Starting phenix.real_space_refine on Sat Jun 14 07:26:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzj_45069/06_2025/9bzj_45069_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzj_45069/06_2025/9bzj_45069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bzj_45069/06_2025/9bzj_45069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzj_45069/06_2025/9bzj_45069.map" model { file = "/net/cci-nas-00/data/ceres_data/9bzj_45069/06_2025/9bzj_45069_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzj_45069/06_2025/9bzj_45069_neut.cif" } resolution = 4.12 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): 0.05s 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: 9.46, per 1000 atoms: 0.59 Number of scatterers: 16038 At special positions: 0 Unit cell: (93.288, 128.778, 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: 4.55 Conformation dependent library (CDL) restraints added in 2.1 seconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.515A 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: 3.986A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.954A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.665A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.694A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.627A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.073A 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: 6.027A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.069A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.546A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.669A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.876A 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: 6.360A 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: 6.200A 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: 6.477A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.478A pdb=" N LEU A 656 " --> pdb=" O ARG A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.185A 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: 7.228A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.050A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.548A 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: 6.474A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.13 Time building geometry restraints manager: 5.35 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: 4752 1.34 - 1.46: 3107 1.46 - 1.58: 8345 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 -0.061 1.25e-02 6.40e+03 2.39e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.039 1.20e-02 6.94e+03 1.04e+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 8.79e+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 7.31e+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 6.81e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21576 2.09 - 4.18: 516 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 110.54 116.59 -6.05 1.36e+00 5.41e-01 1.98e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.14 -4.43 1.15e+00 7.56e-01 1.48e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.82 -4.32 1.23e+00 6.61e-01 1.23e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.68 -3.97 1.15e+00 7.56e-01 1.19e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.54 3.65 1.06e+00 8.90e-01 1.18e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 9468 35.81 - 71.61: 339 71.61 - 107.42: 37 107.42 - 143.22: 3 143.22 - 179.03: 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 -58.32 120.71 -179.03 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 301.68 151.19 150.50 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" C5' TTP A 803 " pdb=" O5' TTP A 803 " pdb=" PA TTP A 803 " pdb=" O3A TTP A 803 " ideal model delta sinusoidal sigma weight residual 179.97 31.92 148.05 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 9847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2142 0.094 - 0.187: 184 0.187 - 0.281: 29 0.281 - 0.374: 3 0.374 - 0.468: 2 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.48e+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 4.65e+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 2.90e+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 4.10e-02 2.70e+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 " -0.018 2.00e-02 2.50e+03 1.13e-02 2.23e+00 pdb=" CG PHE D 92 " 0.021 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 169 " 0.017 2.00e-02 2.50e+03 9.83e-03 1.93e+00 pdb=" CG TYR C 169 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 169 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 169 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 169 " 0.009 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 130 2.51 - 3.11: 11553 3.11 - 3.70: 27047 3.70 - 4.30: 41558 4.30 - 4.90: 65430 Nonbonded interactions: 145718 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 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 145713 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 38.220 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16386 Z= 0.315 Angle : 0.740 10.445 22134 Z= 0.463 Chirality : 0.058 0.468 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.952 179.028 6154 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.34 % Allowed : 15.38 % Favored : 83.28 % 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: 0.55 (0.18), residues: 1932 helix: 0.58 (0.14), residues: 1151 sheet: 0.46 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile 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 0.003 0.000 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.15420 ( 871) hydrogen bonds : angle 6.51774 ( 2571) covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.73993 (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 1022 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 999 time to evaluate : 1.745 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: A 12 LEU cc_start: 0.8765 (mt) cc_final: 0.8500 (mp) REVERT: A 55 LEU cc_start: 0.8884 (mt) cc_final: 0.8611 (mt) REVERT: A 76 ASP cc_start: 0.8075 (m-30) cc_final: 0.7582 (m-30) REVERT: A 152 SER cc_start: 0.8599 (p) cc_final: 0.8240 (p) REVERT: A 157 LEU cc_start: 0.9274 (tp) cc_final: 0.8862 (tp) REVERT: A 172 LEU cc_start: 0.9261 (mp) cc_final: 0.8971 (mp) REVERT: A 188 ILE cc_start: 0.9093 (mt) cc_final: 0.8801 (mt) REVERT: A 192 LEU cc_start: 0.9318 (mt) cc_final: 0.8863 (mt) REVERT: A 211 GLU cc_start: 0.6249 (mt-10) cc_final: 0.5867 (tp30) REVERT: A 236 TYR cc_start: 0.7661 (t80) cc_final: 0.7361 (t80) REVERT: A 238 ASP cc_start: 0.7874 (p0) cc_final: 0.7554 (p0) REVERT: A 259 ASN cc_start: 0.8087 (m-40) cc_final: 0.7612 (m-40) REVERT: A 265 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8516 (mmmt) REVERT: A 308 LYS cc_start: 0.8783 (mtmm) cc_final: 0.8522 (mtmm) REVERT: A 322 MET cc_start: 0.7756 (mmp) cc_final: 0.6265 (mmm) REVERT: A 326 PHE cc_start: 0.8518 (m-10) cc_final: 0.7921 (m-80) REVERT: A 355 TYR cc_start: 0.7427 (m-80) cc_final: 0.7205 (m-80) REVERT: A 367 VAL cc_start: 0.8652 (m) cc_final: 0.8449 (p) REVERT: A 373 ILE cc_start: 0.9100 (mt) cc_final: 0.8794 (mt) REVERT: A 377 LYS cc_start: 0.8839 (mttt) cc_final: 0.8499 (mttm) REVERT: A 407 ILE cc_start: 0.8904 (mt) cc_final: 0.8463 (mt) REVERT: A 415 ASN cc_start: 0.8025 (t0) cc_final: 0.7711 (t0) REVERT: A 417 LEU cc_start: 0.8059 (tt) cc_final: 0.7705 (tt) REVERT: A 418 ASN cc_start: 0.8250 (m-40) cc_final: 0.7390 (m110) REVERT: A 435 SER cc_start: 0.9330 (p) cc_final: 0.8991 (t) REVERT: A 447 ASN cc_start: 0.8127 (m-40) cc_final: 0.7799 (m-40) REVERT: A 480 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7745 (mt-10) REVERT: A 490 THR cc_start: 0.8511 (m) cc_final: 0.8183 (m) REVERT: A 500 ILE cc_start: 0.9186 (mt) cc_final: 0.8967 (mt) REVERT: A 546 LEU cc_start: 0.9075 (mt) cc_final: 0.8846 (mt) REVERT: A 550 MET cc_start: 0.7294 (mtm) cc_final: 0.7026 (mtm) REVERT: A 594 VAL cc_start: 0.8906 (m) cc_final: 0.8580 (t) REVERT: A 597 ILE cc_start: 0.8719 (pt) cc_final: 0.8369 (pt) REVERT: A 611 THR cc_start: 0.7322 (t) cc_final: 0.7084 (p) REVERT: A 644 ILE cc_start: 0.8380 (mt) cc_final: 0.7909 (mt) REVERT: A 653 SER cc_start: 0.9125 (OUTLIER) cc_final: 0.8844 (p) REVERT: B 12 LEU cc_start: 0.8951 (mt) cc_final: 0.8660 (mp) REVERT: B 51 LEU cc_start: 0.8137 (tp) cc_final: 0.7887 (tp) REVERT: B 147 GLN cc_start: 0.7969 (mt0) cc_final: 0.7604 (mt0) REVERT: B 175 VAL cc_start: 0.8898 (t) cc_final: 0.8637 (t) REVERT: B 204 SER cc_start: 0.8988 (m) cc_final: 0.7894 (t) REVERT: B 261 PHE cc_start: 0.8606 (t80) cc_final: 0.8322 (t80) REVERT: B 265 LYS cc_start: 0.8801 (mmtt) cc_final: 0.7939 (mmmt) REVERT: B 286 ASP cc_start: 0.6400 (OUTLIER) cc_final: 0.6144 (m-30) REVERT: B 315 ASP cc_start: 0.8332 (p0) cc_final: 0.7908 (p0) REVERT: B 326 PHE cc_start: 0.8294 (m-10) cc_final: 0.8073 (m-10) REVERT: B 362 ASP cc_start: 0.6385 (m-30) cc_final: 0.5902 (m-30) REVERT: B 366 LYS cc_start: 0.8586 (ptpp) cc_final: 0.8328 (ptpp) REVERT: B 373 ILE cc_start: 0.9115 (mt) cc_final: 0.8851 (mt) REVERT: B 384 GLU cc_start: 0.9052 (pm20) cc_final: 0.8311 (pm20) REVERT: B 425 ILE cc_start: 0.8783 (mt) cc_final: 0.8517 (mt) REVERT: B 467 ASN cc_start: 0.8197 (t0) cc_final: 0.7927 (t0) REVERT: B 494 MET cc_start: 0.7580 (mtp) cc_final: 0.7129 (mtp) REVERT: B 496 ASN cc_start: 0.7643 (t0) cc_final: 0.7393 (t0) REVERT: B 500 ILE cc_start: 0.9131 (mt) cc_final: 0.8905 (mt) REVERT: B 561 LEU cc_start: 0.8483 (tp) cc_final: 0.8128 (tp) REVERT: B 570 MET cc_start: 0.6811 (mtm) cc_final: 0.6470 (mtm) REVERT: B 605 THR cc_start: 0.7613 (m) cc_final: 0.6870 (m) REVERT: B 640 MET cc_start: 0.7912 (tpp) cc_final: 0.7138 (tpp) REVERT: B 644 ILE cc_start: 0.8665 (mt) cc_final: 0.8272 (mt) REVERT: C 43 THR cc_start: 0.4801 (p) cc_final: 0.4514 (m) REVERT: C 92 PHE cc_start: 0.6653 (t80) cc_final: 0.6162 (t80) REVERT: C 96 MET cc_start: 0.4835 (mmm) cc_final: 0.4378 (mmm) REVERT: C 169 TYR cc_start: 0.4145 (m-80) cc_final: 0.3724 (m-80) REVERT: C 185 MET cc_start: 0.3037 (mtp) cc_final: 0.2614 (ptt) REVERT: C 195 LEU cc_start: 0.7441 (tt) cc_final: 0.7165 (tt) REVERT: D 95 MET cc_start: 0.1773 (tmm) cc_final: 0.0989 (tmm) REVERT: D 151 ILE cc_start: 0.5937 (mm) cc_final: 0.5205 (mm) REVERT: D 178 PHE cc_start: 0.4551 (m-80) cc_final: 0.4118 (m-80) REVERT: D 194 ILE cc_start: 0.6907 (mt) cc_final: 0.6641 (mt) REVERT: D 286 VAL cc_start: 0.2691 (t) cc_final: 0.1560 (p) outliers start: 23 outliers final: 5 residues processed: 1010 average time/residue: 0.3086 time to fit residues: 445.9467 Evaluate side-chains 673 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 666 time to evaluate : 1.755 ------------------------------------------------------------------------------- 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: 3.9990 chunk 145 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 0.3980 chunk 98 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 174 optimal weight: 0.9980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 232 ASN A 242 GLN A 361 GLN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN B 676 HIS C 249 GLN C 263 ASN D 71 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 128 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.137900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.097394 restraints weight = 38745.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.101375 restraints weight = 20465.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.103910 restraints weight = 12720.816| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16386 Z= 0.190 Angle : 0.646 8.240 22134 Z= 0.346 Chirality : 0.045 0.316 2360 Planarity : 0.004 0.061 2818 Dihedral : 11.313 176.907 2242 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.17 % Allowed : 2.74 % Favored : 97.09 % 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: 1.16 (0.18), residues: 1932 helix: 1.27 (0.15), residues: 1124 sheet: -0.25 (0.40), residues: 144 loop : 0.34 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 124 HIS 0.009 0.002 HIS A 304 PHE 0.029 0.002 PHE D 320 TYR 0.021 0.002 TYR D 262 ARG 0.005 0.001 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.04846 ( 871) hydrogen bonds : angle 5.02682 ( 2571) covalent geometry : bond 0.00408 (16386) covalent geometry : angle 0.64582 (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 781 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 778 time to evaluate : 1.732 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 8 LYS cc_start: 0.9278 (tttt) cc_final: 0.9005 (tttm) REVERT: A 27 ASP cc_start: 0.9420 (p0) cc_final: 0.9144 (p0) REVERT: A 31 GLU cc_start: 0.9414 (mm-30) cc_final: 0.9025 (mp0) REVERT: A 41 ILE cc_start: 0.9506 (mm) cc_final: 0.9247 (mm) REVERT: A 118 TYR cc_start: 0.9003 (t80) cc_final: 0.8624 (t80) REVERT: A 144 MET cc_start: 0.9101 (mtm) cc_final: 0.8786 (mtm) REVERT: A 147 GLN cc_start: 0.8903 (mt0) cc_final: 0.8355 (mt0) REVERT: A 157 LEU cc_start: 0.9254 (tp) cc_final: 0.9003 (tp) REVERT: A 161 ARG cc_start: 0.8331 (ttm110) cc_final: 0.7821 (ttm110) REVERT: A 172 LEU cc_start: 0.9655 (mp) cc_final: 0.8968 (mp) REVERT: A 173 LEU cc_start: 0.9592 (mt) cc_final: 0.9318 (mt) REVERT: A 204 SER cc_start: 0.9591 (m) cc_final: 0.9237 (t) REVERT: A 236 TYR cc_start: 0.9049 (t80) cc_final: 0.8194 (t80) REVERT: A 315 ASP cc_start: 0.8701 (p0) cc_final: 0.8387 (p0) REVERT: A 322 MET cc_start: 0.8543 (mmp) cc_final: 0.7546 (tpp) REVERT: A 326 PHE cc_start: 0.9631 (m-10) cc_final: 0.9018 (m-80) REVERT: A 333 LYS cc_start: 0.8976 (tmtt) cc_final: 0.8591 (tptt) REVERT: A 344 GLU cc_start: 0.8790 (mp0) cc_final: 0.8586 (mp0) REVERT: A 357 TYR cc_start: 0.8857 (m-10) cc_final: 0.8457 (m-10) REVERT: A 406 ASP cc_start: 0.8764 (m-30) cc_final: 0.8104 (m-30) REVERT: A 407 ILE cc_start: 0.9292 (mt) cc_final: 0.8799 (mt) REVERT: A 435 SER cc_start: 0.9570 (p) cc_final: 0.9294 (t) REVERT: A 456 LYS cc_start: 0.9076 (mtmt) cc_final: 0.8866 (ptpt) REVERT: A 505 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8550 (mt-10) REVERT: A 508 LYS cc_start: 0.9519 (tttm) cc_final: 0.9312 (ttpp) REVERT: A 515 ASP cc_start: 0.8871 (m-30) cc_final: 0.8578 (m-30) REVERT: A 550 MET cc_start: 0.7481 (mtm) cc_final: 0.6441 (mtm) REVERT: A 615 MET cc_start: 0.9098 (mmp) cc_final: 0.8894 (mmp) REVERT: A 632 MET cc_start: 0.8808 (mtp) cc_final: 0.8558 (mtp) REVERT: A 645 GLN cc_start: 0.8748 (tp-100) cc_final: 0.8535 (tp40) REVERT: A 672 LEU cc_start: 0.9327 (mt) cc_final: 0.9075 (mt) REVERT: B 51 LEU cc_start: 0.9423 (tp) cc_final: 0.8878 (tp) REVERT: B 71 LEU cc_start: 0.9444 (mm) cc_final: 0.8974 (mm) REVERT: B 81 PHE cc_start: 0.9516 (m-80) cc_final: 0.9258 (m-80) REVERT: B 87 LYS cc_start: 0.9393 (tptm) cc_final: 0.9078 (tptm) REVERT: B 95 MET cc_start: 0.9198 (tpp) cc_final: 0.8889 (tpp) REVERT: B 119 GLU cc_start: 0.9193 (mp0) cc_final: 0.8987 (mp0) REVERT: B 162 LYS cc_start: 0.9548 (tppt) cc_final: 0.9224 (mmmm) REVERT: B 186 ILE cc_start: 0.9751 (mt) cc_final: 0.9491 (mt) REVERT: B 191 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8735 (mm-40) REVERT: B 211 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8220 (mm-30) REVERT: B 223 VAL cc_start: 0.9372 (m) cc_final: 0.9041 (m) REVERT: B 227 MET cc_start: 0.9145 (mtt) cc_final: 0.8653 (mtt) REVERT: B 266 LYS cc_start: 0.9434 (mtpp) cc_final: 0.9221 (mtpp) REVERT: B 333 LYS cc_start: 0.9216 (tptt) cc_final: 0.8952 (ttmm) REVERT: B 362 ASP cc_start: 0.8644 (m-30) cc_final: 0.8358 (m-30) REVERT: B 370 ASN cc_start: 0.9433 (m-40) cc_final: 0.8862 (m-40) REVERT: B 390 GLN cc_start: 0.9119 (mt0) cc_final: 0.8840 (mm110) REVERT: B 398 ASP cc_start: 0.8686 (t0) cc_final: 0.8455 (t70) REVERT: B 410 ASN cc_start: 0.8747 (m110) cc_final: 0.8487 (m110) REVERT: B 413 SER cc_start: 0.9607 (m) cc_final: 0.9264 (t) REVERT: B 415 ASN cc_start: 0.9510 (t0) cc_final: 0.9177 (t0) REVERT: B 446 ARG cc_start: 0.8340 (mtp85) cc_final: 0.7956 (mmm-85) REVERT: B 447 ASN cc_start: 0.8567 (m-40) cc_final: 0.7443 (m-40) REVERT: B 458 MET cc_start: 0.9412 (mmm) cc_final: 0.8953 (mmm) REVERT: B 467 ASN cc_start: 0.9187 (t0) cc_final: 0.8901 (t0) REVERT: B 480 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8156 (mt-10) REVERT: B 493 MET cc_start: 0.9596 (tmm) cc_final: 0.9384 (tmm) REVERT: B 494 MET cc_start: 0.9467 (mtp) cc_final: 0.9095 (mtp) REVERT: B 496 ASN cc_start: 0.9741 (t0) cc_final: 0.9398 (t0) REVERT: B 499 SER cc_start: 0.9883 (t) cc_final: 0.9628 (p) REVERT: B 561 LEU cc_start: 0.9645 (tp) cc_final: 0.9419 (tp) REVERT: B 574 TYR cc_start: 0.8512 (m-80) cc_final: 0.8140 (m-80) REVERT: B 602 GLU cc_start: 0.8366 (pt0) cc_final: 0.8007 (pt0) REVERT: B 627 LYS cc_start: 0.9059 (tttt) cc_final: 0.8606 (tttm) REVERT: B 636 LYS cc_start: 0.9673 (mmmm) cc_final: 0.9383 (mmmm) REVERT: B 640 MET cc_start: 0.9590 (tpp) cc_final: 0.9292 (tpp) REVERT: B 682 ILE cc_start: 0.9719 (mt) cc_final: 0.9466 (mt) REVERT: C 92 PHE cc_start: 0.8789 (t80) cc_final: 0.7334 (t80) REVERT: C 95 MET cc_start: 0.8141 (tmm) cc_final: 0.7700 (tmm) REVERT: C 96 MET cc_start: 0.7534 (mmm) cc_final: 0.6630 (mmm) REVERT: C 118 ILE cc_start: 0.8255 (mm) cc_final: 0.8025 (mm) REVERT: C 196 ARG cc_start: 0.8382 (ptp-110) cc_final: 0.8034 (ttm110) REVERT: C 198 GLU cc_start: 0.9515 (mm-30) cc_final: 0.9261 (mm-30) REVERT: D 95 MET cc_start: 0.3626 (tmm) cc_final: 0.2933 (tmm) REVERT: D 137 MET cc_start: 0.6613 (mtm) cc_final: 0.6294 (mmp) REVERT: D 149 ASP cc_start: 0.9105 (m-30) cc_final: 0.8874 (m-30) REVERT: D 151 ILE cc_start: 0.6973 (mm) cc_final: 0.6472 (mm) REVERT: D 233 ASN cc_start: 0.8617 (m110) cc_final: 0.8391 (m110) REVERT: D 318 ASP cc_start: 0.8743 (m-30) cc_final: 0.8478 (m-30) outliers start: 3 outliers final: 0 residues processed: 779 average time/residue: 0.2867 time to fit residues: 327.9886 Evaluate side-chains 637 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 637 time to evaluate : 1.804 ------------------------------------------------------------------------------- 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: 4.9990 chunk 168 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 191 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 171 optimal weight: 0.9990 chunk 189 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN B 645 GLN C 132 GLN C 249 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.138103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.098255 restraints weight = 39124.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.102181 restraints weight = 20797.