN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN D 265 ASN ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.115642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.084290 restraints weight = 37817.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.087367 restraints weight = 18431.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.089484 restraints weight = 11218.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.090927 restraints weight = 7868.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.091798 restraints weight = 6026.994| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.7032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 16386 Z= 0.305 Angle : 0.809 15.021 22134 Z= 0.421 Chirality : 0.049 0.280 2360 Planarity : 0.004 0.051 2818 Dihedral : 8.982 140.801 2291 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.49 % Allowed : 32.23 % Favored : 63.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.19), residues: 1932 helix: 0.66 (0.15), residues: 1141 sheet: -0.88 (0.37), residues: 162 loop : 0.19 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 686 TYR 0.038 0.002 TYR D 142 PHE 0.052 0.003 PHE C 109 TRP 0.039 0.003 TRP D 30 HIS 0.010 0.002 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00664 / 0.30 (16386) covalent geometry : angle 0.80905 / 0.42 (22134) hydrogen bonds : bond 0.04537 / 2.90 ( 871) hydrogen bonds : angle 5.52985 / 3.94 ( 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 756 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 679 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.9602 (mm) cc_final: 0.9397 (tp) REVERT: A 56 ASP cc_start: 0.9151 (m-30) cc_final: 0.8807 (m-30) REVERT: A 178 SER cc_start: 0.8737 (OUTLIER) cc_final: 0.8432 (t) REVERT: A 190 MET cc_start: 0.9279 (mtp) cc_final: 0.9023 (mtp) REVERT: A 221 LYS cc_start: 0.9362 (mmtp) cc_final: 0.9080 (mmtp) REVERT: A 232 ASN cc_start: 0.9473 (m-40) cc_final: 0.9150 (m110) REVERT: A 243 ARG cc_start: 0.7903 (ptm-80) cc_final: 0.7598 (ppt170) REVERT: A 250 TYR cc_start: 0.9040 (m-80) cc_final: 0.8694 (m-80) REVERT: A 286 ASP cc_start: 0.8321 (m-30) cc_final: 0.8082 (m-30) REVERT: A 290 GLU cc_start: 0.9222 (tt0) cc_final: 0.8874 (tm-30) REVERT: A 335 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8061 (mt-10) REVERT: A 362 ASP cc_start: 0.8167 (m-30) cc_final: 0.7634 (m-30) REVERT: A 384 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.7643 (pm20) REVERT: A 390 GLN cc_start: 0.8975 (mt0) cc_final: 0.8535 (mt0) REVERT: A 406 ASP cc_start: 0.8118 (m-30) cc_final: 0.7872 (t70) REVERT: A 446 ARG cc_start: 0.7771 (mtp85) cc_final: 0.7139 (mmm160) REVERT: A 498 TYR cc_start: 0.8956 (m-80) cc_final: 0.8726 (m-80) REVERT: A 515 ASP cc_start: 0.9112 (m-30) cc_final: 0.8728 (m-30) REVERT: A 588 GLN cc_start: 0.9121 (mm-40) cc_final: 0.8650 (mm-40) REVERT: A 599 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8187 (pt0) REVERT: A 618 LEU cc_start: 0.9509 (tp) cc_final: 0.9252 (tt) REVERT: A 639 ASP cc_start: 0.8742 (m-30) cc_final: 0.8202 (m-30) REVERT: A 640 MET cc_start: 0.9508 (OUTLIER) cc_final: 0.8696 (tpp) REVERT: A 645 GLN cc_start: 0.9503 (tp40) cc_final: 0.9270 (tp-100) REVERT: A 684 TYR cc_start: 0.8253 (OUTLIER) cc_final: 0.7530 (m-10) REVERT: B 15 GLU cc_start: 0.8865 (tp30) cc_final: 0.8591 (tp30) REVERT: B 65 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8023 (mp0) REVERT: B 112 LYS cc_start: 0.9547 (mmmt) cc_final: 0.9242 (mmmt) REVERT: B 