Starting phenix.real_space_refine on Sat May 17 16:29:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz6_45054/05_2025/9bz6_45054_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz6_45054/05_2025/9bz6_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bz6_45054/05_2025/9bz6_45054.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz6_45054/05_2025/9bz6_45054.map" model { file = "/net/cci-nas-00/data/ceres_data/9bz6_45054/05_2025/9bz6_45054_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz6_45054/05_2025/9bz6_45054_neut.cif" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 8.95, per 1000 atoms: 0.56 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: 3.66 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.53 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: 4.67 Time building geometry restraints manager: 4.30 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=" 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=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.579 -0.039 1.20e-02 6.94e+03 1.07e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.033 1.08e-02 8.57e+03 9.10e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.570 -0.032 1.17e-02 7.31e+03 7.72e+00 bond pdb=" CA ILE C 35 " pdb=" CB ILE C 35 " ideal model delta sigma weight residual 1.537 1.568 -0.031 1.21e-02 6.83e+03 6.66e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21579 2.09 - 4.19: 512 4.19 - 6.28: 36 6.28 - 8.37: 3 8.37 - 10.46: 4 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.61 -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 - 35.79: 9471 35.79 - 71.59: 336 71.59 - 107.38: 37 107.38 - 143.17: 3 143.17 - 178.96: 3 Dihedral angle restraints: 9850 sinusoidal: 4092 harmonic: 5758 Sorted by residual: dihedral pdb=" C2 TTP A 803 " pdb=" C1' TTP A 803 " pdb=" N1 TTP A 803 " pdb=" O4' TTP A 803 " ideal model delta sinusoidal sigma weight residual -58.32 120.65 -178.96 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 TTP B 801 " pdb=" C1' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " ideal model delta sinusoidal sigma weight residual 301.68 151.18 150.50 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" C5' TTP A 803 " pdb=" O5' TTP A 803 " pdb=" PA TTP A 803 " pdb=" O3A TTP A 803 " ideal model delta sinusoidal sigma weight residual 179.97 31.90 148.07 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 9847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2147 0.093 - 0.187: 181 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 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 33.650 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.070 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 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 0.061 16386 Z= 0.316 Angle : 0.740 10.463 22134 Z= 0.463 Chirality : 0.058 0.467 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.907 178.963 6154 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.25 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 PHE 0.021 0.002 PHE C 168 TYR 0.020 0.002 TYR D 179 ARG 0.004 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.15421 ( 871) hydrogen bonds : angle 6.51761 ( 2571) covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.74027 (22134) *********************** 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 : 1.816 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: symmetry clash REVERT: A 12 LEU cc_start: 0.8399 (mt) cc_final: 0.7104 (mp) REVERT: A 76 ASP cc_start: 0.8141 (m-30) cc_final: 0.7766 (m-30) REVERT: A 172 LEU cc_start: 0.9016 (mp) cc_final: 0.8788 (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: 0.8689 (tp) REVERT: A 267 ILE cc_start: 0.8497 (mp) cc_final: 0.7415 (mm) REVERT: A 345 LYS cc_start: 0.8631 (tttt) cc_final: 0.8415 (ttmm) REVERT: A 378 PHE cc_start: 0.8737 (p90) cc_final: 0.8536 (p90) REVERT: A 447 ASN cc_start: 0.7436 (m-40) cc_final: 0.6725 (m110) REVERT: A 501 GLN cc_start: 0.8009 (tt0) cc_final: 0.7769 (tt0) REVERT: A 550 MET cc_start: 0.7374 (mtm) cc_final: 0.7101 (mtm) REVERT: A 597 ILE cc_start: 0.8819 (pt) cc_final: 0.8576 (pt) REVERT: A 618 LEU cc_start: 0.9315 (tp) cc_final: 0.9088 (tt) REVERT: A 624 PHE cc_start: 0.6889 (t80) cc_final: 0.6471 (t80) REVERT: A 630 TYR cc_start: 0.7985 (m-80) cc_final: 0.7430 (m-80) REVERT: B 11 GLN cc_start: 0.7869 (mt0) cc_final: 0.7579 (mt0) REVERT: B 27 ASP cc_start: 0.8050 (p0) cc_final: 0.7834 (p0) REVERT: B 157 LEU cc_start: 0.8567 (tp) cc_final: 0.8316 (tp) REVERT: B 177 ASP cc_start: 0.8070 (t0) cc_final: 0.7382 (t0) REVERT: B 204 SER cc_start: 0.8823 (m) cc_final: 0.8303 (t) REVERT: B 288 PHE cc_start: 0.8348 (t80) cc_final: 0.7486 (t80) REVERT: B 294 GLU cc_start: 0.6937 (mt-10) cc_final: 0.5196 (mt-10) REVERT: B 295 ASP cc_start: 0.7755 (t0) cc_final: 0.7381 (t0) REVERT: B 366 LYS cc_start: 0.8551 (ptpp) cc_final: 0.8319 (ptmt) REVERT: B 376 VAL cc_start: 0.9423 (t) cc_final: 0.9144 (m) REVERT: B 384 GLU cc_start: 0.8925 (pm20) cc_final: 0.8240 (pm20) REVERT: B 387 GLN cc_start: 0.7499 (mt0) cc_final: 0.7025 (mt0) REVERT: B 435 SER cc_start: 0.9153 (p) cc_final: 0.8886 (p) REVERT: B 480 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6881 (mt-10) REVERT: B 543 ILE cc_start: 0.8870 (mm) cc_final: 0.8652 (mm) REVERT: B 550 MET cc_start: 0.7979 (mtm) cc_final: 0.7714 (mtp) REVERT: B 597 ILE cc_start: 0.9119 (pt) cc_final: 0.8870 (pt) REVERT: B 640 MET cc_start: 0.7348 (tpp) cc_final: 0.7141 (tpp) REVERT: C 24 GLN cc_start: 0.6658 (tp40) cc_final: 0.6399 (tp40) REVERT: C 112 LEU cc_start: 0.3589 (mt) cc_final: 0.3254 (mt) REVERT: C 118 ILE cc_start: 0.6611 (mt) cc_final: 0.6382 (mt) REVERT: C 163 LEU cc_start: 0.6487 (tt) cc_final: 0.6147 (tt) REVERT: D 80 HIS cc_start: 0.7053 (m-70) cc_final: 0.6702 (m170) REVERT: D 104 SER cc_start: 0.7255 (m) cc_final: 0.6977 (m) REVERT: D 119 ASN cc_start: 0.5381 (m-40) cc_final: 0.5115 (m-40) REVERT: D 125 VAL cc_start: 0.6417 (t) cc_final: 0.6118 (p) REVERT: D 131 LEU cc_start: 0.5783 (tp) cc_final: 0.5216 (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: 0.2911 time to fit residues: 453.3878 Evaluate side-chains 745 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 738 time to evaluate : 1.727 ------------------------------------------------------------------------------- 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 162 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 320 ASN B 329 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN B 676 HIS C 24 GLN C 28 GLN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN D 28 GLN D 71 ASN D 80 HIS D 181 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.128288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.093661 restraints weight = 35950.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.097300 restraints weight = 17399.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.099756 restraints weight = 10418.009| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16386 Z= 0.202 Angle : 0.721 11.393 22134 Z= 0.377 Chirality : 0.046 0.227 2360 Planarity : 0.004 0.041 2818 Dihedral : 11.504 174.969 2253 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.37 % Allowed : 21.21 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.19), residues: 1932 helix: 1.24 (0.15), residues: 1136 sheet: 0.13 (0.43), residues: 126 loop : 0.50 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 30 HIS 0.011 0.001 HIS C 201 PHE 0.038 0.003 PHE D 172 TYR 0.057 0.002 TYR D 262 ARG 0.008 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.05066 ( 871) hydrogen bonds : angle 5.34887 ( 2571) covalent geometry : bond 0.00449 (16386) covalent geometry : angle 0.72064 (22134) *********************** 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 855 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 780 time to evaluate : 1.783 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: symmetry clash REVERT: A 39 ASP cc_start: 0.8964 (m-30) cc_final: 0.8650 (m-30) REVERT: A 76 ASP cc_start: 0.9180 (m-30) cc_final: 0.8866 (m-30) REVERT: A 174 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8292 (mm-30) REVERT: A 191 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8599 (mm-40) REVERT: A 221 LYS cc_start: 0.9331 (mmtp) cc_final: 0.9002 (mttp) REVERT: A 290 GLU cc_start: 0.9354 (tt0) cc_final: 0.9045 (tm-30) REVERT: A 335 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8063 (mt-10) REVERT: A 375 LYS cc_start: 0.8598 (mttt) cc_final: 0.8358 (mmmm) REVERT: A 415 ASN cc_start: 0.9311 (t0) cc_final: 0.8903 (t0) REVERT: A 447 ASN cc_start: 0.8506 (m-40) cc_final: 0.8025 (m-40) REVERT: A 561 LEU cc_start: 0.9201 (tp) cc_final: 0.8905 (tp) REVERT: A 588 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8695 (mm-40) REVERT: A 618 LEU cc_start: 0.9509 (tp) cc_final: 0.9193 (tt) REVERT: A 639 ASP cc_start: 0.8556 (m-30) cc_final: 0.8196 (m-30) REVERT: A 663 THR cc_start: 0.9476 (OUTLIER) cc_final: 0.9255 (t) REVERT: A 668 ASN cc_start: 0.9489 (m-40) cc_final: 0.9185 (m-40) REVERT: A 684 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.7403 (m-10) REVERT: B 12 LEU cc_start: 0.9309 (mt) cc_final: 0.9094 (mp) REVERT: B 15 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8315 (mt-10) REVERT: B 87 LYS cc_start: 0.9354 (tptm) cc_final: 0.9080 (tppt) REVERT: B 172 LEU cc_start: 0.9287 (mp) cc_final: 0.8944 (mp) REVERT: B 181 ASP cc_start: 0.8844 (m-30) cc_final: 0.8597 (m-30) REVERT: B 211 GLU cc_start: 0.8625 (mm-30) cc_final: 0.7967 (mm-30) REVERT: B 288 PHE cc_start: 0.9325 (t80) cc_final: 0.8952 (t80) REVERT: B 290 GLU cc_start: 0.8106 (tp30) cc_final: 0.7875 (tp30) REVERT: B 350 ARG cc_start: 0.8669 (mtp85) cc_final: 0.7725 (mtp85) REVERT: B 352 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8352 (mm-30) REVERT: B 355 TYR cc_start: 0.8307 (m-80) cc_final: 0.7668 (m-80) REVERT: B 361 GLN cc_start: 0.9093 (tt0) cc_final: 0.8501 (tt0) REVERT: B 374 SER cc_start: 0.9064 (t) cc_final: 0.8461 (p) REVERT: B 375 LYS