Starting phenix.real_space_refine on Sat May 17 16:36:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzo_45072/05_2025/9bzo_45072_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzo_45072/05_2025/9bzo_45072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bzo_45072/05_2025/9bzo_45072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzo_45072/05_2025/9bzo_45072.map" model { file = "/net/cci-nas-00/data/ceres_data/9bzo_45072/05_2025/9bzo_45072_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzo_45072/05_2025/9bzo_45072_neut.cif" } resolution = 4.48 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): 0.07s 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: 9.62, per 1000 atoms: 0.60 Number of scatterers: 16038 At special positions: 0 Unit cell: (94.302, 130.806, 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: 4.29 Conformation dependent library (CDL) restraints added in 2.1 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: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.104A 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: 3.515A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.984A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.953A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.664A 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: 4.851A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.628A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.018A 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: 4.073A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.677A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.645A 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: 3.730A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.026A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.632A 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: 4.067A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.514A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.668A 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: 7.901A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.478A pdb=" N LEU A 656 " --> pdb=" O ARG A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.185A 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: 6.383A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.063A 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: 4.516A 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: 7.905A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.548A 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: 7.593A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.39 Time building geometry restraints manager: 4.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4874 1.34 - 1.46: 3050 1.46 - 1.58: 8280 1.58 - 1.70: 26 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.060 1.25e-02 6.40e+03 2.34e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.038 1.20e-02 6.94e+03 1.01e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.032 1.08e-02 8.57e+03 8.93e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.569 -0.032 1.17e-02 7.31e+03 7.37e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.573 -0.033 1.25e-02 6.40e+03 7.09e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21573 2.09 - 4.18: 519 4.18 - 6.27: 37 6.27 - 8.36: 1 8.36 - 10.45: 4 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.64 -6.10 1.36e+00 5.41e-01 2.01e+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 TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.83 -4.33 1.23e+00 6.61e-01 1.24e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.71 -4.00 1.15e+00 7.56e-01 1.21e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.56 3.63 1.06e+00 8.90e-01 1.17e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 9468 35.80 - 71.60: 339 71.60 - 107.40: 37 107.40 - 143.21: 3 143.21 - 179.01: 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 -58.32 120.69 -179.01 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 301.68 151.14 150.54 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 31.89 148.08 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: 2143 0.093 - 0.185: 182 0.185 - 0.277: 30 0.277 - 0.370: 3 0.370 - 0.462: 2 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.35e+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 4.55e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.96e+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 2.71e+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 1.11e-02 2.17e+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 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 177 " -0.017 2.00e-02 2.50e+03 9.87e-03 1.95e+00 pdb=" CG TYR C 177 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR C 177 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR C 177 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C 177 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 177 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 177 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 177 " -0.010 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 129 2.51 - 3.11: 11552 3.11 - 3.70: 27036 3.70 - 4.30: 41525 4.30 - 4.90: 65391 Nonbonded interactions: 145633 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 1.961 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.991 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.013 3.040 ... (remaining 145628 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: 0.840 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: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 38.440 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.060 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6206 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 16386 Z= 0.315 Angle : 0.740 10.446 22134 Z= 0.463 Chirality : 0.058 0.462 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.953 179.007 6154 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.34 % Allowed : 15.33 % Favored : 83.33 % 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 227 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 6.51764 ( 2571) covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.74021 (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 974 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 951 time to evaluate : 1.787 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7829 (tp) cc_final: 0.7552 (tp) REVERT: A 71 LEU cc_start: 0.9357 (mt) cc_final: 0.9120 (mm) REVERT: A 95 MET cc_start: 0.8236 (tpp) cc_final: 0.7778 (mmm) REVERT: A 129 PHE cc_start: 0.7706 (m-10) cc_final: 0.7334 (m-10) REVERT: A 143 LEU cc_start: 0.8767 (tp) cc_final: 0.8528 (tp) REVERT: A 147 GLN cc_start: 0.8532 (mt0) cc_final: 0.8332 (mt0) REVERT: A 149 TYR cc_start: 0.7936 (t80) cc_final: 0.7580 (t80) REVERT: A 162 LYS cc_start: 0.7852 (ttpt) cc_final: 0.7306 (ttmm) REVERT: A 171 PHE cc_start: 0.8423 (m-80) cc_final: 0.8042 (m-80) REVERT: A 199 VAL cc_start: 0.9238 (t) cc_final: 0.9026 (t) REVERT: A 226 VAL cc_start: 0.9057 (t) cc_final: 0.8740 (t) REVERT: A 267 ILE cc_start: 0.8851 (mp) cc_final: 0.8583 (tp) REVERT: A 278 LEU cc_start: 0.8842 (tp) cc_final: 0.8324 (tp) REVERT: A 300 VAL cc_start: 0.7976 (m) cc_final: 0.7722 (m) REVERT: A 320 ASN cc_start: 0.8214 (m110) cc_final: 0.7981 (t0) REVERT: A 322 MET cc_start: 0.6879 (mmp) cc_final: 0.6192 (mmm) REVERT: A 345 LYS cc_start: 0.7944 (tttt) cc_final: 0.7732 (tttt) REVERT: A 349 LEU cc_start: 0.8582 (mt) cc_final: 0.8050 (mt) REVERT: A 377 LYS cc_start: 0.8334 (mttt) cc_final: 0.7382 (mtmm) REVERT: A 385 VAL cc_start: 0.8338 (t) cc_final: 0.8135 (t) REVERT: A 407 ILE cc_start: 0.8376 (mt) cc_final: 0.7960 (mt) REVERT: A 431 LEU cc_start: 0.9208 (mt) cc_final: 0.8817 (mt) REVERT: A 435 SER cc_start: 0.9237 (p) cc_final: 0.8123 (p) REVERT: A 436 LEU cc_start: 0.9338 (mt) cc_final: 0.8688 (mt) REVERT: A 493 MET cc_start: 0.8014 (tmm) cc_final: 0.7699 (tmm) REVERT: A 515 ASP cc_start: 0.7742 (m-30) cc_final: 0.7431 (m-30) REVERT: A 547 PHE cc_start: 0.7693 (m-80) cc_final: 0.7111 (m-10) REVERT: A 561 LEU cc_start: 0.9084 (tp) cc_final: 0.8860 (tp) REVERT: A 630 TYR cc_start: 0.7064 (m-80) cc_final: 0.6417 (m-10) REVERT: A 634 MET cc_start: 0.8595 (mmp) cc_final: 0.8293 (mmm) REVERT: A 648 ILE cc_start: 0.8283 (mm) cc_final: 0.8030 (mm) REVERT: A 650 GLN cc_start: 0.7405 (mt0) cc_final: 0.7124 (mt0) REVERT: A 653 SER cc_start: 0.9117 (OUTLIER) cc_final: 0.8896 (p) REVERT: A 664 THR cc_start: 0.8780 (p) cc_final: 0.8559 (p) REVERT: B 18 ILE cc_start: 0.8623 (mt) cc_final: 0.8401 (mp) REVERT: B 21 ASP cc_start: 0.7903 (m-30) cc_final: 0.7605 (m-30) REVERT: B 81 PHE cc_start: 0.7397 (m-80) cc_final: 0.7196 (m-80) REVERT: B 99 LYS cc_start: 0.9215 (mmtt) cc_final: 0.8760 (mmmt) REVERT: B 109 ASN cc_start: 0.8797 (m-40) cc_final: 0.8072 (m-40) REVERT: B 122 ILE cc_start: 0.9114 (mt) cc_final: 0.8767 (mt) REVERT: B 179 LEU cc_start: 0.8301 (tp) cc_final: 0.8024 (tp) REVERT: B 186 ILE cc_start: 0.9327 (mt) cc_final: 0.9102 (mt) REVERT: B 187 ASP cc_start: 0.7738 (t70) cc_final: 0.7204 (t0) REVERT: B 191 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8073 (mm-40) REVERT: B 192 LEU cc_start: 0.9001 (mt) cc_final: 0.8706 (mt) REVERT: B 204 SER cc_start: 0.8623 (m) cc_final: 0.8000 (m) REVERT: B 206 LEU cc_start: 0.9174 (mt) cc_final: 0.8686 (mt) REVERT: B 250 TYR cc_start: 0.7617 (m-80) cc_final: 0.7406 (m-80) REVERT: B 264 THR cc_start: 0.8002 (p) cc_final: 0.7358 (p) REVERT: B 265 LYS cc_start: 0.8508 (mmtt) cc_final: 0.8208 (mmmt) REVERT: B 286 ASP cc_start: 0.5893 (OUTLIER) cc_final: 0.5575 (m-30) REVERT: B 291 LEU cc_start: 0.9109 (mt) cc_final: 0.8896 (mt) REVERT: B 300 VAL cc_start: 0.8796 (m) cc_final: 0.8520 (m) REVERT: B 322 MET cc_start: 0.7844 (mmm) cc_final: 0.6023 (mmm) REVERT: B 337 ILE cc_start: 0.8650 (pt) cc_final: 0.8246 (mp) REVERT: B 359 MET cc_start: 0.8120 (ttt) cc_final: 0.7715 (ttt) REVERT: B 364 VAL cc_start: 0.8175 (t) cc_final: 0.7907 (t) REVERT: B 373 ILE cc_start: 0.9172 (mt) cc_final: 0.8131 (mt) REVERT: B 410 ASN cc_start: 0.8395 (m110) cc_final: 0.8152 (m110) REVERT: B 430 LYS cc_start: 0.8042 (mttt) cc_final: 0.7253 (mtpp) REVERT: B 431 LEU cc_start: 0.9080 (mt) cc_final: 0.8550 (mt) REVERT: B 436 LEU cc_start: 0.9402 (mt) cc_final: 0.9160 (mt) REVERT: B 508 LYS cc_start: 0.8646 (tttt) cc_final: 0.8371 (ttpt) REVERT: B 575 ARG cc_start: 0.8151 (mtm110) cc_final: 0.7856 (mtm-85) REVERT: B 586 TYR cc_start: 0.6731 (m-80) cc_final: 0.6399 (m-10) REVERT: B 612 TYR cc_start: 0.6928 (m-80) cc_final: 0.6568 (m-80) REVERT: B 656 LEU cc_start: 0.8166 (mt) cc_final: 0.7962 (mt) REVERT: B 683 TYR cc_start: 0.7618 (t80) cc_final: 0.7363 (t80) REVERT: C 17 PHE cc_start: 0.5346 (p90) cc_final: 0.4532 (p90) REVERT: C 67 THR cc_start: 0.6971 (m) cc_final: 0.6704 (m) REVERT: C 100 VAL cc_start: 0.3793 (t) cc_final: 0.2973 (t) REVERT: C 108 ILE cc_start: 0.7782 (mt) cc_final: 0.7084 (mm) REVERT: C 118 ILE cc_start: 0.6148 (mt) cc_final: 0.5579 (mp) REVERT: C 163 LEU cc_start: 0.7081 (tt) cc_final: 0.6099 (tt) REVERT: C 174 TYR cc_start: 0.3126 (OUTLIER) cc_final: 0.2866 (t80) REVERT: C 212 ILE cc_start: 0.8024 (mt) cc_final: 0.7125 (mt) REVERT: D 130 TYR cc_start: 0.4062 (m-80) cc_final: 0.2565 (m-80) outliers start: 23 outliers final: 6 residues processed: 967 average time/residue: 0.3252 time to fit residues: 437.8074 Evaluate side-chains 664 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 655 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN A 242 GLN A 320 ASN ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 HIS B 49 HIS ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN B 645 GLN B 676 HIS ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN C 233 ASN C 238 ASN ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.119320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.091357 restraints weight = 41580.