147 GLN cc_start: 0.9519 (mt0) cc_final: 0.9233 (mt0) REVERT: B 172 LEU cc_start: 0.9560 (mp) cc_final: 0.9316 (mp) REVERT: B 181 ASP cc_start: 0.8731 (m-30) cc_final: 0.8258 (m-30) REVERT: B 232 ASN cc_start: 0.9297 (OUTLIER) cc_final: 0.8912 (t0) REVERT: B 235 ARG cc_start: 0.9070 (mtm110) cc_final: 0.8761 (ttp-110) REVERT: B 251 LEU cc_start: 0.9559 (tp) cc_final: 0.9278 (tp) REVERT: B 257 ASP cc_start: 0.8837 (m-30) cc_final: 0.8515 (m-30) REVERT: B 290 GLU cc_start: 0.8392 (tp30) cc_final: 0.8070 (tp30) REVERT: B 352 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8133 (mm-30) REVERT: B 375 LYS cc_start: 0.9359 (mtpp) cc_final: 0.9042 (mtpp) REVERT: B 423 LYS cc_start: 0.9613 (mtmm) cc_final: 0.9349 (mtpp) REVERT: B 434 ASP cc_start: 0.8703 (m-30) cc_final: 0.8470 (m-30) REVERT: B 458 MET cc_start: 0.9252 (mmm) cc_final: 0.8903 (mmp) REVERT: B 493 MET cc_start: 0.9608 (tmm) cc_final: 0.9207 (tmm) REVERT: B 515 ASP cc_start: 0.9038 (m-30) cc_final: 0.8727 (m-30) REVERT: B 599 GLU cc_start: 0.8450 (pt0) cc_final: 0.8042 (pt0) REVERT: B 604 ARG cc_start: 0.8385 (mmt-90) cc_final: 0.8064 (mmt-90) REVERT: B 610 LYS cc_start: 0.9088 (mtpp) cc_final: 0.8789 (mtpp) REVERT: B 686 ARG cc_start: 0.8539 (mtp85) cc_final: 0.7927 (mtp85) REVERT: C 74 MET cc_start: 0.9479 (mpp) cc_final: 0.9147 (pmm) REVERT: C 86 ARG cc_start: 0.8782 (mtt180) cc_final: 0.8414 (mpt180) REVERT: C 96 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8017 (mmt) REVERT: C 137 MET cc_start: 0.9406 (tpp) cc_final: 0.9112 (tpt) REVERT: C 147 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7693 (ptmm) REVERT: C 174 TYR cc_start: 0.8948 (OUTLIER) cc_final: 0.7811 (t80) REVERT: C 178 PHE cc_start: 0.8805 (t80) cc_final: 0.8525 (t80) REVERT: C 242 TYR cc_start: 0.9464 (t80) cc_final: 0.8932 (t80) REVERT: C 268 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8528 (mt) REVERT: C 269 MET cc_start: 0.9508 (tmm) cc_final: 0.9074 (mmp) REVERT: D 20 MET cc_start: 0.8785 (ttt) cc_final: 0.8523 (ppp) REVERT: D 28 GLN cc_start: 0.9136 (mt0) cc_final: 0.8914 (tt0) REVERT: D 46 TYR cc_start: 0.8855 (m-10) cc_final: 0.8445 (m-10) REVERT: D 47 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7669 (mt) REVERT: D 74 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7825 (tpt) REVERT: D 109 PHE cc_start: 0.8655 (m-80) cc_final: 0.8134 (m-80) REVERT: D 130 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.8219 (m-10) REVERT: D 137 MET cc_start: 0.9592 (mtt) cc_final: 0.9341 (mtp) REVERT: D 265 ASN cc_start: 0.8601 (m-40) cc_final: 0.7809 (m110) REVERT: D 270 ASN cc_start: 0.8526 (m-40) cc_final: 0.8317 (m-40) REVERT: D 287 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7732 (mt) outliers start: 77 outliers final: 54 residues processed: 711 average time/residue: 0.1123 time to fit residues: 121.8475 Evaluate side-chains 716 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 649 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 SER 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 472 LEU Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 314 MET 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 443 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 287 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 61 optimal weight: 0.0170 chunk 19 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 153 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 GLN A 447 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 25 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN D 270 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.122930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.091587 restraints weight = 37275.