Starting phenix.real_space_refine on Sat Jun 14 07:08:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzo_45072/06_2025/9bzo_45072_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzo_45072/06_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_45072/06_2025/9bzo_45072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzo_45072/06_2025/9bzo_45072.map" model { file = "/net/cci-nas-00/data/ceres_data/9bzo_45072/06_2025/9bzo_45072_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzo_45072/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 10.37, per 1000 atoms: 0.65 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: 4.33 Conformation dependent library (CDL) restraints added in 2.3 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: 2.17 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: 7.40 Time building geometry restraints manager: 5.20 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 0.060 Extract box with map and model: 0.680 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 44.780 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.090 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.710 ------------------------------------------------------------------------------- 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 : 2.003 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: 0.9119 (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: 0.8331 (mt0) REVERT: A 149 TYR cc_start: 0.7936 (t80) cc_final: 0.7581 (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: 0.8136 (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: 0.8816 (mt) REVERT: A 435 SER cc_start: 0.9237 (p) cc_final: 0.8124 (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: 0.7700 (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: 0.8558 (p) REVERT: B 18 ILE cc_start: 0.8623 (mt) cc_final: 0.8400 (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: 0.7192 (m-80) REVERT: B 99 LYS cc_start: 0.9215 (mmtt) cc_final: 0.8763 (mmmt) REVERT: B 109 ASN cc_start: 0.8797 (m-40) cc_final: 0.8074 (m-40) REVERT: B 122 ILE cc_start: 0.9114 (mt) cc_final: 0.8766 (mt) REVERT: B 179 LEU cc_start: 0.8301 (tp) cc_final: 0.8023 (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: 0.8207 (mmmt) REVERT: B 286 ASP cc_start: 0.5893 (OUTLIER) cc_final: 0.5574 (m-30) REVERT: B 291 LEU cc_start: 0.9109 (mt) cc_final: 0.8897 (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: 0.6022 (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: 0.8150 (m110) REVERT: B 430 LYS cc_start: 0.8042 (mttt) cc_final: 0.7252 (mtpp) REVERT: B 431 LEU cc_start: 0.9080 (mt) cc_final: 0.8549 (mt) REVERT: B 436 LEU cc_start: 0.9402 (mt) cc_final: 0.9159 (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: 0.6401 (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: 0.4531 (p90) REVERT: C 67 THR cc_start: 0.6971 (m) cc_final: 0.6705 (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: 0.7085 (mm) REVERT: C 118 ILE cc_start: 0.6148 (mt) cc_final: 0.5578 (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: 0.3393 time to fit residues: 457.8946 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 : 1.751 ------------------------------------------------------------------------------- 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: 9.9990 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 = 0.3581 r_free = 0.3581 target = 0.121512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.090402 restraints weight = 47621.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.093730 restraints weight = 29084.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.096086 restraints weight = 20191.846| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16386 Z= 0.198 Angle : 0.667 9.728 22134 Z= 0.359 Chirality : 0.044 0.206 2360 Planarity : 0.004 0.051 2818 Dihedral : 11.370 177.059 2242 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.41 % Allowed : 2.86 % Favored : 96.74 % 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: 1.21 (0.15), residues: 1131 sheet: 0.06 (0.41), residues: 138 loop : 0.50 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 558 HIS 0.008 0.002 HIS A 438 PHE 0.038 0.003 PHE C 166 TYR 0.028 0.002 TYR D 174 ARG 0.011 0.001 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.04740 ( 871) hydrogen bonds : angle 5.26787 ( 2571) covalent geometry : bond 0.00423 (16386) covalent geometry : angle 0.66735 (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 : 1.738 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 54 LYS cc_start: 0.9715 (ttmm) cc_final: 0.9499 (tttp) REVERT: A 101 TYR cc_start: 0.9431 (m-80) cc_final: 0.9196 (m-10) REVERT: A 109 ASN cc_start: 0.9555 (p0) cc_final: 0.9320 (m-40) REVERT: A 115 LEU cc_start: 0.9482 (mt) cc_final: 0.9004 (mt) REVERT: A 119 GLU cc_start: 0.9191 (mp0) cc_final: 0.8178 (tm-30) REVERT: A 120 ASP cc_start: 0.9233 (m-30) cc_final: 0.8728 (m-30) REVERT: A 122 ILE cc_start: 0.9439 (mt) cc_final: 0.9189 (mt) REVERT: A 136 LYS cc_start: 0.9516 (tttp) cc_final: 0.9221 (tttp) REVERT: A 144 MET cc_start: 0.8799 (mtm) cc_final: 0.8385 (mtm) REVERT: A 147 GLN cc_start: 0.9005 (mt0) cc_final: 0.8477 (mt0) REVERT: A 149 TYR cc_start: 0.9500 (t80) cc_final: 0.9243 (t80) REVERT: A 173 LEU cc_start: 0.9472 (mt) cc_final: 0.9269 (mt) REVERT: A 199 VAL cc_start: 0.9397 (t) cc_final: 0.9171 (t) REVERT: A 236 TYR cc_start: 0.8709 (t80) cc_final: 0.8216 (t80) REVERT: A 278 LEU cc_start: 0.9562 (tp) cc_final: 0.9190 (tp) REVERT: A 280 ILE cc_start: 0.8755 (pt) cc_final: 0.8547 (pt) REVERT: A 286 ASP cc_start: 0.9385 (m-30) cc_final: 0.9041 (m-30) REVERT: A 300 VAL cc_start: 0.9602 (m) cc_final: 0.9163 (m) REVERT: A 322 MET cc_start: 0.8573 (mmp) cc_final: 0.8156 (mmm) REVERT: A 326 PHE cc_start: 0.9530 (m-80) cc_final: 0.9062 (m-80) REVERT: A 335 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8449 (mp0) REVERT: A 349 LEU cc_start: 0.9538 (mt) cc_final: 0.9313 (mt) REVERT: A 359 MET cc_start: 0.8748 (ttp) cc_final: 0.8275 (ttp) REVERT: A 370 ASN cc_start: 0.9417 (m-40) cc_final: 0.8976 (m-40) REVERT: A 375 LYS cc_start: 0.8757 (mmmt) cc_final: 0.8243 (mmtm) REVERT: A 377 LYS cc_start: 0.8751 (mttt) cc_final: 0.8289 (mtmm) REVERT: A 386 LEU cc_start: 0.9375 (mt) cc_final: 0.9165 (mt) REVERT: A 407 ILE cc_start: 0.9002 (mt) cc_final: 0.8696 (mt) REVERT: A 459 LYS cc_start: 0.9099 (mttp) cc_final: 0.8403 (mtpt) REVERT: A 466 MET cc_start: 0.9357 (ptt) cc_final: 0.9070 (ptt) REVERT: A 468 LEU cc_start: 0.9740 (tp) cc_final: 0.9487 (tp) REVERT: A 474 GLN cc_start: 0.9335 (tm-30) cc_final: 0.9083 (tm-30) REVERT: A 493 MET cc_start: 0.9323 (tmm) cc_final: 0.9057 (tmm) REVERT: A 494 MET cc_start: 0.9694 (mpp) cc_final: 0.9395 (mpp) REVERT: A 501 GLN cc_start: 0.9492 (mm-40) cc_final: 0.8847 (tp-100) REVERT: A 515 ASP cc_start: 0.9252 (m-30) cc_final: 0.8670 (m-30) REVERT: A 516 GLN cc_start: 0.9180 (mp10) cc_final: 0.8815 (mp10) REVERT: A 561 LEU cc_start: 0.9614 (tp) cc_final: 0.9342 (tp) REVERT: A 586 TYR cc_start: 0.9095 (m-10) cc_final: 0.8664 (m-10) REVERT: A 598 MET cc_start: 0.8520 (ttt) cc_final: 0.8183 (ttt) REVERT: A 615 MET cc_start: 0.8733 (mmt) cc_final: 0.8465 (mmt) REVERT: A 650 GLN cc_start: 0.8569 (mt0) cc_final: 0.8109 (mt0) REVERT: A 658 LEU cc_start: 0.9441 (mt) cc_final: 0.9166 (mt) REVERT: A 662 MET cc_start: 0.8642 (pmm) cc_final: 0.8319 (pmm) REVERT: A 677 ARG cc_start: 0.9347 (mmm-85) cc_final: 0.8755 (mmm-85) REVERT: A 686 ARG cc_start: 0.7379 (mmm160) cc_final: 0.7070 (mmm160) REVERT: B 8 LYS cc_start: 0.9331 (tptp) cc_final: 0.8999 (tptp) REVERT: B 16 ILE cc_start: 0.9749 (pt) cc_final: 0.9504 (pt) REVERT: B 30 LYS cc_start: 0.9743 (tmtt) cc_final: 0.9374 (tptt) REVERT: B 41 ILE cc_start: 0.9624 (mm) cc_final: 0.9333 (mt) REVERT: B 54 LYS cc_start: 0.9787 (ttmm) cc_final: 0.9480 (ttmm) REVERT: B 67 GLU cc_start: 0.9433 (mm-30) cc_final: 0.9212 (mm-30) REVERT: B 95 MET cc_start: 0.9534 (mmp) cc_final: 0.9107 (mmm) REVERT: B 99 LYS cc_start: 0.9487 (mmmt) cc_final: 0.8996 (mptt) REVERT: B 144 MET cc_start: 0.9445 (mtm) cc_final: 0.9185 (mtm) REVERT: B 191 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8861 (mm-40) REVERT: B 195 LEU cc_start: 0.9481 (mt) cc_final: 0.9263 (mt) REVERT: B 211 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8236 (mm-30) REVERT: B 227 MET cc_start: 0.9169 (mtp) cc_final: 0.8802 (mtp) REVERT: B 250 TYR cc_start: 0.8505 (m-80) cc_final: 0.7567 (m-80) REVERT: B 286 ASP cc_start: 0.8686 (m-30) cc_final: 0.8037 (m-30) REVERT: B 291 LEU cc_start: 0.9561 (mt) cc_final: 0.9303 (mt) REVERT: B 322 MET cc_start: 0.8720 (mmm) cc_final: 0.8281 (mmm) REVERT: B 362 ASP cc_start: 0.8509 (m-30) cc_final: 0.7362 (m-30) REVERT: B 373 ILE cc_start: 0.9661 (mt) cc_final: 0.9381 (mt) REVERT: B 375 LYS cc_start: 0.9280 (mmmm) cc_final: 0.9064 (mmmm) REVERT: B 379 SER cc_start: 0.9175 (t) cc_final: 0.8824 (t) REVERT: B 386 LEU cc_start: 0.9028 (mt) cc_final: 0.8647 (mt) REVERT: B 387 GLN cc_start: 0.8619 (mt0) cc_final: 0.8302 (mm-40) REVERT: B 393 SER cc_start: 0.9546 (t) cc_final: 0.9299 (p) REVERT: B 410 ASN cc_start: 0.8932 (m110) cc_final: 0.8601 (m110) REVERT: B 458 MET cc_start: 0.9604 (mmm) cc_final: 0.9235 (mmm) REVERT: B 468 LEU cc_start: 0.9638 (tp) cc_final: 0.9434 (tp) REVERT: B 500 ILE cc_start: 0.9655 (mt) cc_final: 0.9427 (mt) REVERT: B 516 GLN cc_start: 0.8950 (tt0) cc_final: 0.8595 (tt0) REVERT: B 570 MET cc_start: 0.8881 (mmm) cc_final: 0.8278 (mmm) REVERT: B 574 TYR cc_start: 0.7499 (m-80) cc_final: 0.6843 (m-80) REVERT: B 586 TYR cc_start: 0.9281 (m-80) cc_final: 0.8956 (m-10) REVERT: B 598 MET cc_start: 0.9287 (mtm) cc_final: 0.8979 (mtm) REVERT: B 612 TYR cc_start: 0.9190 (m-80) cc_final: 0.7908 (m-80) REVERT: B 613 TYR cc_start: 0.9088 (t80) cc_final: 0.8759 (t80) REVERT: B 648 ILE cc_start: 0.9366 (mm) cc_final: 0.9026 (mm) REVERT: B 650 GLN cc_start: 0.7628 (mt0) cc_final: 0.7221 (mt0) REVERT: B 673 TYR cc_start: 0.9197 (t80) cc_final: 0.8903 (t80) REVERT: C 17 PHE cc_start: 0.8669 (p90) cc_final: 0.7511 (p90) REVERT: C 21 PHE cc_start: 0.9161 (m-10) cc_final: 0.8604 (m-80) REVERT: C 157 MET cc_start: 0.9678 (mtm) cc_final: 0.9339 (ptm) REVERT: C 163 LEU cc_start: 0.9562 (tt) cc_final: 0.9281 (tt) REVERT: C 178 PHE cc_start: 0.9208 (m-80) cc_final: 0.8998 (m-10) REVERT: C 214 ASN cc_start: 0.8647 (m-40) cc_final: 0.8156 (p0) REVERT: C 227 PHE cc_start: 0.7345 (m-80) cc_final: 0.7102 (m-80) REVERT: C 263 ASN cc_start: 0.6772 (m-40) cc_final: 0.6315 (p0) REVERT: C 288 ASN cc_start: 0.8703 (m110) cc_final: 0.8495 (m-40) REVERT: C 318 ASP cc_start: 0.9342 (m-30) cc_final: 0.9061 (m-30) REVERT: D 17 PHE cc_start: 0.5300 (m-80) cc_final: 0.5027 (m-80) REVERT: D 21 PHE cc_start: 0.9098 (m-10) cc_final: 0.8829 (m-10) REVERT: D 74 MET cc_start: 0.8389 (mmp) cc_final: 0.8087 (mmt) REVERT: D 109 PHE cc_start: 0.8467 (m-80) cc_final: 0.7971 (m-10) REVERT: D 172 PHE cc_start: 0.9339 (m-80) cc_final: 0.8901 (m-80) REVERT: D 189 GLU cc_start: 0.9206 (pt0) cc_final: 0.8760 (pt0) REVERT: D 214 ASN cc_start: 0.9172 (m110) cc_final: 0.8764 (p0) REVERT: D 239 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8625 (pp20) outliers start: 7 outliers final: 1 residues processed: 766 average time/residue: 0.2906 time to fit residues: 322.1742 Evaluate side-chains 616 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 614 time to evaluate : 1.873 ------------------------------------------------------------------------------- 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: 5.9990 chunk 168 optimal weight: 9.9990 chunk 175 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 171 optimal weight: 0.9990 chunk 189 optimal weight: 9.