cc_start: 0.9003 (mmmm) cc_final: 0.8415 (mmmm) REVERT: B 378 PHE cc_start: 0.9361 (p90) cc_final: 0.9076 (p90) REVERT: B 399 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8717 (tp30) REVERT: B 415 ASN cc_start: 0.9458 (t0) cc_final: 0.9251 (t0) REVERT: B 425 ILE cc_start: 0.9470 (mt) cc_final: 0.9233 (mt) REVERT: B 458 MET cc_start: 0.9468 (mmm) cc_final: 0.9188 (mmp) REVERT: B 493 MET cc_start: 0.9671 (tmm) cc_final: 0.9287 (tmm) REVERT: B 515 ASP cc_start: 0.9141 (m-30) cc_final: 0.8796 (m-30) REVERT: B 543 ILE cc_start: 0.9515 (mm) cc_final: 0.9207 (mm) REVERT: B 550 MET cc_start: 0.8019 (mtm) cc_final: 0.7700 (mtm) REVERT: B 558 TRP cc_start: 0.9549 (m100) cc_final: 0.8610 (m100) REVERT: B 588 GLN cc_start: 0.9228 (mm-40) cc_final: 0.8952 (mm-40) REVERT: B 599 GLU cc_start: 0.8521 (pt0) cc_final: 0.8278 (pt0) REVERT: B 604 ARG cc_start: 0.8320 (mmp80) cc_final: 0.8049 (mmt-90) REVERT: B 640 MET cc_start: 0.9349 (tpp) cc_final: 0.8908 (tpp) REVERT: B 672 LEU cc_start: 0.9605 (mt) cc_final: 0.9382 (mt) REVERT: B 686 ARG cc_start: 0.8382 (mtp85) cc_final: 0.8001 (mtp85) REVERT: C 56 MET cc_start: 0.8551 (ttm) cc_final: 0.8350 (ttt) REVERT: C 86 ARG cc_start: 0.8421 (mtt180) cc_final: 0.7921 (mpt180) REVERT: C 96 MET cc_start: 0.8501 (mmm) cc_final: 0.8278 (mmm) REVERT: C 109 PHE cc_start: 0.8788 (m-80) cc_final: 0.8559 (m-80) REVERT: C 116 GLU cc_start: 0.9190 (pm20) cc_final: 0.8869 (pm20) REVERT: C 118 ILE cc_start: 0.9824 (mt) cc_final: 0.9605 (mm) REVERT: C 120 GLU cc_start: 0.9377 (tm-30) cc_final: 0.9139 (pt0) REVERT: C 122 PHE cc_start: 0.8899 (m-80) cc_final: 0.8504 (m-80) REVERT: C 137 MET cc_start: 0.9092 (tpp) cc_final: 0.8839 (tpp) REVERT: C 157 MET cc_start: 0.9005 (mtt) cc_final: 0.8555 (mtt) REVERT: C 163 LEU cc_start: 0.9462 (tt) cc_final: 0.9105 (tt) REVERT: C 185 MET cc_start: 0.7956 (mmm) cc_final: 0.7546 (mmm) REVERT: C 268 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9304 (mt) REVERT: C 269 MET cc_start: 0.9484 (tmm) cc_final: 0.9203 (tmm) REVERT: C 271 LEU cc_start: 0.9379 (mt) cc_final: 0.9071 (mt) REVERT: C 320 PHE cc_start: 0.8662 (m-80) cc_final: 0.8400 (m-80) REVERT: D 18 THR cc_start: 0.9037 (p) cc_final: 0.8316 (m) REVERT: D 33 GLU cc_start: 0.9245 (mp0) cc_final: 0.8921 (pp20) REVERT: D 109 PHE cc_start: 0.8558 (m-80) cc_final: 0.8286 (m-80) REVERT: D 131 LEU cc_start: 0.7595 (tp) cc_final: 0.7268 (tt) REVERT: D 137 MET cc_start: 0.9228 (mtt) cc_final: 0.8978 (mtp) REVERT: D 178 PHE cc_start: 0.8938 (m-80) cc_final: 0.8641 (m-80) REVERT: D 184 LEU cc_start: 0.8696 (mt) cc_final: 0.8377 (mt) REVERT: D 224 LEU cc_start: 0.8795 (mt) cc_final: 0.8439 (mt) REVERT: D 233 ASN cc_start: 0.9053 (m110) cc_final: 0.8819 (p0) REVERT: D 242 TYR cc_start: 0.8418 (t80) cc_final: 0.7906 (t80) REVERT: D 259 PHE cc_start: 0.8325 (t80) cc_final: 0.7419 (t80) REVERT: D 262 TYR cc_start: 0.9002 (t80) cc_final: 0.8750 (t80) outliers start: 75 outliers final: 38 residues processed: 809 average time/residue: 0.2679 time to fit residues: 322.8744 Evaluate side-chains 751 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 710 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 79 GLU 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 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 663 THR 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 410 ASN 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 660 ASP Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain C residue 18 THR 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 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 153 LEU Chi-restraints excluded: chain D residue 174 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 2.9990 chunk 168 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 191 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 171 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 chunk 141 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS A 438 HIS ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN C 263 ASN D 28 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.123864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.091179 restraints weight = 37103.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.094796 restraints weight = 17400.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.097237 restraints weight = 10300.635| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16386 Z= 0.194 Angle : 0.698 15.232 22134 Z= 0.359 Chirality : 0.046 0.175 2360 Planarity : 0.004 0.037 2818 Dihedral : 11.313 173.480 2249 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.20 % Allowed : 23.43 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.19), residues: 1932 helix: 1.19 (0.15), residues: 1146 sheet: -0.23 (0.40), residues: 144 loop : 0.43 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 30 HIS 0.006 0.001 HIS C 201 PHE 0.053 0.003 PHE C 168 TYR 0.044 0.002 TYR D 262 ARG 0.007 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.04450 ( 871) hydrogen bonds : angle 5.33686 ( 2571) covalent geometry : bond 0.00432 (16386) covalent geometry : angle 0.69788 (22134) *********************** 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 834 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 762 time to evaluate : 1.724 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 12 LEU cc_start: 0.9444 (mt) cc_final: 0.9039 (mt) REVERT: A 15 GLU cc_start: 0.8889 (tp30) cc_final: 0.8446 (tp30) REVERT: A 51 LEU cc_start: 0.9398 (tp) cc_final: 0.9118 (tp) REVERT: A 150 GLN cc_start: 0.9178 (tp40) cc_final: 0.8776 (tp40) REVERT: A 163 ARG cc_start: 0.8110 (tpp80) cc_final: 0.7722 (mmm-85) REVERT: A 220 THR cc_start: 0.9405 (m) cc_final: 0.9042 (p) REVERT: A 221 LYS cc_start: 0.9330 (mmtp) cc_final: 0.8987 (mttp) REVERT: A 290 GLU cc_start: 0.9312 (tt0) cc_final: 0.8936 (tm-30) REVERT: A 312 GLN cc_start: 0.8407 (mp10) cc_final: 0.8200 (mp10) REVERT: A 335 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8124 (mt-10) REVERT: A 386 LEU cc_start: 0.9343 (mt) cc_final: 0.9127 (mt) REVERT: A 390 GLN cc_start: 0.8820 (mt0) cc_final: 0.8394 (mt0) REVERT: A 393 SER cc_start: 0.9608 (m) cc_final: 0.9380 (t) REVERT: A 415 ASN cc_start: 0.9189 (t0) cc_final: 0.8927 (t0) REVERT: A 444 ASP cc_start: 0.8624 (t0) cc_final: 0.7433 (t0) REVERT: A 446 ARG cc_start: 0.7492 (mtp85) cc_final: 0.7084 (mmm160) REVERT: A 447 ASN cc_start: 0.8488 (m-40) cc_final: 0.7764 (m-40) REVERT: A 453 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.8339 (ttp80) REVERT: A 459 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.8927 (mtmm) REVERT: A 512 GLU cc_start: 0.8447 (pt0) cc_final: 0.8226 (pm20) REVERT: A 515 ASP cc_start: 0.9097 (m-30) cc_final: 0.8846 (m-30) REVERT: A 558 TRP cc_start: 0.9361 (m100) cc_final: 0.8973 (m100) REVERT: A 588 GLN cc_start: 0.8953 (mm-40) cc_final: 0.8635 (mm-40) REVERT: A 590 SER cc_start: 0.9543 (t) cc_final: 0.9017 (p) REVERT: A 639 ASP cc_start: 0.8719 (m-30) cc_final: 0.8268 (m-30) REVERT: A 640 MET cc_start: 0.9489 (OUTLIER) cc_final: 0.8553 (tpp) REVERT: A 654 PHE cc_start: 0.9408 (t80) cc_final: 0.8865 (t80) REVERT: A 663 THR cc_start: 0.9585 (OUTLIER) cc_final: 0.9371 (t) REVERT: A 668 ASN cc_start: 0.9529 (m-40) cc_final: 0.9277 (m-40) REVERT: A 683 TYR cc_start: 0.8806 (t80) cc_final: 0.8511 (t80) REVERT: A 684 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.7351 (m-10) REVERT: B 99 LYS cc_start: 0.9160 (mmtt) cc_final: 0.8611 (mmmm) REVERT: B 109 ASN cc_start: 0.9321 (m-40) cc_final: 0.9053 (m-40) REVERT: B 172 LEU cc_start: 0.9427 (mp) cc_final: 0.9125 (mp) REVERT: B 235 ARG cc_start: 0.8847 (mtm110) cc_final: 0.8488 (mtm110) REVERT: B 257 ASP cc_start: 0.8984 (m-30) cc_final: 0.8722 (m-30) REVERT: B 288 PHE cc_start: 0.9280 (t80) cc_final: 0.8898 (t80) REVERT: B 344 GLU cc_start: 0.8899 (pt0) cc_final: 0.8643 (pp20) REVERT: B 355 TYR cc_start: 0.8469 (m-80) cc_final: 0.7725 (m-80) REVERT: B 361 GLN cc_start: 0.9177 (tt0) cc_final: 0.8915 (tt0) REVERT: B 374 SER cc_start: 0.9071 (t) cc_final: 0.8643 (p) REVERT: B 375 LYS cc_start: 0.9125 (mmmm) cc_final: 0.8575 (mmmm) REVERT: B 378 PHE cc_start: 0.9348 (p90) cc_final: 0.9109 (p90) REVERT: B 399 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8255 (tp30) REVERT: B 415 ASN cc_start: 0.9476 (t0) cc_final: 0.9224 (t0) REVERT: B 446 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7832 (mmm-85) REVERT: B 458 MET cc_start: 0.9331 (mmm) cc_final: 0.9047 (mmp) REVERT: B 493 MET cc_start: 0.9649 (tmm) cc_final: 0.9391 (tmm) REVERT: B 515 ASP cc_start: 0.9141 (m-30) cc_final: 0.8752 (m-30) REVERT: B 543 ILE cc_start: 0.9536 (mm) cc_final: 0.9198 (mm) REVERT: B 550 MET cc_start: 0.8297 (mtm) cc_final: 0.7878 (mtm) REVERT: B 588 GLN cc_start: 0.9353 (mm-40) cc_final: 0.8893 (mm-40) REVERT: B 595 MET cc_start: 0.8789 (mmm) cc_final: 0.7909 (mmm) REVERT: B 598 MET cc_start: 0.8641 (mtm) cc_final: 0.8106 (mtm) REVERT: B 599 GLU cc_start: 0.8562 (pt0) cc_final: 0.8345 (pt0) REVERT: B 604 ARG cc_start: 0.8614 (mmp80) cc_final: 0.8352 (mmt-90) REVERT: B 610 LYS cc_start: 0.8967 (mtpp) cc_final: 0.8682 (mtpp) REVERT: B 640 MET cc_start: 0.9329 (tpp) cc_final: 0.9013 (tpp) REVERT: B 686 ARG cc_start: 0.8486 (mtp85) cc_final: 0.7817 (mtp85) REVERT: C 66 ASP cc_start: 0.8870 (OUTLIER) cc_final: 0.8419 (t70) REVERT: C 69 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8375 (tm-30) REVERT: C 86 ARG cc_start: 0.8633 (mtt180) cc_final: 0.8183 (mpt180) REVERT: C 95 MET cc_start: 0.8590 (tmm) cc_final: 0.8158 (tmm) REVERT: C 96 MET cc_start: 0.8678 (mmm) cc_final: 0.8458 (mmm) REVERT: C 116 GLU cc_start: 0.9213 (pm20) cc_final: 0.8863 (pm20) REVERT: C 120 GLU cc_start: 0.9315 (tm-30) cc_final: 0.9041 (pt0) REVERT: C 122 PHE cc_start: 0.8891 (m-80) cc_final: 0.8462 (m-80) REVERT: C 157 MET cc_start: 0.9365 (mtt) cc_final: 0.9062 (mtt) REVERT: C 179 TYR cc_start: 0.8785 (t80) cc_final: 0.8582 (t80) REVERT: C 269 MET cc_start: 0.9521 (tmm) cc_final: 0.9236 (tmm) REVERT: C 313 GLU