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.104715 restraints weight = 12901.880| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16386 Z= 0.153 Angle : 0.598 9.916 22134 Z= 0.318 Chirality : 0.043 0.170 2360 Planarity : 0.003 0.039 2818 Dihedral : 11.096 177.114 2242 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % 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: 1.04 (0.18), residues: 1932 helix: 1.15 (0.15), residues: 1124 sheet: -0.14 (0.41), residues: 130 loop : 0.27 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 124 HIS 0.005 0.001 HIS A 438 PHE 0.026 0.002 PHE D 166 TYR 0.023 0.002 TYR A 522 ARG 0.007 0.001 ARG A 274 Details of bonding type rmsd hydrogen bonds : bond 0.04164 ( 871) hydrogen bonds : angle 4.91760 ( 2571) covalent geometry : bond 0.00340 (16386) covalent geometry : angle 0.59831 (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 708 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 706 time to evaluate : 1.732 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: A 8 LYS cc_start: 0.9349 (tttt) cc_final: 0.9133 (tttm) REVERT: A 31 GLU cc_start: 0.9356 (mm-30) cc_final: 0.9148 (mm-30) REVERT: A 147 GLN cc_start: 0.8899 (mt0) cc_final: 0.8441 (mt0) REVERT: A 172 LEU cc_start: 0.9623 (mp) cc_final: 0.8923 (mp) REVERT: A 173 LEU cc_start: 0.9616 (mt) cc_final: 0.9360 (mt) REVERT: A 204 SER cc_start: 0.9553 (m) cc_final: 0.9177 (t) REVERT: A 227 MET cc_start: 0.9397 (mtp) cc_final: 0.9000 (mtp) REVERT: A 236 TYR cc_start: 0.9051 (t80) cc_final: 0.8274 (t80) REVERT: A 251 LEU cc_start: 0.9353 (tp) cc_final: 0.9135 (tp) REVERT: A 278 LEU cc_start: 0.9302 (tp) cc_final: 0.9067 (tp) REVERT: A 286 ASP cc_start: 0.8426 (p0) cc_final: 0.7272 (p0) REVERT: A 315 ASP cc_start: 0.8752 (p0) cc_final: 0.8443 (p0) REVERT: A 317 MET cc_start: 0.8949 (ptm) cc_final: 0.8593 (ptm) REVERT: A 320 ASN cc_start: 0.9233 (t0) cc_final: 0.8711 (t0) REVERT: A 322 MET cc_start: 0.8932 (mmp) cc_final: 0.7881 (tpp) REVERT: A 326 PHE cc_start: 0.9692 (m-10) cc_final: 0.8856 (m-80) REVERT: A 333 LYS cc_start: 0.9067 (tmtt) cc_final: 0.8561 (tptp) REVERT: A 348 MET cc_start: 0.9051 (ptp) cc_final: 0.8736 (ptp) REVERT: A 357 TYR cc_start: 0.8859 (m-10) cc_final: 0.8458 (m-10) REVERT: A 375 LYS cc_start: 0.9256 (mttm) cc_final: 0.8911 (mtpp) REVERT: A 406 ASP cc_start: 0.8696 (m-30) cc_final: 0.8116 (m-30) REVERT: A 407 ILE cc_start: 0.9278 (mt) cc_final: 0.8808 (mt) REVERT: A 435 SER cc_start: 0.9597 (p) cc_final: 0.9360 (t) REVERT: A 436 LEU cc_start: 0.9676 (mt) cc_final: 0.9441 (mt) REVERT: A 456 LYS cc_start: 0.9069 (mtmt) cc_final: 0.8814 (ptpt) REVERT: A 505 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8558 (mt-10) REVERT: A 515 ASP cc_start: 0.8818 (m-30) cc_final: 0.8522 (m-30) REVERT: A 550 MET cc_start: 0.7875 (mtm) cc_final: 0.7598 (mtm) REVERT: A 572 HIS cc_start: 0.8948 (m90) cc_final: 0.8742 (m-70) REVERT: A 604 ARG cc_start: 0.8970 (mmp80) cc_final: 0.8465 (mmp80) REVERT: A 615 MET cc_start: 0.9203 (mmp) cc_final: 0.8983 (mmp) REVERT: A 640 MET cc_start: 0.9280 (tpp) cc_final: 0.9041 (tpp) REVERT: A 645 GLN cc_start: 0.8752 (tp-100) cc_final: 0.8257 (tp-100) REVERT: B 51 LEU cc_start: 0.9400 (tp) cc_final: 0.8877 (tp) REVERT: B 71 LEU cc_start: 0.9422 (mm) cc_final: 0.8948 (mt) REVERT: B 95 MET cc_start: 0.9218 (tpp) cc_final: 0.8732 (tpp) REVERT: B 119 GLU cc_start: 0.9088 (mp0) cc_final: 0.8866 (mp0) REVERT: B 128 PHE cc_start: 0.9565 (t80) cc_final: 0.9349 (t80) REVERT: B 139 GLU cc_start: 0.9378 (mm-30) cc_final: 0.9159 (mm-30) REVERT: B 162 LYS cc_start: 0.9550 (tppt) cc_final: 0.8835 (tppp) REVERT: B 191 GLN cc_start: 0.8951 (mm-40) cc_final: 0.8623 (mm-40) REVERT: B 211 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8157 (mm-30) REVERT: B 223 VAL cc_start: 0.9350 (m) cc_final: 0.9116 (m) REVERT: B 227 MET cc_start: 0.9127 (mtt) cc_final: 0.8673 (mtt) REVERT: B 257 ASP cc_start: 0.8771 (m-30) cc_final: 0.8310 (m-30) REVERT: B 266 LYS cc_start: 0.9458 (mtpp) cc_final: 0.9209 (mtpp) REVERT: B 286 ASP cc_start: 0.8483 (m-30) cc_final: 0.7486 (m-30) REVERT: B 294 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8369 (tm-30) REVERT: B 312 GLN cc_start: 0.8661 (pm20) cc_final: 0.8238 (pm20) REVERT: B 321 GLU cc_start: 0.8738 (pp20) cc_final: 0.8498 (pp20) REVERT: B 333 LYS cc_start: 0.9262 (tptt) cc_final: 0.9050 (ttmm) REVERT: B 362 ASP cc_start: 0.8564 (m-30) cc_final: 0.7536 (m-30) REVERT: B 370 ASN cc_start: 0.9394 (m-40) cc_final: 0.8640 (m-40) REVERT: B 390 GLN cc_start: 0.9174 (mt0) cc_final: 0.8878 (mm110) REVERT: B 393 SER cc_start: 0.9591 (t) cc_final: 0.9373 (p) REVERT: B 398 ASP cc_start: 0.8694 (t0) cc_final: 0.8447 (t70) REVERT: B 402 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8800 (mm-30) REVERT: B 403 ILE cc_start: 0.9555 (mp) cc_final: 0.9270 (tp) REVERT: B 410 ASN cc_start: 0.8820 (m110) cc_final: 0.8474 (m110) REVERT: B 413 SER cc_start: 0.9633 (m) cc_final: 0.9294 (t) REVERT: B 415 ASN cc_start: 0.9636 (t0) cc_final: 0.9073 (t0) REVERT: B 447 ASN cc_start: 0.8542 (m-40) cc_final: 0.7266 (m-40) REVERT: B 458 MET cc_start: 0.9331 (mmm) cc_final: 0.8820 (mmm) REVERT: B 494 MET cc_start: 0.9502 (mtp) cc_final: 0.9268 (mtp) REVERT: B 496 ASN cc_start: 0.9758 (t0) cc_final: 0.9353 (t0) REVERT: B 499 SER cc_start: 0.9889 (t) cc_final: 0.9628 (p) REVERT: B 505 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8798 (mt-10) REVERT: B 515 ASP cc_start: 0.9143 (t0) cc_final: 0.8935 (t0) REVERT: B 516 GLN cc_start: 0.9145 (tp-100) cc_final: 0.8859 (tp-100) REVERT: B 550 MET cc_start: 0.7486 (mtt) cc_final: 0.7099 (mtp) REVERT: B 561 LEU cc_start: 0.9643 (tp) cc_final: 0.9366 (tp) REVERT: B 574 TYR cc_start: 0.8517 (m-80) cc_final: 0.8168 (m-10) REVERT: B 598 MET cc_start: 0.9276 (mtm) cc_final: 0.9059 (mtm) REVERT: B 599 GLU cc_start: 0.8818 (pt0) cc_final: 0.8599 (pt0) REVERT: B 601 ILE cc_start: 0.9521 (mm) cc_final: 0.8766 (mm) REVERT: B 602 GLU cc_start: 0.8471 (pt0) cc_final: 0.8181 (pt0) REVERT: B 604 ARG cc_start: 0.9360 (mmm-85) cc_final: 0.9153 (mmm-85) REVERT: B 610 LYS cc_start: 0.9279 (ttpp) cc_final: 0.8959 (tttm) REVERT: B 627 LYS cc_start: 0.9134 (tttt) cc_final: 0.8759 (tttm) REVERT: B 628 GLU cc_start: 0.8479 (mm-30) cc_final: 0.7691 (mm-30) REVERT: B 636 LYS cc_start: 0.9699 (mmmm) cc_final: 0.9423 (mmmm) REVERT: B 640 MET cc_start: 0.9627 (tpp) cc_final: 0.8845 (tpp) REVERT: B 667 LEU cc_start: 0.9609 (tp) cc_final: 0.9187 (tp) REVERT: B 682 ILE cc_start: 0.9684 (mt) cc_final: 0.9430 (mt) REVERT: C 92 PHE cc_start: 0.8875 (t80) cc_final: 0.8225 (t80) REVERT: C 233 ASN cc_start: 0.9283 (m110) cc_final: 0.9068 (m110) REVERT: D 79 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8682 (pt0) REVERT: D 95 MET cc_start: 0.3785 (tmm) cc_final: 0.3174 (tmm) REVERT: D 109 PHE cc_start: 0.7905 (m-80) cc_final: 0.7697 (m-80) REVERT: D 137 MET cc_start: 0.8206 (mtm) cc_final: 0.7751 (mmp) REVERT: D 151 ILE cc_start: 0.6723 (mm) cc_final: 0.6431 (mm) REVERT: D 174 TYR cc_start: 0.8515 (t80) cc_final: 0.8206 (t80) REVERT: D 189 GLU cc_start: 0.8794 (tt0) cc_final: 0.8535 (mp0) outliers start: 2 outliers final: 0 residues processed: 706 average time/residue: 0.2730 time to fit residues: 286.6735 Evaluate side-chains 630 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 630 time to evaluate : 1.704 ------------------------------------------------------------------------------- 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: 0.9990 chunk 99 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 361 GLN A 365 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN C 263 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN ** D 132 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 = 0.3723 r_free = 0.3723 target = 0.132845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.093863 restraints weight = 39823.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.097625 restraints weight = 21324.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.100085 restraints weight = 13281.903| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16386 Z= 0.210 Angle : 0.616 8.219 22134 Z= 0.328 Chirality : 0.043 0.196 2360 Planarity : 0.004 0.066 2818 Dihedral : 10.974 174.494 2242 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.06 % Allowed : 2.10 % Favored : 97.84 % 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: 0.95 (0.19), residues: 1932 helix: 1.16 (0.15), residues: 1138 sheet: -0.36 (0.39), residues: 144 loop : 0.11 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 124 HIS 0.005 0.001 HIS A 368 PHE 0.026 0.002 PHE D 178 TYR 0.023 0.002 TYR A 394 ARG 0.005 0.001 ARG A 446 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 871) hydrogen bonds : angle 4.86407 ( 2571) covalent geometry : bond 0.00448 (16386) covalent geometry : angle 0.61560 (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 689 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 688 time to evaluate : 1.789 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 10 ILE cc_start: 0.9490 (OUTLIER) cc_final: 0.9211 (mm) REVERT: A 14 ASN cc_start: 0.9330 (m-40) cc_final: 0.9035 (m110) REVERT: A 31 GLU cc_start: 0.9357 (mm-30) cc_final: 0.9144 (mm-30) REVERT: A 69 LEU cc_start: 0.9562 (mt) cc_final: 0.9334 (pp) REVERT: A 95 MET cc_start: 0.9179 (mmm) cc_final: 0.8943 (tpp) REVERT: A 139 GLU cc_start: 0.9460 (tp30) cc_final: 0.9236 (tp30) REVERT: A 144 MET cc_start: 0.9060 (mtm) cc_final: 0.8601 (mtm) REVERT: A 147 GLN cc_start: 0.8925 (mt0) cc_final: 0.7968 (mt0) REVERT: A 172 LEU cc_start: 0.9649 (mp) cc_final: 0.9383 (mp) REVERT: A 205 LYS cc_start: 0.8639 (mttp) cc_final: 0.8345 (mtpp) REVERT: A 227 MET cc_start: 0.9393 (mtp) cc_final: 0.9020 (mtp) REVERT: A 236 TYR cc_start: 0.9178 (t80) cc_final: 0.8518 (t80) REVERT: A 322 MET cc_start: 0.8990 (mmp) cc_final: 0.7878 (tpp) REVERT: A 326 PHE cc_start: 0.9662 (m-10) cc_final: 0.8853 (m-80) REVERT: A 333 LYS cc_start: 0.9153 (tmtt) cc_final: 0.8615 (tptt) REVERT: A 348 MET cc_start: 0.9054 (ptp) cc_final: 0.8679 (ptp) REVERT: A 361 GLN cc_start: 0.9019 (tp40) cc_final: 0.8632 (tp-100) REVERT: A 407 ILE cc_start: 0.9245 (mt) cc_final: 0.8792 (mt) REVERT: A 418 ASN cc_start: 0.9064 (m-40) cc_final: 0.8507 (m110) REVERT: A 456 LYS cc_start: 0.9124 (mtmt) cc_final: 0.8692 (ptpt) REVERT: A 458 MET cc_start: 0.9112 (mmp) cc_final: 0.8588 (mmp) REVERT: A 505 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8306 (mt-10) REVERT: A 515 ASP cc_start: 0.8847 (m-30) cc_final: 0.8503 (m-30) REVERT: A 562 LYS cc_start: 0.9792 (tttm) cc_final: 0.9454 (ttmm) REVERT: A 588 GLN cc_start: 0.9135 (mm-40) cc_final: 0.8588 (mm-40) REVERT: A 604 ARG cc_start: 0.8924 (mmp80) cc_final: 0.8558 (mmp80) REVERT: A 615 MET cc_start: 0.9122 (mmp) cc_final: 0.8748 (mmm) REVERT: A 632 MET cc_start: 0.8852 (mtp) cc_final: 0.8604 (mtp) REVERT: A 672 LEU cc_start: 0.9433 (mt) cc_final: 0.9188 (mt) REVERT: A 683 TYR cc_start: 0.8672 (t80) cc_final: 0.8354 (t80) REVERT: B 51 LEU cc_start: 0.9494 (tp) cc_final: 0.9118 (tp) REVERT: B 55 LEU cc_start: 0.9797 (mt) cc_final: 0.9587 (mt) REVERT: B 67 GLU cc_start: 0.9258 (tm-30) cc_final: 0.8808 (tm-30) REVERT: B 71 LEU cc_start: 0.9484 (mm) cc_final: 0.9279 (mm) REVERT: B 95 MET cc_start: 0.9229 (tpp) cc_final: 0.9019 (tpp) REVERT: B 119 GLU cc_start: 0.9200 (mp0) cc_final: 0.8887 (mp0) REVERT: B 139 GLU cc_start: 0.9386 (mm-30) cc_final: 0.9174 (mm-30) REVERT: B 172 LEU cc_start: 0.9406 (mp) cc_final: 0.9157 (mp) REVERT: B 173 LEU cc_start: 0.9661 (mt) cc_final: 0.9374 (mt) REVERT: B 184 ARG cc_start: 0.9223 (mmm-85) cc_final: 0.9006 (mmm-85) REVERT: B 191 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8546 (mm-40) REVERT: B 211 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8271 (mm-30) REVERT: B 227 MET cc_start: 0.9070 (mtt) cc_final: 0.8792 (mtt) REVERT: B 258 ILE cc_start: 0.9417 (tp) cc_final: 0.9212 (tp) REVERT: B 286 ASP cc_start: 0.8557 (m-30) cc_final: 0.7621 (m-30) REVERT: B 316 GLU cc_start: 0.9185 (tt0) cc_final: 0.8971 (tt0) REVERT: B 321 GLU cc_start: 0.8905 (pp20) cc_final: 0.8554 (pp20) REVERT: B 333 LYS cc_start: 0.9269 (tptt) cc_final: 0.8997 (ttmm) REVERT: B 362 ASP cc_start: 0.8568 (m-30) cc_final: 0.7544 (m-30) REVERT: B 370 ASN cc_start: 0.9486 (m-40) cc_final: 0.8911 (m-40) REVERT: B 393 SER cc_start: 0.9630 (t) cc_final: 0.9341 (p) REVERT: B 398 ASP cc_start: 0.8788 (t0) cc_final: 0.8507 (t70) REVERT: B 402 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8859 (mm-30) REVERT: B 403 ILE cc_start: 0.9560 (mp) cc_final: 0.9257 (tp) REVERT: B 406 ASP cc_start: 0.8065 (m-30) cc_final: 0.7712 (m-30) REVERT: B 410 ASN cc_start: 0.9030 (m110) cc_final: 0.8765 (m110) REVERT: B 413 SER cc_start: 0.9625 (m) cc_final: 0.9247 (t) REVERT: B 415 ASN cc_start: 0.9633 (t0) cc_final: 0.9014 (t0) REVERT: B 447 ASN cc_start: 0.8627 (m-40) cc_final: 0.7402 (m-40) REVERT: B 515 ASP cc_start: 0.9189 (t0) cc_final: 0.8980 (t0) REVERT: B 599 GLU cc_start: 0.8895 (pt0) cc_final: 0.8622 (pt0) REVERT: B 601 ILE cc_start: 0.9503 (mm) cc_final: 0.8856 (mm) REVERT: B 602 GLU cc_start: 0.8350 (pt0) cc_final: 0.7985 (pt0) REVERT: B 610 LYS cc_start: 0.9272 (ttpp) cc_final: 0.9014 (tttp) REVERT: B 615 MET cc_start: 0.9282 (mmm) cc_final: 0.9076 (mmp) REVERT: B 627 LYS cc_start: 0.9405 (tttt) cc_final: 0.8880 (tttp) REVERT: B 628 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8285 (mm-30) REVERT: B 632 MET cc_start: 0.8977 (mtm) cc_final: 0.8776 (mtp) REVERT: B 640 MET cc_start: 0.9626 (tpp) cc_final: 0.8939 (tpp) REVERT: B 655 THR cc_start: 0.9532 (m) cc_final: 0.9089 (t) REVERT: B 667 LEU cc_start: 0.9581 (tp) cc_final: 0.9118 (tp) REVERT: C 233 ASN cc_start: 0.9290 (m110) cc_final: 0.9082 (m110) REVERT: D 137 MET cc_start: 0.8316 (mtm) cc_final: 0.7874 (mmp) REVERT: D 151 ILE cc_start: 0.6789 (mm) cc_final: 0.6444 (mm) REVERT: D 174 TYR cc_start: 0.8571 (t80) cc_final: 0.8331 (t80) REVERT: D 185 MET cc_start: 0.5353 (mmp) cc_final: 0.4991 (tpp) REVERT: D 189 GLU cc_start: 0.8972 (tt0) cc_final: 0.8702 (mp0) REVERT: D 211 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8613 (tm-30) REVERT: D 263 ASN cc_start: 0.8916 (m-40) cc_final: 0.8688 (m-40) outliers start: 1 outliers final: 0 residues processed: 688 average time/residue: 0.2847 time to fit residues: 294.3049 Evaluate side-chains 604 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 603 time to evaluate : 1.896 ------------------------------------------------------------------------------- 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: 7.9990 chunk 41 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 51 optimal weight: 0.0020 chunk 175 optimal weight: 4.9990 chunk 182 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS B 438 HIS C 28 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.138938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.100010 restraints weight = 39861.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.103846 restraints weight = 20888.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.106434 restraints weight = 12958.096| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.6185 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= 0.128 Angle : 0.563 6.595 22134 Z= 0.300 Chirality : 0.042 0.189 2360 Planarity : 0.004 0.050 2818 Dihedral : 10.674 179.210 2242 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.12 % Allowed : 2.21 % Favored : 97.67 % 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: 0.98 (0.19), residues: 1932 helix: 1.21 (0.15), residues: 1117 sheet: -0.50 (0.39), residues: 146 loop : 0.16 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 124 HIS 0.006 0.001 HIS B 368 PHE 0.028 0.002 PHE D 227 TYR 0.021 0.001 TYR B 574 ARG 0.006 0.001 ARG A 446 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 871) hydrogen bonds : angle 4.80917 ( 2571) covalent geometry : bond 0.00278 (16386) covalent geometry : angle 0.56288 (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 709 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 707 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.9494 (mp) cc_final: 0.9162 (mm) REVERT: A 14 ASN cc_start: 0.9389 (m-40) cc_final: 0.9066 (m110) REVERT: A 30 LYS cc_start: 0.9417 (tmmt) cc_final: 0.9213 (tptt) REVERT: A 69 LEU cc_start: 0.9570 (mt) cc_final: 0.9337 (pp) REVERT: A 95 MET cc_start: 0.9136 (mmm) cc_final: 0.8838 (tpp) REVERT: A 147 GLN cc_start: 0.8845 (mt0) cc_final: 0.8276 (mt0) REVERT: A 172 LEU cc_start: 0.9641 (mp) cc_final: 0.9290 (mp) REVERT: A 227 MET cc_start: 0.9384 (mtp) cc_final: 0.9025 (mtp) REVERT: A 236 TYR cc_start: 0.9080 (t80) cc_final: 0.8318 (t80) REVERT: A 251 LEU cc_start: 0.9451 (tp) cc_final: 0.9196 (tp) REVERT: A 257 ASP cc_start: 0.9131 (m-30) cc_final: 0.8905 (m-30) REVERT: A 259 ASN cc_start: 0.9204 (m-40) cc_final: 0.8892 (m-40) REVERT: A 278 LEU cc_start: 0.9265 (tp) cc_final: 0.9020 (tp) REVERT: A 290 GLU cc_start: 0.8931 (tp30) cc_final: 0.8547 (tp30) REVERT: A 322 MET cc_start: 0.9011 (mmp) cc_final: 0.8577 (tpp) REVERT: A 326 PHE cc_start: 0.9641 (m-10) cc_final: 0.9149 (m-80) REVERT: A 333 LYS cc_start: 0.9177 (tmtt) cc_final: 0.8779 (tptt) REVERT: A 345 LYS cc_start: 0.9506 (tttt) cc_final: 0.9287 (ttpt) REVERT: A 357 TYR cc_start: 0.8780 (m-10) cc_final: 0.8496 (m-10) REVERT: A 361 GLN cc_start: 0.9042 (tp40) cc_final: 0.8599 (tp-100) REVERT: A 365 ASN cc_start: 0.9151 (m110) cc_final: 0.8867 (m110) REVERT: A 407 ILE cc_start: 0.9295 (mt) cc_final: 0.8814 (mt) REVERT: A 413 SER cc_start: 0.9392 (m) cc_final: 0.9138 (m) REVERT: A 447 ASN cc_start: 0.8568 (m110) cc_final: 0.8315 (m-40) REVERT: A 456 LYS cc_start: 0.9082 (mtmt) cc_final: 0.8757 (ptpt) REVERT: A 458 MET cc_start: 0.9043 (mmp) cc_final: 0.8552 (mmp) REVERT: A 501 GLN cc_start: 0.9405 (tt0) cc_final: 0.8813 (tm-30) REVERT: A 505 GLU cc_start: 0.8968 (mt-10) cc_final: 0.7775 (mt-10) REVERT: A 515 ASP cc_start: 0.8760 (m-30) cc_final: 0.8467 (m-30) REVERT: A 550 MET cc_start: 0.8159 (mtm) cc_final: 0.7941 (mtm) REVERT: A 562 LYS cc_start: 0.9800 (tttm) cc_final: 0.9466 (ttmm) REVERT: A 604 ARG cc_start: 0.8890 (mmp80) cc_final: 0.8583 (mmp80) REVERT: A 615 MET cc_start: 0.9174 (mmp) cc_final: 0.8779 (mmm) REVERT: A 672 LEU cc_start: 0.9408 (mt) cc_final: 0.9177 (mt) REVERT: B 51 LEU cc_start: 0.9371 (tp) cc_final: 0.8981 (tp) REVERT: B 67 GLU cc_start: 0.9245 (tm-30) cc_final: 0.8742 (tm-30) REVERT: B 95 MET cc_start: 0.9203 (tpp) cc_final: 0.8725 (tpp) REVERT: B 98 PHE cc_start: 0.9529 (t80) cc_final: 0.9153 (t80) REVERT: B 115 LEU cc_start: 0.9572 (mp) cc_final: 0.9198 (mp) REVERT: B 119 GLU cc_start: 0.9153 (mp0) cc_final: 0.8857 (mp0) REVERT: B 172 LEU cc_start: 0.9366 (mp) cc_final: 