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 HIS B 320 ASN B 361 GLN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN D 91 ASN D 216 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.112001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.082222 restraints weight = 49534.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.085288 restraints weight = 29995.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.087638 restraints weight = 20915.734| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16386 Z= 0.169 Angle : 0.608 7.205 22134 Z= 0.326 Chirality : 0.043 0.212 2360 Planarity : 0.004 0.046 2818 Dihedral : 11.138 177.563 2242 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.12 % Allowed : 2.62 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.03 (0.19), residues: 1932 helix: 1.11 (0.15), residues: 1130 sheet: -0.10 (0.41), residues: 134 loop : 0.34 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 623 HIS 0.008 0.001 HIS A 469 PHE 0.033 0.003 PHE B 81 TYR 0.027 0.002 TYR D 174 ARG 0.006 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 871) hydrogen bonds : angle 5.05264 ( 2571) covalent geometry : bond 0.00356 (16386) covalent geometry : angle 0.60766 (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 714 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 712 time to evaluate : 1.842 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: A 29 ASP cc_start: 0.9373 (t0) cc_final: 0.9119 (t70) REVERT: A 54 LYS cc_start: 0.9735 (ttmm) cc_final: 0.9528 (tttp) REVERT: A 67 GLU cc_start: 0.9601 (mp0) cc_final: 0.9364 (pm20) REVERT: A 101 TYR cc_start: 0.9464 (m-80) cc_final: 0.9000 (m-10) REVERT: A 115 LEU cc_start: 0.9587 (mt) cc_final: 0.9323 (mt) REVERT: A 119 GLU cc_start: 0.9110 (mp0) cc_final: 0.8643 (mp0) REVERT: A 136 LYS cc_start: 0.9537 (tttp) cc_final: 0.9327 (ttmm) REVERT: A 144 MET cc_start: 0.8825 (mtm) cc_final: 0.8365 (mtm) REVERT: A 147 GLN cc_start: 0.8931 (mt0) cc_final: 0.8337 (mt0) REVERT: A 150 GLN cc_start: 0.9196 (tp40) cc_final: 0.8987 (tp40) REVERT: A 164 ARG cc_start: 0.7512 (ptm-80) cc_final: 0.6209 (ptm-80) REVERT: A 172 LEU cc_start: 0.9338 (mp) cc_final: 0.8984 (mp) REVERT: A 173 LEU cc_start: 0.9497 (mt) cc_final: 0.9290 (mt) REVERT: A 190 MET cc_start: 0.9185 (mtp) cc_final: 0.8953 (mtp) REVERT: A 199 VAL cc_start: 0.9512 (t) cc_final: 0.9287 (t) REVERT: A 236 TYR cc_start: 0.8825 (t80) cc_final: 0.8406 (t80) REVERT: A 279 SER cc_start: 0.8164 (m) cc_final: 0.7369 (p) REVERT: A 280 ILE cc_start: 0.8743 (pt) cc_final: 0.8519 (pt) REVERT: A 283 VAL cc_start: 0.9186 (t) cc_final: 0.8915 (t) REVERT: A 286 ASP cc_start: 0.9046 (m-30) cc_final: 0.8821 (m-30) REVERT: A 300 VAL cc_start: 0.9615 (m) cc_final: 0.9397 (m) REVERT: A 322 MET cc_start: 0.8869 (mmp) cc_final: 0.8223 (tmm) REVERT: A 326 PHE cc_start: 0.9665 (m-10) cc_final: 0.9064 (m-80) REVERT: A 335 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8393 (mp0) REVERT: A 359 MET cc_start: 0.8735 (ttp) cc_final: 0.8395 (ttp) REVERT: A 362 ASP cc_start: 0.9084 (m-30) cc_final: 0.8796 (m-30) REVERT: A 370 ASN cc_start: 0.9476 (m-40) cc_final: 0.8994 (m-40) REVERT: A 375 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8539 (mmtm) REVERT: A 377 LYS cc_start: 0.8860 (mttt) cc_final: 0.8297 (mtmm) REVERT: A 406 ASP cc_start: 0.8505 (m-30) cc_final: 0.8212 (m-30) REVERT: A 407 ILE cc_start: 0.9032 (mt) cc_final: 0.8685 (mt) REVERT: A 459 LYS cc_start: 0.9062 (mttp) cc_final: 0.8354 (mtmm) REVERT: A 468 LEU cc_start: 0.9684 (tp) cc_final: 0.9412 (tp) REVERT: A 469 HIS cc_start: 0.9064 (t-170) cc_final: 0.8692 (t-170) REVERT: A 479 TYR cc_start: 0.9033 (t80) cc_final: 0.8482 (t80) REVERT: A 490 THR cc_start: 0.9692 (m) cc_final: 0.9246 (p) REVERT: A 493 MET cc_start: 0.9357 (tmm) cc_final: 0.9080 (tmm) REVERT: A 494 MET cc_start: 0.9676 (mpp) cc_final: 0.9362 (mpp) REVERT: A 501 GLN cc_start: 0.9390 (tp-100) cc_final: 0.8691 (tp-100) REVERT: A 515 ASP cc_start: 0.9289 (m-30) cc_final: 0.8412 (m-30) REVERT: A 516 GLN cc_start: 0.9188 (mp10) cc_final: 0.8524 (mp10) REVERT: A 598 MET cc_start: 0.8511 (ttt) cc_final: 0.8252 (ttt) REVERT: A 599 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8054 (tm-30) REVERT: A 662 MET cc_start: 0.8663 (pmm) cc_final: 0.8109 (pmm) REVERT: A 677 ARG cc_start: 0.9405 (mmm-85) cc_final: 0.8909 (mmm-85) REVERT: B 8 LYS cc_start: 0.9379 (tptp) cc_final: 0.9056 (tptp) REVERT: B 16 ILE cc_start: 0.9763 (pt) cc_final: 0.9477 (pt) REVERT: B 30 LYS cc_start: 0.9769 (tmtt) cc_final: 0.9415 (tptt) REVERT: B 95 MET cc_start: 0.9520 (mmp) cc_final: 0.9309 (mmm) REVERT: B 99 LYS cc_start: 0.9531 (mmmt) cc_final: 0.9063 (mttt) REVERT: B 119 GLU cc_start: 0.9180 (mp0) cc_final: 0.8734 (mp0) REVERT: B 195 LEU cc_start: 0.9566 (mt) cc_final: 0.9354 (mt) REVERT: B 211 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8261 (mm-30) REVERT: B 235 ARG cc_start: 0.8766 (ttm110) cc_final: 0.8279 (ttm110) REVERT: B 250 TYR cc_start: 0.8644 (m-80) cc_final: 0.7406 (m-80) REVERT: B 263 ASP cc_start: 0.9128 (m-30) cc_final: 0.8883 (m-30) REVERT: B 283 VAL cc_start: 0.9444 (t) cc_final: 0.9013 (t) REVERT: B 286 ASP cc_start: 0.8811 (m-30) cc_final: 0.8274 (m-30) REVERT: B 322 MET cc_start: 0.8982 (mmm) cc_final: 0.8140 (mmm) REVERT: B 326 PHE cc_start: 0.9495 (m-10) cc_final: 0.9175 (m-80) REVERT: B 349 LEU cc_start: 0.9335 (mm) cc_final: 0.9101 (mt) REVERT: B 359 MET cc_start: 0.8942 (ttt) cc_final: 0.8408 (tmm) REVERT: B 362 ASP cc_start: 0.8474 (m-30) cc_final: 0.7570 (m-30) REVERT: B 375 LYS cc_start: 0.9256 (mmmm) cc_final: 0.9020 (mmmm) REVERT: B 379 SER cc_start: 0.9186 (t) cc_final: 0.8492 (t) REVERT: B 391 VAL cc_start: 0.9364 (t) cc_final: 0.9133 (t) REVERT: B 393 SER cc_start: 0.9632 (t) cc_final: 0.9351 (p) REVERT: B 402 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8291 (tm-30) REVERT: B 403 ILE cc_start: 0.9448 (mp) cc_final: 0.9072 (tp) REVERT: B 410 ASN cc_start: 0.8860 (m110) cc_final: 0.8535 (m110) REVERT: B 458 MET cc_start: 0.9606 (mmm) cc_final: 0.9310 (mmm) REVERT: B 468 LEU cc_start: 0.9648 (tp) cc_final: 0.9402 (tp) REVERT: B 500 ILE cc_start: 0.9637 (mt) cc_final: 0.9410 (mt) REVERT: B 570 MET cc_start: 0.8951 (mmm) cc_final: 0.8248 (mmm) REVERT: B 575 ARG cc_start: 0.8498 (mtm-85) cc_final: 0.8181 (mtm-85) REVERT: B 588 GLN cc_start: 0.9414 (mm110) cc_final: 0.9082 (mm-40) REVERT: B 598 MET cc_start: 0.9352 (mtm) cc_final: 0.9001 (mtm) REVERT: B 599 GLU cc_start: 0.8893 (pt0) cc_final: 0.8574 (pt0) REVERT: B 612 TYR cc_start: 0.9010 (m-80) cc_final: 0.7946 (m-80) REVERT: B 613 TYR cc_start: 0.9026 (t80) cc_final: 0.8327 (t80) REVERT: B 631 ASP cc_start: 0.9418 (t70) cc_final: 0.9137 (t0) REVERT: B 637 VAL cc_start: 0.9790 (t) cc_final: 0.9589 (t) REVERT: B 640 MET cc_start: 0.9545 (tpp) cc_final: 0.9302 (tpp) REVERT: B 645 GLN cc_start: 0.9038 (tp40) cc_final: 0.8820 (tp-100) REVERT: B 648 ILE cc_start: 0.9349 (mm) cc_final: 0.9017 (mm) REVERT: B 673 TYR cc_start: 0.9158 (t80) cc_final: 0.8761 (t80) REVERT: B 679 ILE cc_start: 0.9654 (mm) cc_final: 0.9424 (mm) REVERT: C 17 PHE cc_start: 0.8516 (p90) cc_final: 0.7466 (p90) REVERT: C 20 MET cc_start: 0.8909 (ptp) cc_final: 0.8679 (pmm) REVERT: C 21 PHE cc_start: 0.9159 (m-10) cc_final: 0.8458 (m-80) REVERT: C 96 MET cc_start: 0.8175 (tpt) cc_final: 0.7940 (tpt) REVERT: C 157 MET cc_start: 0.9680 (mtm) cc_final: 0.9249 (ptm) REVERT: C 163 LEU cc_start: 0.9544 (tt) cc_final: 0.9222 (tt) REVERT: C 178 PHE cc_start: 0.9244 (m-80) cc_final: 0.8879 (m-10) REVERT: C 214 ASN cc_start: 0.8760 (m-40) cc_final: 0.8303 (p0) REVERT: C 239 GLU cc_start: 0.8669 (pt0) cc_final: 0.8147 (pt0) REVERT: C 263 ASN cc_start: 0.6843 (m110) cc_final: 0.6561 (p0) REVERT: C 283 ASN cc_start: 0.7804 (t0) cc_final: 0.7556 (t0) REVERT: D 66 ASP cc_start: 0.6077 (OUTLIER) cc_final: 0.5749 (p0) REVERT: D 109 PHE cc_start: 0.8887 (m-80) cc_final: 0.8098 (m-80) REVERT: D 164 GLU cc_start: 0.8359 (pt0) cc_final: 0.7817 (pt0) REVERT: D 172 PHE cc_start: 0.9417 (m-80) cc_final: 0.8725 (m-80) REVERT: D 185 MET cc_start: 0.5293 (mmp) cc_final: 0.4458 (mmm) REVERT: D 224 LEU cc_start: 0.9516 (mt) cc_final: 0.9244 (mt) outliers start: 2 outliers final: 0 residues processed: 713 average time/residue: 0.2847 time to fit residues: 297.6161 Evaluate side-chains 607 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 606 time to evaluate : 1.886 ------------------------------------------------------------------------------- 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: 10.0000 chunk 1 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 313 HIS ** 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 501 GLN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN B 410 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN C 233 ASN C 270 ASN D 23 ASN D 52 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.103443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.076091 restraints weight = 53552.