cc_start: 0.8964 (tt0) cc_final: 0.8662 (tp30) REVERT: C 320 PHE cc_start: 0.9040 (m-80) cc_final: 0.8722 (m-80) REVERT: D 18 THR cc_start: 0.9021 (p) cc_final: 0.8489 (m) REVERT: D 24 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8655 (mp10) REVERT: D 33 GLU cc_start: 0.9235 (mp0) cc_final: 0.8922 (pp20) REVERT: D 74 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.7069 (tpt) REVERT: D 109 PHE cc_start: 0.8533 (m-80) cc_final: 0.8113 (m-80) REVERT: D 128 ASN cc_start: 0.9084 (t0) cc_final: 0.8715 (m-40) REVERT: D 137 MET cc_start: 0.9370 (mtt) cc_final: 0.9073 (mtp) REVERT: D 178 PHE cc_start: 0.8824 (m-80) cc_final: 0.7946 (m-80) REVERT: D 184 LEU cc_start: 0.8887 (mt) cc_final: 0.8525 (mt) REVERT: D 198 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8741 (mm-30) REVERT: D 231 LEU cc_start: 0.9342 (mm) cc_final: 0.8674 (mm) outliers start: 72 outliers final: 44 residues processed: 792 average time/residue: 0.2667 time to fit residues: 315.8413 Evaluate side-chains 738 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 686 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 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 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 459 LYS 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 632 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 71 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 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 410 ASN Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 446 ARG 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 682 ILE Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 180 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 39 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 418 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 GLN C 216 GLN D 25 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.116622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.084917 restraints weight = 38180.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.088150 restraints weight = 17989.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.090302 restraints weight = 10904.729| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.6159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 16386 Z= 0.296 Angle : 0.752 10.928 22134 Z= 0.394 Chirality : 0.048 0.223 2360 Planarity : 0.004 0.059 2818 Dihedral : 10.800 164.913 2245 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 6.29 % Allowed : 24.18 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.18), residues: 1932 helix: 0.86 (0.15), residues: 1160 sheet: -0.47 (0.38), residues: 148 loop : 0.27 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 44 HIS 0.005 0.001 HIS A 438 PHE 0.048 0.003 PHE C 109 TYR 0.043 0.002 TYR D 142 ARG 0.007 0.001 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.04434 ( 871) hydrogen bonds : angle 5.44579 ( 2571) covalent geometry : bond 0.00640 (16386) covalent geometry : angle 0.75167 (22134) *********************** 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 822 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 714 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8774 (tppt) cc_final: 0.8550 (tppt) REVERT: A 51 LEU cc_start: 0.9522 (tp) cc_final: 0.9161 (tp) REVERT: A 102 ASN cc_start: 0.9257 (OUTLIER) cc_final: 0.8831 (m110) REVERT: A 163 ARG cc_start: 0.8210 (tpp80) cc_final: 0.7929 (mmm-85) REVERT: A 166 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8686 (mm-30) REVERT: A 178 SER cc_start: 0.8786 (OUTLIER) cc_final: 0.8386 (t) REVERT: A 194 LYS cc_start: 0.9504 (ttpp) cc_final: 0.9271 (ttpp) REVERT: A 232 ASN cc_start: 0.9368 (m-40) cc_final: 0.9133 (m110) REVERT: A 252 ASN cc_start: 0.9387 (t0) cc_final: 0.9136 (t0) REVERT: A 290 GLU cc_start: 0.9292 (tt0) cc_final: 0.8977 (tm-30) REVERT: A 335 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8117 (mt-10) REVERT: A 359 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8369 (ttp) REVERT: A 384 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.7726 (pm20) REVERT: A 390 GLN cc_start: 0.8882 (mt0) cc_final: 0.8535 (mt0) REVERT: A 415 ASN cc_start: 0.9087 (t0) cc_final: 0.8611 (t0) REVERT: A 418 ASN cc_start: 0.9237 (m110) cc_final: 0.8774 (m110) REVERT: A 444 ASP cc_start: 0.8661 (t0) cc_final: 0.8064 (t0) REVERT: A 446 ARG cc_start: 0.7618 (mtp85) cc_final: 0.7211 (mmm160) REVERT: A 459 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.8941 (mtmm) REVERT: A 590 SER cc_start: 0.9488 (t) cc_final: 0.9174 (p) REVERT: A 595 MET cc_start: 0.9202 (mmp) cc_final: 0.8959 (mmp) REVERT: A 598 MET cc_start: 0.8881 (tpp) cc_final: 0.8657 (mmm) REVERT: A 618 LEU cc_start: 0.9504 (tp) cc_final: 0.9253 (tt) REVERT: A 639 ASP cc_start: 0.8815 (m-30) cc_final: 0.8246 (m-30) REVERT: A 640 MET cc_start: 0.9520 (OUTLIER) cc_final: 0.8639 (tpp) REVERT: A 645 GLN cc_start: 0.9504 (tp40) cc_final: 0.9182 (tp-100) REVERT: A 668 ASN cc_start: 0.9610 (m-40) cc_final: 0.9347 (m-40) REVERT: A 672 LEU cc_start: 0.9804 (mm) cc_final: 0.9587 (mm) REVERT: A 683 TYR cc_start: 0.8949 (t80) cc_final: 0.8666 (t80) REVERT: A 684 TYR cc_start: 0.8202 (OUTLIER) cc_final: 0.7687 (m-80) REVERT: B 31 GLU cc_start: 0.8934 (mp0) cc_final: 0.8711 (mp0) REVERT: B 99 LYS cc_start: 0.9297 (mmtt) cc_final: 0.8758 (mmmm) REVERT: B 154 PRO cc_start: 0.9560 (Cg_exo) cc_final: 0.9354 (Cg_endo) REVERT: B 172 LEU cc_start: 0.9566 (mp) cc_final: 0.9325 (mp) REVERT: B 181 ASP cc_start: 0.8797 (m-30) cc_final: 0.8368 (m-30) REVERT: B 238 ASP cc_start: 0.7926 (t0) cc_final: 0.7684 (t0) REVERT: B 251 LEU cc_start: 0.9552 (tp) cc_final: 0.9335 (tp) REVERT: B 257 ASP cc_start: 0.8866 (m-30) cc_final: 0.8578 (m-30) REVERT: B 423 LYS cc_start: 0.9531 (mtmt) cc_final: 0.9239 (mmtp) REVERT: B 434 ASP cc_start: 0.8710 (m-30) cc_final: 0.8461 (m-30) REVERT: B 446 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7927 (mmm-85) REVERT: B 458 MET cc_start: 0.9351 (mmm) cc_final: 0.9031 (mmp) REVERT: B 493 MET cc_start: 0.9614 (tmm) cc_final: 0.9289 (tmm) REVERT: B 515 ASP cc_start: 0.9143 (m-30) cc_final: 0.8835 (m-30) REVERT: B 543 ILE cc_start: 0.9598 (mm) cc_final: 0.9394 (mm) REVERT: B 595 MET cc_start: 0.8989 (mmm) cc_final: 0.8320 (mmm) REVERT: B 598 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8083 (mtm) REVERT: B 599 GLU cc_start: 0.8480 (pt0) cc_final: 0.8264 (pt0) REVERT: B 602 GLU cc_start: 0.8618 (pt0) cc_final: 0.8342 (pt0) REVERT: B 631 ASP cc_start: 0.8839 (t0) cc_final: 0.8523 (t0) REVERT: B 640 MET cc_start: 0.9281 (tpp) cc_final: 0.8913 (tpp) REVERT: B 686 ARG cc_start: 0.8478 (mtp85) cc_final: 0.7811 (mtp85) REVERT: C 55 TYR cc_start: 0.9113 (t80) cc_final: 0.8727 (t80) REVERT: C 56 MET cc_start: 0.8198 (ttt) cc_final: 0.7690 (ppp) REVERT: C 66 ASP cc_start: 0.8945 (OUTLIER) cc_final: 0.8472 (t70) REVERT: C 69 GLN cc_start: 0.8478 (tm-30) cc_final: 0.8126 (tm-30) REVERT: C 86 ARG cc_start: 0.8845 (mtt180) cc_final: 0.8431 (mpt180) REVERT: C 92 PHE cc_start: 0.9115 (t80) cc_final: 0.8913 (t80) REVERT: C 95 MET cc_start: 0.8572 (tmm) cc_final: 0.8132 (tmm) REVERT: C 96 MET cc_start: 0.8724 (mmm) cc_final: 0.8492 (mmm) REVERT: C 111 THR cc_start: 0.8424 (m) cc_final: 0.8198 (p) REVERT: C 174 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.7393 (t80) REVERT: C 179 TYR cc_start: 0.8817 (t80) cc_final: 0.8525 (t80) REVERT: C 242 TYR cc_start: 0.9446 (t80) cc_final: 0.8875 (t80) REVERT: C 269 MET cc_start: 0.9618 (tmm) cc_final: 0.9356 (tmm) REVERT: C 320 PHE cc_start: 0.9152 (m-80) cc_final: 0.8696 (m-80) REVERT: D 20 MET cc_start: 0.8707 (ttt) cc_final: 0.8500 (ptm) REVERT: D 30 TRP cc_start: 0.8222 (p-90) cc_final: 0.7563 (p-90) REVERT: D 33 GLU cc_start: 0.9212 (mp0) cc_final: 0.8995 (tm-30) REVERT: D 74 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7277 (tpt) REVERT: D 109 PHE cc_start: 0.8597 (m-80) cc_final: 0.8205 (m-80) REVERT: D 123 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8829 (mp0) REVERT: D 137 MET cc_start: 0.9543 (mtt) cc_final: 0.9281 (mtp) REVERT: D 186 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8545 (mm-40) REVERT: D 196 ARG cc_start: 0.9307 (tmm-80) cc_final: 0.9067 (ttt180) REVERT: D 198 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8676 (mm-30) REVERT: D 224 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8603 (mt) REVERT: D 231 LEU cc_start: 0.9125 (mm) cc_final: 0.8902 (mm) outliers start: 108 outliers final: 74 residues processed: 756 average time/residue: 0.2618 time to fit residues: 297.5757 Evaluate side-chains 737 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 650 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 429 VAL 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 584 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 71 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 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 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 417 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 594 VAL 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 660 ASP Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 287 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 175 optimal weight: 9.9990 chunk 182 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 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 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.118304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.086464 restraints weight = 37255.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.089840 restraints weight = 17451.