0.9066 (mp) REVERT: B 173 LEU cc_start: 0.9643 (mt) cc_final: 0.9399 (mt) REVERT: B 191 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8482 (mt0) REVERT: B 211 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8110 (mm-30) REVERT: B 223 VAL cc_start: 0.9466 (m) cc_final: 0.9231 (m) REVERT: B 257 ASP cc_start: 0.8805 (m-30) cc_final: 0.8502 (m-30) REVERT: B 266 LYS cc_start: 0.9446 (mtpp) cc_final: 0.9179 (mtpp) REVERT: B 286 ASP cc_start: 0.8573 (m-30) cc_final: 0.7621 (m-30) REVERT: B 290 GLU cc_start: 0.9234 (tp30) cc_final: 0.9028 (tp30) REVERT: B 316 GLU cc_start: 0.9165 (tt0) cc_final: 0.8961 (tt0) REVERT: B 321 GLU cc_start: 0.8933 (pp20) cc_final: 0.8651 (pp20) REVERT: B 333 LYS cc_start: 0.9265 (tptt) cc_final: 0.9011 (ttmm) REVERT: B 362 ASP cc_start: 0.8556 (m-30) cc_final: 0.7591 (m-30) REVERT: B 370 ASN cc_start: 0.9556 (m-40) cc_final: 0.9253 (m110) REVERT: B 390 GLN cc_start: 0.9206 (mt0) cc_final: 0.8870 (mm110) REVERT: B 393 SER cc_start: 0.9600 (t) cc_final: 0.9335 (p) REVERT: B 398 ASP cc_start: 0.8738 (t0) cc_final: 0.8435 (t70) REVERT: B 403 ILE cc_start: 0.9551 (mp) cc_final: 0.9222 (tp) REVERT: B 406 ASP cc_start: 0.8072 (m-30) cc_final: 0.7831 (m-30) REVERT: B 413 SER cc_start: 0.9640 (m) cc_final: 0.9335 (t) REVERT: B 415 ASN cc_start: 0.9648 (t0) cc_final: 0.8719 (t0) REVERT: B 445 ILE cc_start: 0.9356 (mp) cc_final: 0.8781 (mp) REVERT: B 458 MET cc_start: 0.9216 (mmm) cc_final: 0.8720 (mmm) REVERT: B 505 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8573 (mt-10) REVERT: B 561 LEU cc_start: 0.9676 (tp) cc_final: 0.9424 (tp) REVERT: B 599 GLU cc_start: 0.8877 (pt0) cc_final: 0.8584 (pt0) REVERT: B 601 ILE cc_start: 0.9457 (mm) cc_final: 0.8749 (mm) REVERT: B 615 MET cc_start: 0.9306 (mmm) cc_final: 0.9064 (mmp) REVERT: B 627 LYS cc_start: 0.9421 (tttt) cc_final: 0.8921 (tttp) REVERT: B 628 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8452 (mm-30) REVERT: B 640 MET cc_start: 0.9601 (tpp) cc_final: 0.9136 (tpp) REVERT: B 648 ILE cc_start: 0.9431 (mm) cc_final: 0.9203 (mm) REVERT: B 655 THR cc_start: 0.9566 (m) cc_final: 0.9048 (t) REVERT: B 667 LEU cc_start: 0.9609 (tp) cc_final: 0.9163 (tp) REVERT: C 197 ASP cc_start: 0.9148 (m-30) cc_final: 0.8932 (m-30) REVERT: C 198 GLU cc_start: 0.9268 (mm-30) cc_final: 0.8918 (mm-30) REVERT: C 233 ASN cc_start: 0.9270 (m110) cc_final: 0.9047 (m110) REVERT: C 241 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7875 (pm20) REVERT: D 74 MET cc_start: 0.4239 (tmm) cc_final: 0.3704 (tmm) REVERT: D 137 MET cc_start: 0.8248 (mtm) cc_final: 0.7787 (mmp) REVERT: D 172 PHE cc_start: 0.9038 (m-80) cc_final: 0.8529 (m-80) REVERT: D 174 TYR cc_start: 0.8565 (t80) cc_final: 0.8323 (t80) REVERT: D 189 GLU cc_start: 0.9008 (tt0) cc_final: 0.8767 (mp0) REVERT: D 211 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8691 (tm-30) REVERT: D 231 LEU cc_start: 0.8950 (mm) cc_final: 0.8666 (pp) REVERT: D 244 GLU cc_start: 0.9172 (tp30) cc_final: 0.8833 (tp30) REVERT: D 320 PHE cc_start: 0.8356 (m-10) cc_final: 0.7968 (m-10) outliers start: 2 outliers final: 0 residues processed: 708 average time/residue: 0.2708 time to fit residues: 285.2086 Evaluate side-chains 616 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 615 time to evaluate : 1.811 ------------------------------------------------------------------------------- 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: 5.9990 chunk 126 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 115 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 chunk 169 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS A 447 ASN ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN C 249 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 119 ASN D 127 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.130862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.093213 restraints weight = 40869.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.096692 restraints weight = 21653.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.098975 restraints weight = 13506.908| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.6700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16386 Z= 0.290 Angle : 0.698 9.409 22134 Z= 0.371 Chirality : 0.045 0.252 2360 Planarity : 0.004 0.055 2818 Dihedral : 11.034 178.587 2242 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: 0.87 (0.15), residues: 1134 sheet: -0.78 (0.38), residues: 148 loop : -0.04 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 623 HIS 0.005 0.002 HIS B 304 PHE 0.024 0.002 PHE A 360 TYR 0.041 0.002 TYR B 574 ARG 0.006 0.001 ARG A 350 Details of bonding type rmsd hydrogen bonds : bond 0.04206 ( 871) hydrogen bonds : angle 5.04643 ( 2571) covalent geometry : bond 0.00612 (16386) covalent geometry : angle 0.69799 (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 664 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 664 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.9526 (mp) cc_final: 0.9183 (mm) REVERT: A 14 ASN cc_start: 0.9485 (m-40) cc_final: 0.9193 (m110) REVERT: A 119 GLU cc_start: 0.9063 (mp0) cc_final: 0.8595 (mp0) REVERT: A 120 ASP cc_start: 0.9041 (m-30) cc_final: 0.8764 (m-30) REVERT: A 122 ILE cc_start: 0.9684 (mp) cc_final: 0.9417 (mp) REVERT: A 139 GLU cc_start: 0.9392 (tp30) cc_final: 0.9181 (tp30) REVERT: A 144 MET cc_start: 0.9002 (mtm) cc_final: 0.8510 (mtm) REVERT: A 166 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8322 (mm-30) REVERT: A 172 LEU cc_start: 0.9717 (mp) cc_final: 0.9368 (mp) REVERT: A 227 MET cc_start: 0.9368 (mtp) cc_final: 0.8974 (mtp) REVERT: A 236 TYR cc_start: 0.9269 (t80) cc_final: 0.8603 (t80) REVERT: A 257 ASP cc_start: 0.9212 (m-30) cc_final: 0.8947 (m-30) REVERT: A 259 ASN cc_start: 0.9159 (m-40) cc_final: 0.8933 (m-40) REVERT: A 291 LEU cc_start: 0.9520 (mt) cc_final: 0.9264 (mt) REVERT: A 319 MET cc_start: 0.8785 (ttp) cc_final: 0.8407 (tmm) REVERT: A 333 LYS cc_start: 0.9370 (tmtt) cc_final: 0.8898 (tptp) REVERT: A 357 TYR cc_start: 0.8876 (m-10) cc_final: 0.8604 (m-10) REVERT: A 407 ILE cc_start: 0.9380 (mt) cc_final: 0.8883 (mt) REVERT: A 458 MET cc_start: 0.9159 (mmp) cc_final: 0.8587 (mmp) REVERT: A 505 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8361 (mt-10) REVERT: A 515 ASP cc_start: 0.8818 (m-30) cc_final: 0.8422 (m-30) REVERT: A 550 MET cc_start: 0.8104 (mtm) cc_final: 0.7662 (mtm) REVERT: A 562 LYS cc_start: 0.9807 (tttm) cc_final: 0.9535 (ttmm) REVERT: A 588 GLN cc_start: 0.9017 (mm-40) cc_final: 0.8718 (mm-40) REVERT: A 606 TYR cc_start: 0.8204 (m-80) cc_final: 0.7952 (m-80) REVERT: A 615 MET cc_start: 0.9118 (mmp) cc_final: 0.8778 (mmm) REVERT: A 683 TYR cc_start: 0.8789 (t80) cc_final: 0.8067 (t80) REVERT: B 51 LEU cc_start: 0.9454 (tp) cc_final: 0.9144 (tp) REVERT: B 55 LEU cc_start: 0.9825 (mt) cc_final: 0.9575 (mt) REVERT: B 67 GLU cc_start: 0.9322 (tm-30) cc_final: 0.8840 (tm-30) REVERT: B 95 MET cc_start: 0.9077 (tpp) cc_final: 0.8723 (tpp) REVERT: B 119 GLU cc_start: 0.9265 (mp0) cc_final: 0.8861 (mp0) REVERT: B 173 LEU cc_start: 0.9614 (mt) cc_final: 0.9355 (mt) REVERT: B 211 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8627 (tp30) REVERT: B 257 ASP cc_start: 0.8949 (m-30) cc_final: 0.8644 (m-30) REVERT: B 258 ILE cc_start: 0.9479 (tp) cc_final: 0.9178 (tp) REVERT: B 286 ASP cc_start: 0.8558 (m-30) cc_final: 0.7590 (m-30) REVERT: B 317 MET cc_start: 0.9216 (mtm) cc_final: 0.8892 (mpp) REVERT: B 321 GLU cc_start: 0.8950 (pp20) cc_final: 0.8367 (pp20) REVERT: B 322 MET cc_start: 0.9465 (tpt) cc_final: 0.8953 (mmm) REVERT: B 333 LYS cc_start: 0.9251 (tptt) cc_final: 0.8811 (ttmm) REVERT: B 362 ASP cc_start: 0.8635 (m-30) cc_final: 0.7689 (m-30) REVERT: B 373 ILE cc_start: 0.9601 (mt) cc_final: 0.9378 (tp) REVERT: B 393 SER cc_start: 0.9609 (t) cc_final: 0.9254 (p) REVERT: B 398 ASP cc_start: 0.8762 (t0) cc_final: 0.8492 (t70) REVERT: B 406 ASP cc_start: 0.8197 (m-30) cc_final: 0.7850 (m-30) REVERT: B 413 SER cc_start: 0.9589 (m) cc_final: 0.9246 (t) REVERT: B 415 ASN cc_start: 0.9617 (t0) cc_final: 0.9048 (t0) REVERT: B 447 ASN cc_start: 0.8549 (m-40) cc_final: 0.8147 (m-40) REVERT: B 505 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8485 (mt-10) REVERT: B 599 GLU cc_start: 0.8897 (pt0) cc_final: 0.8554 (pt0) REVERT: B 601 ILE cc_start: 0.9619 (mm) cc_final: 0.8939 (mm) REVERT: B 610 LYS cc_start: 0.9393 (ttpp) cc_final: 0.9009 (tttp) REVERT: B 615 MET cc_start: 0.9310 (mmm) cc_final: 0.8871 (mmp) REVERT: B 627 LYS cc_start: 0.9341 (tttt) cc_final: 0.8855 (tttp) REVERT: B 628 GLU cc_start: 0.8709 (mm-30) cc_final: 0.7747 (mm-30) REVERT: B 633 ASP cc_start: 0.8980 (t0) cc_final: 0.8601 (t0) REVERT: B 640 MET cc_start: 0.9475 (tpp) cc_final: 0.9051 (tpp) REVERT: B 648 ILE cc_start: 0.9402 (mm) cc_final: 0.9197 (mm) REVERT: B 655 THR cc_start: 0.9520 (m) cc_final: 0.9311 (t) REVERT: B 667 LEU cc_start: 0.9575 (tp) cc_final: 0.9127 (tp) REVERT: B 668 ASN cc_start: 0.9417 (m-40) cc_final: 0.9178 (m110) REVERT: B 671 ASP cc_start: 0.8885 (m-30) cc_final: 0.8684 (m-30) REVERT: C 55 TYR cc_start: 0.8456 (t80) cc_final: 0.7972 (t80) REVERT: C 68 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7832 (pp20) REVERT: C 108 ILE cc_start: 0.8661 (pt) cc_final: 0.8459 (pt) REVERT: C 110 MET cc_start: 0.8007 (mtm) cc_final: 0.7740 (mtm) REVERT: C 183 LYS cc_start: 0.5426 (mppt) cc_final: 0.4938 (ptmt) REVERT: C 233 ASN cc_start: 0.9305 (m110) cc_final: 0.9101 (m110) REVERT: D 74 MET cc_start: 0.5023 (tmm) cc_final: 0.4425 (tmm) REVERT: D 109 PHE cc_start: 0.8237 (m-80) cc_final: 0.7697 (m-80) REVERT: D 137 MET cc_start: 0.8387 (mtm) cc_final: 0.7832 (mmp) REVERT: D 172 PHE cc_start: 0.9257 (m-80) cc_final: 0.8785 (m-80) REVERT: D 189 GLU cc_start: 0.9191 (tt0) cc_final: 0.8933 (mp0) outliers start: 0 outliers final: 0 residues processed: 664 average time/residue: 0.2758 time to fit residues: 270.8391 Evaluate side-chains 587 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 587 time to evaluate : 1.987 ------------------------------------------------------------------------------- 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: 6.9990 chunk 85 optimal weight: 5.9990 chunk 161 optimal weight: 0.0370 chunk 23 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 146 optimal weight: 0.8980 chunk 184 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN B 447 ASN B 645 GLN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.136078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.098033 restraints weight = 39979.