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.078750 restraints weight = 31899.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.080885 restraints weight = 22237.621| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.6822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 16386 Z= 0.323 Angle : 0.785 8.586 22134 Z= 0.418 Chirality : 0.047 0.173 2360 Planarity : 0.005 0.050 2818 Dihedral : 11.545 177.698 2242 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 22.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.17 % Favored : 97.77 % Rotamer: Outliers : 0.12 % Allowed : 3.67 % Favored : 96.21 % 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: 0.19 (0.18), residues: 1932 helix: 0.51 (0.15), residues: 1128 sheet: -0.49 (0.39), residues: 152 loop : -0.16 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP D 124 HIS 0.007 0.002 HIS A 568 PHE 0.036 0.003 PHE C 168 TYR 0.044 0.003 TYR A 612 ARG 0.006 0.001 ARG D 261 Details of bonding type rmsd hydrogen bonds : bond 0.04710 ( 871) hydrogen bonds : angle 5.40478 ( 2571) covalent geometry : bond 0.00660 (16386) covalent geometry : angle 0.78526 (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 673 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 671 time to evaluate : 1.954 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 41 ILE cc_start: 0.9787 (mm) cc_final: 0.9581 (mt) REVERT: A 106 LEU cc_start: 0.9232 (tp) cc_final: 0.8979 (tp) REVERT: A 115 LEU cc_start: 0.9649 (mt) cc_final: 0.9415 (mt) REVERT: A 136 LYS cc_start: 0.9606 (tttp) cc_final: 0.9353 (ttmm) REVERT: A 144 MET cc_start: 0.8886 (mtm) cc_final: 0.8297 (mtm) REVERT: A 172 LEU cc_start: 0.9393 (mp) cc_final: 0.9064 (mp) REVERT: A 184 ARG cc_start: 0.9094 (tpp80) cc_final: 0.8818 (tpp80) REVERT: A 190 MET cc_start: 0.9200 (mtp) cc_final: 0.8883 (mtp) REVERT: A 191 GLN cc_start: 0.8926 (mm-40) cc_final: 0.8578 (mm-40) REVERT: A 199 VAL cc_start: 0.9462 (t) cc_final: 0.9207 (t) REVERT: A 228 LYS cc_start: 0.8684 (mmmm) cc_final: 0.8464 (mmtm) REVERT: A 236 TYR cc_start: 0.9028 (t80) cc_final: 0.8470 (t80) REVERT: A 252 ASN cc_start: 0.9416 (t0) cc_final: 0.9173 (t0) REVERT: A 286 ASP cc_start: 0.9004 (m-30) cc_final: 0.8614 (m-30) REVERT: A 335 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8604 (mp0) REVERT: A 359 MET cc_start: 0.8885 (ttp) cc_final: 0.8537 (ttp) REVERT: A 362 ASP cc_start: 0.9206 (m-30) cc_final: 0.8948 (m-30) REVERT: A 370 ASN cc_start: 0.9634 (m-40) cc_final: 0.9383 (m-40) REVERT: A 375 LYS cc_start: 0.8997 (mmmt) cc_final: 0.8556 (mmtm) REVERT: A 377 LYS cc_start: 0.8902 (mttt) cc_final: 0.8495 (mttp) REVERT: A 406 ASP cc_start: 0.8790 (m-30) cc_final: 0.8435 (m-30) REVERT: A 407 ILE cc_start: 0.9109 (mt) cc_final: 0.8684 (mt) REVERT: A 441 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8936 (mm-30) REVERT: A 469 HIS cc_start: 0.9344 (t-170) cc_final: 0.9038 (t-170) REVERT: A 494 MET cc_start: 0.9481 (mpp) cc_final: 0.9057 (mmm) REVERT: A 501 GLN cc_start: 0.9449 (tp40) cc_final: 0.8630 (tp-100) REVERT: A 515 ASP cc_start: 0.9405 (m-30) cc_final: 0.8939 (m-30) REVERT: A 550 MET cc_start: 0.8530 (pmm) cc_final: 0.7870 (pmm) REVERT: A 561 LEU cc_start: 0.9614 (tp) cc_final: 0.9413 (tp) REVERT: A 570 MET cc_start: 0.9078 (mtp) cc_final: 0.8793 (mtp) REVERT: A 583 SER cc_start: 0.9647 (m) cc_final: 0.9414 (p) REVERT: A 598 MET cc_start: 0.8626 (ttt) cc_final: 0.8308 (ttt) REVERT: A 599 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8128 (tm-30) REVERT: A 615 MET cc_start: 0.8940 (mmp) cc_final: 0.8707 (mmp) REVERT: A 636 LYS cc_start: 0.9821 (mmtp) cc_final: 0.9618 (mmmm) REVERT: A 647 HIS cc_start: 0.9213 (m-70) cc_final: 0.8517 (m170) REVERT: A 675 HIS cc_start: 0.9228 (t-90) cc_final: 0.8489 (t70) REVERT: B 8 LYS cc_start: 0.9346 (tptp) cc_final: 0.9096 (tptp) REVERT: B 30 LYS cc_start: 0.9786 (tmtt) cc_final: 0.9399 (tptt) REVERT: B 54 LYS cc_start: 0.9758 (ttmm) cc_final: 0.9429 (tttp) REVERT: B 116 GLU cc_start: 0.8530 (mt-10) cc_final: 0.7778 (mt-10) REVERT: B 139 GLU cc_start: 0.9506 (mm-30) cc_final: 0.9219 (mp0) REVERT: B 179 LEU cc_start: 0.9761 (tp) cc_final: 0.9492 (tp) REVERT: B 199 VAL cc_start: 0.9003 (t) cc_final: 0.8714 (p) REVERT: B 211 GLU cc_start: 0.8983 (mm-30) cc_final: 0.7952 (mt-10) REVERT: B 235 ARG cc_start: 0.8660 (ttm110) cc_final: 0.8138 (ttm110) REVERT: B 250 TYR cc_start: 0.8832 (m-80) cc_final: 0.7955 (m-80) REVERT: B 263 ASP cc_start: 0.9315 (m-30) cc_final: 0.9047 (m-30) REVERT: B 291 LEU cc_start: 0.9514 (mt) cc_final: 0.9227 (mt) REVERT: B 322 MET cc_start: 0.8810 (mmm) cc_final: 0.8571 (mmm) REVERT: B 349 LEU cc_start: 0.9379 (mm) cc_final: 0.9165 (mt) REVERT: B 359 MET cc_start: 0.8980 (ttt) cc_final: 0.8473 (tmm) REVERT: B 403 ILE cc_start: 0.9367 (mp) cc_final: 0.9035 (tp) REVERT: B 407 ILE cc_start: 0.8844 (mt) cc_final: 0.8615 (mt) REVERT: B 415 ASN cc_start: 0.9324 (t0) cc_final: 0.8964 (t0) REVERT: B 420 MET cc_start: 0.9307 (mmm) cc_final: 0.8994 (mmm) REVERT: B 459 LYS cc_start: 0.9171 (mttp) cc_final: 0.8475 (mtmt) REVERT: B 468 LEU cc_start: 0.9592 (tp) cc_final: 0.9324 (tp) REVERT: B 493 MET cc_start: 0.9209 (ppp) cc_final: 0.8907 (ppp) REVERT: B 494 MET cc_start: 0.9504 (mmt) cc_final: 0.9078 (mmt) REVERT: B 510 LYS cc_start: 0.9337 (mmtm) cc_final: 0.9107 (mmtm) REVERT: B 598 MET cc_start: 0.9407 (mtm) cc_final: 0.9019 (mtm) REVERT: B 602 GLU cc_start: 0.8088 (mp0) cc_final: 0.7510 (mp0) REVERT: B 612 TYR cc_start: 0.8896 (m-80) cc_final: 0.7983 (m-80) REVERT: B 613 TYR cc_start: 0.9075 (t80) cc_final: 0.7997 (t80) REVERT: B 615 MET cc_start: 0.8870 (mmp) cc_final: 0.8042 (mmp) REVERT: B 631 ASP cc_start: 0.9355 (t70) cc_final: 0.9064 (t0) REVERT: B 639 ASP cc_start: 0.9339 (m-30) cc_final: 0.8909 (m-30) REVERT: B 640 MET cc_start: 0.9537 (tpp) cc_final: 0.8954 (tpp) REVERT: B 673 TYR cc_start: 0.9138 (t80) cc_final: 0.8728 (t80) REVERT: B 679 ILE cc_start: 0.9516 (mm) cc_final: 0.9290 (mm) REVERT: C 20 MET cc_start: 0.8985 (ptp) cc_final: 0.8711 (ptp) REVERT: C 21 PHE cc_start: 0.9143 (m-10) cc_final: 0.8752 (m-80) REVERT: C 66 ASP cc_start: 0.8492 (p0) cc_final: 0.7989 (p0) REVERT: C 105 TYR cc_start: 0.8706 (m-80) cc_final: 0.8435 (m-80) REVERT: C 122 PHE cc_start: 0.8543 (m-80) cc_final: 0.8242 (m-80) REVERT: C 157 MET cc_start: 0.9716 (mtm) cc_final: 0.9380 (ttm) REVERT: C 178 PHE cc_start: 0.9217 (m-80) cc_final: 0.8821 (m-10) REVERT: C 239 GLU cc_start: 0.8699 (pt0) cc_final: 0.8179 (pt0) REVERT: C 263 ASN cc_start: 0.6730 (m110) cc_final: 0.6465 (t0) REVERT: D 109 PHE cc_start: 0.8857 (m-80) cc_final: 0.8223 (m-80) REVERT: D 112 LEU cc_start: 0.8561 (mm) cc_final: 0.7647 (pp) REVERT: D 166 PHE cc_start: 0.8176 (t80) cc_final: 0.7845 (t80) REVERT: D 172 PHE cc_start: 0.9466 (m-80) cc_final: 0.8991 (m-80) REVERT: D 179 TYR cc_start: 0.8014 (t80) cc_final: 0.7788 (t80) REVERT: D 185 MET cc_start: 0.5658 (mmp) cc_final: 0.5265 (mmp) outliers start: 2 outliers final: 0 residues processed: 671 average time/residue: 0.2951 time to fit residues: 293.4202 Evaluate side-chains 564 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 564 time to evaluate : 2.025 ------------------------------------------------------------------------------- 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: 1.9990 chunk 41 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 645 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN D 52 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.109514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.081176 restraints weight = 51710.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.084282 restraints weight = 30788.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.086580 restraints weight = 20997.501| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.6982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16386 Z= 0.142 Angle : 0.633 8.000 22134 Z= 0.338 Chirality : 0.044 0.257 2360 Planarity : 0.004 0.046 2818 Dihedral : 10.941 176.159 2242 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.12 % Allowed : 2.10 % Favored : 97.79 % 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: 0.49 (0.18), residues: 1932 helix: 0.77 (0.15), residues: 1144 sheet: -0.23 (0.42), residues: 148 loop : -0.14 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP D 124 HIS 0.017 0.002 HIS B 675 PHE 0.036 0.002 PHE C 168 TYR 0.027 0.002 TYR D 130 ARG 0.007 0.001 ARG A 575 Details of bonding type rmsd hydrogen bonds : bond 0.04117 ( 871) hydrogen bonds : angle 5.02869 ( 2571) covalent geometry : bond 0.00311 (16386) covalent geometry : angle 0.63297 (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 696 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 694 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9200 (tptp) cc_final: 0.8771 (tppt) REVERT: A 41 ILE cc_start: 0.9714 (mm) cc_final: 0.9413 (mt) REVERT: A 81 PHE cc_start: 0.9673 (m-80) cc_final: 0.9426 (m-80) REVERT: A 119 GLU cc_start: 0.9207 (mp0) cc_final: 0.7998 (tm-30) REVERT: A 136 LYS cc_start: 0.9603 (tttp) cc_final: 0.9309 (ttmm) REVERT: A 147 GLN cc_start: 0.8052 (tp-100) cc_final: 0.7571 (mm-40) REVERT: A 150 GLN cc_start: 0.8974 (tp40) cc_final: 0.8760 (tp40) REVERT: A 172 LEU cc_start: 0.9349 (mp) cc_final: 0.9140 (mp) REVERT: A 184 ARG cc_start: 0.9074 (tpp80) cc_final: 0.8716 (tpp80) REVERT: A 187 ASP cc_start: 0.9413 (t70) cc_final: 0.8921 (t70) REVERT: A 190 MET cc_start: 0.9122 (mtp) cc_final: 0.8908 (mtp) REVERT: A 191 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8381 (mp10) REVERT: A 199 VAL cc_start: 0.9485 (t) cc_final: 0.9264 (t) REVERT: A 235 ARG cc_start: 0.8312 (mtm110) cc_final: 0.7996 (mtm110) REVERT: A 236 TYR cc_start: 0.8860 (t80) cc_final: 0.8364 (t80) REVERT: A 254 PHE cc_start: 0.8806 (m-80) cc_final: 0.7975 (m-80) REVERT: A 280 ILE cc_start: 0.8609 (pt) cc_final: 0.8183 (mp) REVERT: A 335 