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.092142 restraints weight = 10360.538| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.6577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16386 Z= 0.166 Angle : 0.719 12.909 22134 Z= 0.365 Chirality : 0.046 0.201 2360 Planarity : 0.004 0.043 2818 Dihedral : 10.367 160.819 2245 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.66 % Allowed : 29.20 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.19), residues: 1932 helix: 0.89 (0.15), residues: 1154 sheet: -0.59 (0.38), residues: 150 loop : 0.28 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 124 HIS 0.005 0.001 HIS B 438 PHE 0.044 0.002 PHE D 172 TYR 0.038 0.002 TYR D 142 ARG 0.006 0.001 ARG B 164 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 871) hydrogen bonds : angle 5.28487 ( 2571) covalent geometry : bond 0.00373 (16386) covalent geometry : angle 0.71866 (22134) *********************** 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 821 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 741 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8789 (tppt) cc_final: 0.8424 (tppt) REVERT: A 12 LEU cc_start: 0.9571 (mt) cc_final: 0.9349 (mt) REVERT: A 51 LEU cc_start: 0.9396 (tp) cc_final: 0.9110 (tp) REVERT: A 56 ASP cc_start: 0.9241 (m-30) cc_final: 0.8973 (m-30) REVERT: A 123 SER cc_start: 0.9614 (OUTLIER) cc_final: 0.9192 (p) REVERT: A 139 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8792 (mt-10) REVERT: A 162 LYS cc_start: 0.9214 (tmmt) cc_final: 0.8971 (ttpt) REVERT: A 163 ARG cc_start: 0.8306 (tpp80) cc_final: 0.8093 (mmm-85) REVERT: A 191 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8242 (mt0) REVERT: A 220 THR cc_start: 0.9370 (m) cc_final: 0.8935 (p) REVERT: A 232 ASN cc_start: 0.9413 (m-40) cc_final: 0.8989 (m110) REVERT: A 286 ASP cc_start: 0.8364 (m-30) cc_final: 0.8150 (m-30) REVERT: A 290 GLU cc_start: 0.9331 (tt0) cc_final: 0.8865 (tm-30) REVERT: A 312 GLN cc_start: 0.8463 (mp10) cc_final: 0.8207 (mp10) REVERT: A 335 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8207 (mt-10) REVERT: A 359 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8306 (ttp) REVERT: A 362 ASP cc_start: 0.8357 (m-30) cc_final: 0.7768 (m-30) REVERT: A 390 GLN cc_start: 0.8871 (mt0) cc_final: 0.8349 (mt0) REVERT: A 406 ASP cc_start: 0.8139 (m-30) cc_final: 0.7825 (t0) REVERT: A 415 ASN cc_start: 0.9044 (t0) cc_final: 0.8377 (t0) REVERT: A 418 ASN cc_start: 0.9067 (m110) cc_final: 0.8375 (m-40) REVERT: A 444 ASP cc_start: 0.8726 (t0) cc_final: 0.8133 (t0) REVERT: A 446 ARG cc_start: 0.7539 (mtp85) cc_final: 0.7133 (mmm160) REVERT: A 515 ASP cc_start: 0.9189 (m-30) cc_final: 0.8954 (m-30) REVERT: A 590 SER cc_start: 0.9519 (t) cc_final: 0.9054 (p) REVERT: A 639 ASP cc_start: 0.8851 (m-30) cc_final: 0.8252 (m-30) REVERT: A 640 MET cc_start: 0.9554 (OUTLIER) cc_final: 0.8543 (tpp) REVERT: A 668 ASN cc_start: 0.9659 (m-40) cc_final: 0.9459 (m-40) REVERT: A 684 TYR cc_start: 0.8108 (OUTLIER) cc_final: 0.7481 (m-10) REVERT: B 60 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8881 (mp0) REVERT: B 128 PHE cc_start: 0.9781 (t80) cc_final: 0.9389 (t80) REVERT: B 154 PRO cc_start: 0.9467 (Cg_exo) cc_final: 0.9261 (Cg_endo) REVERT: B 167 LEU cc_start: 0.9395 (mt) cc_final: 0.9099 (mt) REVERT: B 172 LEU cc_start: 0.9489 (mp) cc_final: 0.9222 (mp) REVERT: B 181 ASP cc_start: 0.8688 (m-30) cc_final: 0.8218 (m-30) REVERT: B 202 ASN cc_start: 0.9433 (t0) cc_final: 0.8824 (t0) REVERT: B 238 ASP cc_start: 0.7933 (t0) cc_final: 0.7560 (t0) REVERT: B 251 LEU cc_start: 0.9489 (tp) cc_final: 0.9259 (tp) REVERT: B 257 ASP cc_start: 0.9036 (m-30) cc_final: 0.8768 (m-30) REVERT: B 274 ARG cc_start: 0.8602 (ttm-80) cc_final: 0.8400 (ttm-80) REVERT: B 423 LYS cc_start: 0.9611 (mtmm) cc_final: 0.9288 (mmtp) REVERT: B 446 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7929 (mmm-85) REVERT: B 447 ASN cc_start: 0.8738 (m-40) cc_final: 0.8030 (m110) REVERT: B 458 MET cc_start: 0.9203 (mmm) cc_final: 0.8822 (mmp) REVERT: B 493 MET cc_start: 0.9630 (tmm) cc_final: 0.9309 (tmm) REVERT: B 515 ASP cc_start: 0.9149 (m-30) cc_final: 0.8764 (m-30) REVERT: B 595 MET cc_start: 0.9025 (mmm) cc_final: 0.8351 (mmm) REVERT: B 598 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8146 (mtm) REVERT: B 599 GLU cc_start: 0.8487 (pt0) cc_final: 0.8077 (pt0) REVERT: B 610 LYS cc_start: 0.9116 (mtpp) cc_final: 0.8720 (mtpp) REVERT: B 631 ASP cc_start: 0.8892 (t0) cc_final: 0.8642 (t0) REVERT: B 640 MET cc_start: 0.9298 (tpp) cc_final: 0.9022 (tpp) REVERT: B 686 ARG cc_start: 0.8580 (mtp85) cc_final: 0.7776 (mtp85) REVERT: C 55 TYR cc_start: 0.9086 (t80) cc_final: 0.8768 (t80) REVERT: C 56 MET cc_start: 0.8294 (ttt) cc_final: 0.7786 (ppp) REVERT: C 66 ASP cc_start: 0.8969 (OUTLIER) cc_final: 0.8570 (t70) REVERT: C 69 GLN cc_start: 0.8399 (tm-30) cc_final: 0.8075 (tm-30) REVERT: C 86 ARG cc_start: 0.8753 (mtt180) cc_final: 0.8424 (mpt180) REVERT: C 95 MET cc_start: 0.8581 (tmm) cc_final: 0.8262 (tmm) REVERT: C 122 PHE cc_start: 0.8879 (m-80) cc_final: 0.8426 (m-80) REVERT: C 157 MET cc_start: 0.9121 (mtt) cc_final: 0.8915 (mtt) REVERT: C 174 TYR cc_start: 0.8818 (OUTLIER) cc_final: 0.7415 (t80) REVERT: C 178 PHE cc_start: 0.8874 (t80) cc_final: 0.8573 (t80) REVERT: C 179 TYR cc_start: 0.8781 (t80) cc_final: 0.8540 (t80) REVERT: C 237 GLU cc_start: 0.9464 (pt0) cc_final: 0.9082 (pp20) REVERT: C 242 TYR cc_start: 0.9492 (t80) cc_final: 0.9005 (t80) REVERT: C 269 MET cc_start: 0.9660 (tmm) cc_final: 0.9451 (tmm) REVERT: C 320 PHE cc_start: 0.9148 (m-80) cc_final: 0.8729 (m-80) REVERT: D 20 MET cc_start: 0.8820 (ttt) cc_final: 0.8589 (ptm) REVERT: D 30 TRP cc_start: 0.8189 (p-90) cc_final: 0.7666 (p-90) REVERT: D 74 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7372 (tpt) REVERT: D 92 PHE cc_start: 0.8269 (t80) cc_final: 0.7932 (t80) REVERT: D 109 PHE cc_start: 0.8634 (m-80) cc_final: 0.8215 (m-80) REVERT: D 128 ASN cc_start: 0.9049 (t0) cc_final: 0.8771 (m-40) REVERT: D 137 MET cc_start: 0.9605 (mtt) cc_final: 0.9334 (mtp) REVERT: D 164 GLU cc_start: 0.8611 (mm-30) cc_final: 0.7415 (mm-30) REVERT: D 178 PHE cc_start: 0.9227 (m-80) cc_final: 0.8714 (t80) REVERT: D 196 ARG cc_start: 0.9229 (tmm-80) cc_final: 0.9023 (ttt180) REVERT: D 198 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8074 (mm-30) REVERT: D 231 LEU cc_start: 0.9128 (mm) cc_final: 0.8825 (mm) REVERT: D 259 PHE cc_start: 0.8569 (t80) cc_final: 0.7757 (t80) REVERT: D 270 ASN cc_start: 0.8661 (m-40) cc_final: 0.8454 (m-40) outliers start: 80 outliers final: 52 residues processed: 773 average time/residue: 0.2615 time to fit residues: 304.4264 Evaluate side-chains 750 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 688 time to evaluate : 1.711 ------------------------------------------------------------------------------- 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 134 THR 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 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 THR 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 60 GLU 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 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 446 ARG Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 594 VAL 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 662 MET Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 312 VAL 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 161 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 31 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 156 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 ASN A 645 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 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 216 GLN D 233 ASN ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN D 270 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.115281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.083023 restraints weight = 37842.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.086299 restraints weight = 18113.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.088490 restraints weight = 10872.591| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.6969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16386 Z= 0.245 Angle : 0.758 12.218 22134 Z= 0.389 Chirality : 0.048 0.204 2360 Planarity : 0.004 0.046 2818 Dihedral : 10.281 145.163 2245 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 5.13 % Allowed : 30.83 % Favored : 64.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.19), residues: 1932 helix: 0.88 (0.15), residues: 1138 sheet: -0.77 (0.39), residues: 148 loop : 0.14 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 124 HIS 0.016 0.002 HIS C 201 PHE 0.036 0.003 PHE D 172 TYR 0.049 0.002 TYR D 142 ARG 0.006 0.001 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.04275 ( 871) hydrogen bonds : angle 5.40441 ( 2571) covalent geometry : bond 0.00540 (16386) covalent geometry : angle 0.75789 (22134) *********************** 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 779 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 691 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8818 (tppt) cc_final: 0.8573 (tppt) REVERT: A 15 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8527 (mm-30) REVERT: A 51 LEU cc_start: 0.9519 (tp) cc_final: 0.9230 (tp) REVERT: A 119 GLU cc_start: 0.8749 (mp0) cc_final: 0.8082 (mm-30) REVERT: A 139 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8800 (mt-10) REVERT: A 147 GLN cc_start: 0.9137 (mt0) cc_final: 0.8728 (mt0) REVERT: A 162 LYS cc_start: 0.9256 (tmmt) cc_final: 0.9010 (ttpt) REVERT: A 163 ARG cc_start: 0.8456 (tpp80) cc_final: 0.8232 (mmm-85) REVERT: A 194 LYS cc_start: 0.9384 (ttpp) cc_final: 0.9147 (ttpp) REVERT: A 214 LYS cc_start: 0.8941 (mmtt) cc_final: 0.8719 (mmtt) REVERT: A 232 ASN cc_start: 0.9425 (m-40) cc_final: 0.9002 (m110) REVERT: A 266 LYS cc_start: 0.9232 (mtmm) cc_final: 0.9004 (mtmm) REVERT: A 290 GLU cc_start: 0.9339 (tt0) cc_final: 0.8981 (tm-30) REVERT: A 312 GLN cc_start: 0.8451 (mp10) cc_final: 0.8236 (mp10) REVERT: A 335 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8199 (mt-10) REVERT: A 390 GLN cc_start: 0.8959 (mt0) cc_final: 0.8490 (mt0) REVERT: A 406 ASP cc_start: 0.8044 (m-30) cc_final: 0.7791 (t0) REVERT: A 415 ASN cc_start: 0.9167 (t0) cc_final: 0.8333 (t0) REVERT: A 418 ASN cc_start: 0.9100 (m110) cc_final: 0.8346 (m110) REVERT: A 459 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8909 (mtmm) REVERT: A 494 MET cc_start: 0.9226 (mtp) cc_final: 0.9016 (tpp) REVERT: A 515 ASP cc_start: 0.9238 (m-30) cc_final: 0.9018 (m-30) REVERT: A 590 SER cc_start: 0.9516 (t) cc_final: 0.9173 (p) REVERT: A 599 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8173 (pt0) REVERT: A 639 ASP cc_start: 0.8869 (m-30) cc_final: 0.8297 (m-30) REVERT: A 640 MET cc_start: 0.9500 (OUTLIER) cc_final: 0.8596 (tpp) REVERT: A 645 GLN cc_start: 0.9406 (tp40) cc_final: 0.8899 (tp-100) REVERT: A 684 TYR cc_start: 0.8263 (OUTLIER) cc_final: 0.7629 (m-10) REVERT: B 128 PHE cc_start: 0.9771 (t80) cc_final: 0.9327 (t80) REVERT: B 154 PRO cc_start: 0.9497 (Cg_exo) cc_final: 0.9281 (Cg_endo) REVERT: B 172 LEU cc_start: 0.9503 (mp) cc_final: 0.9256 (mp) REVERT: B 235 ARG cc_start: 0.9080 (mtm110) cc_final: 0.8793 (ttp-110) REVERT: B 238 ASP cc_start: 0.8116 (t0) cc_final: 0.7670 (t0) REVERT: B 251 LEU cc_start: 0.9571 (tp) cc_final: 0.9364 (tp) REVERT: B 257 ASP cc_start: 0.8911 (m-30) cc_final: 0.8570 (m-30) REVERT: B 290 GLU cc_start: 0.8715 (tp30) cc_final: 0.7913 (tp30) REVERT: B 294 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8816 (mp0) REVERT: B 308 LYS cc_start: 0.9483 (mtpp) cc_final: 0.9082 (ptpp) REVERT: B 350 ARG cc_start: 0.9118 (mtp85) cc_final: 0.8717 (mmm-85) REVERT: B 383 SER cc_start: 0.9719 (t) cc_final: 0.9283 (p) REVERT: B 423 LYS cc_start: 0.9634 (mtmt) cc_final: 0.9240 (mtpp) REVERT: B 434 ASP cc_start: 0.8758 (m-30) cc_final: 0.8448 (m-30) REVERT: B 446 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.8027 (mmm-85) REVERT: B 458 MET cc_start: 0.9215 (mmm) cc_final: 0.8850 (mmp) REVERT: B 493 MET cc_start: 0.9622 (tmm) cc_final: 0.9257 (tmm) REVERT: B 515 ASP cc_start: 0.9195 (m-30) cc_final: 0.8833 (m-30) REVERT: B 529 ASP cc_start: 0.9014 (m-30) cc_final: 0.8738 (m-30) REVERT: B 595 MET cc_start: 0.9062 (mmm) cc_final: 0.8472 (mmm) REVERT: B 598 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8175 (mtm) REVERT: B 599 GLU cc_start: 0.8496 (pt0) cc_final: 0.8157 (pt0) REVERT: B 602 GLU cc_start: 0.8893 (pt0) cc_final: 0.8300 (pt0) REVERT: B 610 LYS cc_start: 0.9043 (mtpp) cc_final: 0.8802 (mtpp) REVERT: B 631 ASP cc_start: 0.8934 (t0) cc_final: 0.8612 (t0) REVERT: B 640 MET cc_start: 0.9184 (tpp) cc_final: 0.8958 (tpp) REVERT: B 686 ARG cc_start: 0.8552 (mtp85) cc_final: 0.7763 (mtp85) REVERT: C 56 MET cc_start: 0.8470 (ttt) cc_final: 0.7794 (ppp) REVERT: C 66 ASP cc_start: 0.8992 (OUTLIER) cc_final: 0.8616 (t70) REVERT: C 69 GLN cc_start: 0.8313 (tm-30) cc_final: 0.7945 (tm-30) REVERT: C 86 ARG cc_start: 0.8863 (mtt180) cc_final: 0.8516 (mpt180) REVERT: C 137 MET cc_start: 0.9347 (tpp) cc_final: 0.9134 (tpp) REVERT: C 157 MET cc_start: 0.9214 (mtt) cc_final: 0.8852 (mtt) REVERT: C 162 TYR cc_start: 0.9171 (m-80) cc_final: 0.8698 (t80) REVERT: C 179 TYR cc_start: 0.8817 (t80) cc_final: 0.8613 (t80) REVERT: C 242 TYR cc_start: 0.9521 (t80) cc_final: 0.8903 (t80) REVERT: C 259 PHE cc_start: 0.8280 (t80) cc_final: 0.7309 (t80) REVERT: C 270 ASN cc_start: 0.8388 (m-40) cc_final: 0.8172 (m110) REVERT: D 20 MET cc_start: 0.8801 (ttt) cc_final: 0.8570 (ptm) REVERT: D 40 ASP cc_start: 0.8803 (m-30) cc_final: 0.8470 (m-30) REVERT: D 74 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7760 (tpt) REVERT: D 109 PHE cc_start: 0.8643 (m-80) cc_final: 0.8239 (m-80) REVERT: D 137 MET cc_start: 0.9645 (mtt) cc_final: 0.9369 (mtp) REVERT: D 178 PHE cc_start: 0.9324 (m-80) cc_final: 0.8588 (t80) REVERT: D 231 LEU cc_start: 0.9194 (mm) cc_final: 0.8939 (mm) REVERT: D 259 PHE cc_start: 0.8828 (t80) cc_final: 0.8089 (t80) REVERT: D 261 ARG cc_start: 0.8085 (mtm-85) cc_final: 0.7747 (mtm-85) REVERT: D 265 ASN cc_start: 0.8783 (m-40) cc_final: 0.8566 (m-40) outliers start: 88 outliers final: 63 residues processed: 730 average time/residue: 0.2549 time to fit residues: 281.6320 Evaluate side-chains 736 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 666 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 69 LEU 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 155 THR Chi-restraints excluded: chain A residue 180 ASN 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 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 408 SER Chi-restraints excluded: chain A residue 409 CYS 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 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 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 60 GLU 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 200 SER 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 391 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 594 VAL 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 660 ASP Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain D residue 25 ASN 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 145 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 39 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 161 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 184 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 650 GLN ** 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 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN C 238 ASN D 28 GLN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 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 = 0.3533 r_free = 0.3533 target = 0.119464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.087937 restraints weight = 37276.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.091253 restraints weight = 17408.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.093528 restraints weight = 10303.620| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.7225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16386 Z= 0.167 Angle : 0.756 13.876 22134 Z= 0.383 Chirality : 0.048 0.240 2360 Planarity : 0.004 0.051 2818 Dihedral : 10.140 140.922 2245 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.96 % Allowed : 32.34 % Favored : 63.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.19), residues: 1932 helix: 0.82 (0.15), residues: 1150 sheet: -0.63 (0.39), residues: 146 loop : 0.14 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 30 HIS 0.016 0.001 HIS C 201 PHE 0.039 0.002 PHE D 172 TYR 0.059 0.002 TYR D 142 ARG 0.006 0.001 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 871) hydrogen bonds : angle 5.36827 ( 2571) covalent geometry : bond 0.00375 (16386) covalent geometry : angle 0.75606 (22134) *********************** 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 784 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 716 time to evaluate : 1.895 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 8 LYS cc_start: 0.8867 (tppt) cc_final: 0.8573 (tppt) REVERT: A 15 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8534 (mm-30) REVERT: A 51 LEU cc_start: 0.9469 (tp) cc_final: 0.9241 (tp) REVERT: A 119 GLU cc_start: 0.8740 (mp0) cc_final: 0.8031 (mm-30) REVERT: A 123 SER cc_start: 0.9579 (OUTLIER) cc_final: 0.9028 (p) REVERT: A 139 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8766 (mt-10) REVERT: A 147 GLN cc_start: 0.9093 (mt0) cc_final: 0.8671 (mt0) REVERT: A 162 LYS cc_start: 0.9267 (tmmt) cc_final: 0.9007 (ttpt) REVERT: A 163 ARG cc_start: 0.8461 (tpp80) cc_final: 0.8247 (mmm-85) REVERT: A 191 GLN cc_start: 0.8524 (mm-40) cc_final: 0.8002 (mt0) REVERT: A 214 LYS cc_start: 0.8802 (mmtt) cc_final: 0.8568 (mmtt) REVERT: A 220 THR cc_start: 0.9399 (m) cc_final: 0.8978 (p) REVERT: A 232 ASN cc_start: 0.9436 (m-40) cc_final: 0.9005 (m110) REVERT: A 266 LYS cc_start: 0.9201 (mtmm) cc_final: 0.8936 (mtmm) REVERT: A 290 GLU cc_start: 0.9313 (tt0) cc_final: 0.8861 (tm-30) REVERT: A 312 GLN cc_start: 0.8424 (mp10) cc_final: 0.8213 (mp10) REVERT: A 335 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8186 (mt-10) REVERT: A 359 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8383 (ttp) REVERT: A 362 ASP cc_start: 0.8384 (m-30) cc_final: 0.7931 (m-30) REVERT: A 381 LEU cc_start: 0.9514 (tp) cc_final: 0.9187 (tp) REVERT: A 384 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.7366 (pm20) REVERT: A 390 GLN cc_start: 0.8942 (mt0) cc_final: 0.8426 (mt0) REVERT: A 406 ASP cc_start: 0.8072 (m-30) cc_final: 0.7731 (t0) REVERT: A 415 ASN cc_start: 0.9159 (t0) cc_final: 0.8832 (t0) REVERT: A 447 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.7222 (m110) REVERT: A 459 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8950 (mtmm) REVERT: A 515 ASP cc_start: 0.9163 (m-30) cc_final: 0.8913 (m-30) REVERT: A 590 SER cc_start: 0.9602 (t) cc_final: 0.9127 (p) REVERT: A 599 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8058 (pt0) REVERT: A 639 ASP cc_start: 0.8811 (m-30) cc_final: 0.8210 (m-30) REVERT: A 645 GLN cc_start: 0.9452 (tp40) cc_final: 0.9192 (tp-100) REVERT: A 684 TYR cc_start: 0.8176 (OUTLIER) cc_final: 0.7548 (m-10) REVERT: B 18 ILE cc_start: 0.9639 (mp) cc_final: 0.9402 (pt) REVERT: B 82 LYS cc_start: 0.9638 (mmmm) cc_final: 0.9326 (mmtt) REVERT: B 128 PHE cc_start: 0.9763 (t80) cc_final: 0.9304 (t80) REVERT: B 154 PRO cc_start: 0.9446 (Cg_exo) cc_final: 0.9230 (Cg_endo) REVERT: B 172 LEU cc_start: 0.9421 (mp) cc_final: 0.9183 (mp) REVERT: B 214 LYS cc_start: 0.9072 (ttpp) cc_final: 0.8778 (ttpp) REVERT: B 238 ASP cc_start: 0.8294 (t0) cc_final: 0.7847 (t0) REVERT: B 251 LEU cc_start: 0.9516 (tp) cc_final: 0.9262 (tp) REVERT: B 263 ASP cc_start: 0.8985 (m-30) cc_final: 0.8583 (m-30) REVERT: B 423 LYS cc_start: 0.9637 (mtmt) cc_final: 0.9285 (mtpp) REVERT: B 434 ASP cc_start: 0.8727 (m-30) cc_final: 0.8413 (m-30) REVERT: B 446 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7776 (mmm-85) REVERT: B 458 MET cc_start: 0.9122 (mmm) cc_final: 0.8785 (mmp) REVERT: B 493 MET cc_start: 0.9588 (tmm) cc_final: 0.9269 (tmm) REVERT: B 515 ASP cc_start: 0.9162 (m-30) cc_final: 0.8768 (m-30) REVERT: B 595 MET cc_start: 0.9014 (mmm) cc_final: 0.8388 (mmm) REVERT: B 598 