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.094064 restraints weight = 27615.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.096169 restraints weight = 20279.497| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16386 Z= 0.203 Angle : 0.661 9.741 22134 Z= 0.357 Chirality : 0.044 0.215 2360 Planarity : 0.004 0.052 2818 Dihedral : 11.421 177.273 2242 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.41 % Allowed : 2.74 % Favored : 96.85 % 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: 1.22 (0.19), residues: 1932 helix: 1.18 (0.15), residues: 1143 sheet: 0.04 (0.41), residues: 138 loop : 0.55 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 558 HIS 0.008 0.002 HIS A 438 PHE 0.038 0.003 PHE C 166 TYR 0.026 0.002 TYR D 174 ARG 0.007 0.001 ARG A 256 Details of bonding type rmsd hydrogen bonds : bond 0.04776 ( 871) hydrogen bonds : angle 5.26472 ( 2571) covalent geometry : bond 0.00420 (16386) covalent geometry : angle 0.66134 (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 768 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 761 time to evaluate : 1.771 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: A 89 PHE cc_start: 0.8823 (t80) cc_final: 0.8579 (t80) REVERT: A 101 TYR cc_start: 0.9422 (m-80) cc_final: 0.9121 (m-10) REVERT: A 109 ASN cc_start: 0.9530 (p0) cc_final: 0.9281 (m-40) REVERT: A 115 LEU cc_start: 0.9462 (mt) cc_final: 0.9102 (mt) REVERT: A 119 GLU cc_start: 0.9224 (mp0) cc_final: 0.8168 (tm-30) REVERT: A 120 ASP cc_start: 0.9251 (m-30) cc_final: 0.8677 (m-30) REVERT: A 122 ILE cc_start: 0.9474 (mt) cc_final: 0.9262 (mt) REVERT: A 136 LYS cc_start: 0.9506 (tttp) cc_final: 0.9233 (tttp) REVERT: A 144 MET cc_start: 0.8952 (mtm) cc_final: 0.8498 (mtm) REVERT: A 147 GLN cc_start: 0.8950 (mt0) cc_final: 0.8441 (mt0) REVERT: A 149 TYR cc_start: 0.9476 (t80) cc_final: 0.9163 (t80) REVERT: A 168 VAL cc_start: 0.8758 (t) cc_final: 0.8501 (t) REVERT: A 173 LEU cc_start: 0.9443 (mt) cc_final: 0.9217 (mt) REVERT: A 199 VAL cc_start: 0.9179 (t) cc_final: 0.8915 (t) REVERT: A 236 TYR cc_start: 0.8704 (t80) cc_final: 0.8103 (t80) REVERT: A 278 LEU cc_start: 0.9523 (tp) cc_final: 0.9152 (tp) REVERT: A 280 ILE cc_start: 0.8603 (pt) cc_final: 0.8337 (pt) REVERT: A 286 ASP cc_start: 0.9341 (m-30) cc_final: 0.8925 (m-30) REVERT: A 322 MET cc_start: 0.8575 (mmp) cc_final: 0.8135 (mmm) REVERT: A 326 PHE cc_start: 0.9544 (m-80) cc_final: 0.9048 (m-80) REVERT: A 349 LEU cc_start: 0.9534 (mt) cc_final: 0.9292 (mt) REVERT: A 359 MET cc_start: 0.8559 (ttp) cc_final: 0.8213 (ttp) REVERT: A 370 ASN cc_start: 0.9454 (m-40) cc_final: 0.9035 (m-40) REVERT: A 375 LYS cc_start: 0.8670 (mmmt) cc_final: 0.8155 (mmtm) REVERT: A 377 LYS cc_start: 0.8701 (mttt) cc_final: 0.8205 (mtmm) REVERT: A 386 LEU cc_start: 0.9318 (mt) cc_final: 0.9096 (mt) REVERT: A 407 ILE cc_start: 0.8803 (mt) cc_final: 0.8478 (mt) REVERT: A 408 SER cc_start: 0.9194 (p) cc_final: 0.8985 (t) REVERT: A 459 LYS cc_start: 0.8984 (mttp) cc_final: 0.8289 (mtpt) REVERT: A 466 MET cc_start: 0.9443 (ptt) cc_final: 0.9139 (ptt) REVERT: A 468 LEU cc_start: 0.9757 (tp) cc_final: 0.9542 (tp) REVERT: A 493 MET cc_start: 0.9292 (tmm) cc_final: 0.9033 (tmm) REVERT: A 494 MET cc_start: 0.9697 (mpp) cc_final: 0.9366 (mpp) REVERT: A 501 GLN cc_start: 0.9509 (mm-40) cc_final: 0.8808 (tp-100) REVERT: A 515 ASP cc_start: 0.9230 (m-30) cc_final: 0.8664 (m-30) REVERT: A 516 GLN cc_start: 0.9128 (mp10) cc_final: 0.8774 (mp10) REVERT: A 550 MET cc_start: 0.7110 (mtm) cc_final: 0.6628 (ptp) REVERT: A 561 LEU cc_start: 0.9633 (tp) cc_final: 0.9362 (tp) REVERT: A 586 TYR cc_start: 0.9100 (m-10) cc_final: 0.8729 (m-10) REVERT: A 598 MET cc_start: 0.8447 (ttt) cc_final: 0.8206 (ttt) REVERT: A 615 MET cc_start: 0.8649 (mmt) cc_final: 0.8443 (mmt) REVERT: A 650 GLN cc_start: 0.8296 (mt0) cc_final: 0.8025 (mt0) REVERT: A 658 LEU cc_start: 0.9392 (mt) cc_final: 0.9077 (mt) REVERT: A 662 MET cc_start: 0.8647 (pmm) cc_final: 0.8323 (pmm) REVERT: A 677 ARG cc_start: 0.9310 (mmm-85) cc_final: 0.8704 (mmm-85) REVERT: A 686 ARG cc_start: 0.7556 (mmm160) cc_final: 0.7286 (mmm160) REVERT: B 8 LYS cc_start: 0.9333 (tptp) cc_final: 0.9006 (tptp) REVERT: B 16 ILE cc_start: 0.9736 (pt) cc_final: 0.9462 (pt) REVERT: B 30 LYS cc_start: 0.9746 (tmtt) cc_final: 0.9385 (tptt) REVERT: B 41 ILE cc_start: 0.9589 (mm) cc_final: 0.9306 (mt) REVERT: B 51 LEU cc_start: 0.9053 (tp) cc_final: 0.8738 (tp) REVERT: B 67 GLU cc_start: 0.9375 (mm-30) cc_final: 0.9164 (mm-30) REVERT: B 95 MET cc_start: 0.9526 (mmp) cc_final: 0.9078 (mmm) REVERT: B 99 LYS cc_start: 0.9510 (mmmt) cc_final: 0.9021 (mptt) REVERT: B 144 MET cc_start: 0.9506 (mtm) cc_final: 0.9212 (mtm) REVERT: B 195 LEU cc_start: 0.9400 (mt) cc_final: 0.9184 (mt) REVERT: B 211 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8316 (mm-30) REVERT: B 227 MET cc_start: 0.9176 (mtp) cc_final: 0.8826 (mtp) REVERT: B 250 TYR cc_start: 0.8229 (m-80) cc_final: 0.7183 (m-80) REVERT: B 286 ASP cc_start: 0.8575 (m-30) cc_final: 0.8373 (m-30) REVERT: B 291 LEU cc_start: 0.9581 (mt) cc_final: 0.9259 (mt) REVERT: B 322 MET cc_start: 0.8642 (mmm) cc_final: 0.8164 (mmm) REVERT: B 375 LYS cc_start: 0.9267 (mmmm) cc_final: 0.9063 (mmmm) REVERT: B 379 SER cc_start: 0.8967 (t) cc_final: 0.8562 (t) REVERT: B 410 ASN cc_start: 0.8825 (m110) cc_final: 0.8466 (m110) REVERT: B 420 MET cc_start: 0.9078 (mmm) cc_final: 0.8831 (mmm) REVERT: B 458 MET cc_start: 0.9633 (mmm) cc_final: 0.9309 (mmm) REVERT: B 468 LEU cc_start: 0.9655 (tp) cc_final: 0.9439 (tp) REVERT: B 500 ILE cc_start: 0.9673 (mt) cc_final: 0.9444 (mt) REVERT: B 570 MET cc_start: 0.8837 (mmm) cc_final: 0.8207 (mmm) REVERT: B 586 TYR cc_start: 0.9249 (m-80) cc_final: 0.8976 (m-10) REVERT: B 598 MET cc_start: 0.9228 (mtm) cc_final: 0.8949 (mtm) REVERT: B 612 TYR cc_start: 0.9188 (m-80) cc_final: 0.7904 (m-80) REVERT: B 613 TYR cc_start: 0.9119 (t80) cc_final: 0.8842 (t80) REVERT: B 648 ILE cc_start: 0.9374 (mm) cc_final: 0.9058 (mm) REVERT: B 656 LEU cc_start: 0.9604 (mt) cc_final: 0.9381 (mt) REVERT: B 673 TYR cc_start: 0.9129 (t80) cc_final: 0.8836 (t80) REVERT: B 686 ARG cc_start: 0.8211 (tpt170) cc_final: 0.7991 (tpm170) REVERT: C 17 PHE cc_start: 0.8710 (p90) cc_final: 0.7546 (p90) REVERT: C 21 PHE cc_start: 0.9217 (m-10) cc_final: 0.8614 (m-80) REVERT: C 92 PHE cc_start: 0.8140 (t80) cc_final: 0.7931 (t80) REVERT: C 96 MET cc_start: 0.8284 (tpt) cc_final: 0.8042 (tpt) REVERT: C 157 MET cc_start: 0.9608 (mtm) cc_final: 0.9290 (ptm) REVERT: C 163 LEU cc_start: 0.9559 (tt) cc_final: 0.9175 (tt) REVERT: C 178 PHE cc_start: 0.9223 (m-80) cc_final: 0.9006 (m-10) REVERT: C 214 ASN cc_start: 0.8532 (m-40) cc_final: 0.7972 (p0) REVERT: C 263 ASN cc_start: 0.6659 (m-40) cc_final: 0.6370 (p0) REVERT: C 285 ILE cc_start: 0.8991 (mm) cc_final: 0.8755 (mm) REVERT: C 318 ASP cc_start: 0.9122 (m-30) cc_final: 0.8891 (m-30) REVERT: D 17 PHE cc_start: 0.5354 (m-80) cc_final: 0.5104 (m-80) REVERT: D 21 PHE cc_start: 0.9156 (m-10) cc_final: 0.8888 (m-10) REVERT: D 109 PHE cc_start: 0.8433 (m-80) cc_final: 0.7935 (m-10) REVERT: D 172 PHE cc_start: 0.9262 (m-80) cc_final: 0.8854 (m-80) REVERT: D 189 GLU cc_start: 0.9208 (pt0) cc_final: 0.8651 (pt0) REVERT: D 214 ASN cc_start: 0.9157 (m110) cc_final: 0.8764 (p0) REVERT: D 239 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8536 (pp20) outliers start: 7 outliers final: 1 residues processed: 767 average time/residue: 0.2838 time to fit residues: 315.0542 Evaluate side-chains 610 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 608 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 chunk 175 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 191 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 189 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN B 147 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 HIS B 320 ASN B 361 GLN B 418 ASN B 645 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN C 263 ASN D 71 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.109349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.079631 restraints weight = 50292.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.082585 restraints weight = 30861.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.084983 restraints weight = 21494.359| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.5651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16386 Z= 0.215 Angle : 0.650 6.953 22134 Z= 0.346 Chirality : 0.043 0.171 2360 Planarity : 0.004 0.069 2818 Dihedral : 11.286 177.899 2242 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.12 % Allowed : 2.91 % Favored : 96.97 % 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: 1.00 (0.19), residues: 1932 helix: 1.09 (0.15), residues: 1130 sheet: -0.21 (0.39), residues: 144 loop : 0.34 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 623 HIS 0.008 0.002 HIS A 469 PHE 0.036 0.003 PHE D 320 TYR 0.033 0.002 TYR B 574 ARG 0.006 0.001 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.04308 ( 871) hydrogen bonds : angle 5.11348 ( 2571) covalent geometry : bond 0.00449 (16386) covalent geometry : angle 0.64974 (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 695 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 693 time to evaluate : 1.851 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: A 29 ASP cc_start: 0.9368 (t0) cc_final: 0.9116 (t70) REVERT: A 95 MET cc_start: 0.9269 (mmm) cc_final: 0.8929 (tpp) REVERT: A 100 PHE cc_start: 0.9520 (t80) cc_final: 0.9221 (t80) REVERT: A 101 TYR cc_start: 0.9525 (m-80) cc_final: 0.9259 (m-10) REVERT: A 115 LEU cc_start: 0.9629 (mt) cc_final: 0.9348 (mt) REVERT: A 116 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7580 (tt0) REVERT: A 119 GLU cc_start: 0.9258 (mp0) cc_final: 0.8845 (mp0) REVERT: A 120 ASP cc_start: 0.9280 (m-30) cc_final: 0.9064 (m-30) REVERT: A 136 LYS cc_start: 0.9554 (tttp) cc_final: 0.9341 (ttmm) REVERT: A 144 MET cc_start: 0.8818 (mtm) cc_final: 0.8392 (mtm) REVERT: A 147 GLN cc_start: 0.8857 (mt0) cc_final: 0.8391 (mt0) REVERT: A 176 ASN cc_start: 0.8045 (t0) cc_final: 0.7724 (t0) REVERT: A 190 MET cc_start: 0.9193 (mtp) cc_final: 0.8958 (mtp) REVERT: A 199 VAL cc_start: 0.9544 (t) cc_final: 0.9321 (t) REVERT: A 205 LYS cc_start: 0.8308 (mttm) cc_final: 0.8028 (mttm) REVERT: A 221 LYS cc_start: 0.9070 (mmtm) cc_final: 0.8676 (mptt) REVERT: A 236 TYR cc_start: 0.8918 (t80) cc_final: 0.8546 (t80) REVERT: A 279 SER cc_start: 0.8212 (m) cc_final: 0.7660 (p) REVERT: A 283 VAL cc_start: 0.9179 (t) cc_final: 0.8903 (t) REVERT: A 286 ASP cc_start: 0.9068 (m-30) cc_final: 0.8846 (m-30) REVERT: A 300 VAL cc_start: 0.9648 (m) cc_final: 0.9400 (m) REVERT: A 322 MET cc_start: 0.8894 (mmp) cc_final: 0.8304 (tmm) REVERT: A 326 PHE cc_start: 0.9677 (m-10) cc_final: 0.9077 (m-80) REVERT: A 335 GLU cc_start: 0.9268 (mm-30) cc_final: 0.8770 (mp0) REVERT: A 359 MET cc_start: 0.8698 (ttp) cc_final: 0.8390 (ttp) REVERT: A 362 ASP cc_start: 0.9132 (m-30) cc_final: 0.8849 (m-30) REVERT: A 370 ASN cc_start: 0.9531 (m-40) cc_final: 0.9113 (m-40) REVERT: A 375 LYS cc_start: 0.8923 (mmmt) cc_final: 0.8526 (mmtm) REVERT: A 377 LYS cc_start: 0.8863 (mttt) cc_final: 0.8446 (mttp) REVERT: A 407 ILE cc_start: 0.9036 (mt) cc_final: 0.8680 (mt) REVERT: A 441 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8962 (mm-30) REVERT: A 459 LYS cc_start: 0.9092 (mttp) cc_final: 0.8416 (mtmm) REVERT: A 469 HIS cc_start: 0.9214 (t-170) cc_final: 0.8896 (t-170) REVERT: A 493 MET cc_start: 0.9307 (tmm) cc_final: 0.9027 (tmm) REVERT: A 494 MET cc_start: 0.9639 (mpp) cc_final: 0.9274 (mpp) REVERT: A 501 GLN cc_start: 0.9430 (tp40) cc_final: 0.8718 (tp-100) REVERT: A 515 ASP cc_start: 0.9288 (m-30) cc_final: 0.8743 (m-30) REVERT: A 561 LEU cc_start: 0.9604 (tp) cc_final: 0.9382 (tp) REVERT: A 595 MET cc_start: 0.9516 (mmm) cc_final: 0.9274 (tpp) REVERT: A 598 MET cc_start: 0.8606 (ttt) cc_final: 0.8342 (ttt) REVERT: A 599 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7950 (tm-30) REVERT: A 657 PHE cc_start: 0.8824 (m-80) cc_final: 0.8558 (m-80) REVERT: A 662 MET cc_start: 0.8629 (pmm) cc_final: 0.8148 (pmm) REVERT: A 686 ARG cc_start: 0.7438 (mmm160) cc_final: 0.7203 (mmm160) REVERT: B 8 LYS cc_start: 0.9367 (tptp) cc_final: 0.9054 (tptp) REVERT: B 30 LYS cc_start: 0.9772 (tmtt) cc_final: 0.9411 (tptt) REVERT: B 95 MET cc_start: 0.9521 (mmp) cc_final: 0.9306 (mmm) REVERT: B 99 LYS cc_start: 0.9555 (mmmt) cc_final: 0.9121 (mttt) REVERT: B 119 GLU cc_start: 0.9242 (mp0) cc_final: 0.8814 (mp0) REVERT: B 211 GLU cc_start: 0.8710 (mm-30) cc_final: 0.7457 (mt-10) REVERT: B 250 TYR cc_start: 0.8728 (m-80) cc_final: 0.7443 (m-80) REVERT: B 283 VAL cc_start: 0.9541 (t) cc_final: 0.9233 (t) REVERT: B 286 ASP cc_start: 0.8867 (m-30) cc_final: 0.8142 (m-30) REVERT: B 290 GLU cc_start: 0.9240 (pp20) cc_final: 0.9004 (pp20) REVERT: B 291 LEU cc_start: 0.9540 (mt) cc_final: 0.9268 (mt) REVERT: B 322 MET cc_start: 0.8946 (mmm) cc_final: 0.8128 (mmm) REVERT: B 326 PHE cc_start: 0.9531 (m-10) cc_final: 0.9066 (m-80) REVERT: B 349 LEU cc_start: 0.9336 (mm) cc_final: 0.9089 (mt) REVERT: B 359 MET cc_start: 0.8933 (ttt) cc_final: 0.8474 (tmm) REVERT: B 362 ASP cc_start: 0.8534 (m-30) cc_final: 0.7432 (m-30) REVERT: B 375 LYS cc_start: 0.9283 (mmmm) cc_final: 0.9070 (mmmm) REVERT: B 379 SER cc_start: 0.9149 (t) cc_final: 0.8387 (t) REVERT: B 402 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8326 (tm-30) REVERT: B 403 ILE cc_start: 0.9388 (mp) cc_final: 0.8987 (tp) REVERT: B 410 ASN cc_start: 0.8922 (m110) cc_final: 0.8547 (m110) REVERT: B 416 ILE cc_start: 0.9645 (mt) cc_final: 0.9356 (mt) REVERT: B 420 MET cc_start: 0.9365 (mmm) cc_final: 0.8894 (mmm) REVERT: B 468 LEU cc_start: 0.9644 (tp) cc_final: 0.9382 (tp) REVERT: B 500 ILE cc_start: 0.9687 (mt) cc_final: 0.9448 (mt) REVERT: B 510 LYS cc_start: 0.9358 (mppt) cc_final: 0.9146 (mmtm) REVERT: B 550 MET cc_start: 0.8197 (mmp) cc_final: 0.7951 (mmm) REVERT: B 570 MET cc_start: 0.9030 (mmm) cc_final: 0.8315 (mmm) REVERT: B 572 HIS cc_start: 0.9297 (m90) cc_final: 0.9031 (m90) REVERT: B 574 TYR cc_start: 0.8643 (m-10) cc_final: 0.8346 (m-10) REVERT: B 598 MET cc_start: 0.9383 (mtm) cc_final: 0.9042 (mtm) REVERT: B 599 GLU cc_start: 0.8918 (pt0) cc_final: 0.8415 (pt0) REVERT: B 612 TYR cc_start: 0.9054 (m-80) cc_final: 0.7877 (m-80) REVERT: B 613 TYR cc_start: 0.9082 (t80) cc_final: 0.8318 (t80) REVERT: B 615 MET cc_start: 0.8939 (mmp) cc_final: 0.7091 (mmt) REVERT: B 631 ASP cc_start: 0.9419 (t70) cc_final: 0.9142 (t0) REVERT: B 636 LYS cc_start: 0.9630 (mptt) cc_final: 0.9313 (mmtt) REVERT: B 640 MET cc_start: 0.9544 (tpp) cc_final: 0.9044 (tpp) REVERT: B 656 LEU cc_start: 0.9620 (mt) cc_final: 0.9394 (mt) REVERT: B 673 TYR cc_start: 0.9169 (t80) cc_final: 0.8714 (t80) REVERT: B 679 ILE cc_start: 0.9596 (mm) cc_final: 0.9343 (mm) REVERT: B 687 THR cc_start: 0.8577 (t) cc_final: 0.8327 (t) REVERT: C 17 PHE cc_start: 0.8480 (p90) cc_final: 0.7488 (p90) REVERT: C 20 MET cc_start: 0.8930 (ptp) cc_final: 0.8605 (pmm) REVERT: C 21 PHE cc_start: 0.9174 (m-10) cc_final: 0.8452 (m-80) REVERT: C 122 PHE cc_start: 0.8711 (m-80) cc_final: 0.8391 (m-80) REVERT: C 157 MET cc_start: 0.9706 (mtm) cc_final: 0.9241 (ptm) REVERT: C 163 LEU cc_start: 0.9552 (tt) cc_final: 0.9201 (tt) REVERT: C 178 PHE cc_start: 0.9224 (m-80) cc_final: 0.8854 (m-10) REVERT: C 239 GLU cc_start: 0.8755 (pt0) cc_final: 0.8258 (pt0) REVERT: C 263 ASN cc_start: 0.6739 (m110) cc_final: 0.6440 (p0) REVERT: D 93 MET cc_start: 0.9434 (mtm) cc_final: 0.9203 (mtm) REVERT: D 109 PHE cc_start: 0.8925 (m-80) cc_final: 0.8160 (m-80) REVERT: D 164 GLU cc_start: 0.8564 (pt0) cc_final: 0.8288 (pt0) REVERT: D 172 PHE cc_start: 0.9394 (m-80) cc_final: 0.8330 (m-80) outliers start: 2 outliers final: 0 residues processed: 694 average time/residue: 0.2752 time to fit residues: 280.4806 Evaluate side-chains 595 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 595 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 180 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 39 optimal weight: 0.0470 chunk 50 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 overall best weight: 2.0084 ------------------------------------------------------------------------------- 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 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN D 23 ASN D 91 ASN ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.109135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.080079 restraints weight = 49979.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.083157 restraints weight = 30396.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.085341 restraints weight = 21056.034| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.6169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16386 Z= 0.169 Angle : 0.612 8.319 22134 Z= 0.325 Chirality : 0.043 0.163 2360 Planarity : 0.004 0.045 2818 Dihedral : 11.060 179.881 2242 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % 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: 0.89 (0.19), residues: 1932 helix: 1.04 (0.15), residues: 1132 sheet: -0.23 (0.41), residues: 140 loop : 0.20 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 124 HIS 0.005 0.001 HIS A 438 PHE 0.043 0.002 PHE C 168 TYR 0.045 0.002 TYR A 612 ARG 0.006 0.001 ARG A 575 Details of bonding type rmsd hydrogen bonds : bond 0.04039 ( 871) hydrogen bonds : angle 5.00382 ( 2571) covalent geometry : bond 0.00356 (16386) covalent geometry : angle 0.61242 (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 695 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 695 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9343 (t0) cc_final: 0.9071 (t0) REVERT: A 95 MET cc_start: 0.9185 (mmm) cc_final: 0.8726 (tpt) REVERT: A 99 LYS cc_start: 0.9662 (mmtp) cc_final: 0.9461 (mmmm) REVERT: A 116 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7688 (tt0) REVERT: A 119 GLU cc_start: 0.9192 (mp0) cc_final: 0.8864 (mp0) REVERT: A 136 LYS cc_start: 0.9580 (tttp) cc_final: 0.9327 (ttmm) REVERT: A 144 MET cc_start: 0.8722 (mtm) cc_final: 0.8292 (mtm) REVERT: A 147 GLN cc_start: 0.8752 (mt0) cc_final: 0.8378 (mt0) REVERT: A 164 ARG cc_start: 0.7838 (ptm-80) cc_final: 0.6710 (ptm-80) REVERT: A 172 LEU cc_start: 0.9398 (mp) cc_final: 0.9071 (mp) REVERT: A 173 LEU cc_start: 0.9482 (mt) cc_final: 0.9265 (mt) REVERT: A 176 ASN cc_start: 0.8046 (t0) cc_final: 0.7718 (t0) REVERT: A 190 MET cc_start: 0.9168 (mtp) cc_final: 0.8940 (mtp) REVERT: A 199 VAL cc_start: 0.9570 (t) cc_final: 0.9259 (t) REVERT: A 235 ARG cc_start: 0.8340 (mtm110) cc_final: 0.8025 (mtm110) REVERT: A 236 TYR cc_start: 0.8951 (t80) cc_final: 0.8623 (t80) REVERT: A 280 ILE cc_start: 0.8599 (pt) cc_final: 0.8387 (mp) REVERT: A 283 VAL cc_start: 0.9223 (t) cc_final: 0.8993 (t) REVERT: A 286 ASP cc_start: 0.9028 (m-30) cc_final: 0.8719 (m-30) REVERT: A 316 GLU cc_start: 0.9495 (tt0) cc_final: 0.9294 (tt0) REVERT: A 322 MET cc_start: 0.9031 (mmp) cc_final: 0.8454 (mmm) REVERT: A 326 PHE cc_start: 0.9681 (m-10) cc_final: 0.9184 (m-80) REVERT: A 335 GLU cc_start: 0.9239 (mm-30) cc_final: 0.8810 (mp0) REVERT: A 359 MET cc_start: 0.8819 (ttp) cc_final: 0.8577 (ttp) REVERT: A 362 ASP cc_start: 0.9113 (m-30) cc_final: 0.8851 (m-30) REVERT: A 370 ASN cc_start: 0.9553 (m-40) cc_final: 0.9030 (m110) REVERT: A 375 LYS cc_start: 0.9002 (mmmt) cc_final: 0.8622 (mmtm) REVERT: A 377 LYS cc_start: 0.8901 (mttt) cc_final: 0.8344 (mtmm) REVERT: A 406 ASP cc_start: 0.8673 (m-30) cc_final: 0.8331 (m-30) REVERT: A 407 ILE cc_start: 0.9095 (mt) cc_final: 0.8751 (mt) REVERT: A 441 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8955 (mm-30) REVERT: A 458 MET cc_start: 0.8863 (mmp) cc_final: 0.8460 (mmp) REVERT: A 459 LYS cc_start: 0.9176 (mttp) cc_final: 0.8482 (mtmm) REVERT: A 469 HIS cc_start: 0.9137 (t-170) cc_final: 0.8909 (t-170) REVERT: A 493 MET cc_start: 0.9295 (tmm) cc_final: 0.8858 (tmm) REVERT: A 494 MET cc_start: 0.9555 (mpp) cc_final: 0.9103 (mmm) REVERT: A 501 GLN cc_start: 0.9391 (tp40) cc_final: 0.8709 (tp40) REVERT: A 515 ASP cc_start: 0.9338 (m-30) cc_final: 0.8480 (m-30) REVERT: A 516 GLN cc_start: 0.9322 (mp10) cc_final: 0.8836 (mp10) REVERT: A 561 LEU cc_start: 0.9644 (tp) cc_final: 0.9105 (tp) REVERT: A 570 MET cc_start: 0.9316 (mtp) cc_final: 0.8921 (mtp) REVERT: A 595 MET cc_start: 0.9403 (mmm) cc_final: 0.9150 (tpp) REVERT: A 598 MET cc_start: 0.8577 (ttt) cc_final: 0.8261 (ttt) REVERT: A 602 GLU cc_start: 0.8110 (pp20) cc_final: 0.7642 (pp20) REVERT: A 615 MET cc_start: 0.8935 (mmp) cc_final: 0.8646 (mmp) REVERT: A 640 MET cc_start: 0.9403 (tpp) cc_final: 0.9006 (tpp) REVERT: A 657 PHE cc_start: 0.8839 (m-80) cc_final: 0.8529 (m-80) REVERT: A 662 MET cc_start: 0.8626 (pmm) cc_final: 0.8269 (pmm) REVERT: A 675 HIS cc_start: 0.9224 (t-90) cc_final: 0.8662 (t70) REVERT: A 686 ARG cc_start: 0.7477 (mmm160) cc_final: 0.7041 (mmm160) REVERT: B 8 LYS cc_start: 0.9342 (tptp) cc_final: 0.9036 (tptp) REVERT: B 30 LYS cc_start: 0.9780 (tmtt) cc_final: 0.9409 (tptt) REVERT: B 99 LYS cc_start: 0.9558 (mmmt) cc_final: 0.9320 (mmmt) REVERT: B 116 GLU cc_start: 0.8388 (tt0) cc_final: 0.8048 (tt0) REVERT: B 117 ARG cc_start: 0.9067 (mtp180) cc_final: 0.8713 (mtp180) REVERT: B 119 GLU cc_start: 0.9194 (mp0) cc_final: 0.8819 (mp0) REVERT: B 168 VAL cc_start: 0.9522 (t) cc_final: 0.9289 (m) REVERT: B 191 GLN cc_start: 0.9034 (mm-40) cc_final: 0.8825 (mm-40) REVERT: B 211 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8169 (mm-30) REVERT: B 250 TYR cc_start: 0.8716 (m-80) cc_final: 0.7465 (m-80) REVERT: B 263 ASP cc_start: 0.9131 (m-30) cc_final: 0.8841 (m-30) REVERT: B 283 VAL cc_start: 0.9541 (t) cc_final: 0.9154 (t) REVERT: B 322 MET cc_start: 0.8838 (mmm) cc_final: 0.8137 (mmm) REVERT: B 326 PHE cc_start: 0.9495 (m-10) cc_final: 0.9029 (m-80) REVERT: B 349 LEU cc_start: 0.9342 (mm) cc_final: 0.9123 (mt) REVERT: B 359 MET cc_start: 0.8892 (ttt) cc_final: 0.8442 (tmm) REVERT: B 375 LYS cc_start: 0.9288 (mmmm) cc_final: 0.9016 (mmmm) REVERT: B 379 SER cc_start: 0.9167 (t) cc_final: 0.8490 (t) REVERT: B 402 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8298 (tm-30) REVERT: B 403 ILE