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8759 (mp0) REVERT: A 359 MET cc_start: 0.8828 (ttp) cc_final: 0.8391 (ttp) REVERT: A 362 ASP cc_start: 0.9081 (m-30) cc_final: 0.8842 (m-30) REVERT: A 370 ASN cc_start: 0.9533 (m-40) cc_final: 0.9226 (m110) REVERT: A 375 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8687 (mmtm) REVERT: A 377 LYS cc_start: 0.8924 (mttt) cc_final: 0.8351 (mttp) REVERT: A 398 ASP cc_start: 0.8725 (p0) cc_final: 0.8423 (p0) REVERT: A 406 ASP cc_start: 0.8825 (m-30) cc_final: 0.8500 (m-30) REVERT: A 407 ILE cc_start: 0.9133 (mt) cc_final: 0.8743 (mt) REVERT: A 469 HIS cc_start: 0.9223 (t-170) cc_final: 0.8927 (t-170) REVERT: A 490 THR cc_start: 0.9597 (m) cc_final: 0.8982 (m) REVERT: A 494 MET cc_start: 0.9448 (mpp) cc_final: 0.9101 (mmm) REVERT: A 501 GLN cc_start: 0.9384 (tp40) cc_final: 0.8598 (tp-100) REVERT: A 515 ASP cc_start: 0.9325 (m-30) cc_final: 0.8826 (m-30) REVERT: A 516 GLN cc_start: 0.9198 (mp10) cc_final: 0.8976 (mp10) REVERT: A 561 LEU cc_start: 0.9601 (tp) cc_final: 0.9381 (tp) REVERT: A 570 MET cc_start: 0.9237 (mtp) cc_final: 0.8816 (mtp) REVERT: A 583 SER cc_start: 0.9562 (m) cc_final: 0.9310 (t) REVERT: A 615 MET cc_start: 0.8943 (mmp) cc_final: 0.8707 (mmp) REVERT: A 636 LYS cc_start: 0.9797 (mmtp) cc_final: 0.9583 (mmmm) REVERT: A 653 SER cc_start: 0.8693 (p) cc_final: 0.8416 (p) REVERT: A 686 ARG cc_start: 0.7411 (mmm160) cc_final: 0.7136 (mmm160) REVERT: B 8 LYS cc_start: 0.9385 (tptp) cc_final: 0.9135 (tptp) REVERT: B 30 LYS cc_start: 0.9782 (tmtt) cc_final: 0.9379 (tptt) REVERT: B 82 LYS cc_start: 0.9531 (ptpp) cc_final: 0.9200 (ptpt) REVERT: B 95 MET cc_start: 0.9287 (tpp) cc_final: 0.8840 (tpp) REVERT: B 119 GLU cc_start: 0.9276 (mp0) cc_final: 0.8887 (mp0) REVERT: B 120 ASP cc_start: 0.9369 (m-30) cc_final: 0.9126 (m-30) REVERT: B 124 ILE cc_start: 0.9639 (mm) cc_final: 0.9298 (mm) REVERT: B 139 GLU cc_start: 0.9491 (mm-30) cc_final: 0.9200 (mp0) REVERT: B 168 VAL cc_start: 0.9552 (t) cc_final: 0.9351 (m) REVERT: B 191 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8645 (mm-40) REVERT: B 211 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8356 (mm-30) REVERT: B 235 ARG cc_start: 0.8730 (ttm110) cc_final: 0.8160 (ttm110) REVERT: B 250 TYR cc_start: 0.8481 (m-80) cc_final: 0.7204 (m-80) REVERT: B 263 ASP cc_start: 0.9174 (m-30) cc_final: 0.8973 (m-30) REVERT: B 283 VAL cc_start: 0.9468 (t) cc_final: 0.9196 (t) REVERT: B 286 ASP cc_start: 0.9267 (m-30) cc_final: 0.8600 (m-30) REVERT: B 291 LEU cc_start: 0.9558 (mt) cc_final: 0.9206 (mt) REVERT: B 359 MET cc_start: 0.8939 (ttt) cc_final: 0.8206 (tmm) REVERT: B 362 ASP cc_start: 0.8582 (m-30) cc_final: 0.7651 (m-30) REVERT: B 375 LYS cc_start: 0.9357 (mmmm) cc_final: 0.9129 (mmmm) REVERT: B 379 SER cc_start: 0.8815 (t) cc_final: 0.8260 (t) REVERT: B 403 ILE cc_start: 0.9323 (mp) cc_final: 0.8913 (tp) REVERT: B 420 MET cc_start: 0.9271 (mmm) cc_final: 0.9014 (mmm) REVERT: B 446 ARG cc_start: 0.9140 (mmm-85) cc_final: 0.8614 (mmm-85) REVERT: B 459 LYS cc_start: 0.9158 (mttp) cc_final: 0.8387 (mtmt) REVERT: B 467 ASN cc_start: 0.8658 (m110) cc_final: 0.8410 (m-40) REVERT: B 468 LEU cc_start: 0.9521 (tp) cc_final: 0.9236 (tp) REVERT: B 493 MET cc_start: 0.9148 (ppp) cc_final: 0.8826 (ppp) REVERT: B 494 MET cc_start: 0.9496 (mmt) cc_final: 0.9038 (mmt) REVERT: B 570 MET cc_start: 0.8743 (mmm) cc_final: 0.8266 (mmm) REVERT: B 571 TYR cc_start: 0.9268 (t80) cc_final: 0.9042 (t80) REVERT: B 598 MET cc_start: 0.9516 (mtm) cc_final: 0.9236 (mtm) REVERT: B 606 TYR cc_start: 0.8825 (m-80) cc_final: 0.8159 (m-80) REVERT: B 612 TYR cc_start: 0.8718 (m-80) cc_final: 0.7838 (m-80) REVERT: B 613 TYR cc_start: 0.9307 (t80) cc_final: 0.8370 (t80) REVERT: B 615 MET cc_start: 0.9044 (mmp) cc_final: 0.8505 (mmp) REVERT: B 631 ASP cc_start: 0.9359 (t70) cc_final: 0.9086 (t0) REVERT: B 640 MET cc_start: 0.9380 (tpp) cc_final: 0.8902 (tpp) REVERT: B 648 ILE cc_start: 0.9398 (mm) cc_final: 0.9197 (mm) REVERT: C 17 PHE cc_start: 0.8682 (p90) cc_final: 0.7911 (p90) REVERT: C 20 MET cc_start: 0.8992 (ptp) cc_final: 0.8696 (pmm) REVERT: C 21 PHE cc_start: 0.9122 (m-10) cc_final: 0.8672 (m-80) REVERT: C 66 ASP cc_start: 0.8176 (p0) cc_final: 0.7851 (p0) REVERT: C 105 TYR cc_start: 0.8753 (m-80) cc_final: 0.8435 (m-80) REVERT: C 122 PHE cc_start: 0.8465 (m-80) cc_final: 0.8206 (m-80) REVERT: C 178 PHE cc_start: 0.9221 (m-80) cc_final: 0.8850 (m-10) REVERT: C 239 GLU cc_start: 0.8578 (pt0) cc_final: 0.7979 (pt0) REVERT: C 263 ASN cc_start: 0.6859 (m110) cc_final: 0.6641 (p0) REVERT: D 21 PHE cc_start: 0.8667 (m-10) cc_final: 0.8329 (m-10) REVERT: D 109 PHE cc_start: 0.8942 (m-80) cc_final: 0.8200 (m-80) REVERT: D 166 PHE cc_start: 0.7901 (t80) cc_final: 0.7626 (t80) REVERT: D 172 PHE cc_start: 0.9447 (m-80) cc_final: 0.8874 (m-80) REVERT: D 179 TYR cc_start: 0.7895 (t80) cc_final: 0.7664 (t80) REVERT: D 185 MET cc_start: 0.5186 (mmp) cc_final: 0.4669 (mmm) REVERT: D 252 LEU cc_start: 0.8216 (mt) cc_final: 0.7883 (mp) REVERT: D 271 LEU cc_start: 0.8338 (mt) cc_final: 0.8056 (mt) outliers start: 2 outliers final: 0 residues processed: 696 average time/residue: 0.2782 time to fit residues: 284.6894 Evaluate side-chains 585 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 585 time to evaluate : 1.807 ------------------------------------------------------------------------------- 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: 0.9980 chunk 126 optimal weight: 2.9990 chunk 62 optimal weight: 0.0670 chunk 69 optimal weight: 8.9990 chunk 156 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 177 optimal weight: 0.0670 overall best weight: 1.4260 ------------------------------------------------------------------------------- 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 ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** 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 475 ASN A 645 GLN B 320 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.109001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.080275 restraints weight = 50799.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.083231 restraints weight = 30615.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.085484 restraints weight = 21260.375| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 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 = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.7320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16386 Z= 0.147 Angle : 0.635 8.378 22134 Z= 0.338 Chirality : 0.044 0.272 2360 Planarity : 0.004 0.057 2818 Dihedral : 10.756 175.696 2242 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.17 % Allowed : 1.57 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.55 (0.18), residues: 1932 helix: 0.86 (0.15), residues: 1131 sheet: -0.39 (0.42), residues: 148 loop : -0.12 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP D 124 HIS 0.007 0.001 HIS B 438 PHE 0.048 0.002 PHE D 227 TYR 0.034 0.002 TYR D 130 ARG 0.007 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 871) hydrogen bonds : angle 5.07444 ( 2571) covalent geometry : bond 0.00318 (16386) covalent geometry : angle 0.63526 (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 684 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 681 time to evaluate : 1.954 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: A 8 LYS cc_start: 0.9221 (tptp) cc_final: 0.8768 (tppt) REVERT: A 81 PHE cc_start: 0.9670 (m-80) cc_final: 0.9453 (m-80) REVERT: A 106 LEU cc_start: 0.9084 (tp) cc_final: 0.8836 (tp) REVERT: A 119 GLU cc_start: 0.9137 (mp0) cc_final: 0.7982 (tm-30) REVERT: A 120 ASP cc_start: 0.9452 (m-30) cc_final: 0.9091 (m-30) REVERT: A 129 PHE cc_start: 0.9705 (m-10) cc_final: 0.9504 (m-80) REVERT: A 136 LYS cc_start: 0.9628 (tttp) cc_final: 0.9234 (tttp) REVERT: A 172 LEU cc_start: 0.9365 (mp) cc_final: 0.9134 (mp) REVERT: A 176 ASN cc_start: 0.8435 (t0) cc_final: 0.7738 (m-40) REVERT: A 184 ARG cc_start: 0.9029 (tpp80) cc_final: 0.8807 (tpp80) REVERT: A 190 MET cc_start: 0.9072 (mtp) cc_final: 0.8852 (mtp) REVERT: A 191 GLN cc_start: 0.8724 (mm-40) cc_final: 0.8446 (mm-40) REVERT: A 205 LYS cc_start: 0.8800 (mtpp) cc_final: 0.8550 (mtpp) REVERT: A 236 TYR cc_start: 0.8826 (t80) cc_final: 0.8258 (t80) REVERT: A 252 ASN cc_start: 0.9509 (t0) cc_final: 0.9260 (t0) REVERT: A 279 SER cc_start: 0.8323 (m) cc_final: 0.8052 (p) REVERT: A 280 ILE cc_start: 0.8707 (pt) cc_final: 0.8088 (mp) REVERT: A 286 ASP cc_start: 0.9095 (m-30) cc_final: 0.8678 (m-30) REVERT: A 322 MET cc_start: 0.9091 (mmm) cc_final: 0.8577 (tmm) REVERT: A 345 LYS cc_start: 0.9053 (tttt) cc_final: 0.8812 (tttt) REVERT: A 349 LEU cc_start: 0.9469 (mt) cc_final: 0.9200 (mt) REVERT: A 359 MET cc_start: 0.8837 (ttp) cc_final: 0.8633 (ttp) REVERT: A 362 ASP cc_start: 0.8934 (m-30) cc_final: 0.8560 (m-30) REVERT: A 370 ASN cc_start: 0.9515 (m-40) cc_final: 0.9228 (m110) REVERT: A 375 LYS cc_start: 0.9038 (mmmt) cc_final: 0.8632 (mmtm) REVERT: A 377 LYS cc_start: 0.8915 (mttt) cc_final: 0.8321 (mttp) REVERT: A 381 LEU cc_start: 0.8971 (tp) cc_final: 0.8448 (pt) REVERT: A 398 ASP cc_start: 0.8609 (p0) cc_final: 0.8334 (p0) REVERT: A 403 ILE cc_start: 0.8923 (tp) cc_final: 0.8579 (tp) REVERT: A 406 ASP cc_start: 0.8810 (m-30) cc_final: 0.8371 (m-30) REVERT: A 407 ILE cc_start: 0.9129 (mt) cc_final: 0.8721 (mt) REVERT: A 469 HIS cc_start: 0.9189 (t-170) cc_final: 0.8963 (t-170) REVERT: A 490 THR cc_start: 0.9587 (m) cc_final: 0.8888 (m) REVERT: A 494 MET cc_start: 0.9454 (mpp) cc_final: 0.9120 (mmm) REVERT: A 515 ASP cc_start: 0.9312 (m-30) cc_final: 0.8879 (m-30) REVERT: A 570 MET cc_start: 0.9288 (mtp) cc_final: 0.8802 (mtp) REVERT: A 583 SER cc_start: 0.9617 (m) cc_final: 0.9392 (t) REVERT: A 604 ARG cc_start: 0.9137 (tpp80) cc_final: 0.8738 (ttm110) REVERT: A 628 GLU cc_start: 0.9298 (mt-10) cc_final: 0.8548 (mm-30) REVERT: A 636 LYS cc_start: 0.9791 (mmtp) cc_final: 0.9573 (mmmm) REVERT: A 640 MET cc_start: 0.9357 (tpp) cc_final: 0.8879 (tpp) REVERT: A 647 HIS cc_start: 0.9044 (m-70) cc_final: 0.7844 (m170) REVERT: A 653 SER cc_start: 0.8724 (p) cc_final: 0.8455 (p) REVERT: A 675 HIS cc_start: 0.9379 (t-90) cc_final: 0.8729 (t70) REVERT: A 677 ARG cc_start: 0.9405 (mmm-85) cc_final: 0.8922 (mmm-85) REVERT: A 686 ARG cc_start: 0.7267 (mmm160) cc_final: 0.7064 (mmm160) REVERT: B 8 LYS cc_start: 0.9396 (tptp) cc_final: 0.9159 (tptp) REVERT: B 30 LYS cc_start: 0.9783 (tmtt) cc_final: 0.9371 (tptt) REVERT: B 65 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8272 (tp30) REVERT: B 82 LYS cc_start: 0.9481 (ptpp) cc_final: 0.9138 (ptpt) REVERT: B 95 MET cc_start: 0.9305 (tpp) cc_final: 0.8861 (tpp) REVERT: B 107 LYS cc_start: 0.9340 (mtpp) cc_final: 0.9118 (mtpp) REVERT: B 116 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8082 (tp30) REVERT: B 119 GLU cc_start: 0.9150 (mp0) cc_final: 0.8761 (mp0) REVERT: B 120 ASP cc_start: 0.9427 (m-30) cc_final: 0.8913 (m-30) REVERT: B 124 ILE cc_start: 0.9598 (mm) cc_final: 0.9183 (mm) REVERT: B 202 ASN cc_start: 0.6847 (p0) cc_final: 0.6550 (p0) REVERT: B 211 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8432 (mm-30) REVERT: B 227 MET cc_start: 0.9201 (ttp) cc_final: 0.8951 (ttp) REVERT: B 235 ARG cc_start: 0.8723 (ttm110) cc_final: 0.8120 (ttm110) REVERT: B 250 TYR cc_start: 0.8532 (m-80) cc_final: 0.7293 (m-80) REVERT: B 263 ASP cc_start: 0.9181 (m-30) cc_final: 0.8899 (m-30) REVERT: B 283 VAL cc_start: 0.9401 (t) cc_final: 0.9100 (t) REVERT: B 286 ASP cc_start: 0.9260 (m-30) cc_final: 0.8917 (t0) REVERT: B 291 LEU cc_start: 0.9529 (mt) cc_final: 0.9189 (mt) REVERT: B 322 MET cc_start: 0.8801 (mmm) cc_final: 0.8417 (mmm) REVERT: B 359 MET cc_start: 0.8889 (ttt) cc_final: 0.8158 (tmm) REVERT: B 375 LYS cc_start: 0.9315 (mmmm) cc_final: 0.9057 (mmmm) REVERT: B 379 SER cc_start: 0.8908 (t) cc_final: 0.8312 (t) REVERT: B 403 ILE cc_start: 0.9331 (mp) cc_final: 0.8860 (tp) REVERT: B 407 ILE cc_start: 0.8914 (mt) cc_final: 0.8713 (mt) REVERT: B 410 ASN cc_start: 0.9072 (m110) cc_final: 0.8817 (m110) REVERT: B 418 ASN cc_start: 0.9463 (m-40) cc_final: 0.9127 (m110) REVERT: B 420 MET cc_start: 0.9359 (mmm) cc_final: 0.8972 (mmm) REVERT: B 446 ARG cc_start: 0.9060 (mmm-85) cc_final: 0.8453 (mmm-85) REVERT: B 459 LYS cc_start: 0.9034 (mttp) cc_final: 0.8305 (mtmt) REVERT: B 467 ASN cc_start: 0.8698 (m110) cc_final: 0.7920 (m110) REVERT: B 506 ILE cc_start: 0.9594 (mm) cc_final: 0.9374 (mm) REVERT: B 598 MET cc_start: 0.9456 (mtm) cc_final: 0.9194 (mtm) REVERT: B 602 GLU cc_start: 0.8018 (mp0) cc_final: 0.7703 (mp0) REVERT: B 612 TYR cc_start: 0.8638 (m-80) cc_final: 0.7665 (m-80) REVERT: B 613 TYR cc_start: 0.9307 (t80) cc_final: 0.7829 (t80) REVERT: B 615 MET cc_start: 0.9072 (mmp) cc_final: 0.8261 (mmp) REVERT: B 631 ASP cc_start: 0.9371 (t70) cc_final: 0.9107 (t0) REVERT: B 640 MET cc_start: 0.9373 (tpp) cc_final: 0.8850 (tpp) REVERT: B 679 ILE cc_start: 0.9625 (mm) cc_final: 0.9400 (mm) REVERT: C 17 PHE cc_start: 0.8741 (p90) cc_final: 0.7894 (p90) REVERT: C 21 PHE cc_start: 0.9060 (m-10) cc_final: 0.8576 (m-80) REVERT: C 105 TYR cc_start: 0.8884 (m-80) cc_final: 0.8533 (m-80) REVERT: C 122 PHE cc_start: 0.8560 (m-80) cc_final: 0.8296 (m-80) REVERT: C 157 MET cc_start: 0.9600 (ptm) cc_final: 0.9010 (ppp) REVERT: C 178 PHE cc_start: 0.9223 (m-80) cc_final: 0.8836 (m-10) REVERT: C 233 ASN cc_start: 0.9535 (m110) cc_final: 0.9331 (p0) REVERT: C 239 GLU cc_start: 0.8606 (pt0) cc_final: 0.8029 (pt0) REVERT: C 271 LEU cc_start: 0.8608 (mp) cc_final: 0.8408 (mp) REVERT: C 283 ASN cc_start: 0.7769 (t0) cc_final: 0.7481 (t0) REVERT: C 285 ILE cc_start: 0.9181 (mm) cc_final: 0.8957 (mm) REVERT: D 17 PHE cc_start: 0.4964 (m-80) cc_final: 0.4631 (m-80) REVERT: D 21 PHE cc_start: 0.8549 (m-10) cc_final: 0.8181 (m-10) REVERT: D 108 ILE cc_start: 0.9452 (mt) cc_final: 0.9231 (pt) REVERT: D 109 PHE cc_start: 0.8907 (m-80) cc_final: 0.8198 (m-80) REVERT: D 112 LEU cc_start: 0.8595 (mm) cc_final: 0.7736 (pp) REVERT: D 172 PHE cc_start: 0.9399 (m-80) cc_final: 0.8853 (m-80) REVERT: D 179 TYR cc_start: 0.7959 (t80) cc_final: 0.7719 (t80) REVERT: D 185 MET cc_start: 0.5510 (mmp) cc_final: 0.5035 (mmm) outliers start: 3 outliers final: 2 residues processed: 684 average time/residue: 0.2779 time to fit residues: 281.5973 Evaluate side-chains 569 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 567 time to evaluate : 1.798 ------------------------------------------------------------------------------- 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: 3.9990 chunk 85 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 23 optimal weight: 0.0370 chunk 40 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 175 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.3464 ------------------------------------------------------------------------------- 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 ** 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 668 ASN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN B 361 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 HIS ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN C 270 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN D 238 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.105723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.078501 restraints weight = 52236.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.081464 restraints weight = 31898.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.083512 restraints weight = 21773.722| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 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 = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.7624 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= 0.181 Angle : 0.663 8.714 22134 Z= 0.355 Chirality : 0.045 0.292 2360 Planarity : 0.004 0.049 2818 Dihedral : 10.721 174.531 2242 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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: 0.53 (0.19), residues: 1932 helix: 0.86 (0.15), residues: 1125 sheet: -0.57 (0.42), residues: 148 loop : -0.12 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP D 124 HIS 0.008 0.001 HIS D 201 PHE 0.035 0.002 PHE C 168 TYR 0.031 0.002 TYR C 247 ARG 0.007 0.001 ARG C 225 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 871) hydrogen bonds : angle 5.17780 ( 2571) covalent geometry : bond 0.00388 (16386) covalent geometry : angle 0.66279 (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 653 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 653 time to evaluate : 1.878 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: A 8 LYS cc_start: 0.9281 (tptp) cc_final: 0.8860 (tppt) REVERT: A 119 GLU cc_start: 0.9149 (mp0) cc_final: 0.7860 (tm-30) REVERT: A 120 ASP cc_start: 0.9480 (m-30) cc_final: 0.9100 (m-30) REVERT: A 128 PHE cc_start: 0.9546 (t80) cc_final: 0.9281 (t80) REVERT: A 136 LYS cc_start: 0.9612 (tttp) cc_final: 0.9273 (tppp) REVERT: A 176 ASN cc_start: 0.8400 (t0) cc_final: 0.7742 (m-40) REVERT: A 184 ARG cc_start: 0.9129 (tpp80) cc_final: 0.8903 (tpp80) REVERT: A 190 MET cc_start: 0.9090 (mtp) cc_final: 0.8856 (mtp) REVERT: A 191 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8428 (mm-40) REVERT: A 235 ARG cc_start: 0.8274 (mtm110) cc_final: 0.7990 (mtm110) REVERT: A 236 TYR cc_start: 0.8881 (t80) cc_final: 0.8298 (t80) REVERT: A 280 ILE cc_start: 0.8642 (pt) cc_final: 0.8337 (mp) REVERT: A 283 VAL cc_start: 0.9179 (t) cc_final: 0.8899 (t) REVERT: A 286 ASP cc_start: 0.9053 (m-30) cc_final: 0.8523 (m-30) REVERT: A 345 LYS cc_start: 0.9052 (tttt) cc_final: 0.8804 (tttt) REVERT: A 349 LEU cc_start: 0.9461 (mt) cc_final: 0.9172 (mt) REVERT: A 359 MET cc_start: 0.8942 (ttp) cc_final: 0.8374 (ttp) REVERT: A 362 ASP cc_start: 0.8994 (m-30) cc_final: 0.8784 (m-30) REVERT: A 370 ASN cc_start: 0.9576 (m-40) cc_final: 0.9319 (m110) REVERT: A 375 LYS cc_start: 0.8993 (mmmt) cc_final: 0.8517 (mmtm) REVERT: A 377 LYS cc_start: 0.8900 (mttt) cc_final: 0.8344 (mttp) REVERT: A 381 LEU cc_start: 0.9001 (tp) cc_final: 0.8475 (pt) REVERT: A 398 ASP cc_start: 0.8641 (p0) cc_final: 0.8351 (p0) REVERT: A 407 ILE cc_start: 0.9099 (mt) cc_final: 0.8780 (mt) REVERT: A 469 HIS cc_start: 0.9121 (t-170) cc_final: 0.8863 (t-170) REVERT: A 515 ASP cc_start: 0.9395 (m-30) cc_final: 0.8895 (m-30) REVERT: A 570 MET cc_start: 0.9316 (mtp) cc_final: 0.8947 (mtp) REVERT: A 583 SER cc_start: 0.9578 (m) cc_final: 0.9290 (t) REVERT: A 598 MET cc_start: 0.8974 (ttt) cc_final: 0.8692 (ttt) REVERT: A 604 ARG cc_start: 0.9173 (tpp80) cc_final: 0.8750 (ttm110) REVERT: A 615 MET cc_start: 0.8981 (mmp) cc_final: 0.8774 (mmp) REVERT: A 628 GLU cc_start: 0.9306 (mt-10) cc_final: 0.9017 (mt-10) REVERT: A 636 LYS cc_start: 0.9789 (mmtp) cc_final: 0.9565 (mmmm) REVERT: A 640 MET cc_start: 0.9340 (tpp) cc_final: 0.8961 (tpp) REVERT: A 647 HIS cc_start: 0.9158 (m-70) cc_final: 0.7721 (m170) REVERT: A 675 HIS cc_start: 0.9336 (t-90) cc_final: 0.8568 (t-90) REVERT: B 8 LYS cc_start: 0.9375 (tptp) cc_final: 0.9167 (tptp) REVERT: B 30 LYS cc_start: 0.9791 (tmtt) cc_final: 0.9377 (tptt) REVERT: B 65 GLU cc_start: 0.8651 (tm-30) cc_final: 0.7693 (tm-30) REVERT: B 95 MET cc_start: 0.9248 (tpp) cc_final: 0.8867 (tpp) REVERT: B 107 LYS cc_start: 0.9303 (mtpp) cc_final: 0.9087 (mtpp) REVERT: B 116 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8155 (tp30) REVERT: B 117 ARG cc_start: 0.9079 (mtp180) cc_final: 0.8493 (mmm160) REVERT: B 119 GLU cc_start: 0.9196 (mp0) cc_final: 0.8816 (mp0) REVERT: B 120 ASP cc_start: 0.9411 (m-30) cc_final: 0.8979 (m-30) REVERT: B 124 ILE cc_start: 0.9624 (mm) cc_final: 0.9308 (mm) REVERT: B 144 MET cc_start: 0.9363 (mtm) cc_final: 0.9157 (mtm) REVERT: B 187 ASP cc_start: 0.9525 (t70) cc_final: 0.9310 (t0) REVERT: B 202 ASN cc_start: 0.6963 (p0) cc_final: 0.6618 (p0) REVERT: B 211 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8418 (mm-30) REVERT: B 227 MET cc_start: 0.9164 (ttp) cc_final: 0.8939 (ttp) REVERT: B 235 ARG cc_start: 0.8732 (ttm110) cc_final: 0.8121 (ttm110) REVERT: B 250 TYR cc_start: 0.8631 (m-80) cc_final: 0.7408 (m-80) REVERT: B 263 ASP cc_start: 0.9173 (m-30) cc_final: 0.8868 (m-30) REVERT: B 291 LEU cc_start: 0.9497 (mt) cc_final: 0.9224 (mt) REVERT: B 322 MET cc_start: 0.8855 (mmm) cc_final: 0.8508 (mmm) REVERT: B 375 LYS cc_start: 0.9332 (mmmm) cc_final: 0.9065 (mmmm) REVERT: B 379 SER cc_start: 0.9011 (t) cc_final: 0.8555 (t) REVERT: B 392 SER cc_start: 0.9259 (m) cc_final: 0.8298 (t) REVERT: B 403 ILE cc_start: 0.9330 (mp) cc_final: 0.8906 (tp) REVERT: B 410 ASN cc_start: 0.9006 (m110) cc_final: 0.8773 (m110) REVERT: B 418 ASN cc_start: 0.9438 (m-40) cc_final: 0.9039 (m110) REVERT: B 426 GLU cc_start: 0.9502 (pm20) cc_final: 0.9285 (pm20) REVERT: B 446 ARG cc_start: 0.9090 (mmm-85) cc_final: 0.8483 (mmm-85) REVERT: B 459 LYS cc_start: 0.9102 (mttp) cc_final: 0.8385 (mtmt) REVERT: B 460 SER cc_start: 0.8489 (t) cc_final: 0.8230 (t) REVERT: B 467 ASN cc_start: 0.8629 (m110) cc_final: 0.7839 (m110) REVERT: B 493 MET cc_start: 0.9262 (tmm) cc_final: 0.9053 (tmm) REVERT: B 494 MET cc_start: 0.9538 (mmt) cc_final: 0.9071 (mmt) REVERT: B 574 TYR cc_start: 0.8239 (m-80) cc_final: 0.7804 (m-80) REVERT: B 598 MET cc_start: 0.9489 (mtm) cc_final: 0.9204 (mtm) REVERT: B 612 TYR cc_start: 0.8658 (m-80) cc_final: 0.7788 (m-80) REVERT: B 631 ASP cc_start: 0.9376 (t70) cc_final: 0.9089 (t0) REVERT: B 636 LYS cc_start: 0.9607 (mptt) cc_final: 0.9313 (mmtt) REVERT: B 640 MET cc_start: 0.9370 (tpp) cc_final: 0.8849 (tpp) REVERT: B 641 ILE cc_start: 0.9727 (mm) cc_final: 0.9509 (mm) REVERT: B 679 ILE cc_start: 0.9616 (mm) cc_final: 0.9396 (mm) REVERT: C 17 PHE cc_start: 0.8766 (p90) cc_final: 0.8032 (p90) REVERT: C 21 PHE cc_start: 0.9057 (m-10) cc_final: 0.8435 (m-80) REVERT: C 105 TYR cc_start: 0.8787 (m-80) cc_final: 0.8511 (m-80) REVERT: C 122 PHE cc_start: 0.8555 (m-80) cc_final: 0.8275 (m-80) REVERT: C 157 MET cc_start: 0.9564 (ptm) cc_final: 0.8995 (ppp) REVERT: C 239 GLU cc_start: 0.8413 (pt0) cc_final: 0.7929 (pt0) REVERT: D 109 PHE cc_start: 0.8837 (m-80) cc_final: 0.8216 (m-80) REVERT: D 112 LEU cc_start: 0.8660 (mm) cc_final: 0.7730 (pp) REVERT: D 166 PHE cc_start: 0.7916 (t80) cc_final: 0.7512 (t80) REVERT: D 172 PHE cc_start: 0.9437 (m-80) cc_final: 0.8899 (m-80) REVERT: D 177 TYR cc_start: 0.9411 (t80) cc_final: 0.9051 (t80) REVERT: D 179 TYR cc_start: 0.8026 (t80) cc_final: 0.7646 (t80) REVERT: D 185 MET cc_start: 0.5497 (mmp) cc_final: 0.4977 (mmm) REVERT: D 244 GLU cc_start: 0.9127 (mp0) cc_final: 0.8865 (mm-30) outliers start: 0 outliers final: 0 residues processed: 653 average time/residue: 0.2781 time to fit residues: 268.0097 Evaluate side-chains 560 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 560 time to evaluate : 1.957 ------------------------------------------------------------------------------- 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: 1.9990 chunk 30 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 183 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** 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 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 HIS ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.111684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.084153 restraints weight = 50917.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.087228 restraints weight = 30458.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.089272 restraints weight = 20769.956| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 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 = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.7853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16386 Z= 0.136 Angle : 0.646 8.127 22134 Z= 0.344 Chirality : 0.045 0.322 2360 Planarity : 0.004 0.047 2818 Dihedral : 10.502 172.999 2242 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: 0.52 (0.19), residues: 1932 helix: 0.87 (0.15), residues: 1138 sheet: -0.57 (0.42), residues: 148 loop : -0.18 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP D 124 HIS 0.006 0.001 HIS A 438 PHE 0.033 0.002 PHE C 168 TYR 0.040 0.001 TYR C 142 ARG 0.008 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 871) hydrogen bonds : angle 5.07032 ( 2571) covalent geometry : bond 0.00299 (16386) covalent geometry : angle 0.64567 (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 658 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 658 time to evaluate : 1.758 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: A 8 LYS cc_start: 0.9273 (tptp) cc_final: 0.8838 (tppt) REVERT: A 15 GLU cc_start: 0.9219 (tp30) cc_final: 0.8849 (tp30) REVERT: A 29 ASP cc_start: 0.9308 (t70) cc_final: 0.9089 (p0) REVERT: A 58 LEU cc_start: 0.9789 (mm) cc_final: 0.9352 (mm) REVERT: A 106 LEU cc_start: 0.9088 (tp) cc_final: 0.8775 (tp) REVERT: A 116 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8493 (mt-10) REVERT: A 119 GLU cc_start: 0.9081 (mp0) cc_final: 0.7870 (tm-30) REVERT: A 120 ASP cc_start: 0.9474 (m-30) cc_final: 0.9108 (m-30) REVERT: A 128 PHE cc_start: 0.9473 (t80) cc_final: 0.9184 (t80) REVERT: A 144 MET cc_start: 0.8792 (mmm) cc_final: 0.8330 (ptp) REVERT: A 176 ASN cc_start: 0.8424 (t0) cc_final: 0.7707 (m-40) REVERT: A 190 MET cc_start: 0.9100 (mtp) cc_final: 0.8842 (mtp) REVERT: A 235 ARG cc_start: 0.8243 (mtm110) cc_final: 0.7992 (mtm110) REVERT: A 236 TYR cc_start: 0.8854 (t80) cc_final: 0.8167 (t80) REVERT: A 280 ILE cc_start: 0.8625 (pt) cc_final: 0.8292 (mp) REVERT: A 286 ASP cc_start: 0.9108 (m-30) cc_final: 0.8754 (m-30) REVERT: A 345 LYS cc_start: 0.9029 (tttt) cc_final: 0.8794 (tttt) REVERT: A 349 LEU cc_start: 0.9435 (mt) cc_final: 0.9167 (mt) REVERT: A 359 MET cc_start: 0.8927 (ttp) cc_final: 0.8539 (ttp) REVERT: A 370 ASN cc_start: 0.9532 (m-40) cc_final: 0.9301 (m110) REVERT: A 375 LYS cc_start: 0.8919 (mmmt) cc_final: 0.8303 (mmtm) REVERT: A 377 LYS cc_start: 0.8837 (mttt) cc_final: 0.8232 (mttp) REVERT: A 381 LEU cc_start: 0.9046 (tp) cc_final: 0.8525 (pt) REVERT: A 407 ILE cc_start: 0.9058 (mt) cc_final: 0.8817 (mt) REVERT: A 426 GLU cc_start: 0.9208 (tm-30) cc_final: 0.8789 (tm-30) REVERT: A 469 HIS cc_start: 0.9000 (t-170) cc_final: 0.8786 (t-170) REVERT: A 494 MET cc_start: 0.9488 (mmp) cc_final: 0.8895 (mmt) REVERT: A 496 ASN cc_start: 0.8951 (m-40) cc_final: 0.8584 (m110) REVERT: A 515 ASP cc_start: 0.9373 (m-30) cc_final: 0.8895 (m-30) REVERT: A 570 MET cc_start: 0.9366 (mtp) cc_final: 0.8809 (mtp) REVERT: A 583 SER cc_start: 0.9552 (m) cc_final: 0.9343 (t) REVERT: A 588 GLN cc_start: 0.9031 (tp40) cc_final: 0.8436 (tp-100) REVERT: A 604 ARG cc_start: 0.9151 (tpp80) cc_final: 0.8659 (ttm110) REVERT: A 606 TYR cc_start: 0.7941 (m-80) cc_final: 0.7330 (m-10) REVERT: A 628 GLU cc_start: 0.9308 (mt-10) cc_final: 0.8808 (mp0) REVERT: A 636 LYS cc_start: 0.9768 (mmtp) cc_final: 0.9544 (mmmm) REVERT: A 640 MET cc_start: 0.9401 (tpp) cc_final: 0.8999 (tpp) REVERT: A 647 HIS cc_start: 0.9144 (m-70) cc_final: 0.7617 (m170) REVERT: A 653 SER cc_start: 0.8629 (p) cc_final: 0.8282 (p) REVERT: A 675 HIS cc_start: 0.9249 (t70) cc_final: 0.9020 (t70) REVERT: A 677 ARG cc_start: 0.9416 (mmm-85) cc_final: 0.8935 (mmm-85) REVERT: B 30 LYS cc_start: 0.9780 (tmtt) cc_final: 0.9364 (tptt) REVERT: B 65 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7836 (tm-30) REVERT: B 95 MET cc_start: 0.9157 (tpp) cc_final: 0.8767 (tpp) REVERT: B 107 LYS cc_start: 0.9286 (mtpp) cc_final: 0.9045 (mtpp) REVERT: B 116 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8208 (tp30) REVERT: B 117 ARG cc_start: 0.9076 (mtp180) cc_final: 0.8740 (mmt180) REVERT: B 119 GLU cc_start: 0.9156 (mp0) cc_final: 0.8751 (mp0) REVERT: B 120 ASP cc_start: 0.9342 (m-30) cc_final: 0.8887 (m-30) REVERT: B 124 ILE cc_start: 0.9636 (mm) cc_final: 0.9315 (mm) REVERT: B 139 GLU cc_start: 0.9285 (mp0) cc_final: 0.8985 (mp0) REVERT: B 156 PHE cc_start: 0.9484 (t80) cc_final: 0.9199 (t80) REVERT: B 202 ASN cc_start: 0.6871 (p0) cc_final: 0.6511 (p0) REVERT: B 211 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8229 (mm-30) REVERT: B 227 MET cc_start: 0.9128 (ttp) cc_final: 0.8924 (ttp) REVERT: B 235 ARG cc_start: 0.8731 (ttm110) cc_final: 0.8120 (ttm110) REVERT: B 250 TYR cc_start: 0.8612 (m-80) cc_final: 0.7335 (m-80) REVERT: B 263 ASP cc_start: 0.9139 (m-30) cc_final: 0.8785 (m-30) REVERT: B 291 LEU cc_start: 0.9498 (mt) cc_final: 0.9237 (mt) REVERT: B 322 MET cc_start: 0.8881 (mmm) cc_final: 0.8534 (mmm) REVERT: B 375 LYS cc_start: 0.9204 (mmmm) cc_final: 0.8871 (mmmm) REVERT: B 379 SER cc_start: 0.8895 (t) cc_final: 0.8399 (t) REVERT: B 392 SER cc_start: 0.9205 (m) cc_final: 0.8472 (m) REVERT: B 396 ASP cc_start: 0.8671 (m-30) cc_final: 0.8467 (m-30) REVERT: B 403 ILE cc_start: 0.9361 (mp) cc_final: 0.8932 (tp) REVERT: B 410 ASN cc_start: 0.8915 (m110) cc_final: 0.8676 (m110) REVERT: B 415 ASN cc_start: 0.9159 (t0) cc_final: 0.8479 (t0) REVERT: B 418 ASN cc_start: 0.9478 (m-40) cc_final: 0.9171 (m110) REVERT: B 446 ARG cc_start: 0.9047 (mmm-85) cc_final: 0.8513 (mmm-85) REVERT: B 459 LYS cc_start: 0.9032 (mttp) cc_final: 0.8331 (mtmt) REVERT: B 460 SER cc_start: 0.8539 (t) cc_final: 0.8252 (t) REVERT: B 467 ASN cc_start: 0.8629 (m110) cc_final: 0.8325 (m-40) REVERT: B 469 HIS cc_start: 0.8769 (t-170) cc_final: 0.8465 (t70) REVERT: B 493 MET cc_start: 0.9204 (tmm) cc_final: 0.8992 (tmm) REVERT: B 494 MET cc_start: 0.9520 (mmt) cc_final: 0.9003 (mmt) REVERT: B 574 TYR cc_start: 0.8271 (m-80) cc_final: 0.7783 (m-80) REVERT: B 598 MET cc_start: 0.9415 (mtm) cc_final: 0.9189 (mtm) REVERT: B 612 TYR cc_start: 0.8682 (m-80) cc_final: 0.7720 (m-80) REVERT: B 613 TYR cc_start: 0.9325 (t80) cc_final: 0.9071 (t80) REVERT: B 615 MET cc_start: 0.8815 (mmp) cc_final: 0.8563 (mmp) REVERT: B 631 ASP cc_start: 0.9330 (t70) cc_final: 0.9105 (t0) REVERT: B 636 LYS cc_start: 0.9607 (mptt) cc_final: 0.9304 (mmtt) REVERT: B 640 MET cc_start: 0.9328 (tpp) cc_final: 0.8772 (tpp) REVERT: B 641 ILE cc_start: 0.9678 (mm) cc_final: 0.9433 (mm) REVERT: B 646 GLN cc_start: 0.9485 (pt0) cc_final: 0.9066 (pm20) REVERT: B 679 ILE cc_start: 0.9602 (mm) cc_final: 0.9387 (mm) REVERT: C 17 PHE cc_start: 0.8684 (p90) cc_final: 0.7977 (p90) REVERT: C 21 PHE cc_start: 0.9031 (m-10) cc_final: 0.8532 (m-80) REVERT: C 24 GLN cc_start: 0.8845 (mp10) cc_final: 0.8600 (mp10) REVERT: C 55 TYR cc_start: 0.7427 (t80) cc_final: 0.7202 (t80) REVERT: C 105 TYR cc_start: 0.8863 (m-80) cc_final: 0.8575 (m-80) REVERT: C 122 PHE cc_start: 0.8461 (m-80) cc_final: 0.8188 (m-80) REVERT: C 157 MET cc_start: 0.9524 (ptm) cc_final: 0.8976 (ppp) REVERT: C 172 PHE cc_start: 0.9167 (m-80) cc_final: 0.8937 (m-80) REVERT: C 239 GLU cc_start: 0.8332 (pt0) cc_final: 0.7914 (pt0) REVERT: D 21 PHE cc_start: 0.8699 (m-10) cc_final: 0.8256 (m-10) REVERT: D 56 MET cc_start: 0.6482 (mpp) cc_final: 0.5994 (ptp) REVERT: D 109 PHE cc_start: 0.8829 (m-80) cc_final: 0.8209 (m-80) REVERT: D 112 LEU cc_start: 0.8736 (mm) cc_final: 0.7874 (pp) REVERT: D 157 MET cc_start: 0.9462 (ptm) cc_final: 0.8831 (ppp) REVERT: D 166 PHE cc_start: 0.7762 (t80) cc_final: 0.7272 (t80) REVERT: D 172 PHE cc_start: 0.9463 (m-80) cc_final: 0.8903 (m-80) REVERT: D 177 TYR cc_start: 0.9370 (t80) cc_final: 0.9031 (t80) REVERT: D 179 TYR cc_start: 0.7997 (t80) cc_final: 0.7697 (t80) REVERT: D 244 GLU cc_start: 0.9124 (mp0) cc_final: 0.8846 (mm-30) REVERT: D 318 ASP cc_start: 0.9219 (t0) cc_final: 0.8931 (t70) outliers start: 0 outliers final: 0 residues processed: 658 average time/residue: 0.2754 time to fit residues: 268.8859 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 : 1.982 ------------------------------------------------------------------------------- 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: 3.9990 chunk 102 optimal weight: 1.9990 chunk 182 optimal weight: 9.9990 chunk 107 optimal weight: 0.0070 chunk 77 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.7802 ------------------------------------------------------------------------------- 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 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.113213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.084409 restraints weight = 50913.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.087603 restraints weight = 30690.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.089854 restraints weight = 20866.724| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.8075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16386 Z= 0.137 Angle : 0.675 12.041 22134 Z= 0.357 Chirality : 0.045 0.357 2360 Planarity : 0.004 0.045 2818 Dihedral : 10.337 170.130 2242 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: 0.49 (0.19), residues: 1932 helix: 0.81 (0.15), residues: 1140 sheet: -0.64 (0.41), residues: 148 loop : -0.09 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP D 124 HIS 0.010 0.001 HIS D 201 PHE 0.028 0.002 PHE C 168 TYR 0.034 0.002 TYR C 142 ARG 0.009 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 871) hydrogen bonds : angle 5.17006 ( 2571) covalent geometry : bond 0.00304 (16386) covalent geometry : angle 0.67536 (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 655 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 655 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: A 8 LYS cc_start: 0.9254 (tptp) cc_final: 0.8798 (tppt) REVERT: A 15 GLU cc_start: 0.9206 (tp30) cc_final: 0.8780 (tp30) REVERT: A 29 ASP cc_start: 0.9313 (t70) cc_final: 0.9077 (t70) REVERT: A 81 PHE cc_start: 0.9461 (m-80) cc_final: 0.9139 (m-80) REVERT: A 119 GLU cc_start: 0.9031 (mp0) cc_final: 0.7880 (tm-30) REVERT: A 120 ASP cc_start: 0.9454 (m-30) cc_final: 0.9058 (m-30) REVERT: A 142 ASN cc_start: 0.9469 (m110) cc_final: 0.9254 (m110) REVERT: A 188 ILE cc_start: 0.9146 (mm) cc_final: 0.8820 (mm) REVERT: A 221 LYS cc_start: 0.9022 (mmtm) cc_final: 0.8802 (mmtm) REVERT: A 235 ARG cc_start: 0.8222 (mtm110) cc_final: 0.7998 (mtm110) REVERT: A 236 TYR cc_start: 0.8857 (t80) cc_final: 0.8279 (t80) REVERT: A 280 ILE cc_start: 0.8597 (pt) cc_final: 0.8171 (mp) REVERT: A 345 LYS cc_start: 0.8996 (tttt) cc_final: 0.8727 (tttt) REVERT: A 349 LEU cc_start: 0.9435 (mt) cc_final: 0.9101 (mt) REVERT: A 359 MET cc_start: 0.8939 (ttp) cc_final: 0.8522 (ttp) REVERT: A 370 ASN cc_start: 0.9493 (m-40) cc_final: 0.9263 (m110) REVERT: A 375 LYS cc_start: 0.8950 (mmmt) cc_final: 0.8209 (mmtm) REVERT: A 377 LYS cc_start: 0.8852 (mttt) cc_final: 0.8198 (mttp) REVERT: A 381 LEU cc_start: 0.9059 (tp) cc_final: 0.8560 (pt) REVERT: A 494 MET cc_start: 0.9471 (mmp) cc_final: 0.8889 (mmm) REVERT: A 515 ASP cc_start: 0.9366 (m-30) cc_final: 0.8908 (m-30) REVERT: A 570 MET cc_start: 0.9368 (mtp) cc_final: 0.8778 (mtp) REVERT: A 583 SER cc_start: 0.9532 (m) cc_final: 0.9271 (t) REVERT: A 588 GLN cc_start: 0.9064 (tp40) cc_final: 0.8436 (tp-100) REVERT: A 598 MET cc_start: 0.9090 (ttt) cc_final: 0.8862 (ttt) REVERT: A 628 GLU cc_start: 0.9306 (mt-10) cc_final: 0.8839 (mp0) REVERT: A 636 LYS cc_start: 0.9782 (mmtp) cc_final: 0.9576 (mmmm) REVERT: A 640 MET cc_start: 0.9371 (tpp) cc_final: 0.8988 (tpp) REVERT: A 647 HIS cc_start: 0.8941 (m-70) cc_final: 0.8498 (m90) REVERT: A 653 SER cc_start: 0.8605 (p) cc_final: 0.8304 (p) REVERT: A 675 HIS cc_start: 0.9254 (t70) cc_final: 0.8902 (t70) REVERT: A 677 ARG cc_start: 0.9394 (mmm-85) cc_final: 0.8947 (mmm-85) REVERT: A 686 ARG cc_start: 0.7056 (tpt90) cc_final: 0.6826 (tpt170) REVERT: B 30 LYS cc_start: 0.9712 (tmtt) cc_final: 0.9255 (tptt) REVERT: B 107 LYS cc_start: 0.9306 (mtpp) cc_final: 0.9060 (mtpp) REVERT: B 116 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8248 (tp30) REVERT: B 117 ARG cc_start: 0.9069 (mtp180) cc_final: 0.8564 (mmm160) REVERT: B 119 GLU cc_start: 0.9139 (mp0) cc_final: 0.8720 (mp0) REVERT: B 120 ASP cc_start: 0.9263 (m-30) cc_final: 0.8977 (m-30) REVERT: B 124 ILE cc_start: 0.9618 (mm) cc_final: 0.9293 (mm) REVERT: B 139 GLU cc_start: 0.9233 (mp0) cc_final: 0.8967 (mp0) REVERT: B 144 MET cc_start: 0.9390 (mtm) cc_final: 0.9128 (mtm) REVERT: B 156 PHE cc_start: 0.9454 (t80) cc_final: 0.9227 (t80) REVERT: B 202 ASN cc_start: 0.6851 (p0) cc_final: 0.6487 (p0) REVERT: B 211 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7894 (mm-30) REVERT: B 235 ARG cc_start: 0.8781 (ttm110) cc_final: 0.8215 (ttm110) REVERT: B 250 TYR cc_start: 0.8557 (m-80) cc_final: 0.7416 (m-80) REVERT: B 263 ASP cc_start: 0.8921 (m-30) cc_final: 0.8583 (m-30) REVERT: B 283 VAL cc_start: 0.9461 (t) cc_final: 0.9239 (t) REVERT: B 286 ASP cc_start: 0.8306 (m-30) cc_final: 0.7912 (m-30) REVERT: B 291 LEU cc_start: 0.9533 (mt) cc_final: 0.9266 (mt) REVERT: B 322 MET cc_start: 0.8843 (mmm) cc_final: 0.8450 (mmm) REVERT: B 350 ARG cc_start: 0.8829 (mtm-85) cc_final: 0.8291 (mtm180) REVERT: B 359 MET cc_start: 0.8915 (ttt) cc_final: 0.8318 (tmm) REVERT: B 362 ASP cc_start: 0.7933 (p0) cc_final: 0.6952 (p0) REVERT: B 375 LYS cc_start: 0.9211 (mmmm) cc_final: 0.8873 (mmmm) REVERT: B 379 SER cc_start: 0.8969 (t) cc_final: 0.8371 (t) REVERT: B 392 SER cc_start: 0.9169 (m) cc_final: 0.8418 (m) REVERT: B 403 ILE cc_start: 0.9380 (mp) cc_final: 0.8975 (tp) REVERT: B 410 ASN cc_start: 0.8874 (m-40) cc_final: 0.8665 (m-40) REVERT: B 415 ASN cc_start: 0.9170 (t0) cc_final: 0.8402 (t0) REVERT: B 418 ASN cc_start: 0.9464 (m-40) cc_final: 0.9136 (m-40) REVERT: B 420 MET cc_start: 0.9521 (mmp) cc_final: 0.9298 (mmp) REVERT: B 426 GLU cc_start: 0.9419 (pm20) cc_final: 0.9108 (pm20) REVERT: B 446 ARG cc_start: 0.9017 (mmm-85) cc_final: 0.8508 (mmm-85) REVERT: B 460 SER cc_start: 0.8464 (t) cc_final: 0.8207 (t) REVERT: B 467 ASN cc_start: 0.8579 (m110) cc_final: 0.8289 (m-40) REVERT: B 469 HIS cc_start: 0.8614 (t-170) cc_final: 0.8271 (t70) REVERT: B 493 MET cc_start: 0.9199 (tmm) cc_final: 0.8948 (tmm) REVERT: B 494 MET cc_start: 0.9495 (mmt) cc_final: 0.8915 (mmt) REVERT: B 574 TYR cc_start: 0.8216 (m-80) cc_final: 0.7731 (m-80) REVERT: B 597 ILE cc_start: 0.9395 (pt) cc_final: 0.9119 (pt) REVERT: B 606 TYR cc_start: 0.8591 (m-80) cc_final: 0.8245 (m-80) REVERT: B 612 TYR cc_start: 0.8573 (m-80) cc_final: 0.7715 (m-80) REVERT: B 613 TYR cc_start: 0.9339 (t80) cc_final: 0.9055 (t80) REVERT: B 631 ASP cc_start: 0.9287 (t70) cc_final: 0.9046 (t0) REVERT: B 640 MET cc_start: 0.9329 (tpp) cc_final: 0.8744 (tpp) REVERT: B 641 ILE cc_start: 0.9688 (mm) cc_final: 0.9438 (mm) REVERT: B 667 LEU cc_start: 0.9735 (tp) cc_final: 0.9359 (tp) REVERT: B 671 ASP cc_start: 0.9160 (m-30) cc_final: 0.8927 (m-30) REVERT: B 679 ILE cc_start: 0.9569 (mm) cc_final: 0.9335 (mm) REVERT: C 17 PHE cc_start: 0.8738 (p90) cc_final: 0.8062 (p90) REVERT: C 21 PHE cc_start: 0.8975 (m-10) cc_final: 0.8687 (m-80) REVERT: C 24 GLN cc_start: 0.8840 (mp10) cc_final: 0.8596 (mp10) REVERT: C 55 TYR cc_start: 0.7746 (t80) cc_final: 0.7363 (t80) REVERT: C 105 TYR cc_start: 0.8929 (m-80) cc_final: 0.8619 (m-80) REVERT: C 112 LEU cc_start: 0.7772 (pp) cc_final: 0.7511 (pp) REVERT: C 122 PHE cc_start: 0.8504 (m-80) cc_final: 0.8245 (m-80) REVERT: C 172 PHE cc_start: 0.9174 (m-80) cc_final: 0.8841 (m-80) REVERT: C 204 TYR cc_start: 0.9076 (t80) cc_final: 0.8643 (t80) REVERT: C 239 GLU cc_start: 0.8250 (pt0) cc_final: 0.7759 (pt0) REVERT: C 283 ASN cc_start: 0.7719 (t0) cc_final: 0.7451 (t0) REVERT: C 285 ILE cc_start: 0.9151 (mm) cc_final: 0.8936 (mm) REVERT: D 21 PHE cc_start: 0.8618 (m-10) cc_final: 0.8098 (m-10) REVERT: D 96 MET cc_start: 0.8223 (mmm) cc_final: 0.7720 (mmm) REVERT: D 109 PHE cc_start: 0.8763 (m-80) cc_final: 0.8121 (m-80) REVERT: D 112 LEU cc_start: 0.8747 (mm) cc_final: 0.7872 (pp) REVERT: D 157 MET cc_start: 0.9465 (ptm) cc_final: 0.8833 (ppp) REVERT: D 166 PHE cc_start: 0.7636 (t80) cc_final: 0.7236 (t80) REVERT: D 172 PHE cc_start: 0.9449 (m-80) cc_final: 0.9152 (m-80) REVERT: D 177 TYR cc_start: 0.9392 (t80) cc_final: 0.8986 (t80) REVERT: D 179 TYR cc_start: 0.7995 (t80) cc_final: 0.7625 (t80) REVERT: D 244 GLU cc_start: 0.9179 (mp0) cc_final: 0.8854 (mm-30) outliers start: 0 outliers final: 0 residues processed: 655 average time/residue: 0.2748 time to fit residues: 267.7555 Evaluate side-chains 558 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 558 time to evaluate : 1.770 ------------------------------------------------------------------------------- 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: 0.0060 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 135 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 127 optimal weight: 0.0070 chunk 68 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 overall best weight: 2.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 242 GLN 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 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.110718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.082361 restraints weight = 51570.