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.101780 restraints weight = 20983.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.104213 restraints weight = 13005.422| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.6923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16386 Z= 0.145 Angle : 0.603 7.307 22134 Z= 0.320 Chirality : 0.043 0.236 2360 Planarity : 0.004 0.053 2818 Dihedral : 10.777 178.927 2242 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.06 % Allowed : 1.40 % Favored : 98.54 % 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: 0.81 (0.19), residues: 1932 helix: 1.10 (0.15), residues: 1113 sheet: -0.67 (0.39), residues: 146 loop : 0.05 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 124 HIS 0.004 0.001 HIS A 438 PHE 0.032 0.002 PHE D 178 TYR 0.035 0.001 TYR D 130 ARG 0.007 0.001 ARG A 274 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 871) hydrogen bonds : angle 4.90931 ( 2571) covalent geometry : bond 0.00321 (16386) covalent geometry : angle 0.60293 (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 688 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 687 time to evaluate : 1.732 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 14 ASN cc_start: 0.9450 (m-40) cc_final: 0.9124 (m110) REVERT: A 69 LEU cc_start: 0.9622 (mt) cc_final: 0.9325 (pp) REVERT: A 119 GLU cc_start: 0.8891 (mp0) cc_final: 0.8413 (mp0) REVERT: A 128 PHE cc_start: 0.9486 (t80) cc_final: 0.9227 (t80) REVERT: A 139 GLU cc_start: 0.9353 (tp30) cc_final: 0.9110 (tp30) REVERT: A 150 GLN cc_start: 0.9183 (tm-30) cc_final: 0.8568 (tm-30) REVERT: A 166 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8327 (mm-30) REVERT: A 172 LEU cc_start: 0.9674 (mp) cc_final: 0.9314 (mp) REVERT: A 190 MET cc_start: 0.9019 (mtp) cc_final: 0.8655 (mtp) REVERT: A 227 MET cc_start: 0.9350 (mtp) cc_final: 0.8955 (mtp) REVERT: A 236 TYR cc_start: 0.9091 (t80) cc_final: 0.8101 (t80) REVERT: A 251 LEU cc_start: 0.9506 (tp) cc_final: 0.9259 (tp) REVERT: A 255 HIS cc_start: 0.8745 (t-90) cc_final: 0.7656 (t-90) REVERT: A 257 ASP cc_start: 0.9199 (m-30) cc_final: 0.8727 (m-30) REVERT: A 259 ASN cc_start: 0.9227 (m-40) cc_final: 0.8905 (m-40) REVERT: A 274 ARG cc_start: 0.8684 (ttp-110) cc_final: 0.7605 (ptp90) REVERT: A 318 ASP cc_start: 0.8777 (t0) cc_final: 0.8561 (t0) REVERT: A 333 LYS cc_start: 0.9352 (tmtt) cc_final: 0.8820 (tptp) REVERT: A 357 TYR cc_start: 0.8786 (m-10) cc_final: 0.8406 (m-10) REVERT: A 361 GLN cc_start: 0.9063 (tp40) cc_final: 0.8787 (tp-100) REVERT: A 395 THR cc_start: 0.9594 (p) cc_final: 0.9346 (p) REVERT: A 403 ILE cc_start: 0.9274 (mm) cc_final: 0.8994 (mm) REVERT: A 407 ILE cc_start: 0.9297 (mt) cc_final: 0.8867 (mt) REVERT: A 458 MET cc_start: 0.9085 (mmp) cc_final: 0.8517 (mmp) REVERT: A 505 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8307 (mt-10) REVERT: A 515 ASP cc_start: 0.8829 (m-30) cc_final: 0.8473 (m-30) REVERT: A 550 MET cc_start: 0.8231 (mtm) cc_final: 0.7922 (mtm) REVERT: A 561 LEU cc_start: 0.9667 (tp) cc_final: 0.9436 (tp) REVERT: A 562 LYS cc_start: 0.9829 (tttm) cc_final: 0.9453 (tppt) REVERT: A 588 GLN cc_start: 0.9050 (mm-40) cc_final: 0.8821 (mm110) REVERT: A 606 TYR cc_start: 0.8239 (m-80) cc_final: 0.7921 (m-80) REVERT: A 615 MET cc_start: 0.9316 (mmp) cc_final: 0.8882 (mmp) REVERT: A 640 MET cc_start: 0.9148 (tpp) cc_final: 0.8929 (tpp) REVERT: A 672 LEU cc_start: 0.9448 (mt) cc_final: 0.9230 (mt) REVERT: A 683 TYR cc_start: 0.8675 (t80) cc_final: 0.7826 (t80) REVERT: B 51 LEU cc_start: 0.9373 (tp) cc_final: 0.9017 (tp) REVERT: B 55 LEU cc_start: 0.9830 (mt) cc_final: 0.9598 (mt) REVERT: B 67 GLU cc_start: 0.9348 (tm-30) cc_final: 0.8848 (tm-30) REVERT: B 95 MET cc_start: 0.8984 (tpp) cc_final: 0.8234 (tpp) REVERT: B 98 PHE cc_start: 0.9502 (t80) cc_final: 0.9151 (t80) REVERT: B 106 LEU cc_start: 0.9589 (tp) cc_final: 0.9331 (tp) REVERT: B 107 LYS cc_start: 0.9379 (mttp) cc_final: 0.9060 (mptt) REVERT: B 115 LEU cc_start: 0.9300 (mp) cc_final: 0.9001 (mp) REVERT: B 116 GLU cc_start: 0.8445 (mp0) cc_final: 0.8229 (mp0) REVERT: B 119 GLU cc_start: 0.9204 (mp0) cc_final: 0.8795 (mp0) REVERT: B 173 LEU cc_start: 0.9640 (mt) cc_final: 0.9436 (mt) REVERT: B 191 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8329 (mt0) REVERT: B 257 ASP cc_start: 0.8869 (m-30) cc_final: 0.8590 (m-30) REVERT: B 258 ILE cc_start: 0.9475 (tp) cc_final: 0.9253 (tp) REVERT: B 263 ASP cc_start: 0.8963 (m-30) cc_final: 0.8529 (m-30) REVERT: B 286 ASP cc_start: 0.8569 (m-30) cc_final: 0.7658 (m-30) REVERT: B 312 GLN cc_start: 0.8781 (pm20) cc_final: 0.8497 (pm20) REVERT: B 317 MET cc_start: 0.9137 (mtm) cc_final: 0.8733 (mpp) REVERT: B 321 GLU cc_start: 0.8947 (pp20) cc_final: 0.8654 (pp20) REVERT: B 333 LYS cc_start: 0.9245 (tptt) cc_final: 0.8918 (ttmm) REVERT: B 362 ASP cc_start: 0.8677 (m-30) cc_final: 0.7763 (m-30) REVERT: B 370 ASN cc_start: 0.9571 (m110) cc_final: 0.9085 (m110) REVERT: B 373 ILE cc_start: 0.9490 (mt) cc_final: 0.8998 (tp) REVERT: B 390 GLN cc_start: 0.8997 (mt0) cc_final: 0.8650 (mm110) REVERT: B 393 SER cc_start: 0.9578 (t) cc_final: 0.9258 (p) REVERT: B 398 ASP cc_start: 0.8727 (t0) cc_final: 0.8446 (t70) REVERT: B 403 ILE cc_start: 0.9522 (mp) cc_final: 0.9221 (tp) REVERT: B 406 ASP cc_start: 0.8203 (m-30) cc_final: 0.7943 (m-30) REVERT: B 413 SER cc_start: 0.9621 (m) cc_final: 0.9220 (t) REVERT: B 415 ASN cc_start: 0.9678 (t0) cc_final: 0.8916 (t0) REVERT: B 418 ASN cc_start: 0.9276 (m-40) cc_final: 0.8990 (m-40) REVERT: B 434 ASP cc_start: 0.8984 (m-30) cc_final: 0.8782 (m-30) REVERT: B 447 ASN cc_start: 0.8466 (m110) cc_final: 0.6847 (m110) REVERT: B 458 MET cc_start: 0.9293 (mmm) cc_final: 0.8705 (mmm) REVERT: B 467 ASN cc_start: 0.9166 (t0) cc_final: 0.8906 (t0) REVERT: B 505 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8629 (mt-10) REVERT: B 586 TYR cc_start: 0.9142 (m-80) cc_final: 0.8823 (m-80) REVERT: B 599 GLU cc_start: 0.8867 (pt0) cc_final: 0.8537 (pt0) REVERT: B 601 ILE cc_start: 0.9504 (mm) cc_final: 0.8820 (mm) REVERT: B 610 LYS cc_start: 0.9430 (ttpp) cc_final: 0.9211 (tttm) REVERT: B 615 MET cc_start: 0.9288 (mmm) cc_final: 0.9068 (mmp) REVERT: B 627 LYS cc_start: 0.9338 (tttt) cc_final: 0.8917 (tttt) REVERT: B 628 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8162 (mm-30) REVERT: B 633 ASP cc_start: 0.8867 (t0) cc_final: 0.8311 (t0) REVERT: B 636 LYS cc_start: 0.9609 (mmmm) cc_final: 0.9350 (mmtp) REVERT: B 640 MET cc_start: 0.9509 (tpp) cc_final: 0.9078 (tpp) REVERT: B 655 THR cc_start: 0.9580 (m) cc_final: 0.9305 (t) REVERT: B 667 LEU cc_start: 0.9571 (tp) cc_final: 0.9139 (tp) REVERT: B 668 ASN cc_start: 0.9368 (m-40) cc_final: 0.9105 (m110) REVERT: C 55 TYR cc_start: 0.8235 (t80) cc_final: 0.7840 (t80) REVERT: C 68 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7684 (pp20) REVERT: C 96 MET cc_start: 0.7768 (mmm) cc_final: 0.6771 (mmm) REVERT: C 110 MET cc_start: 0.7880 (mtm) cc_final: 0.7641 (mtm) REVERT: C 197 ASP cc_start: 0.9195 (m-30) cc_final: 0.8893 (m-30) REVERT: C 198 GLU cc_start: 0.9390 (mm-30) cc_final: 0.9159 (mm-30) REVERT: C 233 ASN cc_start: 0.9303 (m110) cc_final: 0.9102 (m110) REVERT: D 74 MET cc_start: 0.4508 (tmm) cc_final: 0.4125 (tmm) REVERT: D 137 MET cc_start: 0.8460 (mtm) cc_final: 0.7900 (mmp) REVERT: D 149 ASP cc_start: 0.8991 (m-30) cc_final: 0.8737 (m-30) REVERT: D 172 PHE cc_start: 0.9157 (m-80) cc_final: 0.8509 (m-80) REVERT: D 174 TYR cc_start: 0.8555 (t80) cc_final: 0.8294 (t80) REVERT: D 189 GLU cc_start: 0.9175 (tt0) cc_final: 0.8928 (mp0) REVERT: D 194 ILE cc_start: 0.9061 (mt) cc_final: 0.8743 (mt) REVERT: D 211 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8763 (tm-30) REVERT: D 278 GLU cc_start: 0.6436 (pm20) cc_final: 0.6187 (pp20) outliers start: 1 outliers final: 0 residues processed: 688 average time/residue: 0.2697 time to fit residues: 276.3270 Evaluate side-chains 610 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 610 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 242 GLN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN B 645 GLN C 249 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.135610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.096821 restraints weight = 40232.