cc_start: 0.9348 (mp) cc_final: 0.8969 (tp) REVERT: B 407 ILE cc_start: 0.8864 (mt) cc_final: 0.8648 (mt) REVERT: B 410 ASN cc_start: 0.8927 (m110) cc_final: 0.8517 (m110) REVERT: B 415 ASN cc_start: 0.9416 (t0) cc_final: 0.8993 (t0) REVERT: B 416 ILE cc_start: 0.9627 (mt) cc_final: 0.9421 (mt) REVERT: B 419 VAL cc_start: 0.9598 (p) cc_final: 0.9385 (p) REVERT: B 420 MET cc_start: 0.9402 (mmm) cc_final: 0.8987 (mmm) REVERT: B 458 MET cc_start: 0.9447 (mmm) cc_final: 0.8714 (mmm) REVERT: B 468 LEU cc_start: 0.9582 (tp) cc_final: 0.9309 (tp) REVERT: B 598 MET cc_start: 0.9446 (mtm) cc_final: 0.9028 (mtm) REVERT: B 612 TYR cc_start: 0.8863 (m-80) cc_final: 0.8087 (m-80) REVERT: B 613 TYR cc_start: 0.9048 (t80) cc_final: 0.7891 (t80) REVERT: B 631 ASP cc_start: 0.9387 (t70) cc_final: 0.9087 (t0) REVERT: B 639 ASP cc_start: 0.9319 (m-30) cc_final: 0.8888 (m-30) REVERT: B 640 MET cc_start: 0.9465 (tpp) cc_final: 0.9035 (tpp) REVERT: B 645 GLN cc_start: 0.9077 (tp40) cc_final: 0.8865 (tp-100) REVERT: B 648 ILE cc_start: 0.9353 (mm) cc_final: 0.9044 (mm) REVERT: B 656 LEU cc_start: 0.9609 (mt) cc_final: 0.9390 (mt) REVERT: B 673 TYR cc_start: 0.9124 (t80) cc_final: 0.8756 (t80) REVERT: B 679 ILE cc_start: 0.9614 (mm) cc_final: 0.9382 (mm) REVERT: B 686 ARG cc_start: 0.8383 (tpm170) cc_final: 0.8139 (tpm170) REVERT: B 687 THR cc_start: 0.8339 (t) cc_final: 0.8001 (t) REVERT: C 17 PHE cc_start: 0.8643 (p90) cc_final: 0.7588 (p90) REVERT: C 20 MET cc_start: 0.8939 (ptp) cc_final: 0.8664 (ptp) REVERT: C 21 PHE cc_start: 0.9186 (m-10) cc_final: 0.8268 (m-80) REVERT: C 96 MET cc_start: 0.8310 (tpt) cc_final: 0.8064 (tpt) REVERT: C 122 PHE cc_start: 0.8618 (m-80) cc_final: 0.8264 (m-80) REVERT: C 157 MET cc_start: 0.9697 (mtm) cc_final: 0.9407 (ttm) REVERT: C 178 PHE cc_start: 0.9233 (m-80) cc_final: 0.8896 (m-10) REVERT: D 109 PHE cc_start: 0.8935 (m-80) cc_final: 0.8266 (m-80) REVERT: D 112 LEU cc_start: 0.8549 (mm) cc_final: 0.7686 (pp) REVERT: D 172 PHE cc_start: 0.9251 (m-80) cc_final: 0.8687 (m-80) REVERT: D 179 TYR cc_start: 0.7798 (t80) cc_final: 0.7596 (t80) REVERT: D 185 MET cc_start: 0.5510 (mmp) cc_final: 0.5066 (mmp) REVERT: D 189 GLU cc_start: 0.9223 (pt0) cc_final: 0.8919 (pt0) REVERT: D 224 LEU cc_start: 0.9388 (mt) cc_final: 0.9163 (mt) REVERT: D 252 LEU cc_start: 0.8177 (mt) cc_final: 0.7885 (mp) outliers start: 0 outliers final: 0 residues processed: 695 average time/residue: 0.2990 time to fit residues: 309.1145 Evaluate side-chains 586 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 586 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 57 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 182 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 ASN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 HIS D 233 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.105694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.077304 restraints weight = 51724.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.080297 restraints weight = 31041.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.082424 restraints weight = 21365.396| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.6751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16386 Z= 0.212 Angle : 0.646 7.122 22134 Z= 0.346 Chirality : 0.043 0.219 2360 Planarity : 0.004 0.043 2818 Dihedral : 11.019 177.530 2242 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: 0.66 (0.18), residues: 1932 helix: 0.93 (0.15), residues: 1137 sheet: -0.40 (0.41), residues: 144 loop : -0.05 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP D 124 HIS 0.008 0.001 HIS B 675 PHE 0.042 0.002 PHE C 168 TYR 0.034 0.002 TYR D 130 ARG 0.005 0.001 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.04140 ( 871) hydrogen bonds : angle 5.11038 ( 2571) covalent geometry : bond 0.00442 (16386) covalent geometry : angle 0.64629 (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 673 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 673 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9170 (tptp) cc_final: 0.8772 (tppt) REVERT: A 29 ASP cc_start: 0.9368 (t0) cc_final: 0.9161 (t70) REVERT: A 41 ILE cc_start: 0.9729 (mm) cc_final: 0.9493 (mt) REVERT: A 95 MET cc_start: 0.9362 (mmm) cc_final: 0.8114 (mmm) REVERT: A 116 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7904 (tt0) REVERT: A 119 GLU cc_start: 0.9136 (mp0) cc_final: 0.8835 (mp0) REVERT: A 136 LYS cc_start: 0.9607 (tttp) cc_final: 0.9329 (ttmm) REVERT: A 144 MET cc_start: 0.8734 (mtm) cc_final: 0.8316 (mtm) REVERT: A 147 GLN cc_start: 0.8734 (mt0) cc_final: 0.8419 (mt0) REVERT: A 172 LEU cc_start: 0.9452 (mp) cc_final: 0.9119 (mp) REVERT: A 190 MET cc_start: 0.9180 (mtp) cc_final: 0.8906 (mtp) REVERT: A 199 VAL cc_start: 0.9555 (t) cc_final: 0.9224 (t) REVERT: A 236 TYR cc_start: 0.8944 (t80) cc_final: 0.8341 (t80) REVERT: A 280 ILE cc_start: 0.8670 (pt) cc_final: 0.8187 (mp) REVERT: A 286 ASP cc_start: 0.9076 (m-30) cc_final: 0.8748 (m-30) REVERT: A 316 GLU cc_start: 0.9452 (tt0) cc_final: 0.9230 (tt0) REVERT: A 322 MET cc_start: 0.9084 (mmp) cc_final: 0.8752 (mmm) REVERT: A 335 GLU cc_start: 0.9308 (mm-30) cc_final: 0.8862 (mp0) REVERT: A 359 MET cc_start: 0.8945 (ttp) cc_final: 0.8577 (ttp) REVERT: A 362 ASP cc_start: 0.9059 (m-30) cc_final: 0.8854 (m-30) REVERT: A 370 ASN cc_start: 0.9567 (m-40) cc_final: 0.9246 (m110) REVERT: A 375 LYS cc_start: 0.9005 (mmmt) cc_final: 0.8484 (mmtm) REVERT: A 377 LYS cc_start: 0.8900 (mttt) cc_final: 0.8508 (mttp) REVERT: A 406 ASP cc_start: 0.8732 (m-30) cc_final: 0.8376 (m-30) REVERT: A 407 ILE cc_start: 0.9126 (mt) cc_final: 0.8773 (mt) REVERT: A 441 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8945 (mm-30) REVERT: A 469 HIS cc_start: 0.9207 (t-170) cc_final: 0.8988 (t-170) REVERT: A 490 THR cc_start: 0.9618 (m) cc_final: 0.8915 (m) REVERT: A 493 MET cc_start: 0.9146 (tmm) cc_final: 0.8664 (tmm) REVERT: A 494 MET cc_start: 0.9525 (mpp) cc_final: 0.9072 (mmm) REVERT: A 501 GLN cc_start: 0.9428 (tp40) cc_final: 0.9214 (mm-40) REVERT: A 506 ILE cc_start: 0.9645 (mt) cc_final: 0.9407 (mt) REVERT: A 515 ASP cc_start: 0.9386 (m-30) cc_final: 0.8858 (m-30) REVERT: A 570 MET cc_start: 0.9324 (mtp) cc_final: 0.8936 (mtp) REVERT: A 595 MET cc_start: 0.9450 (mmm) cc_final: 0.9205 (tpp) REVERT: A 604 ARG cc_start: 0.8700 (ttm110) cc_final: 0.8435 (ttm110) REVERT: A 615 MET cc_start: 0.9012 (mmp) cc_final: 0.8750 (mmp) REVERT: A 632 MET cc_start: 0.8481 (mmp) cc_final: 0.8189 (mmp) REVERT: A 636 LYS cc_start: 0.9802 (mmtp) cc_final: 0.9587 (mmmm) REVERT: A 640 MET cc_start: 0.9390 (tpp) cc_final: 0.8955 (tpp) REVERT: A 657 PHE cc_start: 0.8924 (m-80) cc_final: 0.8591 (m-80) REVERT: A 662 MET cc_start: 0.8499 (pmm) cc_final: 0.8229 (pmm) REVERT: A 675 HIS cc_start: 0.9258 (t-90) cc_final: 0.9037 (t-90) REVERT: B 8 LYS cc_start: 0.9362 (tptp) cc_final: 0.9107 (tptp) REVERT: B 30 LYS cc_start: 0.9782 (tmtt) cc_final: 0.9381 (tptt) REVERT: B 65 GLU cc_start: 0.8415 (tm-30) cc_final: 0.7958 (tm-30) REVERT: B 82 LYS cc_start: 0.9555 (ptpp) cc_final: 0.9252 (ptpt) REVERT: B 95 MET cc_start: 0.9233 (tpp) cc_final: 0.8503 (tpp) REVERT: B 99 LYS cc_start: 0.9544 (mmmt) cc_final: 0.8918 (mmmt) REVERT: B 116 GLU cc_start: 0.8375 (tt0) cc_final: 0.8007 (tt0) REVERT: B 117 ARG cc_start: 0.9104 (mtp180) cc_final: 0.8744 (mtp180) REVERT: B 119 GLU cc_start: 0.9229 (mp0) cc_final: 0.8793 (mp0) REVERT: B 120 ASP cc_start: 0.9427 (m-30) cc_final: 0.9160 (m-30) REVERT: B 124 ILE cc_start: 0.9595 (mm) cc_final: 0.9389 (mm) REVERT: B 139 GLU cc_start: 0.9444 (mp0) cc_final: 0.9236 (mp0) REVERT: B 168 VAL cc_start: 0.9516 (t) cc_final: 0.9267 (m) REVERT: B 191 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8647 (mm-40) REVERT: B 211 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8325 (mm-30) REVERT: B 235 ARG cc_start: 0.8703 (ttm110) cc_final: 0.8096 (ttm110) REVERT: B 250 TYR cc_start: 0.8745 (m-80) cc_final: 0.7564 (m-80) REVERT: B 263 ASP cc_start: 0.9239 (m-30) cc_final: 0.8906 (m-30) REVERT: B 283 VAL cc_start: 0.9554 (t) cc_final: 0.9256 (t) REVERT: B 286 ASP cc_start: 0.8941 (m-30) cc_final: 0.6944 (m-30) REVERT: B 316 GLU cc_start: 0.9392 (tm-30) cc_final: 0.9189 (tm-30) REVERT: B 349 LEU cc_start: 0.9377 (mm) cc_final: 0.9164 (mt) REVERT: B 359 MET cc_start: 0.9051 (ttt) cc_final: 0.8490 (tmm) REVERT: B 362 ASP cc_start: 0.8476 (m-30) cc_final: 0.7757 (p0) REVERT: B 375 LYS cc_start: 0.9336 (mmmm) cc_final: 0.9086 (mmmm) REVERT: B 379 SER cc_start: 0.9109 (t) cc_final: 0.8613 (t) REVERT: B 403 ILE cc_start: 0.9296 (mp) cc_final: 0.8772 (tp) REVERT: B 407 ILE cc_start: 0.8982 (mt) cc_final: 0.8748 (mt) REVERT: B 410 ASN cc_start: 0.9124 (m-40) cc_final: 0.8859 (m-40) REVERT: B 415 ASN cc_start: 0.9310 (t0) cc_final: 0.9000 (t0) REVERT: B 416 ILE cc_start: 0.9636 (mt) cc_final: 0.9435 (mt) REVERT: B 420 MET cc_start: 0.9450 (mmm) cc_final: 0.9056 (mmm) REVERT: B 458 MET cc_start: 0.9466 (mmm) cc_final: 0.8795 (mmm) REVERT: B 459 LYS cc_start: 0.9109 (mttp) cc_final: 0.8457 (mtmt) REVERT: B 467 ASN cc_start: 0.8682 (m110) cc_final: 0.8420 (m-40) REVERT: B 468 LEU cc_start: 0.9571 (tp) cc_final: 0.9283 (tp) REVERT: B 494 MET cc_start: 0.9572 (ttm) cc_final: 0.9228 (ttm) REVERT: B 570 MET cc_start: 0.8919 (mmm) cc_final: 0.8464 (mmm) REVERT: B 602 GLU cc_start: 0.8499 (mp0) cc_final: 0.5624 (mp0) REVERT: B 606 TYR cc_start: 0.8838 (m-80) cc_final: 0.7910 (m-80) REVERT: B 612 TYR cc_start: 0.8726 (m-80) cc_final: 0.7813 (m-80) REVERT: B 613 TYR cc_start: 0.9093 (t80) cc_final: 0.7711 (t80) REVERT: B 615 MET cc_start: 0.9087 (mmp) cc_final: 0.8344 (mmp) REVERT: B 631 ASP cc_start: 0.9368 (t70) cc_final: 0.9098 (t0) REVERT: B 636 LYS cc_start: 0.9632 (mptt) cc_final: 0.9303 (mmtt) REVERT: B 639 ASP cc_start: 0.9340 (m-30) cc_final: 0.8823 (m-30) REVERT: B 640 MET cc_start: 0.9402 (tpp) cc_final: 0.8977 (tpp) REVERT: B 648 ILE cc_start: 0.9365 (mm) cc_final: 0.9083 (mm) REVERT: B 656 LEU cc_start: 0.9487 (mt) cc_final: 0.9227 (mt) REVERT: B 673 TYR cc_start: 0.9130 (t80) cc_final: 0.8638 (t80) REVERT: B 679 ILE cc_start: 0.9612 (mm) cc_final: 0.9351 (mm) REVERT: C 17 PHE cc_start: 0.8671 (p90) cc_final: 0.7665 (p90) REVERT: C 20 MET cc_start: 0.8954 (ptp) cc_final: 0.8629 (ptp) REVERT: C 21 PHE cc_start: 0.9132 (m-10) cc_final: 0.8215 (m-80) REVERT: C 66 ASP cc_start: 0.8205 (p0) cc_final: 0.7927 (p0) REVERT: C 96 MET cc_start: 0.8336 (tpt) cc_final: 0.8081 (tpt) REVERT: C 105 TYR cc_start: 0.8690 (m-80) cc_final: 0.8442 (m-80) REVERT: C 122 PHE cc_start: 0.8612 (m-80) cc_final: 0.8271 (m-80) REVERT: C 178 PHE cc_start: 0.9211 (m-80) cc_final: 0.8876 (m-10) REVERT: C 239 GLU cc_start: 0.8662 (pt0) cc_final: 0.8103 (pt0) REVERT: D 21 PHE cc_start: 0.8844 (m-10) cc_final: 0.8487 (m-10) REVERT: D 109 PHE cc_start: 0.8955 (m-80) cc_final: 0.8296 (m-80) REVERT: D 112 LEU cc_start: 0.8595 (mm) cc_final: 0.7698 (pp) REVERT: D 166 PHE cc_start: 0.8234 (t80) cc_final: 0.7878 (t80) REVERT: D 172 PHE cc_start: 0.9405 (m-80) cc_final: 0.8854 (m-80) REVERT: D 179 TYR cc_start: 0.8119 (t80) cc_final: 0.7828 (t80) REVERT: D 185 MET cc_start: 0.5784 (mmp) cc_final: 0.5496 (mmp) REVERT: D 224 LEU cc_start: 0.9401 (mt) cc_final: 0.9198 (mt) outliers start: 0 outliers final: 0 residues processed: 673 average time/residue: 0.2749 time to fit residues: 272.7992 Evaluate side-chains 580 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 580 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 31 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 156 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 169 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 177 optimal weight: 0.4980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.109580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.080242 restraints weight = 50037.