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.094871 restraints weight = 17759.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.097127 restraints weight = 10648.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.098596 restraints weight = 7301.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.099598 restraints weight = 5553.205| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.7321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16386 Z= 0.155 Angle : 0.799 14.520 22134 Z= 0.403 Chirality : 0.048 0.226 2360 Planarity : 0.004 0.052 2818 Dihedral : 8.635 136.912 2291 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.67 % Allowed : 33.92 % Favored : 62.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.19), residues: 1932 helix: 0.66 (0.15), residues: 1137 sheet: -0.80 (0.38), residues: 160 loop : 0.09 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 164 TYR 0.041 0.002 TYR D 142 PHE 0.056 0.002 PHE C 109 TRP 0.042 0.002 TRP D 30 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (16386) covalent geometry : angle 0.79881 / 0.40 (22134) hydrogen bonds : bond 0.04436 / 2.83 ( 871) hydrogen bonds : angle 5.41919 / 3.87 ( 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 745 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 682 time to evaluate : 0.596 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: A 56 ASP cc_start: 0.9076 (m-30) cc_final: 0.8735 (m-30) REVERT: A 123 SER cc_start: 0.9577 (OUTLIER) cc_final: 0.9154 (p) REVERT: A 139 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8569 (mp0) REVERT: A 178 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8350 (t) REVERT: A 190 MET cc_start: 0.9239 (mtp) cc_final: 0.9023 (mtp) REVERT: A 191 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8011 (mt0) REVERT: A 221 LYS cc_start: 0.9203 (mmtp) cc_final: 0.8854 (mttp) REVERT: A 232 ASN cc_start: 0.9490 (m-40) cc_final: 0.9206 (m110) REVERT: A 243 ARG cc_start: 0.7736 (ptm-80) cc_final: 0.7478 (ppt170) REVERT: A 290 GLU cc_start: 0.9233 (tt0) cc_final: 0.8775 (tm-30) REVERT: A 335 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8149 (mt-10) REVERT: A 362 ASP cc_start: 0.8182 (m-30) cc_final: 0.7628 (m-30) REVERT: A 381 LEU cc_start: 0.9443 (tp) cc_final: 0.9094 (tp) REVERT: A 384 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.7665 (pm20) REVERT: A 390 GLN cc_start: 0.8928 (mt0) cc_final: 0.8623 (mt0) REVERT: A 406 ASP cc_start: 0.8024 (m-30) cc_final: 0.7731 (t70) REVERT: A 447 ASN cc_start: 0.8603 (m110) cc_final: 0.7305 (m110) REVERT: A 459 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.8938 (mtmm) REVERT: A 493 MET cc_start: 0.8959 (tmm) cc_final: 0.8658 (tmm) REVERT: A 498 TYR cc_start: 0.8859 (m-80) cc_final: 0.8562 (m-80) REVERT: A 515 ASP cc_start: 0.9055 (m-30) cc_final: 0.8808 (m-30) REVERT: A 588 GLN cc_start: 0.9114 (mm-40) cc_final: 0.8767 (tp40) REVERT: A 599 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8111 (pt0) REVERT: A 639 ASP cc_start: 0.8715 (m-30) cc_final: 0.8126 (m-30) REVERT: A 640 MET cc_start: 0.9495 (OUTLIER) cc_final: 0.8605 (tpp) REVERT: A 684 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.7294 (m-10) REVERT: B 15 GLU cc_start: 0.8913 (tp30) cc_final: 0.8625 (tp30) REVERT: B 99 