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.100510 restraints weight = 21175.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.102933 restraints weight = 13215.164| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.7129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16386 Z= 0.168 Angle : 0.647 7.560 22134 Z= 0.345 Chirality : 0.044 0.247 2360 Planarity : 0.004 0.056 2818 Dihedral : 10.688 178.973 2242 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.80 (0.19), residues: 1932 helix: 1.09 (0.15), residues: 1111 sheet: -0.50 (0.42), residues: 136 loop : 0.01 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 124 HIS 0.005 0.001 HIS B 313 PHE 0.033 0.002 PHE D 109 TYR 0.029 0.002 TYR A 394 ARG 0.008 0.001 ARG A 446 Details of bonding type rmsd hydrogen bonds : bond 0.04015 ( 871) hydrogen bonds : angle 5.00929 ( 2571) covalent geometry : bond 0.00371 (16386) covalent geometry : angle 0.64716 (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 672 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 672 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.9513 (m-40) cc_final: 0.9184 (m110) REVERT: A 27 ASP cc_start: 0.9443 (p0) cc_final: 0.9211 (p0) REVERT: A 69 LEU cc_start: 0.9622 (mt) cc_final: 0.9327 (pp) REVERT: A 119 GLU cc_start: 0.8865 (mp0) cc_final: 0.8370 (mp0) REVERT: A 128 PHE cc_start: 0.9467 (t80) cc_final: 0.9210 (t80) REVERT: A 139 GLU cc_start: 0.9391 (tp30) cc_final: 0.9126 (tp30) REVERT: A 150 GLN cc_start: 0.9182 (tm-30) cc_final: 0.8556 (tm-30) REVERT: A 166 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8357 (mm-30) REVERT: A 172 LEU cc_start: 0.9677 (mp) cc_final: 0.9274 (mp) REVERT: A 190 MET cc_start: 0.9036 (mtp) cc_final: 0.8693 (mtp) REVERT: A 204 SER cc_start: 0.9248 (p) cc_final: 0.8887 (p) REVERT: A 227 MET cc_start: 0.9371 (mtp) cc_final: 0.8954 (mtp) REVERT: A 236 TYR cc_start: 0.9119 (t80) cc_final: 0.8095 (t80) REVERT: A 251 LEU cc_start: 0.9560 (tp) cc_final: 0.9314 (tp) REVERT: A 255 HIS cc_start: 0.8752 (t-90) cc_final: 0.7665 (t-90) REVERT: A 257 ASP cc_start: 0.9210 (m-30) cc_final: 0.8710 (m-30) REVERT: A 259 ASN cc_start: 0.9226 (m-40) cc_final: 0.8767 (m-40) REVERT: A 274 ARG cc_start: 0.8638 (ttp-110) cc_final: 0.7589 (ptp90) REVERT: A 318 ASP cc_start: 0.8710 (t0) cc_final: 0.8381 (t0) REVERT: A 321 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8521 (tm-30) REVERT: A 333 LYS cc_start: 0.9401 (tmtt) cc_final: 0.8921 (tptp) REVERT: A 345 LYS cc_start: 0.9553 (ttpt) cc_final: 0.9252 (ptmt) REVERT: A 357 TYR cc_start: 0.8764 (m-10) cc_final: 0.8391 (m-10) REVERT: A 361 GLN cc_start: 0.9164 (tp40) cc_final: 0.8704 (tp-100) REVERT: A 403 ILE cc_start: 0.9222 (mm) cc_final: 0.8895 (mm) REVERT: A 405 LEU cc_start: 0.8960 (mt) cc_final: 0.8584 (mt) REVERT: A 407 ILE cc_start: 0.9343 (mt) cc_final: 0.8916 (mt) REVERT: A 458 MET cc_start: 0.9061 (mmp) cc_final: 0.8560 (mmp) REVERT: A 472 LEU cc_start: 0.9487 (mt) cc_final: 0.9243 (mp) REVERT: A 501 GLN cc_start: 0.9410 (tt0) cc_final: 0.8820 (tm-30) REVERT: A 505 GLU cc_start: 0.8909 (mt-10) cc_final: 0.7803 (mt-10) REVERT: A 515 ASP cc_start: 0.8804 (m-30) cc_final: 0.8360 (m-30) REVERT: A 562 LYS cc_start: 0.9815 (tttm) cc_final: 0.9438 (tppt) REVERT: A 588 GLN cc_start: 0.9120 (mm-40) cc_final: 0.8843 (mm110) REVERT: A 615 MET cc_start: 0.9286 (mmp) cc_final: 0.9055 (mmp) REVERT: A 640 MET cc_start: 0.9159 (tpp) cc_final: 0.8908 (tpp) REVERT: A 683 TYR cc_start: 0.8513 (t80) cc_final: 0.7844 (t80) REVERT: B 51 LEU cc_start: 0.9396 (tp) cc_final: 0.9060 (tp) REVERT: B 55 LEU cc_start: 0.9827 (mt) cc_final: 0.9556 (mt) REVERT: B 67 GLU cc_start: 0.9336 (tm-30) cc_final: 0.8861 (tm-30) REVERT: B 71 LEU cc_start: 0.9550 (mm) cc_final: 0.9282 (mp) REVERT: B 95 MET cc_start: 0.9012 (tpp) cc_final: 0.8375 (tpp) REVERT: B 106 LEU cc_start: 0.9574 (tp) cc_final: 0.9283 (tp) REVERT: B 115 LEU cc_start: 0.9405 (mp) cc_final: 0.9114 (mp) REVERT: B 116 GLU cc_start: 0.8469 (mp0) cc_final: 0.8239 (mp0) REVERT: B 119 GLU cc_start: 0.9223 (mp0) cc_final: 0.8808 (mp0) REVERT: B 166 GLU cc_start: 0.8964 (tp30) cc_final: 0.8594 (tp30) REVERT: B 257 ASP cc_start: 0.8894 (m-30) cc_final: 0.8638 (m-30) REVERT: B 258 ILE cc_start: 0.9528 (tp) cc_final: 0.9328 (tp) REVERT: B 286 ASP cc_start: 0.8578 (m-30) cc_final: 0.7669 (m-30) REVERT: B 317 MET cc_start: 0.9171 (mtm) cc_final: 0.8769 (mpp) REVERT: B 333 LYS cc_start: 0.9218 (tptt) cc_final: 0.8767 (ttmm) REVERT: B 362 ASP cc_start: 0.8667 (m-30) cc_final: 0.7746 (m-30) REVERT: B 373 ILE cc_start: 0.9479 (mt) cc_final: 0.9025 (tp) REVERT: B 387 GLN cc_start: 0.9010 (mt0) cc_final: 0.8740 (mt0) REVERT: B 390 GLN cc_start: 0.8979 (mt0) cc_final: 0.8704 (mm110) REVERT: B 393 SER cc_start: 0.9582 (t) cc_final: 0.9270 (p) REVERT: B 398 ASP cc_start: 0.8728 (t0) cc_final: 0.8436 (t70) REVERT: B 403 ILE cc_start: 0.9543 (mp) cc_final: 0.9238 (tp) REVERT: B 406 ASP cc_start: 0.8280 (m-30) cc_final: 0.8013 (m-30) REVERT: B 413 SER cc_start: 0.9616 (m) cc_final: 0.9376 (t) REVERT: B 415 ASN cc_start: 0.9669 (t0) cc_final: 0.8867 (t0) REVERT: B 417 LEU cc_start: 0.9655 (tt) cc_final: 0.9440 (tt) REVERT: B 418 ASN cc_start: 0.9285 (m-40) cc_final: 0.8959 (m-40) REVERT: B 447 ASN cc_start: 0.8687 (m110) cc_final: 0.8406 (m-40) REVERT: B 458 MET cc_start: 0.9291 (mmm) cc_final: 0.8718 (mmm) REVERT: B 460 SER cc_start: 0.9432 (p) cc_final: 0.9148 (p) REVERT: B 467 ASN cc_start: 0.9151 (t0) cc_final: 0.8941 (t0) REVERT: B 586 TYR cc_start: 0.9166 (m-80) cc_final: 0.8933 (m-80) REVERT: B 599 GLU cc_start: 0.8861 (pt0) cc_final: 0.8537 (pt0) REVERT: B 601 ILE cc_start: 0.9551 (mm) cc_final: 0.8855 (mm) REVERT: B 610 LYS cc_start: 0.9454 (ttpp) cc_final: 0.9170 (ttpp) REVERT: B 615 MET cc_start: 0.9293 (mmm) cc_final: 0.9072 (mmp) REVERT: B 627 LYS cc_start: 0.9301 (tttt) cc_final: 0.8827 (tttp) REVERT: B 628 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8041 (mm-30) REVERT: B 633 ASP cc_start: 0.8661 (t0) cc_final: 0.8204 (t0) REVERT: B 636 LYS cc_start: 0.9586 (mmmm) cc_final: 0.9370 (mmmm) REVERT: B 640 MET cc_start: 0.9464 (tpp) cc_final: 0.9064 (tpp) REVERT: B 650 GLN cc_start: 0.8370 (mm-40) cc_final: 0.8091 (mm-40) REVERT: B 655 THR cc_start: 0.9608 (m) cc_final: 0.9344 (t) REVERT: B 667 LEU cc_start: 0.9579 (tp) cc_final: 0.9132 (tp) REVERT: B 668 ASN cc_start: 0.9375 (m-40) cc_final: 0.9155 (m110) REVERT: C 55 TYR cc_start: 0.8124 (t80) cc_final: 0.7732 (t80) REVERT: C 96 MET cc_start: 0.7688 (mmm) cc_final: 0.6692 (mmm) REVERT: C 197 ASP cc_start: 0.9168 (m-30) cc_final: 0.8870 (m-30) REVERT: C 198 GLU cc_start: 0.9483 (mm-30) cc_final: 0.9223 (mm-30) REVERT: C 233 ASN cc_start: 0.9305 (m110) cc_final: 0.9105 (m110) REVERT: D 74 MET cc_start: 0.4402 (tmm) cc_final: 0.4128 (tmm) REVERT: D 109 PHE cc_start: 0.8154 (m-80) cc_final: 0.7744 (m-80) REVERT: D 123 GLU cc_start: 0.8975 (mp0) cc_final: 0.8759 (mp0) REVERT: D 137 MET cc_start: 0.8508 (mtm) cc_final: 0.7831 (mmp) REVERT: D 172 PHE cc_start: 0.8912 (m-80) cc_final: 0.8383 (m-80) REVERT: D 189 GLU cc_start: 0.9284 (tt0) cc_final: 0.9021 (mp0) outliers start: 0 outliers final: 0 residues processed: 672 average time/residue: 0.3120 time to fit residues: 313.5554 Evaluate side-chains 602 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 602 time to evaluate : 1.895 ------------------------------------------------------------------------------- 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: 1.9990 chunk 102 optimal weight: 0.7980 chunk 182 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 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 13 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN D 28 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.134340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.097107 restraints weight = 40356.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.100671 restraints weight = 21222.