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8042 (mtm) REVERT: B 599 GLU cc_start: 0.8372 (pt0) cc_final: 0.7998 (pt0) REVERT: B 602 GLU cc_start: 0.8836 (pt0) cc_final: 0.8231 (pt0) REVERT: B 610 LYS cc_start: 0.8978 (mtpp) cc_final: 0.8692 (mtpp) REVERT: B 631 ASP cc_start: 0.8971 (t0) cc_final: 0.8618 (t0) REVERT: B 640 MET cc_start: 0.9182 (tpp) cc_final: 0.8947 (tpp) REVERT: B 686 ARG cc_start: 0.8547 (mtp85) cc_final: 0.7774 (mtp85) REVERT: C 56 MET cc_start: 0.8389 (ttt) cc_final: 0.7665 (ppp) REVERT: C 66 ASP cc_start: 0.8936 (OUTLIER) cc_final: 0.8616 (t70) REVERT: C 69 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7916 (tm-30) REVERT: C 86 ARG cc_start: 0.8799 (mtt180) cc_final: 0.8509 (mpt180) REVERT: C 157 MET cc_start: 0.9236 (mtt) cc_final: 0.8847 (mtt) REVERT: C 174 TYR cc_start: 0.9016 (OUTLIER) cc_final: 0.7916 (t80) REVERT: C 179 TYR cc_start: 0.8895 (t80) cc_final: 0.8600 (t80) REVERT: C 189 GLU cc_start: 0.9264 (mp0) cc_final: 0.9035 (pm20) REVERT: C 233 ASN cc_start: 0.9370 (m110) cc_final: 0.9066 (p0) REVERT: C 242 TYR cc_start: 0.9482 (t80) cc_final: 0.8913 (t80) REVERT: C 259 PHE cc_start: 0.8175 (t80) cc_final: 0.7369 (t80) REVERT: C 320 PHE cc_start: 0.9187 (m-80) cc_final: 0.8912 (m-80) REVERT: D 18 THR cc_start: 0.9259 (p) cc_final: 0.8916 (m) REVERT: D 20 MET cc_start: 0.8870 (ttt) cc_final: 0.8442 (ptm) REVERT: D 24 GLN cc_start: 0.8969 (mm-40) cc_final: 0.8646 (mp10) REVERT: D 30 TRP cc_start: 0.8149 (p-90) cc_final: 0.7779 (p-90) REVERT: D 40 ASP cc_start: 0.8850 (m-30) cc_final: 0.8539 (m-30) REVERT: D 47 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7993 (mt) REVERT: D 74 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7829 (tpt) REVERT: D 109 PHE cc_start: 0.8677 (m-80) cc_final: 0.8291 (m-80) REVERT: D 137 MET cc_start: 0.9621 (mtt) cc_final: 0.9362 (mtp) REVERT: D 164 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7140 (mm-30) REVERT: D 178 PHE cc_start: 0.9272 (m-80) cc_final: 0.8537 (t80) REVERT: D 196 ARG cc_start: 0.9227 (ptm-80) cc_final: 0.8996 (ptm160) REVERT: D 198 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8154 (mm-30) REVERT: D 231 LEU cc_start: 0.9149 (mm) cc_final: 0.8774 (mm) REVERT: D 259 PHE cc_start: 0.8766 (t80) cc_final: 0.7997 (t80) outliers start: 68 outliers final: 48 residues processed: 741 average time/residue: 0.2475 time to fit residues: 278.6234 Evaluate side-chains 725 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 665 time to evaluate : 1.827 ------------------------------------------------------------------------------- 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 134 THR Chi-restraints excluded: chain A residue 155 THR 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 359 MET 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 447 ASN Chi-restraints excluded: chain A residue 459 LYS 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 632 MET Chi-restraints excluded: chain A residue 638 VAL 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 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 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 446 ARG Chi-restraints excluded: chain B residue 546 LEU 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 624 PHE Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 151 ILE 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 D residue 25 ASN Chi-restraints excluded: chain D residue 28 GLN 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 285 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 159 optimal weight: 20.0000 chunk 72 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 183 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 180 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** 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 ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.120895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.089526 restraints weight = 36701.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.092928 restraints weight = 17232.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.095126 restraints weight = 10185.129| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.7483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16386 Z= 0.156 Angle : 0.795 14.102 22134 Z= 0.398 Chirality : 0.048 0.210 2360 Planarity : 0.004 0.056 2818 Dihedral : 10.021 137.844 2245 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.90 % Allowed : 33.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.19), residues: 1932 helix: 0.76 (0.15), residues: 1148 sheet: -0.73 (0.39), residues: 146 loop : 0.12 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 124 HIS 0.026 0.001 HIS C 201 PHE 0.036 0.002 PHE D 172 TYR 0.054 0.002 TYR D 142 ARG 0.010 0.001 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 871) hydrogen bonds : angle 5.37642 ( 2571) covalent geometry : bond 0.00354 (16386) covalent geometry : angle 0.79513 (22134) *********************** 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 755 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 688 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.9393 (tp) cc_final: 0.9173 (tp) REVERT: A 123 SER cc_start: 0.9575 (OUTLIER) cc_final: 0.9132 (p) REVERT: A 139 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8723 (mt-10) REVERT: A 162 LYS cc_start: 0.9281 (tmmt) cc_final: 0.9025 (ttpt) REVERT: A 163 ARG cc_start: 0.8448 (tpp80) cc_final: 0.8207 (mmm-85) REVERT: A 214 LYS cc_start: 0.8816 (mmtt) cc_final: 0.8605 (mmtt) REVERT: A 220 THR cc_start: 0.9359 (m) cc_final: 0.8973 (p) REVERT: A 232 ASN cc_start: 0.9432 (m-40) cc_final: 0.9105 (m110) REVERT: A 266 LYS cc_start: 0.9175 (mtmm) cc_final: 0.8759 (mtmm) REVERT: A 290 GLU cc_start: 0.9315 (tt0) cc_final: 0.8824 (tm-30) REVERT: A 312 GLN cc_start: 0.8396 (mp10) cc_final: 0.7933 (pm20) REVERT: A 335 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8232 (mt-10) REVERT: A 359 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8449 (ttp) REVERT: A 362 ASP cc_start: 0.8379 (m-30) cc_final: 0.8137 (m-30) REVERT: A 381 LEU cc_start: 0.9530 (tp) cc_final: 0.9198 (tp) REVERT: A 384 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.7462 (pm20) REVERT: A 390 GLN cc_start: 0.8948 (mt0) cc_final: 0.8445 (mt0) REVERT: A 406 ASP cc_start: 0.8115 (m-30) cc_final: 0.7815 (t0) REVERT: A 459 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8944 (mtmm) REVERT: A 471 TYR cc_start: 0.9042 (t80) cc_final: 0.8778 (t80) REVERT: A 493 MET cc_start: 0.8859 (tmm) cc_final: 0.8536 (tmm) REVERT: A 515 ASP cc_start: 0.9125 (m-30) cc_final: 0.8863 (m-30) REVERT: A 550 MET cc_start: 0.8651 (mmt) cc_final: 0.7958 (mmp) REVERT: A 590 SER cc_start: 0.9592 (t) cc_final: 0.9127 (p) REVERT: A 599 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8085 (pt0) REVERT: A 639 ASP cc_start: 0.8644 (m-30) cc_final: 0.8101 (m-30) REVERT: A 645 GLN cc_start: 0.9430 (tp40) cc_final: 0.8973 (tp-100) REVERT: A 684 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.7794 (m-10) REVERT: B 82 LYS cc_start: 0.9609 (mmmm) cc_final: 0.9271 (mmtt) REVERT: B 117 ARG cc_start: 0.8901 (mmm160) cc_final: 0.8167 (mmt180) REVERT: B 128 PHE cc_start: 0.9762 (t80) cc_final: 0.9346 (t80) REVERT: B 172 LEU cc_start: 0.9351 (mp) cc_final: 0.9097 (mp) REVERT: B 213 ILE cc_start: 0.9176 (mp) cc_final: 0.8854 (mt) REVERT: B 214 LYS cc_start: 0.9077 (ttpp) cc_final: 0.8859 (ttpp) REVERT: B 235 ARG cc_start: 0.9029 (mtm110) cc_final: 0.8763 (ttp-110) REVERT: B 238 ASP cc_start: 0.8304 (t0) cc_final: 0.7800 (t0) REVERT: B 251 LEU cc_start: 0.9518 (tp) cc_final: 0.9207 (tp) REVERT: B 263 ASP cc_start: 0.8974 (m-30) cc_final: 0.8574 (m-30) REVERT: B 290 GLU cc_start: 0.8719 (tp30) cc_final: 0.8476 (tp30) REVERT: B 350 ARG cc_start: 0.9125 (mtp85) cc_final: 0.8810 (mmm-85) REVERT: B 423 LYS cc_start: 0.9613 (mtmt) cc_final: 0.9226 (mtpp) REVERT: B 434 ASP cc_start: 0.8759 (m-30) cc_final: 0.8427 (m-30) REVERT: B 446 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7675 (mmm-85) REVERT: B 447 ASN cc_start: 0.8149 (m-40) cc_final: 0.7536 (m-40) REVERT: B 458 MET cc_start: 0.9022 (mmm) cc_final: 0.8721 (mmp) REVERT: B 493 MET cc_start: 0.9523 (tmm) cc_final: 0.9208 (tmm) REVERT: B 515 ASP cc_start: 0.9125 (m-30) cc_final: 0.8772 (m-30) REVERT: B 529 ASP cc_start: 0.8835 (m-30) cc_final: 0.8588 (m-30) REVERT: B 595 MET cc_start: 0.8981 (mmm) cc_final: 0.8418 (mmm) REVERT: B 598 MET cc_start: 0.8723 (mtm) cc_final: 0.8077 (mtm) REVERT: B 599 GLU cc_start: 0.8359 (pt0) cc_final: 0.7977 (pt0) REVERT: B 602 GLU cc_start: 0.8924 (pt0) cc_final: 0.8344 (pt0) REVERT: B 610 LYS cc_start: 0.8951 (mtpp) cc_final: 0.8670 (mtpp) REVERT: B 631 ASP cc_start: 0.8944 (t0) cc_final: 0.8572 (t0) REVERT: B 686 ARG cc_start: 0.8529 (mtp85) cc_final: 0.7799 (mtp85) REVERT: C 66 ASP cc_start: 0.9005 (OUTLIER) cc_final: 0.8563 (t70) REVERT: C 69 GLN cc_start: 0.8299 (tm-30) cc_final: 0.7961 (tm-30) REVERT: C 86 ARG cc_start: 0.8825 (mtt180) cc_final: 0.8492 (mpt180) REVERT: C 122 PHE cc_start: 0.8852 (m-80) cc_final: 0.8411 (m-80) REVERT: C 147 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8041 (ptmm) REVERT: C 157 MET cc_start: 0.9269 (mtt) cc_final: 0.8863 (mtt) REVERT: C 162 TYR cc_start: 0.9163 (m-80) cc_final: 0.8696 (t80) REVERT: C 174 TYR cc_start: 0.9064 (OUTLIER) cc_final: 0.7984 (t80) REVERT: C 178 PHE cc_start: 0.8672 (t80) cc_final: 0.8394 (t80) REVERT: C 233 ASN cc_start: 0.9421 (m110) cc_final: 0.9108 (p0) REVERT: C 240 LEU cc_start: 0.9515 (mm) cc_final: 0.9271 (mm) REVERT: C 242 TYR cc_start: 0.9520 (t80) cc_final: 0.9068 (t80) REVERT: C 259 PHE cc_start: 0.8248 (t80) cc_final: 0.7323 (t80) REVERT: D 20 MET cc_start: 0.8911 (ttt) cc_final: 0.8397 (ppp) REVERT: D 24 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8487 (mp10) REVERT: D 30 TRP cc_start: 0.8128 (p-90) cc_final: 0.7804 (p-90) REVERT: D 40 ASP cc_start: 0.8846 (m-30) cc_final: 0.8510 (m-30) REVERT: D 47 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7793 (mt) REVERT: D 109 PHE cc_start: 0.8642 (m-80) cc_final: 0.8261 (m-80) REVERT: D 123 GLU cc_start: 0.9210 (mp0) cc_final: 0.8850 (pp20) REVERT: D 137 MET cc_start: 0.9610 (mtt) cc_final: 0.9342 (mtp) REVERT: D 164 GLU cc_start: 0.8206 (mm-30) cc_final: 0.6961 (mm-30) REVERT: D 178 PHE cc_start: 0.9263 (m-80) cc_final: 0.8569 (t80) REVERT: D 198 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8180 (mm-30) REVERT: D 243 THR cc_start: 0.9233 (m) cc_final: 0.8872 (p) REVERT: D 259 PHE cc_start: 0.8613 (t80) cc_final: 0.8193 (t80) outliers start: 67 outliers final: 44 residues processed: 713 average time/residue: 0.2548 time to fit residues: 275.9208 Evaluate side-chains 720 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 666 time to evaluate : 1.839 ------------------------------------------------------------------------------- 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 155 THR Chi-restraints excluded: chain A residue 180 ASN 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 359 MET 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 499 SER Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 632 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 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 446 ARG Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 PHE Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 151 ILE 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 D residue 28 GLN 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 115 THR 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 204 TYR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 111 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 GLN ** 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 255 HIS ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN D 136 GLN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 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 = 0.3565 r_free = 0.3565 target = 0.119740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.088500 restraints weight = 37213.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.091610 restraints weight = 18085.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.093892 restraints weight = 10942.942| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.7675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16386 Z= 0.180 Angle : 0.827 14.219 22134 Z= 0.415 Chirality : 0.049 0.225 2360 Planarity : 0.004 0.054 2818 Dihedral : 9.921 138.763 2245 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.79 % Allowed : 33.92 % Favored : 62.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.19), residues: 1932 helix: 0.65 (0.15), residues: 1147 sheet: -0.86 (0.38), residues: 160 loop : 0.15 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 124 HIS 0.029 0.002 HIS C 201 PHE 0.037 0.002 PHE D 172 TYR 0.054 0.002 TYR D 142 ARG 0.008 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04380 ( 871) hydrogen bonds : angle 5.44374 ( 2571) covalent geometry : bond 0.00413 (16386) covalent geometry : angle 0.82685 (22134) *********************** 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 738 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 673 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8495 (mm-30) REVERT: A 51 LEU cc_start: 0.9398 (tp) cc_final: 0.9180 (tp) REVERT: A 56 ASP cc_start: 0.9232 (m-30) cc_final: 0.8888 (m-30) REVERT: A 123 SER cc_start: 0.9582 (OUTLIER) cc_final: 0.9171 (p) REVERT: A 139 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8607 (mt-10) REVERT: A 162 LYS cc_start: 0.9287 (tmmt) cc_final: 0.9011 (ttpt) REVERT: A 214 LYS cc_start: 0.8818 (mmtt) cc_final: 0.8609 (mmtt) REVERT: A 220 THR cc_start: 0.9341 (m) cc_final: 0.9011 (p) REVERT: A 232 ASN cc_start: 0.9504 (m-40) cc_final: 0.9017 (m110) REVERT: A 266 LYS cc_start: 0.9187 (mtmm) cc_final: 0.8800 (mtmm) REVERT: A 290 GLU cc_start: 0.9243 (tt0) cc_final: 0.8827 (tm-30) REVERT: A 335 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8166 (mt-10) REVERT: A 359 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8366 (ttp) REVERT: A 381 LEU cc_start: 0.9505 (tp) cc_final: 0.9186 (tp) REVERT: A 384 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.7627 (pm20) REVERT: A 390 GLN cc_start: 0.8924 (mt0) cc_final: 0.8435 (mt0) REVERT: A 406 ASP cc_start: 0.8063 (m-30) cc_final: 0.7829 (t0) REVERT: A 459 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.9014 (mtmm) REVERT: A 493 MET cc_start: 0.8884 (tmm) cc_final: 0.8513 (tmm) REVERT: A 550 MET cc_start: 0.8637 (mmt) cc_final: 0.8260 (mmm) REVERT: A 590 SER cc_start: 0.9565 (t) cc_final: 0.9209 (p) REVERT: A 599 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8175 (pt0) REVERT: A 639 ASP cc_start: 0.8511 (m-30) cc_final: 0.8031 (m-30) REVERT: A 640 MET cc_start: 0.9309 (tmm) cc_final: 0.8360 (tmm) REVERT: A 645 GLN cc_start: 0.9437 (tp40) cc_final: 0.8970 (tp-100) REVERT: A 684 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.7996 (m-80) REVERT: B 82 LYS cc_start: 0.9555 (mmmm) cc_final: 0.9257 (mmtt) REVERT: B 117 ARG cc_start: 0.8919 (mmm160) cc_final: 0.8214 (mmt180) REVERT: B 128 PHE cc_start: 0.9769 (t80) cc_final: 0.9369 (t80) REVERT: B 172 LEU cc_start: 0.9428 (mp) cc_final: 0.9170 (mp) REVERT: B 211 GLU cc_start: 0.8588 (mm-30) cc_final: 0.7735 (mm-30) REVERT: B 235 ARG cc_start: 0.9007 (mtm110) cc_final: 0.8757 (ttp-110) REVERT: B 238 ASP cc_start: 0.8312 (t0) cc_final: 0.7947 (t0) REVERT: B 251 LEU cc_start: 0.9430 (tp) cc_final: 0.9229 (tp) REVERT: B 263 ASP cc_start: 0.8968 (m-30) cc_final: 0.8551 (m-30) REVERT: B 350 ARG cc_start: 0.9158 (mtp85) cc_final: 0.8875 (mmm-85) REVERT: B 383 SER cc_start: 0.9673 (t) cc_final: 0.9194 (p) REVERT: B 423 LYS cc_start: 0.9609 (mtmt) cc_final: 0.9241 (mtpp) REVERT: B 446 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7729 (mmm-85) REVERT: B 447 ASN cc_start: 0.8022 (m-40) cc_final: 0.7407 (m-40) REVERT: B 458 MET cc_start: 0.9065 (mmm) cc_final: 0.8780 (mmp) REVERT: B 493 MET cc_start: 0.9439 (tmm) cc_final: 0.9085 (tmm) REVERT: B 515 ASP cc_start: 0.9079 (m-30) cc_final: 0.8763 (m-30) REVERT: B 529 ASP cc_start: 0.8817 (m-30) cc_final: 0.8575 (m-30) REVERT: B 595 MET cc_start: 0.8921 (mmm) cc_final: 0.8644 (mmm) REVERT: B 598 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8036 (mtm) REVERT: B 599 GLU cc_start: 0.8370 (pt0) cc_final: 0.8028 (pt0) REVERT: B 602 GLU cc_start: 0.8850 (pt0) cc_final: 0.8190 (pt0) REVERT: B 640 MET cc_start: 0.9081 (tpp) cc_final: 0.8798 (tpp) REVERT: B 686 ARG cc_start: 0.8490 (mtp85) cc_final: 0.7763 (mtp85) REVERT: C 21 PHE cc_start: 0.9424 (m-80) cc_final: 0.8901 (t80) REVERT: C 56 MET cc_start: 0.8213 (ttt) cc_final: 0.7691 (ppp) REVERT: C 66 ASP cc_start: 0.8991 (OUTLIER) cc_final: 0.8619 (t70) REVERT: C 69 GLN cc_start: 0.8307 (tm-30) cc_final: 0.7948 (tm-30) REVERT: C 86 ARG cc_start: 0.8835 (mtt180) cc_final: 0.8551 (mpt180) REVERT: C 96 MET cc_start: 0.8913 (mmm) cc_final: 0.8096 (mmm) REVERT: C 122 PHE cc_start: 0.8806 (m-80) cc_final: 0.8369 (m-80) REVERT: C 147 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8188 (ptmm) REVERT: C 157 MET cc_start: 0.9250 (mtt) cc_final: 0.8904 (mtt) REVERT: C 162 TYR cc_start: 0.9137 (m-80) cc_final: 0.8721 (t80) REVERT: C 174 TYR cc_start: 0.9047 (OUTLIER) cc_final: 0.7915 (t80) REVERT: C 178 PHE cc_start: 0.8671 (t80) cc_final: 0.8454 (t80) REVERT: C 179 TYR cc_start: 0.8942 (t80) cc_final: 0.8693 (t80) REVERT: C 233 ASN cc_start: 0.9410 (m110) cc_final: 0.9108 (p0) REVERT: C 242 TYR cc_start: 0.9506 (t80) cc_final: 0.9057 (t80) REVERT: C 259 PHE cc_start: 0.8228 (t80) cc_final: 0.7354 (t80) REVERT: D 20 MET cc_start: 0.8874 (ttt) cc_final: 0.8357 (ppp) REVERT: D 24 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8491 (mp10) REVERT: D 40 ASP cc_start: 0.8881 (m-30) cc_final: 0.8588 (m-30) REVERT: D 47 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7791 (mt) REVERT: D 79 GLU cc_start: 0.8924 (tt0) cc_final: 0.8544 (pt0) REVERT: D 109 PHE cc_start: 0.8706 (m-80) cc_final: 0.8314 (m-80) REVERT: D 123 GLU cc_start: 0.9152 (mp0) cc_final: 0.8874 (pt0) REVERT: D 137 MET cc_start: 0.9602 (mtt) cc_final: 0.9329 (mtp) REVERT: D 164 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7146 (mm-30) REVERT: D 169 TYR cc_start: 0.8907 (m-80) cc_final: 0.8370 (m-80) REVERT: D 178 PHE cc_start: 0.9261 (m-80) cc_final: 0.8523 (t80) REVERT: D 198 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8192 (mm-30) REVERT: D 231 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8767 (mm) REVERT: D 259 PHE cc_start: 0.8819 (t80) cc_final: 0.8235 (t80) outliers start: 65 outliers final: 47 residues processed: 696 average time/residue: 0.2542 time to fit residues: 269.1906 Evaluate side-chains 693 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 634 time to evaluate : 1.676 ------------------------------------------------------------------------------- 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 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 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 638 VAL 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 190 MET 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 391 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 546 LEU 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 624 PHE Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 151 ILE 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 189 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 115 THR 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 231 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 137 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 160 optimal weight: 9.9990 chunk 106 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 127 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 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** B 410 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** 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 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.122190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.090985 restraints weight = 37254.