LYS cc_start: 0.9262 (mmtt) cc_final: 0.8752 (mmmm) REVERT: B 112 LYS cc_start: 0.9504 (mmmt) cc_final: 0.9194 (mmmt) REVERT: B 128 PHE cc_start: 0.9736 (t80) cc_final: 0.9434 (t80) REVERT: B 172 LEU cc_start: 0.9475 (mp) cc_final: 0.9200 (mp) REVERT: B 232 ASN cc_start: 0.9186 (OUTLIER) cc_final: 0.8945 (t0) REVERT: B 290 GLU cc_start: 0.8399 (tp30) cc_final: 0.8040 (tp30) REVERT: B 308 LYS cc_start: 0.9541 (mtmm) cc_final: 0.9225 (ptpp) REVERT: B 352 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8067 (mm-30) REVERT: B 375 LYS cc_start: 0.9282 (mtpp) cc_final: 0.8947 (mtpp) REVERT: B 423 LYS cc_start: 0.9588 (mtmm) cc_final: 0.9276 (mtpp) REVERT: B 434 ASP cc_start: 0.8681 (m-30) cc_final: 0.8395 (m-30) REVERT: B 458 MET cc_start: 0.9092 (mmm) cc_final: 0.8780 (mmp) REVERT: B 474 GLN cc_start: 0.8964 (mt0) cc_final: 0.8719 (mt0) REVERT: B 493 MET cc_start: 0.9547 (tmm) cc_final: 0.9202 (tmm) REVERT: B 515 ASP cc_start: 0.9016 (m-30) cc_final: 0.8669 (m-30) REVERT: B 598 MET cc_start: 0.8748 (mmm) cc_final: 0.7542 (mmm) REVERT: B 599 GLU cc_start: 0.8269 (pt0) cc_final: 0.7888 (pt0) REVERT: B 604 ARG cc_start: 0.8308 (mmt-90) cc_final: 0.7908 (mmt-90) REVERT: B 610 LYS cc_start: 0.9085 (mtpp) cc_final: 0.8702 (mtpp) REVERT: B 686 ARG cc_start: 0.8444 (mtp85) cc_final: 0.7892 (mtp-110) REVERT: C 55 TYR cc_start: 0.8990 (t80) cc_final: 0.8399 (t80) REVERT: C 66 ASP cc_start: 0.9019 (OUTLIER) cc_final: 0.8615 (t70) REVERT: C 86 ARG cc_start: 0.8729 (mtt180) cc_final: 0.8356 (mpt180) REVERT: C 137 MET cc_start: 0.9448 (tpp) cc_final: 0.9090 (tpt) REVERT: C 147 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7809 (ptmm) REVERT: C 174 TYR cc_start: 0.9009 (OUTLIER) cc_final: 0.7572 (t80) REVERT: C 178 PHE cc_start: 0.8813 (t80) cc_final: 0.8340 (t80) REVERT: C 179 TYR cc_start: 0.9079 (t80) cc_final: 0.8756 (t80) REVERT: C 237 GLU cc_start: 0.9442 (pt0) cc_final: 0.9065 (pp20) REVERT: C 242 TYR cc_start: 0.9433 (t80) cc_final: 0.8940 (t80) REVERT: C 268 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8352 (mp) REVERT: C 269 MET cc_start: 0.9524 (tmm) cc_final: 0.9122 (mmp) REVERT: D 20 MET cc_start: 0.8859 (ttt) cc_final: 0.8545 (ppp) REVERT: D 40 ASP cc_start: 0.8647 (m-30) cc_final: 0.7951 (t0) REVERT: D 74 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7830 (tpt) REVERT: D 109 PHE cc_start: 0.8655 (m-80) cc_final: 0.8221 (m-80) REVERT: D 137 MET cc_start: 0.9586 (mtt) cc_final: 0.9322 (mtp) REVERT: D 231 LEU cc_start: 0.9513 (mm) cc_final: 0.9216 (mm) REVERT: D 246 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8109 (mt) REVERT: D 259 PHE cc_start: 0.8648 (t80) cc_final: 0.8012 (t80) REVERT: D 270 ASN cc_start: 0.8583 (m110) cc_final: 0.8382 (m110) outliers start: 63 outliers final: 43 residues processed: 708 average time/residue: 0.1081 time to fit residues: 116.7414 Evaluate side-chains 710 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 654 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 314 MET 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 611 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 149 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 645 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.120093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.089008 restraints weight = 37395.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.092231 restraints weight = 18129.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.094385 restraints weight = 10912.