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.083250 restraints weight = 30626.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.085494 restraints weight = 21276.474| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.6985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16386 Z= 0.134 Angle : 0.605 7.692 22134 Z= 0.323 Chirality : 0.043 0.181 2360 Planarity : 0.003 0.040 2818 Dihedral : 10.690 176.428 2242 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.17 % Allowed : 1.17 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.79 (0.19), residues: 1932 helix: 1.08 (0.15), residues: 1136 sheet: -0.46 (0.42), residues: 148 loop : -0.03 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP D 124 HIS 0.013 0.001 HIS D 201 PHE 0.038 0.002 PHE C 320 TYR 0.030 0.002 TYR D 130 ARG 0.008 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 871) hydrogen bonds : angle 4.99604 ( 2571) covalent geometry : bond 0.00290 (16386) covalent geometry : angle 0.60504 (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 686 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 683 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9198 (tptp) cc_final: 0.8755 (tppt) REVERT: A 95 MET cc_start: 0.9284 (mmm) cc_final: 0.8107 (mmm) REVERT: A 116 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7861 (tt0) REVERT: A 119 GLU cc_start: 0.9097 (mp0) cc_final: 0.8803 (mp0) REVERT: A 136 LYS cc_start: 0.9610 (tttp) cc_final: 0.9327 (ttmm) REVERT: A 144 MET cc_start: 0.8644 (mtm) cc_final: 0.8305 (mtm) REVERT: A 147 GLN cc_start: 0.8765 (mt0) cc_final: 0.8446 (mt0) REVERT: A 150 GLN cc_start: 0.9268 (tp40) cc_final: 0.9067 (tp40) REVERT: A 172 LEU cc_start: 0.9387 (mp) cc_final: 0.9160 (mp) REVERT: A 187 ASP cc_start: 0.9385 (t70) cc_final: 0.8880 (t70) REVERT: A 190 MET cc_start: 0.9130 (mtp) cc_final: 0.8925 (mtp) REVERT: A 191 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8547 (mp10) REVERT: A 228 LYS cc_start: 0.8538 (mmmm) cc_final: 0.8330 (mmtm) REVERT: A 235 ARG cc_start: 0.8401 (mtm110) cc_final: 0.7901 (mtm110) REVERT: A 236 TYR cc_start: 0.8860 (t80) cc_final: 0.8278 (t80) REVERT: A 280 ILE cc_start: 0.8628 (pt) cc_final: 0.8302 (mp) REVERT: A 286 ASP cc_start: 0.9115 (m-30) cc_final: 0.8878 (m-30) REVERT: A 316 GLU cc_start: 0.9445 (tt0) cc_final: 0.9231 (tt0) REVERT: A 335 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8866 (mp0) REVERT: A 349 LEU cc_start: 0.9482 (mt) cc_final: 0.9212 (mt) REVERT: A 359 MET cc_start: 0.8918 (ttp) cc_final: 0.8583 (ttp) REVERT: A 370 ASN cc_start: 0.9466 (m-40) cc_final: 0.9146 (m110) REVERT: A 375 LYS cc_start: 0.9053 (mmmt) cc_final: 0.8779 (mmtm) REVERT: A 377 LYS cc_start: 0.8902 (mttt) cc_final: 0.8337 (mttp) REVERT: A 381 LEU cc_start: 0.8985 (tp) cc_final: 0.8436 (pt) REVERT: A 406 ASP cc_start: 0.8750 (m-30) cc_final: 0.8432 (m-30) REVERT: A 407 ILE cc_start: 0.9109 (mt) cc_final: 0.8780 (mt) REVERT: A 426 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8416 (tm-30) REVERT: A 441 GLU cc_start: 0.9295 (mm-30) cc_final: 0.9083 (mm-30) REVERT: A 490 THR cc_start: 0.9616 (m) cc_final: 0.8811 (m) REVERT: A 493 MET cc_start: 0.9153 (tmm) cc_final: 0.8545 (tmm) REVERT: A 494 MET cc_start: 0.9515 (mpp) cc_final: 0.9016 (mmm) REVERT: A 501 GLN cc_start: 0.9396 (tp40) cc_final: 0.9125 (mm-40) REVERT: A 515 ASP cc_start: 0.9335 (m-30) cc_final: 0.8988 (m-30) REVERT: A 604 ARG cc_start: 0.8830 (ttm110) cc_final: 0.8365 (ttm110) REVERT: A 615 MET cc_start: 0.9062 (mmp) cc_final: 0.8793 (mmp) REVERT: A 636 LYS cc_start: 0.9781 (mmtp) cc_final: 0.9573 (mmmm) REVERT: A 640 MET cc_start: 0.9405 (tpp) cc_final: 0.9085 (tpp) REVERT: B 8 LYS cc_start: 0.9401 (tptp) cc_final: 0.9134 (tptp) REVERT: B 30 LYS cc_start: 0.9781 (tmtt) cc_final: 0.9374 (tptt) REVERT: B 67 GLU cc_start: 0.8888 (mp0) cc_final: 0.8665 (mp0) REVERT: B 95 MET cc_start: 0.9193 (tpp) cc_final: 0.8489 (tpp) REVERT: B 99 LYS cc_start: 0.9535 (mmmt) cc_final: 0.8930 (mmmt) REVERT: B 116 GLU cc_start: 0.8279 (tt0) cc_final: 0.8059 (tt0) REVERT: B 117 ARG cc_start: 0.8980 (mtp180) cc_final: 0.8640 (mtp180) REVERT: B 119 GLU cc_start: 0.9182 (mp0) cc_final: 0.8720 (mp0) REVERT: B 120 ASP cc_start: 0.9420 (m-30) cc_final: 0.9200 (m-30) REVERT: B 172 LEU cc_start: 0.9068 (mp) cc_final: 0.8855 (mp) REVERT: B 211 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8144 (mt-10) REVERT: B 235 ARG cc_start: 0.8729 (ttm110) cc_final: 0.8127 (ttm110) REVERT: B 250 TYR cc_start: 0.8589 (m-80) cc_final: 0.7403 (m-80) REVERT: B 263 ASP cc_start: 0.9230 (m-30) cc_final: 0.8906 (m-30) REVERT: B 283 VAL cc_start: 0.9542 (t) cc_final: 0.9194 (t) REVERT: B 286 ASP cc_start: 0.8863 (m-30) cc_final: 0.6696 (m-30) REVERT: B 322 MET cc_start: 0.8796 (mmm) cc_final: 0.8445 (mmm) REVERT: B 359 MET cc_start: 0.9076 (ttt) cc_final: 0.8474 (tmm) REVERT: B 362 ASP cc_start: 0.8580 (m-30) cc_final: 0.7786 (p0) REVERT: B 375 LYS cc_start: 0.9298 (mmmm) cc_final: 0.9035 (mmmm) REVERT: B 379 SER cc_start: 0.8952 (t) cc_final: 0.8523 (t) REVERT: B 392 SER cc_start: 0.9349 (m) cc_final: 0.8700 (m) REVERT: B 403 ILE cc_start: 0.9286 (mp) cc_final: 0.8829 (tp) REVERT: B 410 ASN cc_start: 0.9112 (m-40) cc_final: 0.8818 (m-40) REVERT: B 415 ASN cc_start: 0.9252 (t0) cc_final: 0.8873 (t0) REVERT: B 416 ILE cc_start: 0.9623 (mt) cc_final: 0.9411 (mt) REVERT: B 420 MET cc_start: 0.9459 (mmm) cc_final: 0.9131 (mmm) REVERT: B 458 MET cc_start: 0.9376 (mmm) cc_final: 0.8785 (mmm) REVERT: B 459 LYS cc_start: 0.8978 (mttp) cc_final: 0.8299 (mtmt) REVERT: B 460 SER cc_start: 0.8798 (t) cc_final: 0.8568 (t) REVERT: B 467 ASN cc_start: 0.8551 (m110) cc_final: 0.8194 (m-40) REVERT: B 468 LEU cc_start: 0.9525 (tp) cc_final: 0.9232 (tp) REVERT: B 469 HIS cc_start: 0.8926 (t-170) cc_final: 0.8653 (t70) REVERT: B 494 MET cc_start: 0.9559 (ttm) cc_final: 0.9236 (ttm) REVERT: B 506 ILE cc_start: 0.9593 (mm) cc_final: 0.9344 (mm) REVERT: B 571 TYR cc_start: 0.9318 (t80) cc_final: 0.8851 (t80) REVERT: B 599 GLU cc_start: 0.9034 (pm20) cc_final: 0.8801 (pm20) REVERT: B 601 ILE cc_start: 0.9145 (mm) cc_final: 0.8785 (tp) REVERT: B 602 GLU cc_start: 0.8343 (mp0) cc_final: 0.6334 (mp0) REVERT: B 612 TYR cc_start: 0.8729 (m-80) cc_final: 0.7860 (m-80) REVERT: B 613 TYR cc_start: 0.9140 (t80) cc_final: 0.7709 (t80) REVERT: B 615 MET cc_start: 0.9066 (mmp) cc_final: 0.8397 (mmp) REVERT: B 631 ASP cc_start: 0.9372 (t70) cc_final: 0.9129 (t0) REVERT: B 640 MET cc_start: 0.9398 (tpp) cc_final: 0.8942 (tpp) REVERT: B 667 LEU cc_start: 0.9654 (tp) cc_final: 0.9421 (tp) REVERT: B 675 HIS cc_start: 0.9347 (t-90) cc_final: 0.8975 (t-90) REVERT: B 679 ILE cc_start: 0.9643 (mm) cc_final: 0.9411 (mm) REVERT: C 17 PHE cc_start: 0.8593 (p90) cc_final: 0.7630 (p90) REVERT: C 21 PHE cc_start: 0.9112 (m-10) cc_final: 0.8540 (m-80) REVERT: C 96 MET cc_start: 0.8343 (tpt) cc_final: 0.8058 (tpt) REVERT: C 105 TYR cc_start: 0.8800 (m-80) cc_final: 0.8504 (m-80) REVERT: C 122 PHE cc_start: 0.8620 (m-80) cc_final: 0.8250 (m-80) REVERT: C 157 MET cc_start: 0.9554 (ptm) cc_final: 0.8944 (ppp) REVERT: C 178 PHE cc_start: 0.9238 (m-80) cc_final: 0.9004 (m-10) REVERT: C 233 ASN cc_start: 0.9513 (m110) cc_final: 0.9237 (p0) REVERT: C 283 ASN cc_start: 0.7780 (t0) cc_final: 0.7531 (t0) REVERT: C 285 ILE cc_start: 0.9151 (mm) cc_final: 0.8884 (mm) REVERT: D 21 PHE cc_start: 0.8731 (m-10) cc_final: 0.8478 (m-10) REVERT: D 96 MET cc_start: 0.8642 (mmp) cc_final: 0.8134 (mmp) REVERT: D 108 ILE cc_start: 0.9511 (mt) cc_final: 0.9289 (pt) REVERT: D 109 PHE cc_start: 0.8937 (m-80) cc_final: 0.8248 (m-80) REVERT: D 112 LEU cc_start: 0.8617 (mm) cc_final: 0.7763 (pp) REVERT: D 169 TYR cc_start: 0.9148 (m-80) cc_final: 0.8660 (m-80) REVERT: D 172 PHE cc_start: 0.9394 (m-80) cc_final: 0.8841 (m-80) REVERT: D 179 TYR cc_start: 0.8088 (t80) cc_final: 0.7800 (t80) REVERT: D 185 MET cc_start: 0.5875 (mmp) cc_final: 0.5531 (mmm) REVERT: D 211 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8959 (mt-10) REVERT: D 271 LEU cc_start: 0.8602 (mt) cc_final: 0.8320 (mt) outliers start: 3 outliers final: 1 residues processed: 686 average time/residue: 0.2642 time to fit residues: 269.6673 Evaluate side-chains 580 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 579 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 39 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 161 optimal weight: 10.0000 chunk 23 optimal weight: 0.0570 chunk 40 optimal weight: 5.9990 chunk 146 optimal weight: 0.5980 chunk 184 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.9304 ------------------------------------------------------------------------------- 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 242 GLN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN A 668 ASN ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 HIS ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.113783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.084304 restraints weight = 49857.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.087509 restraints weight = 30191.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.089746 restraints weight = 20838.180| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.7322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16386 Z= 0.132 Angle : 0.612 7.115 22134 Z= 0.330 Chirality : 0.043 0.306 2360 Planarity : 0.004 0.069 2818 Dihedral : 10.522 174.975 2242 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.12 % Allowed : 0.99 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.70 (0.19), residues: 1932 helix: 1.01 (0.15), residues: 1138 sheet: -0.42 (0.43), residues: 144 loop : -0.14 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP D 124 HIS 0.029 0.002 HIS D 201 PHE 0.037 0.002 PHE C 168 TYR 0.045 0.002 TYR C 142 ARG 0.006 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 871) hydrogen bonds : angle 5.09934 ( 2571) covalent geometry : bond 0.00283 (16386) covalent geometry : angle 0.61204 (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 676 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 674 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9197 (tptp) cc_final: 0.8736 (tppt) REVERT: A 116 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7776 (tt0) REVERT: A 119 GLU cc_start: 0.9047 (mp0) cc_final: 0.8730 (mp0) REVERT: A 136 LYS cc_start: 0.9617 (tttp) cc_final: 0.9318 (ttmm) REVERT: A 144 MET cc_start: 0.8635 (mtm) cc_final: 0.8268 (mtm) REVERT: A 147 GLN cc_start: 0.8722 (mt0) cc_final: 0.8428 (mt0) REVERT: A 173 LEU cc_start: 0.9449 (mt) cc_final: 0.9213 (mt) REVERT: A 187 ASP cc_start: 0.9362 (t70) cc_final: 0.8866 (t70) REVERT: A 190 MET cc_start: 0.9125 (mtp) cc_final: 0.8902 (mtp) REVERT: A 191 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8513 (mp10) REVERT: A 235 ARG cc_start: 0.8416 (mtm110) cc_final: 0.8168 (mtm110) REVERT: A 236 TYR cc_start: 0.8898 (t80) cc_final: 0.8329 (t80) REVERT: A 254 PHE cc_start: 