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.085434 restraints weight = 31069.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.087563 restraints weight = 21245.762| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 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 = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.8275 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= 0.169 Angle : 0.679 10.647 22134 Z= 0.360 Chirality : 0.045 0.369 2360 Planarity : 0.004 0.049 2818 Dihedral : 10.434 168.961 2242 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 0.45 (0.19), residues: 1932 helix: 0.79 (0.15), residues: 1142 sheet: -0.60 (0.42), residues: 144 loop : -0.17 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP D 124 HIS 0.011 0.001 HIS A 469 PHE 0.029 0.002 PHE C 168 TYR 0.035 0.002 TYR C 142 ARG 0.012 0.001 ARG A 163 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 871) hydrogen bonds : angle 5.23809 ( 2571) covalent geometry : bond 0.00370 (16386) covalent geometry : angle 0.67853 (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 645 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 645 time to evaluate : 2.439 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: 0.9267 (tptp) cc_final: 0.8810 (tppt) REVERT: A 15 GLU cc_start: 0.9193 (tp30) cc_final: 0.8780 (tp30) REVERT: A 29 ASP cc_start: 0.9305 (t70) cc_final: 0.9083 (t70) REVERT: A 64 TYR cc_start: 0.8922 (m-80) cc_final: 0.8698 (m-80) REVERT: A 81 PHE cc_start: 0.9463 (m-80) cc_final: 0.9186 (m-80) REVERT: A 106 LEU cc_start: 0.9175 (tp) cc_final: 0.8851 (tp) REVERT: A 119 GLU cc_start: 0.9074 (mp0) cc_final: 0.7834 (tm-30) REVERT: A 120 ASP cc_start: 0.9461 (m-30) cc_final: 0.8993 (m-30) REVERT: A 128 PHE cc_start: 0.9546 (t80) cc_final: 0.9285 (t80) REVERT: A 142 ASN cc_start: 0.9482 (m110) cc_final: 0.9270 (m110) REVERT: A 188 ILE cc_start: 0.9323 (mm) cc_final: 0.9050 (mm) REVERT: A 236 TYR cc_start: 0.8923 (t80) cc_final: 0.8313 (t80) REVERT: A 263 ASP cc_start: 0.9111 (m-30) cc_final: 0.8860 (m-30) REVERT: A 286 ASP cc_start: 0.9200 (m-30) cc_final: 0.8877 (m-30) REVERT: A 317 MET cc_start: 0.8465 (pmm) cc_final: 0.8233 (pmm) REVERT: A 345 LYS cc_start: 0.9094 (tttt) cc_final: 0.8875 (tttt) REVERT: A 349 LEU cc_start: 0.9469 (mt) cc_final: 0.9140 (mt) REVERT: A 359 MET cc_start: 0.8925 (ttp) cc_final: 0.8593 (ttp) REVERT: A 362 ASP cc_start: 0.8768 (m-30) cc_final: 0.8522 (m-30) REVERT: A 375 LYS cc_start: 0.8965 (mmmt) cc_final: 0.8343 (mmtm) REVERT: A 377 LYS cc_start: 0.8767 (mttt) cc_final: 0.8038 (mttp) REVERT: A 381 LEU cc_start: 0.9087 (tp) cc_final: 0.8564 (pt) REVERT: A 446 ARG cc_start: 0.8605 (tpp80) cc_final: 0.8217 (tpp80) REVERT: A 468 LEU cc_start: 0.9711 (tp) cc_final: 0.9511 (tp) REVERT: A 494 MET cc_start: 0.9457 (mmp) cc_final: 0.8874 (mmm) REVERT: A 515 ASP cc_start: 0.9430 (m-30) cc_final: 0.8987 (m-30) REVERT: A 550 MET cc_start: 0.8706 (pmm) cc_final: 0.8162 (pmm) REVERT: A 570 MET cc_start: 0.9368 (mtp) cc_final: 0.8908 (mtp) REVERT: A 586 TYR cc_start: 0.9079 (m-10) cc_final: 0.8795 (m-10) REVERT: A 588 GLN cc_start: 0.9061 (tp40) cc_final: 0.8443 (tp-100) REVERT: A 602 GLU cc_start: 0.8550 (pp20) cc_final: 0.8318 (pp20) REVERT: A 615 MET cc_start: 0.9116 (mmp) cc_final: 0.8903 (mmp) REVERT: A 628 GLU cc_start: 0.9334 (mt-10) cc_final: 0.8889 (mp0) REVERT: A 636 LYS cc_start: 0.9796 (mmtp) cc_final: 0.9596 (mmmm) REVERT: A 640 MET cc_start: 0.9378 (tpp) cc_final: 0.8854 (tpp) REVERT: A 647 HIS cc_start: 0.9264 (m-70) cc_final: 0.7972 (m170) REVERT: A 653 SER cc_start: 0.8804 (p) cc_final: 0.8490 (p) REVERT: A 675 HIS cc_start: 0.9270 (t70) cc_final: 0.8943 (t70) REVERT: A 677 ARG cc_start: 0.9399 (mmm-85) cc_final: 0.8762 (mmm-85) REVERT: B 30 LYS cc_start: 0.9707 (tmtt) cc_final: 0.9267 (tptt) REVERT: B 65 GLU cc_start: 0.8624 (tp30) cc_final: 0.8179 (tp30) REVERT: B 82 LYS cc_start: 0.9482 (ptpp) cc_final: 0.9110 (ptpt) REVERT: B 107 LYS cc_start: 0.9292 (mtpp) cc_final: 0.9090 (mtpp) REVERT: B 116 GLU cc_start: 0.8725 (mt-10) cc_final: 0.7899 (mt-10) REVERT: B 117 ARG cc_start: 0.9077 (mtp180) cc_final: 0.8563 (mmm160) REVERT: B 119 GLU cc_start: 0.9210 (mp0) cc_final: 0.8809 (mp0) REVERT: B 120 ASP cc_start: 0.9361 (m-30) cc_final: 0.8900 (m-30) REVERT: B 144 MET cc_start: 0.9379 (mtm) cc_final: 0.9176 (mtm) REVERT: B 156 PHE cc_start: 0.9484 (t80) cc_final: 0.9198 (t80) REVERT: B 202 ASN cc_start: 0.6851 (p0) cc_final: 0.6493 (p0) REVERT: B 211 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7927 (mm-30) REVERT: B 227 MET cc_start: 0.9198 (ttp) cc_final: 0.8961 (ttp) REVERT: B 235 ARG cc_start: 0.8727 (ttm110) cc_final: 0.8229 (ttm110) REVERT: B 250 TYR cc_start: 0.8816 (m-80) cc_final: 0.7704 (m-80) REVERT: B 260 ASP cc_start: 0.9400 (p0) cc_final: 0.9196 (p0) REVERT: B 263 ASP cc_start: 0.9051 (m-30) cc_final: 0.8707 (m-30) REVERT: B 286 ASP cc_start: 0.8334 (m-30) cc_final: 0.7936 (m-30) REVERT: B 291 LEU cc_start: 0.9538 (mt) cc_final: 0.9254 (mt) REVERT: B 322 MET cc_start: 0.8925 (mmm) cc_final: 0.8579 (mmm) REVERT: B 359 MET cc_start: 0.8985 (ttt) cc_final: 0.8326 (tmm) REVERT: B 362 ASP cc_start: 0.7946 (p0) cc_final: 0.6971 (p0) REVERT: B 375 LYS cc_start: 0.9260 (mmmm) cc_final: 0.8988 (mmmm) REVERT: B 379 SER cc_start: 0.9004 (t) cc_final: 0.8385 (t) REVERT: B 392 SER cc_start: 0.9169 (m) cc_final: 0.7986 (t) REVERT: B 394 TYR cc_start: 0.9134 (m-80) cc_final: 0.8816 (m-80) REVERT: B 403 ILE cc_start: 0.9388 (mp) cc_final: 0.9001 (tp) REVERT: B 415 ASN cc_start: 0.9147 (t0) cc_final: 0.8420 (t0) REVERT: B 418 ASN cc_start: 0.9493 (m-40) cc_final: 0.9114 (m110) REVERT: B 420 MET cc_start: 0.9507 (mmp) cc_final: 0.9295 (mmp) REVERT: B 426 GLU cc_start: 0.9417 (pm20) cc_final: 0.9120 (pm20) REVERT: B 459 LYS cc_start: 0.9028 (mttp) cc_final: 0.8316 (mtmt) REVERT: B 460 SER cc_start: 0.8415 (t) cc_final: 0.8206 (t) REVERT: B 467 ASN cc_start: 0.8584 (m110) cc_final: 0.8337 (m-40) REVERT: B 493 MET cc_start: 0.9173 (tmm) cc_final: 0.8940 (tmm) REVERT: B 494 MET cc_start: 0.9450 (mmt) cc_final: 0.9002 (mmt) REVERT: B 530 LYS cc_start: 0.9129 (ptmm) cc_final: 0.8699 (ptmm) REVERT: B 574 TYR cc_start: 0.8233 (m-80) cc_final: 0.7853 (m-80) REVERT: B 606 TYR cc_start: 0.8660 (m-80) cc_final: 0.8348 (m-80) REVERT: B 612 TYR cc_start: 0.8567 (m-80) cc_final: 0.7748 (m-80) REVERT: B 613 TYR cc_start: 0.9363 (t80) cc_final: 0.9009 (t80) REVERT: B 615 MET cc_start: 0.8930 (mmp) cc_final: 0.8567 (mmp) REVERT: B 631 ASP cc_start: 0.9340 (t70) cc_final: 0.9027 (t0) REVERT: B 636 LYS cc_start: 0.9626 (mptt) cc_final: 0.9291 (mmtt) REVERT: B 640 MET cc_start: 0.9328 (tpp) cc_final: 0.8767 (tpp) REVERT: B 641 ILE cc_start: 0.9648 (mm) cc_final: 0.9380 (mm) REVERT: B 644 ILE cc_start: 0.9624 (mt) cc_final: 0.9419 (mt) REVERT: B 667 LEU cc_start: 0.9716 (tp) cc_final: 0.9466 (tp) REVERT: B 679 ILE cc_start: 0.9577 (mm) cc_final: 0.9342 (mm) REVERT: C 17 PHE cc_start: 0.8783 (p90) cc_final: 0.8163 (p90) REVERT: C 20 MET cc_start: 0.8674 (pmm) cc_final: 0.8212 (pmm) REVERT: C 21 PHE cc_start: 0.8876 (m-10) cc_final: 0.8505 (m-80) REVERT: C 55 TYR cc_start: 0.7648 (t80) cc_final: 0.7224 (t80) REVERT: C 105 TYR cc_start: 0.9000 (m-80) cc_final: 0.8770 (m-80) REVERT: C 122 PHE cc_start: 0.8444 (m-80) cc_final: 0.8147 (m-80) REVERT: C 157 MET cc_start: 0.9728 (ptm) cc_final: 0.9189 (ppp) REVERT: C 239 GLU cc_start: 0.8435 (pt0) cc_final: 0.8013 (pt0) REVERT: D 21 PHE cc_start: 0.8548 (m-10) cc_final: 0.8112 (m-10) REVERT: D 96 MET cc_start: 0.8217 (mmm) cc_final: 0.7868 (mmm) REVERT: D 108 ILE cc_start: 0.9440 (mt) cc_final: 0.9231 (pt) REVERT: D 109 PHE cc_start: 0.8669 (m-80) cc_final: 0.7966 (m-80) REVERT: D 112 LEU cc_start: 0.8758 (mm) cc_final: 0.7984 (pp) REVERT: D 157 MET cc_start: 0.9533 (ptm) cc_final: 0.8933 (ppp) REVERT: D 166 PHE cc_start: 0.7651 (t80) cc_final: 0.7128 (t80) REVERT: D 172 PHE cc_start: 0.9516 (m-80) cc_final: 0.9156 (m-80) REVERT: D 177 TYR cc_start: 0.9395 (t80) cc_final: 0.9000 (t80) REVERT: D 179 TYR cc_start: 0.8081 (t80) cc_final: 0.7600 (t80) REVERT: D 244 GLU cc_start: 0.9180 (mp0) cc_final: 0.8830 (mm-30) outliers start: 0 outliers final: 0 residues processed: 645 average time/residue: 0.3191 time to fit residues: 308.3875 Evaluate side-chains 549 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 549 time to evaluate : 1.786 ------------------------------------------------------------------------------- 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: 2.9990 chunk 16 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 179 optimal weight: 9.9990 chunk 190 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 43 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 232 ASN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** 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 501 GLN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.109269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.081874 restraints weight = 53479.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.084725 restraints weight = 32220.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.086764 restraints weight = 22369.081| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.8447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16386 Z= 0.216 Angle : 0.727 9.855 22134 Z= 0.390 Chirality : 0.046 0.360 2360 Planarity : 0.004 0.047 2818 Dihedral : 10.611 168.523 2242 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: 0.23 (0.19), residues: 1932 helix: 0.61 (0.15), residues: 1146 sheet: -0.78 (0.40), residues: 144 loop : -0.23 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP D 124 HIS 0.011 0.001 HIS D 201 PHE 0.023 0.002 PHE C 168 TYR 0.031 0.002 TYR C 142 ARG 0.009 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.04383 ( 871) hydrogen bonds : angle 5.40734 ( 2571) covalent geometry : bond 0.00459 (16386) covalent geometry : angle 0.72725 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6974.85 seconds wall clock time: 122 minutes 22.01 seconds (7342.01 seconds total)