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.094381 restraints weight = 17405.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.096671 restraints weight = 10366.668| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.7896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16386 Z= 0.165 Angle : 0.857 15.782 22134 Z= 0.425 Chirality : 0.050 0.237 2360 Planarity : 0.004 0.060 2818 Dihedral : 9.760 138.527 2245 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.50 % Allowed : 35.08 % Favored : 61.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.18), residues: 1932 helix: 0.60 (0.15), residues: 1134 sheet: -1.03 (0.38), residues: 160 loop : 0.06 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP D 124 HIS 0.028 0.001 HIS C 201 PHE 0.045 0.002 PHE B 74 TYR 0.053 0.002 TYR D 142 ARG 0.007 0.001 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.04518 ( 871) hydrogen bonds : angle 5.46840 ( 2571) covalent geometry : bond 0.00378 (16386) covalent geometry : angle 0.85686 (22134) ********************** 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 737 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 677 time to evaluate : 1.897 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 12 LEU cc_start: 0.9524 (mp) cc_final: 0.9201 (mp) REVERT: A 15 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8483 (mm-30) REVERT: A 51 LEU cc_start: 0.9382 (tp) cc_final: 0.9143 (tp) REVERT: A 56 ASP cc_start: 0.9280 (m-30) cc_final: 0.8927 (m-30) REVERT: A 119 GLU cc_start: 0.8737 (mp0) cc_final: 0.8070 (mm-30) REVERT: A 123 SER cc_start: 0.9580 (OUTLIER) cc_final: 0.9056 (p) REVERT: A 139 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8598 (mt-10) REVERT: A 162 LYS cc_start: 0.9291 (tmmt) cc_final: 0.7926 (ttpp) REVERT: A 214 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8575 (mmtt) REVERT: A 220 THR cc_start: 0.9350 (m) cc_final: 0.8981 (p) REVERT: A 232 ASN cc_start: 0.9560 (m-40) cc_final: 0.9085 (m110) REVERT: A 266 LYS cc_start: 0.9159 (mtmm) cc_final: 0.8712 (mtmm) REVERT: A 290 GLU cc_start: 0.9315 (tt0) cc_final: 0.8771 (tm-30) REVERT: A 335 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8210 (mt-10) REVERT: A 359 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8295 (ttp) REVERT: A 381 LEU cc_start: 0.9555 (tp) cc_final: 0.9240 (tp) REVERT: A 384 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.7534 (pm20) REVERT: A 390 GLN cc_start: 0.8983 (mt0) cc_final: 0.8493 (mt0) REVERT: A 406 ASP cc_start: 0.8185 (m-30) cc_final: 0.7935 (t0) REVERT: A 446 ARG cc_start: 0.7852 (mtp85) cc_final: 0.7413 (mmm160) REVERT: A 459 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.8927 (mtmm) REVERT: A 471 TYR cc_start: 0.9002 (t80) cc_final: 0.8731 (t80) REVERT: A 493 MET cc_start: 0.8798 (tmm) cc_final: 0.8414 (tmm) REVERT: A 505 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8316 (mt-10) REVERT: A 515 ASP cc_start: 0.9055 (m-30) cc_final: 0.8780 (m-30) REVERT: A 590 SER cc_start: 0.9544 (t) cc_final: 0.9115 (p) REVERT: A 599 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8127 (pt0) REVERT: A 604 ARG cc_start: 0.8947 (mmm-85) cc_final: 0.8747 (mmm-85) REVERT: A 639 ASP cc_start: 0.8512 (m-30) cc_final: 0.8004 (m-30) REVERT: A 645 GLN cc_start: 0.9412 (tp40) cc_final: 0.8963 (tp-100) REVERT: A 684 TYR cc_start: 0.8200 (OUTLIER) cc_final: 0.7885 (m-80) REVERT: B 82 LYS cc_start: 0.9539 (mmmm) cc_final: 0.9225 (mmtt) REVERT: B 88 LYS cc_start: 0.9189 (mmmm) cc_final: 0.8905 (mmmm) REVERT: B 117 ARG cc_start: 0.8896 (mmm160) cc_final: 0.8161 (mmt180) REVERT: B 128 PHE cc_start: 0.9776 (t80) cc_final: 0.9395 (t80) REVERT: B 211 GLU cc_start: 0.8581 (mm-30) cc_final: 0.7658 (mm-30) REVERT: B 216 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8127 (m) REVERT: B 238 ASP cc_start: 0.8314 (t0) cc_final: 0.7970 (t0) REVERT: B 251 LEU cc_start: 0.9456 (tp) cc_final: 0.9167 (tp) REVERT: B 263 ASP cc_start: 0.8993 (m-30) cc_final: 0.8590 (m-30) REVERT: B 321 GLU cc_start: 0.8718 (pp20) cc_final: 0.8403 (pp20) REVERT: B 350 ARG cc_start: 0.9215 (mtp85) cc_final: 0.8943 (mmm-85) REVERT: B 383 SER cc_start: 0.9690 (t) cc_final: 0.9183 (p) REVERT: B 423 LYS cc_start: 0.9653 (mtmt) cc_final: 0.9262 (mtpp) REVERT: B 434 ASP cc_start: 0.8742 (m-30) cc_final: 0.8516 (m-30) REVERT: B 446 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7746 (mmm-85) REVERT: B 447 ASN cc_start: 0.7942 (m-40) cc_final: 0.7313 (m-40) REVERT: B 458 MET cc_start: 0.9004 (mmm) cc_final: 0.8694 (mmp) REVERT: B 493 MET cc_start: 0.9386 (tmm) cc_final: 0.9106 (tmm) REVERT: B 515 ASP cc_start: 0.9134 (m-30) cc_final: 0.8839 (m-30) REVERT: B 595 MET cc_start: 0.8914 (mmm) cc_final: 0.8624 (mmm) REVERT: B 598 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8085 (mtm) REVERT: B 599 GLU cc_start: 0.8363 (pt0) cc_final: 0.7987 (pt0) REVERT: B 602 GLU cc_start: 0.8936 (pt0) cc_final: 0.8474 (pt0) REVERT: B 610 LYS cc_start: 0.9269 (mtpp) cc_final: 0.8801 (ttmm) REVERT: B 638 VAL cc_start: 0.9579 (t) cc_final: 0.9348 (p) REVERT: B 640 MET cc_start: 0.9182 (tpp) cc_final: 0.8875 (tpp) REVERT: B 686 ARG cc_start: 0.8544 (mtp85) cc_final: 0.7823 (mtp85) REVERT: C 21 PHE cc_start: 0.9480 (m-80) cc_final: 0.9151 (t80) REVERT: C 56 MET cc_start: 0.8178 (ttt) cc_final: 0.7617 (ppp) REVERT: C 66 ASP cc_start: 0.9013 (OUTLIER) cc_final: 0.8631 (t70) REVERT: C 69 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7946 (tm-30) REVERT: C 86 ARG cc_start: 0.8807 (mtt180) cc_final: 0.8491 (mpt180) REVERT: C 96 MET cc_start: 0.8982 (mmm) cc_final: 0.8104 (mmm) REVERT: C 137 MET cc_start: 0.9428 (tpp) cc_final: 0.9218 (tpp) REVERT: C 147 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8231 (ptmm) REVERT: C 157 MET cc_start: 0.9265 (mtt) cc_final: 0.8909 (mtt) REVERT: C 162 TYR cc_start: 0.9137 (m-80) cc_final: 0.8787 (t80) REVERT: C 169 TYR cc_start: 0.9108 (m-80) cc_final: 0.8855 (m-80) REVERT: C 174 TYR cc_start: 0.9096 (OUTLIER) cc_final: 0.8000 (t80) REVERT: C 178 PHE cc_start: 0.8724 (t80) cc_final: 0.8478 (t80) REVERT: C 179 TYR cc_start: 0.8917 (t80) cc_final: 0.8626 (t80) REVERT: C 233 ASN cc_start: 0.9392 (m110) cc_final: 0.9107 (p0) REVERT: C 242 TYR cc_start: 0.9528 (t80) cc_final: 0.9140 (t80) REVERT: C 259 PHE cc_start: 0.8320 (t80) cc_final: 0.7450 (t80) REVERT: D 20 MET cc_start: 0.8902 (ttt) cc_final: 0.8440 (ppp) REVERT: D 24 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8548 (mp10) REVERT: D 40 ASP cc_start: 0.8854 (m-30) cc_final: 0.8530 (m-30) REVERT: D 46 TYR cc_start: 0.8912 (m-80) cc_final: 0.8434 (m-80) REVERT: D 47 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.7923 (mt) REVERT: D 79 GLU cc_start: 0.8853 (tt0) cc_final: 0.8607 (pt0) REVERT: D 109 PHE cc_start: 0.8721 (m-80) cc_final: 0.8317 (m-80) REVERT: D 123 GLU cc_start: 0.9217 (mp0) cc_final: 0.8972 (pt0) REVERT: D 137 MET cc_start: 0.9600 (mtt) cc_final: 0.9340 (mtp) REVERT: D 164 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7174 (mm-30) REVERT: D 169 TYR cc_start: 0.8844 (m-80) cc_final: 0.8392 (m-80) REVERT: D 178 PHE cc_start: 0.9281 (m-80) cc_final: 0.8688 (t80) REVERT: D 198 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8169 (mm-30) REVERT: D 259 PHE cc_start: 0.8796 (t80) cc_final: 0.8359 (t80) REVERT: D 263 ASN cc_start: 0.9129 (p0) cc_final: 0.8812 (p0) outliers start: 60 outliers final: 43 residues processed: 702 average time/residue: 0.2620 time to fit residues: 277.3259 Evaluate side-chains 711 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 656 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 180 ASN 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 346 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 638 VAL 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 190 MET 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 391 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 546 LEU 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 684 TYR Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 151 ILE 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 189 GLU Chi-restraints excluded: chain C residue 226 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 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 231 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 81 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 179 optimal weight: 8.9990 chunk 190 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** 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 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.122178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.091435 restraints weight = 37067.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.094743 restraints weight = 17747.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.096950 restraints weight = 10633.312| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.8063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16386 Z= 0.177 Angle : 0.849 15.641 22134 Z= 0.426 Chirality : 0.050 0.222 2360 Planarity : 0.004 0.052 2818 Dihedral : 9.702 139.293 2245 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.38 % Allowed : 35.43 % Favored : 61.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.19), residues: 1932 helix: 0.64 (0.15), residues: 1131 sheet: -0.99 (0.39), residues: 160 loop : -0.03 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP D 30 HIS 0.027 0.001 HIS C 201 PHE 0.042 0.002 PHE C 172 TYR 0.049 0.002 TYR D 142 ARG 0.008 0.001 ARG A 163 Details of bonding type rmsd hydrogen bonds : bond 0.04453 ( 871) hydrogen bonds : angle 5.50412 ( 2571) covalent geometry : bond 0.00402 (16386) covalent geometry : angle 0.84930 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6635.48 seconds wall clock time: 116 minutes 39.54 seconds (6999.54 seconds total)