0.8445 (m-80) cc_final: 0.7588 (m-10) REVERT: A 280 ILE cc_start: 0.8745 (pt) cc_final: 0.8389 (mp) REVERT: A 286 ASP cc_start: 0.9133 (m-30) cc_final: 0.8836 (m-30) REVERT: A 316 GLU cc_start: 0.9426 (tt0) cc_final: 0.9204 (tt0) REVERT: A 322 MET cc_start: 0.9081 (mmp) cc_final: 0.8741 (tpp) REVERT: A 335 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8888 (mp0) REVERT: A 359 MET cc_start: 0.8826 (ttp) cc_final: 0.8588 (ttp) REVERT: A 362 ASP cc_start: 0.8873 (m-30) cc_final: 0.8635 (m-30) REVERT: A 370 ASN cc_start: 0.9459 (m-40) cc_final: 0.9165 (m110) REVERT: A 375 LYS cc_start: 0.9039 (mmmt) cc_final: 0.8534 (mmtm) REVERT: A 377 LYS cc_start: 0.8858 (mttt) cc_final: 0.8286 (mttp) REVERT: A 381 LEU cc_start: 0.8969 (tp) cc_final: 0.8468 (pt) REVERT: A 403 ILE cc_start: 0.8844 (tp) cc_final: 0.8519 (tp) REVERT: A 407 ILE cc_start: 0.9097 (mt) cc_final: 0.8681 (mt) REVERT: A 426 GLU cc_start: 0.9096 (tm-30) cc_final: 0.8723 (tm-30) REVERT: A 441 GLU cc_start: 0.9291 (mm-30) cc_final: 0.9091 (mm-30) REVERT: A 466 MET cc_start: 0.9207 (ptp) cc_final: 0.8377 (ptp) REVERT: A 469 HIS cc_start: 0.8808 (t-170) cc_final: 0.8601 (t-170) REVERT: A 490 THR cc_start: 0.9478 (m) cc_final: 0.9253 (p) REVERT: A 493 MET cc_start: 0.9053 (tmm) cc_final: 0.8515 (tmm) REVERT: A 494 MET cc_start: 0.9479 (mpp) cc_final: 0.8998 (mmm) REVERT: A 515 ASP cc_start: 0.9367 (m-30) cc_final: 0.8853 (m-30) REVERT: A 570 MET cc_start: 0.9291 (mtp) cc_final: 0.8703 (mtp) REVERT: A 598 MET cc_start: 0.8999 (ttt) cc_final: 0.8495 (ttt) REVERT: A 599 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8019 (tm-30) REVERT: A 628 GLU cc_start: 0.9284 (mt-10) cc_final: 0.8806 (mt-10) REVERT: A 636 LYS cc_start: 0.9775 (mmtp) cc_final: 0.9561 (mmmm) REVERT: A 640 MET cc_start: 0.9440 (tpp) cc_final: 0.8966 (tpp) REVERT: A 677 ARG cc_start: 0.9367 (mmm-85) cc_final: 0.8855 (mmm-85) REVERT: B 8 LYS cc_start: 0.9392 (tptp) cc_final: 0.9163 (tptp) REVERT: B 30 LYS cc_start: 0.9781 (tmtt) cc_final: 0.9380 (tptt) REVERT: B 65 GLU cc_start: 0.8735 (tp30) cc_final: 0.7967 (tp30) REVERT: B 67 GLU cc_start: 0.8804 (mp0) cc_final: 0.8312 (mp0) REVERT: B 95 MET cc_start: 0.9161 (tpp) cc_final: 0.8491 (tpp) REVERT: B 99 LYS cc_start: 0.9531 (mmmt) cc_final: 0.8989 (mmmt) REVERT: B 116 GLU cc_start: 0.8378 (tt0) cc_final: 0.8137 (tt0) REVERT: B 117 ARG cc_start: 0.8966 (mtp180) cc_final: 0.8641 (mtp180) REVERT: B 119 GLU cc_start: 0.9016 (mp0) cc_final: 0.8677 (mp0) REVERT: B 120 ASP cc_start: 0.9368 (m-30) cc_final: 0.9146 (m-30) REVERT: B 144 MET cc_start: 0.9421 (mtm) cc_final: 0.9171 (mtm) REVERT: B 149 TYR cc_start: 0.9114 (t80) cc_final: 0.8681 (t80) REVERT: B 156 PHE cc_start: 0.9496 (t80) cc_final: 0.9192 (t80) REVERT: B 187 ASP cc_start: 0.9446 (t70) cc_final: 0.9166 (t0) REVERT: B 211 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8497 (mm-30) REVERT: B 235 ARG cc_start: 0.8776 (ttm110) cc_final: 0.8226 (ttm110) REVERT: B 250 TYR cc_start: 0.8648 (m-80) cc_final: 0.7459 (m-80) REVERT: B 263 ASP cc_start: 0.9249 (m-30) cc_final: 0.8946 (m-30) REVERT: B 283 VAL cc_start: 0.9553 (t) cc_final: 0.9216 (t) REVERT: B 286 ASP cc_start: 0.8831 (m-30) cc_final: 0.8210 (m-30) REVERT: B 322 MET cc_start: 0.8813 (mmm) cc_final: 0.8483 (mmm) REVERT: B 359 MET cc_start: 0.9022 (ttt) cc_final: 0.8487 (tmm) REVERT: B 375 LYS cc_start: 0.9218 (mmmm) cc_final: 0.8980 (mmmm) REVERT: B 379 SER cc_start: 0.9026 (t) cc_final: 0.8474 (t) REVERT: B 392 SER cc_start: 0.9290 (m) cc_final: 0.8650 (m) REVERT: B 403 ILE cc_start: 0.9322 (mp) cc_final: 0.8968 (tp) REVERT: B 410 ASN cc_start: 0.8863 (m-40) cc_final: 0.8513 (m-40) REVERT: B 415 ASN cc_start: 0.9232 (t0) cc_final: 0.8851 (t0) REVERT: B 416 ILE cc_start: 0.9612 (mt) cc_final: 0.9408 (mt) REVERT: B 420 MET cc_start: 0.9427 (mmm) cc_final: 0.9071 (mmm) REVERT: B 458 MET cc_start: 0.9316 (mmm) cc_final: 0.8767 (mmm) REVERT: B 459 LYS cc_start: 0.8960 (mttp) cc_final: 0.8313 (mtmt) REVERT: B 467 ASN cc_start: 0.8605 (m110) cc_final: 0.8235 (m-40) REVERT: B 469 HIS cc_start: 0.8817 (t-170) cc_final: 0.8485 (t70) REVERT: B 494 MET cc_start: 0.9571 (ttm) cc_final: 0.9255 (ttm) REVERT: B 530 LYS cc_start: 0.8994 (ptmm) cc_final: 0.8758 (ptmm) REVERT: B 574 TYR cc_start: 0.8784 (m-80) cc_final: 0.8524 (m-10) REVERT: B 598 MET cc_start: 0.9247 (mtp) cc_final: 0.9013 (mtp) REVERT: B 601 ILE cc_start: 0.9155 (mm) cc_final: 0.8847 (tp) REVERT: B 602 GLU cc_start: 0.8147 (mp0) cc_final: 0.6323 (mp0) REVERT: B 612 TYR cc_start: 0.8666 (m-80) cc_final: 0.7739 (m-80) REVERT: B 613 TYR cc_start: 0.9204 (t80) cc_final: 0.7776 (t80) REVERT: B 615 MET cc_start: 0.8971 (mmp) cc_final: 0.8398 (mmp) REVERT: B 631 ASP cc_start: 0.9385 (t70) cc_final: 0.9149 (t0) REVERT: B 639 ASP cc_start: 0.9407 (m-30) cc_final: 0.8900 (m-30) REVERT: B 640 MET cc_start: 0.9382 (tpp) cc_final: 0.8827 (tpp) REVERT: B 641 ILE cc_start: 0.9749 (mm) cc_final: 0.9504 (mm) REVERT: B 673 TYR cc_start: 0.9117 (t80) cc_final: 0.8757 (t80) REVERT: B 679 ILE cc_start: 0.9607 (mm) cc_final: 0.9347 (mm) REVERT: C 17 PHE cc_start: 0.8604 (p90) cc_final: 0.7826 (p90) REVERT: C 20 MET cc_start: 0.8883 (ptp) cc_final: 0.8649 (pmm) REVERT: C 21 PHE cc_start: 0.9049 (m-10) cc_final: 0.8429 (m-80) REVERT: C 96 MET cc_start: 0.8396 (tpt) cc_final: 0.8149 (tpt) REVERT: C 105 TYR cc_start: 0.8689 (m-80) cc_final: 0.8428 (m-80) REVERT: C 122 PHE cc_start: 0.8702 (m-80) cc_final: 0.8334 (m-80) REVERT: C 157 MET cc_start: 0.9462 (ptm) cc_final: 0.8892 (ppp) REVERT: C 178 PHE cc_start: 0.9244 (m-80) cc_final: 0.8975 (m-10) REVERT: D 108 ILE cc_start: 0.9479 (mt) cc_final: 0.9246 (pt) REVERT: D 109 PHE cc_start: 0.8916 (m-80) cc_final: 0.8220 (m-80) REVERT: D 112 LEU cc_start: 0.8613 (mm) cc_final: 0.7758 (pp) REVERT: D 166 PHE cc_start: 0.7839 (t80) cc_final: 0.7324 (t80) REVERT: D 169 TYR cc_start: 0.9172 (m-80) cc_final: 0.8691 (m-80) REVERT: D 172 PHE cc_start: 0.9408 (m-80) cc_final: 0.8865 (m-80) REVERT: D 179 TYR cc_start: 0.8158 (t80) cc_final: 0.7822 (t80) REVERT: D 185 MET cc_start: 0.5827 (mmp) cc_final: 0.5485 (mmm) REVERT: D 214 ASN cc_start: 0.9657 (t0) cc_final: 0.9413 (p0) REVERT: D 244 GLU cc_start: 0.9180 (mp0) cc_final: 0.8938 (mm-30) REVERT: D 318 ASP cc_start: 0.9025 (t0) cc_final: 0.8684 (t70) outliers start: 2 outliers final: 1 residues processed: 676 average time/residue: 0.2697 time to fit residues: 270.2056 Evaluate side-chains 582 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 581 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 ASN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 HIS ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN D 132 GLN D 146 GLN ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.109844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.080516 restraints weight = 49764.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.083609 restraints weight = 30399.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.085800 restraints weight = 21133.373| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.7582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16386 Z= 0.168 Angle : 0.645 7.998 22134 Z= 0.345 Chirality : 0.044 0.300 2360 Planarity : 0.004 0.054 2818 Dihedral : 10.548 173.815 2242 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: 0.63 (0.19), residues: 1932 helix: 0.96 (0.15), residues: 1138 sheet: -0.57 (0.42), residues: 144 loop : -0.13 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP D 124 HIS 0.020 0.002 HIS D 201 PHE 0.032 0.002 PHE C 168 TYR 0.033 0.002 TYR C 142 ARG 0.010 0.001 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 871) hydrogen bonds : angle 5.11637 ( 2571) covalent geometry : bond 0.00365 (16386) covalent geometry : angle 0.64463 (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 659 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 659 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9239 (tptp) cc_final: 0.8810 (tppt) REVERT: A 29 ASP cc_start: 0.9298 (t0) cc_final: 0.9072 (t0) REVERT: A 95 MET cc_start: 0.9143 (mmm) cc_final: 0.7551 (tpt) REVERT: A 116 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7729 (tt0) REVERT: A 119 GLU cc_start: 0.9095 (mp0) cc_final: 0.8833 (mp0) REVERT: A 136 LYS cc_start: 0.9614 (tttp) cc_final: 0.9315 (ttmm) REVERT: A 147 GLN cc_start: 0.8719 (mt0) cc_final: 0.8322 (mt0) REVERT: A 164 ARG cc_start: 0.7967 (ptm-80) cc_final: 0.6551 (ptm-80) REVERT: A 190 MET cc_start: 0.9146 (mtp) cc_final: 0.8934 (mtp) REVERT: A 191 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8514 (mm-40) REVERT: A 235 ARG cc_start: 0.8375 (mtm110) cc_final: 0.8143 (mtm110) REVERT: A 236 TYR cc_start: 0.8917 (t80) cc_final: 0.8337 (t80) REVERT: A 261 PHE cc_start: 0.9076 (t80) cc_final: 0.8833 (t80) REVERT: A 280 ILE cc_start: 0.8700 (pt) cc_final: 0.8311 (mp) REVERT: A 286 ASP cc_start: 0.9088 (m-30) cc_final: 0.8802 (m-30) REVERT: A 335 GLU cc_start: 0.9296 (mm-30) cc_final: 0.8927 (mp0) REVERT: A 345 LYS cc_start: 0.8965 (tttt) cc_final: 0.8733 (tttt) REVERT: A 349 LEU cc_start: 0.9446 (mt) cc_final: 0.9185 (mt) REVERT: A 359 MET cc_start: 0.8996 (ttp) cc_final: 0.8632 (ttp) REVERT: A 362 ASP cc_start: 0.8900 (m-30) cc_final: 0.8697 (m-30) REVERT: A 370 ASN cc_start: 0.9500 (m-40) cc_final: 0.9229 (m110) REVERT: A 375 LYS cc_start: 0.8955 (mmmt) cc_final: 0.8421 (mmtm) REVERT: A 377 LYS cc_start: 0.8833 (mttt) cc_final: 0.8272 (mttp) REVERT: A 381 LEU cc_start: 0.9051 (tp) cc_final: 0.8563 (pt) REVERT: A 407 ILE cc_start: 0.9027 (mt) cc_final: 0.8677 (mt) REVERT: A 426 GLU cc_start: 0.9143 (tm-30) cc_final: 0.8457 (tm-30) REVERT: A 441 GLU cc_start: 0.9332 (mm-30) cc_final: 0.9132 (mm-30) REVERT: A 466 MET cc_start: 0.9297 (ptp) cc_final: 0.9071 (ptp) REVERT: A 469 HIS cc_start: 0.8981 (t-170) cc_final: 0.8725 (t-170) REVERT: A 493 MET cc_start: 0.9055 (tmm) cc_final: 0.8706 (tmm) REVERT: A 515 ASP cc_start: 0.9411 (m-30) cc_final: 0.8946 (m-30) REVERT: A 570 MET cc_start: 0.9315 (mtp) cc_final: 0.8996 (mtp) REVERT: A 598 MET cc_start: 0.8916 (ttt) cc_final: 0.8542 (ttt) REVERT: A 604 ARG cc_start: 0.8923 (ttm110) cc_final: 0.8293 (ttm110) REVERT: A 615 MET cc_start: 0.9050 (mmp) cc_final: 0.8764 (mmp) REVERT: A 628 GLU cc_start: 0.9277 (mt-10) cc_final: 0.9001 (mt-10) REVERT: A 636 LYS cc_start: 0.9766 (mmtp) cc_final: 0.9547 (mmmm) REVERT: A 640 MET cc_start: 0.9436 (tpp) cc_final: 0.9010 (tpp) REVERT: B 8 LYS cc_start: 0.9383 (tptp) cc_final: 0.9156 (tptp) REVERT: B 30 LYS cc_start: 0.9786 (tmtt) cc_final: 0.9387 (tptt) REVERT: B 82 LYS cc_start: 0.9509 (ptpp) cc_final: 0.9182 (ptpt) REVERT: B 95 MET cc_start: 0.9168 (tpp) cc_final: 0.8358 (tpp) REVERT: B 99 LYS cc_start: 0.9527 (mmmt) cc_final: 0.8999 (mmmt) REVERT: B 116 GLU cc_start: 0.8406 (tt0) cc_final: 0.8110 (tt0) REVERT: B 117 ARG cc_start: 0.9033 (mtp180) cc_final: 0.8687 (mtp180) REVERT: B 119 GLU cc_start: 0.9085 (mp0) cc_final: 0.8718 (mp0) REVERT: B 139 GLU cc_start: 0.9275 (mp0) cc_final: 0.9013 (mp0) REVERT: B 149 TYR cc_start: 0.9077 (t80) cc_final: 0.8732 (t80) REVERT: B 211 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8428 (mm-30) REVERT: B 235 ARG cc_start: 0.8716 (ttm110) cc_final: 0.8143 (ttm110) REVERT: B 250 TYR cc_start: 0.8752 (m-80) cc_final: 0.7467 (m-80) REVERT: B 263 ASP cc_start: 0.9200 (m-30) cc_final: 0.8824 (m-30) REVERT: B 283 VAL cc_start: 0.9562 (t) cc_final: 