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.095854 restraints weight = 7570.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.096860 restraints weight = 5744.601| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.7504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16386 Z= 0.193 Angle : 0.822 13.967 22134 Z= 0.419 Chirality : 0.049 0.226 2360 Planarity : 0.004 0.054 2818 Dihedral : 8.628 138.460 2291 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.02 % Allowed : 34.32 % Favored : 61.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.19), residues: 1932 helix: 0.64 (0.15), residues: 1135 sheet: -0.80 (0.38), residues: 160 loop : 0.05 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 261 TYR 0.038 0.002 TYR D 142 PHE 0.058 0.002 PHE C 109 TRP 0.045 0.003 TRP D 30 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (16386) covalent geometry : angle 0.82177 / 0.42 (22134) hydrogen bonds : bond 0.04445 / 2.83 ( 871) hydrogen bonds : angle 5.48058 / 3.90 ( 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 724 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 655 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: A 12 LEU cc_start: 0.9551 (mt) cc_final: 0.9326 (mt) REVERT: A 56 ASP cc_start: 0.9109 (m-30) cc_final: 0.8802 (m-30) REVERT: A 123 SER cc_start: 0.9565 (OUTLIER) cc_final: 0.9137 (p) REVERT: A 150 GLN cc_start: 0.9353 (tp40) cc_final: 0.9084 (tp-100) REVERT: A 178 SER cc_start: 0.8560 (OUTLIER) cc_final: 0.8330 (t) REVERT: A 190 MET cc_start: 0.9250 (mtp) cc_final: 0.9030 (mtp) REVERT: A 220 THR cc_start: 0.9437 (m) cc_final: 0.9110 (p) REVERT: A 232 ASN cc_start: 0.9539 (m-40) cc_final: 0.9169 (m110) REVERT: A 243 ARG cc_start: 0.7752 (ptm-80) cc_final: 0.7485 (ppt170) REVERT: A 290 GLU cc_start: 0.9212 (tt0) cc_final: 0.8819 (tm-30) REVERT: A 335 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8063 (mt-10) REVERT: A 362 ASP cc_start: 0.8161 (m-30) cc_final: 0.7915 (m-30) REVERT: A 381 LEU cc_start: 0.9534 (tp) cc_final: 0.9207 (tp) REVERT: A 384 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.7745 (pm20) REVERT: A 406 ASP cc_start: 0.8152 (m-30) cc_final: 0.7941 (t0) REVERT: A 456 LYS cc_start: 0.9157 (mtmm) cc_final: 0.8776 (mtmm) REVERT: A 459 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.9050 (mtmm) REVERT: A 493 MET cc_start: 0.8930 (tmm) cc_final: 0.8582 (tmm) REVERT: A 498 TYR cc_start: 0.8869 (m-80) cc_final: 0.8601 (m-80) REVERT: A 515 ASP cc_start: 0.9064 (m-30) cc_final: 0.8808 (m-30) REVERT: A 588 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8660 (mm-40) REVERT: A 599 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8050 (pt0) REVERT: A 639 ASP cc_start: 0.8747 (m-30) cc_final: 0.8167 (m-30) REVERT: A 640 MET cc_start: 0.9489 (OUTLIER) cc_final: 0.8643 (tpp) REVERT: A 645 GLN cc_start: 0.9415 (tp40) cc_final: 0.8997 (tp-100) REVERT: A 684 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.7467 (m-10) REVERT: B 82 LYS cc_start: 0.9579 (mmmm) cc_final: 0.9266 (mmtt) REVERT: B 112 LYS cc_start: 0.9511 (mmmt) cc_final: 0.9209 (mmmt) REVERT: B 172 LEU cc_start: 0.9499 (mp) cc_final: 0.9276 (mp) REVERT: B 178 SER cc_start: 0.8684 (p) cc_final: 0.8463 (m) REVERT: B 232 ASN cc_start: 0.9254 (OUTLIER) cc_final: 0.8836 (t0) REVERT: B 235 ARG cc_start: 0.9046 (mtm110) cc_final: 0.8781 (ttp-110) REVERT: B 263 ASP cc_start: 0.8930 (m-30) cc_final: 0.8442 (m-30) REVERT: B 290 GLU cc_start: 0.8380 (tp30) cc_final: 