0.9227 (t) REVERT: B 286 ASP cc_start: 0.8918 (m-30) cc_final: 0.8341 (m-30) REVERT: B 322 MET cc_start: 0.8837 (mmm) cc_final: 0.8498 (mmm) REVERT: B 359 MET cc_start: 0.8974 (ttt) cc_final: 0.8494 (tmm) REVERT: B 375 LYS cc_start: 0.9229 (mmmm) cc_final: 0.8970 (mmmm) REVERT: B 379 SER cc_start: 0.9041 (t) cc_final: 0.8478 (t) REVERT: B 392 SER cc_start: 0.9312 (m) cc_final: 0.8432 (t) REVERT: B 402 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8384 (tm-30) REVERT: B 403 ILE cc_start: 0.9319 (mp) cc_final: 0.8979 (tp) REVERT: B 415 ASN cc_start: 0.9237 (t0) cc_final: 0.8833 (t0) REVERT: B 416 ILE cc_start: 0.9627 (mt) cc_final: 0.9407 (mt) REVERT: B 420 MET cc_start: 0.9447 (mmm) cc_final: 0.9105 (mmm) REVERT: B 446 ARG cc_start: 0.9000 (mmm-85) cc_final: 0.8266 (mmm160) REVERT: B 447 ASN cc_start: 0.8447 (m-40) cc_final: 0.7873 (m-40) REVERT: B 458 MET cc_start: 0.9344 (mmm) cc_final: 0.8828 (mmm) REVERT: B 459 LYS cc_start: 0.9051 (mttp) cc_final: 0.8339 (mtmt) REVERT: B 467 ASN cc_start: 0.8577 (m110) cc_final: 0.8241 (m-40) REVERT: B 469 HIS cc_start: 0.8871 (t-170) cc_final: 0.8552 (t70) REVERT: B 494 MET cc_start: 0.9563 (ttm) cc_final: 0.9220 (ttm) REVERT: B 530 LYS cc_start: 0.8967 (ptmm) cc_final: 0.8719 (ptmm) REVERT: B 571 TYR cc_start: 0.9170 (t80) cc_final: 0.8967 (t80) REVERT: B 598 MET cc_start: 0.9186 (mtp) cc_final: 0.8652 (mtp) REVERT: B 602 GLU cc_start: 0.8430 (mp0) cc_final: 0.7428 (mp0) REVERT: B 612 TYR cc_start: 0.8586 (m-80) cc_final: 0.7791 (m-80) REVERT: B 613 TYR cc_start: 0.9178 (t80) cc_final: 0.7869 (t80) REVERT: B 615 MET cc_start: 0.9104 (mmp) cc_final: 0.8606 (mmp) REVERT: B 631 ASP cc_start: 0.9405 (t70) cc_final: 0.9149 (t0) REVERT: B 639 ASP cc_start: 0.9376 (m-30) cc_final: 0.8892 (m-30) REVERT: B 640 MET cc_start: 0.9398 (tpp) cc_final: 0.8829 (tpp) REVERT: B 641 ILE cc_start: 0.9705 (mm) cc_final: 0.9429 (mm) REVERT: B 667 LEU cc_start: 0.9696 (tp) cc_final: 0.9438 (tp) REVERT: B 673 TYR cc_start: 0.9062 (t80) cc_final: 0.8673 (t80) REVERT: B 679 ILE cc_start: 0.9625 (mm) cc_final: 0.9366 (mm) REVERT: C 17 PHE cc_start: 0.8564 (p90) cc_final: 0.7924 (p90) REVERT: C 20 MET cc_start: 0.8932 (ptp) cc_final: 0.8699 (pmm) REVERT: C 21 PHE cc_start: 0.9013 (m-10) cc_final: 0.8544 (m-80) REVERT: C 24 GLN cc_start: 0.8706 (mp10) cc_final: 0.8473 (mp-120) REVERT: C 55 TYR cc_start: 0.7412 (t80) cc_final: 0.7073 (t80) REVERT: C 58 VAL cc_start: 0.8046 (t) cc_final: 0.7763 (t) REVERT: C 96 MET cc_start: 0.8265 (tpt) cc_final: 0.8038 (tpt) REVERT: C 122 PHE cc_start: 0.8675 (m-80) cc_final: 0.8300 (m-80) REVERT: C 157 MET cc_start: 0.9462 (ptm) cc_final: 0.8909 (ppp) REVERT: C 204 TYR cc_start: 0.9075 (t80) cc_final: 0.8552 (t80) REVERT: C 208 LEU cc_start: 0.9359 (mt) cc_final: 0.9129 (mt) REVERT: C 320 PHE cc_start: 0.7816 (m-10) cc_final: 0.7467 (m-10) REVERT: D 21 PHE cc_start: 0.8690 (m-10) cc_final: 0.8265 (m-10) REVERT: D 96 MET cc_start: 0.8634 (mmp) cc_final: 0.8246 (mmm) REVERT: D 108 ILE cc_start: 0.9463 (mt) cc_final: 0.9240 (pt) REVERT: D 109 PHE cc_start: 0.8875 (m-80) cc_final: 0.8189 (m-80) REVERT: D 112 LEU cc_start: 0.8631 (mm) cc_final: 0.7800 (pp) REVERT: D 157 MET cc_start: 0.9480 (ppp) cc_final: 0.8768 (ppp) REVERT: D 166 PHE cc_start: 0.7810 (t80) cc_final: 0.7397 (t80) REVERT: D 169 TYR cc_start: 0.9189 (m-80) cc_final: 0.8852 (m-80) REVERT: D 172 PHE cc_start: 0.9409 (m-80) cc_final: 0.8858 (m-80) REVERT: D 179 TYR cc_start: 0.8208 (t80) cc_final: 0.7764 (t80) REVERT: D 185 MET cc_start: 0.6061 (mmp) cc_final: 0.5725 (mmm) REVERT: D 214 ASN cc_start: 0.9666 (t0) cc_final: 0.9402 (p0) REVERT: D 224 LEU cc_start: 0.9491 (mt) cc_final: 0.9220 (mt) REVERT: D 244 GLU cc_start: 0.9116 (mp0) cc_final: 0.8832 (mm-30) REVERT: D 318 ASP cc_start: 0.8990 (t0) cc_final: 0.8609 (t70) outliers start: 0 outliers final: 0 residues processed: 659 average time/residue: 0.2686 time to fit residues: 262.1360 Evaluate side-chains 572 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 572 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 111 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 182 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 115 optimal weight: 10.0000 chunk 127 optimal weight: 0.0050 chunk 188 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.7796 ------------------------------------------------------------------------------- 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 338 ASN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN C 181 GLN ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.116888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.087314 restraints weight = 49242.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.090289 restraints weight = 29948.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.092659 restraints weight = 21098.263| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.7827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16386 Z= 0.135 Angle : 0.647 12.376 22134 Z= 0.345 Chirality : 0.045 0.328 2360 Planarity : 0.004 0.051 2818 Dihedral : 10.384 172.099 2242 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: 0.54 (0.19), residues: 1932 helix: 0.91 (0.15), residues: 1138 sheet: -0.59 (0.43), residues: 144 loop : -0.22 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP D 124 HIS 0.010 0.001 HIS A 469 PHE 0.037 0.002 PHE C 109 TYR 0.047 0.001 TYR C 142 ARG 0.010 0.001 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.04053 ( 871) hydrogen bonds : angle 5.15999 ( 2571) covalent geometry : bond 0.00290 (16386) covalent geometry : angle 0.64734 (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 672 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 672 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: A 8 LYS cc_start: 0.9220 (tptp) cc_final: 0.8786 (tppt) REVERT: A 15 GLU cc_start: 0.9201 (tp30) cc_final: 0.8842 (tp30) REVERT: A 29 ASP cc_start: 0.9271 (t0) cc_final: 0.9069 (t70) REVERT: A 95 MET cc_start: 0.9103 (mmm) cc_final: 0.7640 (tpt) REVERT: A 116 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7661 (tt0) REVERT: A 119 GLU cc_start: 0.8962 (mp0) cc_final: 0.8680 (mp0) REVERT: A 136 LYS cc_start: 0.9608 (tttp) cc_final: 0.9272 (ttmm) REVERT: A 147 GLN cc_start: 0.8685 (mt0) cc_final: 0.8298 (mt0) REVERT: A 164 ARG cc_start: 0.8095 (ptm-80) cc_final: 0.6595 (ptm-80) REVERT: A 190 MET cc_start: 0.9091 (mtp) cc_final: 0.8867 (mtp) REVERT: A 224 VAL cc_start: 0.8927 (p) cc_final: 0.8542 (t) REVERT: A 235 ARG cc_start: 0.8401 (mtm110) cc_final: 0.8176 (mtm110) REVERT: A 236 TYR cc_start: 0.8848 (t80) cc_final: 0.8271 (t80) REVERT: A 280 ILE cc_start: 0.8655 (pt) cc_final: 0.8353 (mp) REVERT: A 286 ASP cc_start: 0.9147 (m-30) cc_final: 0.8816 (m-30) REVERT: A 335 GLU cc_start: 0.9276 (mm-30) cc_final: 0.9032 (mp0) REVERT: A 345 LYS cc_start: 0.8882 (tttt) cc_final: 0.8635 (tttt) REVERT: A 349 LEU cc_start: 0.9453 (mt) cc_final: 0.9137 (mt) REVERT: A 359 MET cc_start: 0.8937 (ttp) cc_final: 0.8548 (ttp) REVERT: A 370 ASN cc_start: 0.9441 (m-40) cc_final: 0.9195 (m110) REVERT: A 375 LYS cc_start: 0.8958 (mmmt) cc_final: 0.8474 (mmtm) REVERT: A 377 LYS cc_start: 0.8803 (mttt) cc_final: 0.7943 (mtmm) REVERT: A 381 LEU cc_start: 0.9088 (tp) cc_final: 0.8680 (pt) REVERT: A 407 ILE cc_start: 0.9045 (mt) cc_final: 0.8756 (mt) REVERT: A 469 HIS cc_start: 0.8828 (t-170) cc_final: 0.8618 (t-170) REVERT: A 501 GLN cc_start: 0.9442 (mm110) cc_final: 0.9111 (mt0) REVERT: A 515 ASP cc_start: 0.9349 (m-30) cc_final: 0.8905 (m-30) REVERT: A 598 MET cc_start: 0.8896 (ttt) cc_final: 0.8557 (ttt) REVERT: A 604 ARG cc_start: 0.8902 (ttm110) cc_final: 0.8388 (ttm110) REVERT: A 615 MET cc_start: 0.9074 (mmp) cc_final: 0.8801 (mmp) REVERT: A 628 GLU cc_start: 0.9288 (mt-10) cc_final: 0.8986 (mt-10) REVERT: A 640 MET cc_start: 0.9464 (tpp) cc_final: 0.9006 (tpp) REVERT: A 646 GLN cc_start: 0.9191 (pm20) cc_final: 0.8935 (pm20) REVERT: A 647 HIS cc_start: 0.9185 (m-70) cc_final: 0.7736 (m170) REVERT: A 677 ARG cc_start: 0.9360 (mmm-85) cc_final: 0.8855 (mmm-85) REVERT: B 8 LYS cc_start: 0.9375 (tptp) cc_final: 0.9149 (tptp) REVERT: B 30 LYS cc_start: 0.9787 (tmtt) cc_final: 0.9367 (tptt) REVERT: B 67 GLU cc_start: 0.9178 (mp0) cc_final: 0.8871 (mp0) REVERT: B 82 LYS cc_start: 0.9508 (ptpp) cc_final: 0.9138 (ptpt) REVERT: B 99 LYS cc_start: 0.9508 (mmmt) cc_final: 0.9276 (mttt) REVERT: B 117 ARG cc_start: 0.9024 (mtp180) cc_final: 0.8691 (mtp180) REVERT: B 119 GLU cc_start: 0.9025 (mp0) cc_final: 0.8674 (mp0) REVERT: B 144 MET cc_start: 0.9452 (mtm) cc_final: 0.9124 (mtm) REVERT: B 149 TYR cc_start: 0.9092 (t80) cc_final: 0.8581 (t80) REVERT: B 156 PHE cc_start: 0.9488 (t80) cc_final: 0.9245 (t80) REVERT: B 211 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8403 (mm-30) REVERT: B 235 ARG cc_start: 0.8784 (ttm110) cc_final: 0.8289 (ttm110) REVERT: B 250 TYR cc_start: 0.8471 (m-80) cc_final: 0.7259 (m-80) REVERT: B 263 ASP cc_start: 0.9101 (m-30) cc_final: 0.8683 (m-30) REVERT: B 283 VAL cc_start: 0.9584 (t) cc_final: 0.9265 (t) REVERT: B 286 ASP cc_start: 0.8844 (m-30) cc_final: 0.7943 (m-30) REVERT: B 317 MET cc_start: 0.8568 (ptm) cc_final: 0.7998 (ptm) REVERT: B 359 MET cc_start: 0.9002 (ttt) cc_final: 0.8595 (tmm) REVERT: B 362 ASP cc_start: 0.8671 (m-30) cc_final: 0.7595 (m-30) REVERT: B 370 ASN cc_start: 0.9392 (m110) cc_final: 0.9152 (m110) REVERT: B 375 LYS cc_start: 0.9209 (mmmm) cc_final: 0.8941 (mmmm) REVERT: B 379 SER cc_start: 0.8925 (t) cc_final: 0.8394 (t) REVERT: B 392 SER cc_start: 0.9230 (m) cc_final: 0.8584 (m) REVERT: B 402 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8304 (tm-30) REVERT: B 403 ILE cc_start: 0.9277 (mp) cc_final: 0.8920 (tp) REVERT: B 410 ASN cc_start: 0.8671 (m-40) cc_final: 0.8470 (m-40) REVERT: B 415 ASN cc_start: 0.9249 (t0) cc_final: 0.8835 (t0) REVERT: B 420 MET cc_start: 0.9435 (mmm) cc_final: 0.9068 (mmm) REVERT: B 426 GLU cc_start: 0.9402 (pm20) cc_final: 0.9190 (pm20) REVERT: B 446 ARG cc_start: 0.8972 (mmm-85) cc_final: 0.8523 (mmm160) REVERT: B 458 MET cc_start: 0.9295 (mmm) cc_final: 0.8762 (mmm) REVERT: B 459 LYS cc_start: 0.9054 (mttp) cc_final: 0.8375 (mtmt) REVERT: B 467 ASN cc_start: 0.8547 (m110) cc_final: 0.8175 (m-40) REVERT: B 469 HIS cc_start: 0.8799 (t-170) cc_final: 0.8401 (t70) REVERT: B 494 MET cc_start: 0.9568 (ttm) cc_final: 0.9232 (ttm) REVERT: B 530 LYS cc_start: 0.9023 (ptmm) cc_final: 0.8483 (ptmm) REVERT: B 597 ILE cc_start: 0.9272 (pt) cc_final: 0.9054 (pt) REVERT: B 602 GLU cc_start: 0.8605 (mp0) cc_final: 0.7056 (mp0) REVERT: B 612 TYR cc_start: 0.8674 (m-80) cc_final: 0.7898 (m-80) REVERT: B 613 TYR cc_start: 0.9166 (t80) cc_final: 0.8233 (t80) REVERT: B 615 MET cc_start: 0.9037 (mmp) cc_final: 0.8495 (mmp) REVERT: B 627 LYS cc_start: 0.9058 (tttt) cc_final: 0.8721 (tptm) REVERT: B 631 ASP cc_start: 0.9433 (t70) cc_final: 0.8739 (t70) REVERT: B 636 LYS cc_start: 0.9602 (mptt) cc_final: 0.9343 (mmtt) REVERT: B 640 MET cc_start: 0.9372 (tpp) cc_final: 0.8756 (tpp) REVERT: B 641 ILE cc_start: 0.9705 (mm) cc_final: 0.9474 (mm) REVERT: B 648 ILE cc_start: 0.9303 (mm) cc_final: 0.8992 (mm) REVERT: B 667 LEU cc_start: 0.9706 (tp) cc_final: 0.9490 (tp) REVERT: B 679 ILE cc_start: 0.9564 (mm) cc_final: 0.9347 (mm) REVERT: C 17 PHE cc_start: 0.8557 (p90) cc_final: 0.7942 (p90) REVERT: C 21 PHE cc_start: 0.8953 (m-10) cc_final: 0.8404 (m-80) REVERT: C 55 TYR cc_start: 0.7614 (t80) cc_final: 0.7160 (t80) REVERT: C 96 MET cc_start: 0.8427 (tpt) cc_final: 0.8153 (tpt) REVERT: C 122 PHE cc_start: 0.8746 (m-80) cc_final: 0.8429 (m-80) REVERT: C 157 MET cc_start: 0.9435 (ptm) cc_final: 0.9041 (ppp) REVERT: C 204 TYR cc_start: 0.9018 (t80) cc_final: 0.8496 (t80) REVERT: D 21 PHE cc_start: 0.8641 (m-10) cc_final: 0.8199 (m-10) REVERT: D 108 ILE cc_start: 0.9442 (mt) cc_final: 0.9206 (pt) REVERT: D 109 PHE cc_start: 0.8848 (m-80) cc_final: 0.8179 (m-80) REVERT: D 112 LEU cc_start: 0.8654 (mm) cc_final: 0.7777 (pp) REVERT: D 157 MET cc_start: 0.9444 (ppp) cc_final: 0.8682 (ppp) REVERT: D 166 PHE cc_start: 0.7670 (t80) cc_final: 0.7363 (t80) REVERT: D 169 TYR cc_start: 0.9076 (m-80) cc_final: 0.8841 (m-80) REVERT: D 172 PHE cc_start: 0.9437 (m-80) cc_final: 0.8877 (m-80) REVERT: D 179 TYR cc_start: 0.8218 (t80) cc_final: 0.7804 (t80) REVERT: D 185 MET cc_start: 0.6062 (mmp) cc_final: 0.5762 (mmm) REVERT: D 244 GLU cc_start: 0.9121 (mp0) cc_final: 0.8817 (mm-30) REVERT: D 318 ASP cc_start: 0.8925 (t0) cc_final: 0.8520 (t70) outliers start: 0 outliers final: 0 residues processed: 672 average time/residue: 0.2684 time to fit residues: 267.1844 Evaluate side-chains 578 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 578 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 137 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 160 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 148 optimal weight: 0.0980 chunk 127 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 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 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 ASN A 675 HIS ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.109680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.081634 restraints weight = 49786.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.084561 restraints weight = 30738.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.086756 restraints weight = 21465.252| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 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 : 0.003 0.053 16386 Z= 0.159 Angle : 0.694 15.812 22134 Z= 0.367 Chirality : 0.046 0.330 2360 Planarity : 0.004 0.041 2818 Dihedral : 10.447 170.339 2242 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.48 (0.19), residues: 1932 helix: 0.88 (0.15), residues: 1137 sheet: -0.64 (0.43), residues: 148 loop : -0.26 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP D 124 HIS 0.010 0.001 HIS A 469 PHE 0.030 0.002 PHE D 227 TYR 0.038 0.002 TYR C 142 ARG 0.011 0.001 ARG A 163 Details of bonding type rmsd hydrogen bonds : bond 0.04183 ( 871) hydrogen bonds : angle 5.25458 ( 2571) covalent geometry : bond 0.00348 (16386) covalent geometry : angle 0.69420 (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 667 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 667 time to evaluate : 2.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9238 (tptp) cc_final: 0.8796 (tppt) REVERT: A 15 GLU cc_start: 0.9195 (tp30) cc_final: 0.8814 (tp30) REVERT: A 29 ASP cc_start: 0.9234 (t0) cc_final: 0.9021 (t70) REVERT: A 95 MET cc_start: 0.9106 (mmm) cc_final: 0.7854 (tpt) REVERT: A 116 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7722 (tt0) REVERT: A 119 GLU cc_start: 0.9030 (mp0) cc_final: 0.8748 (mp0) REVERT: A 136 LYS cc_start: 0.9611 (tttp) cc_final: 0.9362 (ttmm) REVERT: A 147 GLN cc_start: 0.8693 (mt0) cc_final: 0.8335 (mt0) REVERT: A 164 ARG cc_start: 0.7938 (ptm-80) cc_final: 0.6615 (ptm-80) REVERT: A 235 ARG cc_start: 0.8447 (mtm110) cc_final: 0.8224 (mtm110) REVERT: A 236 TYR cc_start: 0.8904 (t80) cc_final: 0.8342 (t80) REVERT: A 280 ILE cc_start: 0.8623 (pt) cc_final: 0.8056 (mp) REVERT: A 286 ASP cc_start: 0.9169 (m-30) cc_final: 0.8840 (m-30) REVERT: A 335 GLU cc_start: 0.9236 (mm-30) cc_final: 0.8990 (mp0) REVERT: A 345 LYS cc_start: 0.8919 (tttt) cc_final: 0.8682 (tttt) REVERT: A 349 LEU cc_start: 0.9433 (mt) cc_final: 0.9148 (mt) REVERT: A 359 MET cc_start: 0.8950 (ttp) cc_final: 0.8516 (ttp) REVERT: A 370 ASN cc_start: 0.9455 (m-40) cc_final: 0.9159 (m110) REVERT: A 375 LYS cc_start: 0.8946 (mmmt) cc_final: 0.8277 (mmtm) REVERT: A 377 LYS cc_start: 0.8747 (mttt) cc_final: 0.8181 (mttp) REVERT: A 381 LEU cc_start: 0.9092 (tp) cc_final: 0.8628 (pt) REVERT: A 389 SER cc_start: 0.9056 (p) cc_final: 0.8591 (p) REVERT: A 398 ASP cc_start: 0.8425 (p0) cc_final: 0.7861 (p0) REVERT: A 469 HIS cc_start: 0.8951 (t-170) cc_final: 0.8697 (t-170) REVERT: A 515 ASP cc_start: 0.9405 (m-30) cc_final: 0.8993 (m-30) REVERT: A 562 LYS cc_start: 0.9774 (ttmm) cc_final: 0.9308 (tttt) REVERT: A 570 MET cc_start: 0.9362 (mtp) cc_final: 0.8949 (mtp) REVERT: A 595 MET cc_start: 0.9013 (mmm) cc_final: 0.8218 (mtt) REVERT: A 598 MET cc_start: 0.8881 (ttt) cc_final: 0.8140 (ttt) REVERT: A 604 ARG cc_start: 0.8924 (ttm110) cc_final: 0.8417 (ttm110) REVERT: A 628 GLU cc_start: 0.9299 (mt-10) cc_final: 0.8716 (mm-30) REVERT: A 636 LYS cc_start: 0.9770 (mmtp) cc_final: 0.9551 (mmmm) REVERT: A 640 MET cc_start: 0.9418 (tpp) cc_final: 0.8957 (tpp) REVERT: A 646 GLN cc_start: 0.9183 (pm20) cc_final: 0.8901 (pm20) REVERT: A 647 HIS cc_start: 0.9140 (m-70) cc_final: 0.7677 (m170) REVERT: A 677 ARG cc_start: 0.9341 (mmm-85) cc_final: 0.8838 (mmm-85) REVERT: A 679 ILE cc_start: 0.9609 (mm) cc_final: 0.9408 (mm) REVERT: B 8 LYS cc_start: 0.9373 (tptp) cc_final: 0.9145 (tptp) REVERT: B 30 LYS cc_start: 0.9777 (tmtt) cc_final: 0.9357 (tptt) REVERT: B 67 GLU cc_start: 0.9140 (mp0) cc_final: 0.8835 (mp0) REVERT: B 82 LYS cc_start: 0.9519 (ptpp) cc_final: 0.9179 (ptpt) REVERT: B 94 PHE cc_start: 0.9553 (t80) cc_final: 0.8893 (t80) REVERT: B 99 LYS cc_start: 0.9519 (mmmt) cc_final: 0.9273 (mttt) REVERT: B 117 ARG cc_start: 0.8966 (mtp180) cc_final: 0.8692 (mtp180) REVERT: B 119 GLU cc_start: 0.9053 (mp0) cc_final: 0.8715 (mp0) REVERT: B 144 MET cc_start: 0.9464 (mtm) cc_final: 0.9179 (mtm) REVERT: B 149 TYR cc_start: 0.9062 (t80) cc_final: 0.8654 (t80) REVERT: B 211 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8408 (mm-30) REVERT: B 235 ARG cc_start: 0.8683 (ttm110) cc_final: 0.8200 (ttm110) REVERT: B 250 TYR cc_start: 0.8571 (m-80) cc_final: 0.7394 (m-80) REVERT: B 263 ASP cc_start: 0.9104 (m-30) cc_final: 0.8666 (m-30) REVERT: B 283 VAL cc_start: 0.9579 (t) cc_final: 0.9241 (t) REVERT: B 286 ASP cc_start: 0.8822 (m-30) cc_final: 0.7941 (m-30) REVERT: B 350 ARG cc_start: 0.8708 (mtm-85) cc_final: 0.8266 (mtm-85) REVERT: B 359 MET cc_start: 0.8962 (ttt) cc_final: 0.8525 (tmm) REVERT: B 362 ASP cc_start: 0.8572 (m-30) cc_final: 0.7538 (m-30) REVERT: B 375 LYS cc_start: 0.9179 (mmmm) cc_final: 0.8921 (mmmm) REVERT: B 379 SER cc_start: 0.8890 (t) cc_final: 0.8424 (t) REVERT: B 392 SER cc_start: 0.9200 (m) cc_final: 0.8305 (t) REVERT: B 402 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8326 (tm-30) REVERT: B 403 ILE cc_start: 0.9290 (mp) cc_final: 0.8927 (tp) REVERT: B 410 ASN cc_start: 0.8716 (m-40) cc_final: 0.8499 (m-40) REVERT: B 415 ASN cc_start: 0.9224 (t0) cc_final: 0.8889 (t0) REVERT: B 420 MET cc_start: 0.9478 (mmm) cc_final: 0.9124 (mmm) REVERT: B 426 GLU cc_start: 0.9367 (pm20) cc_final: 0.9164 (pm20) REVERT: B 446 ARG cc_start: 0.8915 (mmm-85) cc_final: 0.8174 (mmm160) REVERT: B 458 MET cc_start: 0.9299 (mmm) cc_final: 0.8749 (mmm) REVERT: B 459 LYS cc_start: 0.8993 (mttp) cc_final: 0.8365 (mtmt) REVERT: B 467 ASN cc_start: 0.8428 (m110) cc_final: 0.8214 (m110) REVERT: B 494 MET cc_start: 0.9503 (ttm) cc_final: 0.9199 (ttm) REVERT: B 530 LYS cc_start: 0.9136 (ptmm) cc_final: 0.8758 (ptmm) REVERT: B 599 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7809 (pp20) REVERT: B 602 GLU cc_start: 0.8451 (mp0) cc_final: 0.6957 (mp0) REVERT: B 612 TYR cc_start: 0.8632 (m-80) cc_final: 0.7930 (m-80) REVERT: B 613 TYR cc_start: 0.9191 (t80) cc_final: 0.8296 (t80) REVERT: B 615 MET cc_start: 0.9046 (mmp) cc_final: 0.8521 (mmp) REVERT: B 627 LYS cc_start: 0.9339 (tttt) cc_final: 0.8874 (tttt) REVERT: B 640 MET cc_start: 0.9344 (tpp) cc_final: 0.8658 (tpp) REVERT: B 641 ILE cc_start: 0.9731 (mm) cc_final: 0.9471 (mm) REVERT: B 667 LEU cc_start: 0.9711 (tp) cc_final: 0.9417 (tp) REVERT: B 679 ILE cc_start: 0.9617 (mm) cc_final: 0.9402 (mm) REVERT: C 17 PHE cc_start: 0.8761 (p90) cc_final: 0.8096 (p90) REVERT: C 21 PHE cc_start: 0.9037 (m-10) cc_final: 0.8501 (m-80) REVERT: C 58 VAL cc_start: 0.7928 (t) cc_final: 0.7634 (t) REVERT: C 96 MET cc_start: 0.8309 (tpt) cc_final: 0.8093 (tpt) REVERT: C 122 PHE cc_start: 0.8583 (m-80) cc_final: 0.8244 (m-80) REVERT: C 204 TYR cc_start: 0.9034 (t80) cc_final: 0.8414 (t80) REVERT: C 285 ILE cc_start: 0.9107 (mm) cc_final: 0.8814 (mm) REVERT: D 21 PHE cc_start: 0.8624 (m-10) cc_final: 0.8188 (m-10) REVERT: D 96 MET cc_start: 0.8659 (mmp) cc_final: 0.8234 (mmp) REVERT: D 108 ILE cc_start: 0.9451 (mt) cc_final: 0.9216 (pt) REVERT: D 109 PHE cc_start: 0.8747 (m-80) cc_final: 0.8055 (m-80) REVERT: D 112 LEU cc_start: 0.8746 (mm) cc_final: 0.7885 (pp) REVERT: D 157 MET cc_start: 0.9138 (ppp) cc_final: 0.8500 (ppp) REVERT: D 166 PHE cc_start: 0.7528 (t80) cc_final: 0.7314 (t80) REVERT: D 169 TYR cc_start: 0.9058 (m-80) cc_final: 0.8840 (m-80) REVERT: D 172 PHE cc_start: 0.9419 (m-80) cc_final: 0.8877 (m-80) REVERT: D 177 TYR cc_start: 0.9344 (t80) cc_final: 0.8982 (t80) REVERT: D 179 TYR cc_start: 0.8169 (t80) cc_final: 0.7615 (t80) REVERT: D 185 MET cc_start: 0.6026 (mmp) cc_final: 0.5708 (mmm) REVERT: D 244 GLU cc_start: 0.9139 (mp0) cc_final: 0.8810 (mm-30) REVERT: D 318 ASP cc_start: 0.8886 (t0) cc_final: 0.8485 (t70) outliers start: 0 outliers final: 0 residues processed: 667 average time/residue: 0.2716 time to fit residues: 268.7993 Evaluate side-chains 566 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 566 time to evaluate : 1.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 81 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 190 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 180 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 ASN A 158 ASN A 232 ASN A 313 HIS ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 ASN ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.117801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.088227 restraints weight = 49801.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.091230 restraints weight = 30267.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.093572 restraints weight = 21346.500| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.8239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16386 Z= 0.135 Angle : 0.676 14.343 22134 Z= 0.355 Chirality : 0.045 0.328 2360 Planarity : 0.004 0.043 2818 Dihedral : 10.282 167.080 2242 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.48 (0.19), residues: 1932 helix: 0.91 (0.15), residues: 1131 sheet: -0.66 (0.43), residues: 148 loop : -0.30 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP D 124 HIS 0.010 0.001 HIS D 201 PHE 0.029 0.002 PHE D 227 TYR 0.049 0.001 TYR C 142 ARG 0.010 0.001 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 871) hydrogen bonds : angle 5.18287 ( 2571) covalent geometry : bond 0.00295 (16386) covalent geometry : angle 0.67598 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6616.07 seconds wall clock time: 116 minutes 25.85 seconds (6985.85 seconds total)