0.8026 (tp30) REVERT: B 350 ARG cc_start: 0.9182 (mtp85) cc_final: 0.8800 (mmm-85) REVERT: B 352 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8076 (mm-30) REVERT: B 375 LYS cc_start: 0.9306 (mtpp) cc_final: 0.8956 (mtpp) REVERT: B 423 LYS cc_start: 0.9589 (mtmm) cc_final: 0.9293 (mtpp) REVERT: B 434 ASP cc_start: 0.8666 (m-30) cc_final: 0.8371 (m-30) REVERT: B 446 ARG cc_start: 0.8227 (mmm-85) cc_final: 0.7748 (mmm-85) REVERT: B 458 MET cc_start: 0.9123 (mmm) cc_final: 0.8824 (mmp) REVERT: B 493 MET cc_start: 0.9522 (tmm) cc_final: 0.9171 (tmm) REVERT: B 515 ASP cc_start: 0.8984 (m-30) cc_final: 0.8682 (m-30) REVERT: B 599 GLU cc_start: 0.8357 (pt0) cc_final: 0.8045 (pt0) REVERT: B 610 LYS cc_start: 0.9015 (mtpp) cc_final: 0.8641 (mtpp) REVERT: B 632 MET cc_start: 0.8804 (mmm) cc_final: 0.8142 (mmm) REVERT: C 55 TYR cc_start: 0.8951 (t80) cc_final: 0.8335 (t80) REVERT: C 74 MET cc_start: 0.9139 (ptp) cc_final: 0.8775 (pmm) REVERT: C 81 VAL cc_start: 0.8528 (OUTLIER) cc_final: 0.8327 (t) REVERT: C 86 ARG cc_start: 0.8762 (mtt180) cc_final: 0.8390 (mpt180) REVERT: C 96 MET cc_start: 0.8596 (mmt) cc_final: 0.7935 (mmt) REVERT: C 122 PHE cc_start: 0.8776 (m-80) cc_final: 0.8382 (m-80) REVERT: C 147 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7841 (ptmm) REVERT: C 174 TYR cc_start: 0.8999 (OUTLIER) cc_final: 0.7563 (t80) REVERT: C 178 PHE cc_start: 0.8807 (t80) cc_final: 0.8397 (t80) REVERT: C 179 TYR cc_start: 0.9115 (t80) cc_final: 0.8790 (t80) REVERT: C 239 GLU cc_start: 0.9348 (tp30) cc_final: 0.8984 (mt-10) REVERT: C 242 TYR cc_start: 0.9443 (t80) cc_final: 0.8967 (t80) REVERT: C 268 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8518 (mt) REVERT: C 269 MET cc_start: 0.9501 (tmm) cc_final: 0.9150 (mmp) REVERT: D 20 MET cc_start: 0.8949 (ttt) cc_final: 0.8647 (ppp) REVERT: D 40 ASP cc_start: 0.8644 (m-30) cc_final: 0.7944 (t0) REVERT: D 47 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7460 (mt) REVERT: D 74 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7920 (tpt) REVERT: D 109 PHE cc_start: 0.8653 (m-80) cc_final: 0.8141 (m-80) REVERT: D 124 TRP cc_start: 0.8851 (OUTLIER) cc_final: 0.8466 (p-90) REVERT: D 137 MET cc_start: 0.9591 (mtt) cc_final: 0.9332 (mtp) REVERT: D 169 TYR cc_start: 0.8768 (m-80) cc_final: 0.8214 (m-80) REVERT: D 259 PHE cc_start: 0.8637 (t80) cc_final: 0.8116 (t80) outliers start: 69 outliers final: 51 residues processed: 682 average time/residue: 0.1136 time to fit residues: 118.2451 Evaluate side-chains 700 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 635 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 123 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 124 TRP Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 189 optimal weight: 10.0000 chunk 181 optimal weight: 7.9990 chunk 165 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 54 optimal weight: 0.1980 chunk 132 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 232 ASN B 255 HIS ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.126429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.094882 restraints weight = 37338.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.098330 restraints weight = 17491.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.100371 restraints weight = 10395.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.101963 restraints weight = 7326.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.103027 restraints weight = 5577.724| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.7715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16386 Z= 0.165 Angle : 0.861 14.347 22134 Z= 0.433 Chirality : 0.050 0.307 2360 Planarity : 0.004 0.054 2818 Dihedral : 8.439 137.682 2291 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.85 % Allowed : 35.02 % Favored : 61.13 % 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: 0.16 (0.18), residues: 1932 helix: 0.52 (0.15), residues: 1130 sheet: -0.86 (0.38), residues: 160 loop : -0.12 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 225 TYR 0.040 0.002 TYR D 142 PHE 0.062 0.002 PHE C 109 TRP 0.049 0.002 TRP D 30 HIS 0.006 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (16386) covalent geometry : angle 0.86094 / 0.43 (22134) hydrogen bonds : bond 0.04635 / 2.94 ( 871) hydrogen bonds : angle 5.53101 / 3.94 ( 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 735 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 669 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.9042 (tp) cc_final: 0.8759 (mp) REVERT: A 56 ASP cc_start: 0.9137 (m-30) cc_final: 0.8810 (m-30) REVERT: A 123 SER cc_start: 0.9563 (OUTLIER) cc_final: 0.8965 (p) REVERT: A 139 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8670 (mt-10) REVERT: A 220 THR cc_start: 0.9436 (m) cc_final: 0.9116 (p) REVERT: A 232 ASN cc_start: 0.9575 (m-40) cc_final: 0.9049 (m110) REVERT: A 290 GLU cc_start: 0.9247 (tt0) cc_final: 0.8767 (tm-30) REVERT: A 335 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8212 (mt-10) REVERT: A 381 LEU cc_start: 0.9489 (tp) cc_final: 0.9169 (tp) REVERT: A 384 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.7783 (pm20) REVERT: A 406 ASP cc_start: 0.8119 (m-30) cc_final: 0.7754 (t0) REVERT: A 456 LYS cc_start: 0.9149 (mtmm) cc_final: 0.8709 (mtmm) REVERT: A 459 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.8969 (mtmm) REVERT: A 493 MET cc_start: 0.8935 (tmm) cc_final: 0.8573 (tmm) REVERT: A 498 TYR cc_start: 0.8875 (m-80) cc_final: 0.8586 (m-80) REVERT: A 515 ASP cc_start: 0.9055 (m-30) cc_final: 0.8771 (m-30) REVERT: A 588 GLN cc_start: 0.9075 (mm-40) cc_final: 0.8772 (mm-40) REVERT: A 599 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8174 (pt0) REVERT: A 636 LYS cc_start: 0.9178 (mmmt) cc_final: 0.8976 (mmmm) REVERT: A 639 ASP cc_start: 0.8619 (m-30) cc_final: 0.8211 (m-30) REVERT: A 645 GLN cc_start: 0.9446 (tp40) cc_final: 0.9045 (tp-100) REVERT: A 684 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.7593 (m-10) REVERT: B 82 LYS cc_start: 0.9569 (mmmm) cc_final: 0.9274 (mmtm) REVERT: B 112 LYS cc_start: 0.9474 (mmmt) cc_final: 0.9167 (mmmt) REVERT: B 172 LEU cc_start: 0.9380 (mp) cc_final: 0.9155 (mp) REVERT: B 213 ILE cc_start: 0.9373 (mp) cc_final: 0.9144 (mt) REVERT: B 263 ASP cc_start: 0.8996 (m-30) cc_final: 0.8519 (m-30) REVERT: B 290 GLU cc_start: 0.8341 (tp30) cc_final: 0.7982 (tp30) REVERT: B 321 GLU cc_start: 0.8398 (pp20) cc_final: 0.8126 (pp20) REVERT: B 322 MET cc_start: 0.9409 (tpp) cc_final: 0.9170 (mmt) REVERT: B 350 ARG cc_start: 0.9184 (mtp85) cc_final: 0.8807 (mmm-85) REVERT: B 352 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8085 (mm-30) REVERT: B 375 LYS cc_start: 0.9238 (mtpp) cc_final: 0.8897 (mtpp) REVERT: B 423 LYS cc_start: 0.9601 (mtmm) cc_final: 0.9277 (mtpp) REVERT: B 434 ASP cc_start: 0.8657 (m-30) cc_final: 0.8378 (m-30) REVERT: B 458 MET cc_start: 0.9045 (mmm) cc_final: 0.8742 (mmp) REVERT: B 493 MET cc_start: 0.9518 (tmm) cc_final: 0.9193 (tmm) REVERT: B 515 ASP cc_start: 0.8985 (m-30) cc_final: 0.8692 (m-30) REVERT: B 599 GLU cc_start: 0.8373 (pt0) cc_final: 0.7977 (pt0) REVERT: B 610 LYS cc_start: 0.9017 (mtpp) cc_final: 0.8635 (mtpp) REVERT: C 74 MET cc_start: 0.9239 (ptp) cc_final: 0.8878 (pmm) REVERT: C 86 ARG cc_start: 0.8799 (mtt180) cc_final: 0.8424 (mpt180) REVERT: C 96 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8036 (mmt) REVERT: C 122 PHE cc_start: 0.8750 (m-80) cc_final: 0.8372 (m-80) REVERT: C 147 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7807 (ptmm) REVERT: C 174 TYR cc_start: 0.9010 (OUTLIER) cc_final: 0.7853 (t80) REVERT: C 237 GLU cc_start: 0.9427 (pt0) cc_final: 0.9138 (pp20) REVERT: C 239 GLU cc_start: 0.9365 (tp30) cc_final: 0.8942 (mt-10) REVERT: C 242 TYR cc_start: 0.9453 (t80) cc_final: 0.9028 (t80) REVERT: C 268 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8425 (mt) REVERT: C 269 MET cc_start: 0.9497 (tmm) cc_final: 0.9143 (mmp) REVERT: D 20 MET cc_start: 0.8932 (ttt) cc_final: 0.8702 (ppp) REVERT: D 109 PHE cc_start: 0.8629 (m-80) cc_final: 0.8133 (m-80) REVERT: D 124 TRP cc_start: 0.8871 (OUTLIER) cc_final: 0.8557 (p-90) REVERT: D 137 MET cc_start: 0.9594 (mtt) cc_final: 0.9337 (mtp) REVERT: D 169 TYR cc_start: 0.8749 (m-80) cc_final: 0.8289 (m-80) REVERT: D 236 TYR cc_start: 0.8870 (t80) cc_final: 0.8474 (t80) REVERT: D 259 PHE cc_start: 0.8601 (t80) cc_final: 0.8069 (t80) outliers start: 66 outliers final: 39 residues processed: 692 average time/residue: 0.1146 time to fit residues: 120.8404 Evaluate side-chains 694 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 646 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 124 TRP Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 0.0670 chunk 25 optimal weight: 4.9990 chunk 148 optimal weight: 9.9990 chunk 125 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.124899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.093367 restraints weight = 37147.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.096763 restraints weight = 17643.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.098982 restraints weight = 10562.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.100508 restraints weight = 7259.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.101068 restraints weight = 5526.360| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (14 function evaluations) r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.7768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.414 16386 Z= 0.336 Angle : 1.041 65.876 22134 Z= 0.577 Chirality : 0.053 0.752 2360 Planarity : 0.007 0.299 2818 Dihedral : 8.439 137.682 2291 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 30.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.73 % Allowed : 35.14 % Favored : 61.13 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.18), residues: 1932 helix: 0.52 (0.15), residues: 1130 sheet: -0.88 (0.38), residues: 160 loop : -0.13 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 225 TYR 0.100 0.002 TYR D 162 PHE 0.060 0.003 PHE C 109 TRP 0.039 0.002 TRP D 30 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00708 / 0.34 (16386) covalent geometry : angle 1.04110 / 0.58 (22134) hydrogen bonds : bond 0.04661 / 2.96 ( 871) hydrogen bonds : angle 5.54006 / 3.94 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3360.70 seconds wall clock time: 59 minutes 7.05 seconds (3547.05 seconds total)