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.102965 restraints weight = 13317.191| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.7344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16386 Z= 0.189 Angle : 0.655 9.113 22134 Z= 0.350 Chirality : 0.044 0.221 2360 Planarity : 0.004 0.057 2818 Dihedral : 10.675 177.568 2242 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.19), residues: 1932 helix: 1.05 (0.15), residues: 1115 sheet: -0.66 (0.41), residues: 136 loop : 0.01 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 124 HIS 0.005 0.001 HIS B 255 PHE 0.034 0.002 PHE D 178 TYR 0.028 0.002 TYR D 130 ARG 0.007 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.04029 ( 871) hydrogen bonds : angle 4.99404 ( 2571) covalent geometry : bond 0.00415 (16386) covalent geometry : angle 0.65452 (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 674 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 674 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.9542 (m-40) cc_final: 0.9196 (m110) REVERT: A 27 ASP cc_start: 0.9418 (p0) cc_final: 0.9205 (p0) REVERT: A 30 LYS cc_start: 0.9055 (tptt) cc_final: 0.8816 (tptp) REVERT: A 69 LEU cc_start: 0.9637 (mt) cc_final: 0.9322 (pp) REVERT: A 99 LYS cc_start: 0.9242 (mmtp) cc_final: 0.9024 (mttt) REVERT: A 119 GLU cc_start: 0.8847 (mp0) cc_final: 0.8364 (mp0) REVERT: A 128 PHE cc_start: 0.9476 (t80) cc_final: 0.9263 (t80) REVERT: A 139 GLU cc_start: 0.9385 (tp30) cc_final: 0.9106 (tp30) REVERT: A 144 MET cc_start: 0.8886 (mtm) cc_final: 0.8350 (mtm) REVERT: A 166 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8403 (mm-30) REVERT: A 172 LEU cc_start: 0.9643 (mp) cc_final: 0.9143 (mp) REVERT: A 173 LEU cc_start: 0.9641 (mt) cc_final: 0.9335 (mt) REVERT: A 190 MET cc_start: 0.9045 (mtp) cc_final: 0.8740 (mtp) REVERT: A 227 MET cc_start: 0.9357 (mtp) cc_final: 0.8956 (mtp) REVERT: A 236 TYR cc_start: 0.9192 (t80) cc_final: 0.8207 (t80) REVERT: A 251 LEU cc_start: 0.9519 (tp) cc_final: 0.9279 (tp) REVERT: A 255 HIS cc_start: 0.8826 (t-90) cc_final: 0.7804 (t-90) REVERT: A 257 ASP cc_start: 0.9221 (m-30) cc_final: 0.8757 (m-30) REVERT: A 259 ASN cc_start: 0.9226 (m-40) cc_final: 0.8874 (m-40) REVERT: A 274 ARG cc_start: 0.8558 (ttp-110) cc_final: 0.7436 (ptp90) REVERT: A 318 ASP cc_start: 0.8787 (t0) cc_final: 0.8511 (t0) REVERT: A 321 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8508 (tm-30) REVERT: A 333 LYS cc_start: 0.9398 (tmtt) cc_final: 0.8941 (tptp) REVERT: A 348 MET cc_start: 0.9121 (ptp) cc_final: 0.8764 (ptp) REVERT: A 357 TYR cc_start: 0.8805 (m-10) cc_final: 0.8399 (m-10) REVERT: A 361 GLN cc_start: 0.9138 (tp40) cc_final: 0.8840 (tp-100) REVERT: A 381 LEU cc_start: 0.9236 (tp) cc_final: 0.8935 (tp) REVERT: A 407 ILE cc_start: 0.9285 (mt) cc_final: 0.8787 (mt) REVERT: A 458 MET cc_start: 0.9043 (mmp) cc_final: 0.8524 (mmp) REVERT: A 472 LEU cc_start: 0.9505 (mt) cc_final: 0.9263 (mt) REVERT: A 501 GLN cc_start: 0.9406 (tt0) cc_final: 0.8819 (tm-30) REVERT: A 505 GLU cc_start: 0.8890 (mt-10) cc_final: 0.7794 (mt-10) REVERT: A 515 ASP cc_start: 0.8785 (m-30) cc_final: 0.8471 (m-30) REVERT: A 529 ASP cc_start: 0.8949 (m-30) cc_final: 0.8598 (m-30) REVERT: A 562 LYS cc_start: 0.9808 (tttm) cc_final: 0.9510 (ttmm) REVERT: A 604 ARG cc_start: 0.8862 (mmp80) cc_final: 0.8570 (mmp80) REVERT: A 606 TYR cc_start: 0.8275 (m-80) cc_final: 0.8010 (m-80) REVERT: A 615 MET cc_start: 0.9254 (mmp) cc_final: 0.8988 (mmp) REVERT: A 630 TYR cc_start: 0.8156 (m-80) cc_final: 0.7243 (m-80) REVERT: A 639 ASP cc_start: 0.8996 (m-30) cc_final: 0.8718 (m-30) REVERT: A 683 TYR cc_start: 0.8523 (t80) cc_final: 0.7792 (t80) REVERT: B 51 LEU cc_start: 0.9389 (tp) cc_final: 0.9073 (tp) REVERT: B 55 LEU cc_start: 0.9830 (mt) cc_final: 0.9580 (mt) REVERT: B 67 GLU cc_start: 0.9305 (tm-30) cc_final: 0.8818 (tm-30) REVERT: B 95 MET cc_start: 0.8979 (tpp) cc_final: 0.8549 (tpp) REVERT: B 98 PHE cc_start: 0.9536 (t80) cc_final: 0.9004 (t80) REVERT: B 119 GLU cc_start: 0.9232 (mp0) cc_final: 0.8792 (mp0) REVERT: B 174 GLU cc_start: 0.8109 (tp30) cc_final: 0.7894 (tp30) REVERT: B 257 ASP cc_start: 0.8907 (m-30) cc_final: 0.8647 (m-30) REVERT: B 263 ASP cc_start: 0.8785 (m-30) cc_final: 0.8486 (m-30) REVERT: B 286 ASP cc_start: 0.8580 (m-30) cc_final: 0.7698 (m-30) REVERT: B 290 GLU cc_start: 0.9246 (tp30) cc_final: 0.8984 (tp30) REVERT: B 322 MET cc_start: 0.9403 (tpt) cc_final: 0.8936 (mmm) REVERT: B 333 LYS cc_start: 0.9177 (tptt) cc_final: 0.8811 (ttmm) REVERT: B 362 ASP cc_start: 0.8568 (m-30) cc_final: 0.7627 (m-30) REVERT: B 373 ILE cc_start: 0.9499 (mt) cc_final: 0.9161 (tp) REVERT: B 386 LEU cc_start: 0.9401 (mt) cc_final: 0.9197 (mt) REVERT: B 387 GLN cc_start: 0.8958 (mt0) cc_final: 0.8661 (mt0) REVERT: B 393 SER cc_start: 0.9595 (t) cc_final: 0.9294 (p) REVERT: B 398 ASP cc_start: 0.8682 (t0) cc_final: 0.8391 (t70) REVERT: B 413 SER cc_start: 0.9620 (m) cc_final: 0.9390 (t) REVERT: B 415 ASN cc_start: 0.9654 (t0) cc_final: 0.8978 (t0) REVERT: B 418 ASN cc_start: 0.9306 (m-40) cc_final: 0.9051 (m110) REVERT: B 434 ASP cc_start: 0.9005 (m-30) cc_final: 0.8795 (m-30) REVERT: B 447 ASN cc_start: 0.8663 (m110) cc_final: 0.8400 (m-40) REVERT: B 458 MET cc_start: 0.9257 (mmm) cc_final: 0.8673 (mmm) REVERT: B 460 SER cc_start: 0.9418 (p) cc_final: 0.9130 (p) REVERT: B 501 GLN cc_start: 0.9444 (tt0) cc_final: 0.9212 (tt0) REVERT: B 505 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8537 (mt-10) REVERT: B 599 GLU cc_start: 0.8821 (pt0) cc_final: 0.8482 (pt0) REVERT: B 601 ILE cc_start: 0.9550 (mm) cc_final: 0.8826 (mm) REVERT: B 615 MET cc_start: 0.9307 (mmm) cc_final: 0.9102 (mmp) REVERT: B 627 LYS cc_start: 0.9352 (tttt) cc_final: 0.8888 (tttp) REVERT: B 628 GLU cc_start: 0.8768 (mm-30) cc_final: 0.7994 (mm-30) REVERT: B 633 ASP cc_start: 0.8622 (t0) cc_final: 0.8264 (t0) REVERT: B 640 MET cc_start: 0.9409 (tpp) cc_final: 0.9032 (tpp) REVERT: B 655 THR cc_start: 0.9712 (m) cc_final: 0.9486 (t) REVERT: B 667 LEU cc_start: 0.9592 (tp) cc_final: 0.9131 (tp) REVERT: B 668 ASN cc_start: 0.9325 (m-40) cc_final: 0.9110 (m110) REVERT: B 671 ASP cc_start: 0.8986 (m-30) cc_final: 0.8768 (m-30) REVERT: C 55 TYR cc_start: 0.8167 (t80) cc_final: 0.7776 (t80) REVERT: C 96 MET cc_start: 0.7886 (mmm) cc_final: 0.6865 (mmm) REVERT: C 110 MET cc_start: 0.7633 (mtm) cc_final: 0.7408 (mtm) REVERT: C 111 THR cc_start: 0.3484 (m) cc_final: 0.3108 (p) REVERT: C 197 ASP cc_start: 0.9159 (m-30) cc_final: 0.8934 (m-30) REVERT: C 233 ASN cc_start: 0.9268 (m110) cc_final: 0.9054 (m110) REVERT: D 74 MET cc_start: 0.4396 (tmm) cc_final: 0.4168 (tmm) REVERT: D 109 PHE cc_start: 0.8243 (m-80) cc_final: 0.7837 (m-80) REVERT: D 137 MET cc_start: 0.8419 (mtm) cc_final: 0.7488 (mmp) REVERT: D 151 ILE cc_start: 0.6554 (mm) cc_final: 0.6109 (mm) REVERT: D 179 TYR cc_start: 0.7825 (t80) cc_final: 0.6875 (t80) REVERT: D 189 GLU cc_start: 0.9281 (tt0) cc_final: 0.8726 (mp0) outliers start: 0 outliers final: 0 residues processed: 674 average time/residue: 0.2838 time to fit residues: 285.9053 Evaluate side-chains 597 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 597 time to evaluate : 1.806 ------------------------------------------------------------------------------- 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: 0.9980 chunk 0 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 160 optimal weight: 20.0000 chunk 106 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 chunk 148 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 HIS ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN B 645 GLN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.135681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.098190 restraints weight = 40435.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.101741 restraints weight = 21120.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.104117 restraints weight = 13191.568| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.7536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16386 Z= 0.167 Angle : 0.662 9.392 22134 Z= 0.351 Chirality : 0.044 0.264 2360 Planarity : 0.004 0.058 2818 Dihedral : 10.554 175.768 2242 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.19), residues: 1932 helix: 1.03 (0.15), residues: 1131 sheet: -0.65 (0.39), residues: 148 loop : -0.10 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 124 HIS 0.004 0.001 HIS B 255 PHE 0.032 0.002 PHE D 109 TYR 0.027 0.002 TYR B 574 ARG 0.009 0.001 ARG B 575 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 871) hydrogen bonds : angle 5.01580 ( 2571) covalent geometry : bond 0.00373 (16386) covalent geometry : angle 0.66211 (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 668 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 668 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.9559 (m-40) cc_final: 0.9150 (m110) REVERT: A 27 ASP cc_start: 0.9430 (p0) cc_final: 0.9205 (p0) REVERT: A 30 LYS cc_start: 0.9064 (tptt) cc_final: 0.8821 (tptp) REVERT: A 69 LEU cc_start: 0.9630 (mt) cc_final: 0.9306 (pp) REVERT: A 99 LYS cc_start: 0.9248 (mmtp) cc_final: 0.8987 (mttt) REVERT: A 119 GLU cc_start: 0.8835 (mp0) cc_final: 0.8370 (mp0) REVERT: A 128 PHE cc_start: 0.9460 (t80) cc_final: 0.9240 (t80) REVERT: A 139 GLU cc_start: 0.9388 (tp30) cc_final: 0.9070 (tp30) REVERT: A 147 GLN cc_start: 0.9023 (mt0) cc_final: 0.8328 (mt0) REVERT: A 166 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8423 (mm-30) REVERT: A 172 LEU cc_start: 0.9641 (mp) cc_final: 0.9163 (mp) REVERT: A 173 LEU cc_start: 0.9612 (mt) cc_final: 0.9344 (mt) REVERT: A 190 MET cc_start: 0.9059 (mtp) cc_final: 0.8745 (mtp) REVERT: A 227 MET cc_start: 0.9313 (mtp) cc_final: 0.8956 (mtp) REVERT: A 236 TYR cc_start: 0.9158 (t80) cc_final: 0.8125 (t80) REVERT: A 251 LEU cc_start: 0.9494 (tp) cc_final: 0.9223 (tp) REVERT: A 255 HIS cc_start: 0.8780 (t-90) cc_final: 0.7716 (t-90) REVERT: A 257 ASP cc_start: 0.9189 (m-30) cc_final: 0.8710 (m-30) REVERT: A 259 ASN cc_start: 0.9207 (m-40) cc_final: 0.8893 (m-40) REVERT: A 274 ARG cc_start: 0.8467 (ttp-110) cc_final: 0.7494 (ptp90) REVERT: A 322 MET cc_start: 0.8788 (mmt) cc_final: 0.8550 (tpp) REVERT: A 333 LYS cc_start: 0.9391 (tmtt) cc_final: 0.8950 (tptp) REVERT: A 361 GLN cc_start: 0.9155 (tp40) cc_final: 0.8878 (tp-100) REVERT: A 377 LYS cc_start: 0.9264 (mttt) cc_final: 0.9032 (mttp) REVERT: A 407 ILE cc_start: 0.9155 (mt) cc_final: 0.8707 (mt) REVERT: A 458 MET cc_start: 0.8972 (mmp) cc_final: 0.8490 (mmp) REVERT: A 472 LEU cc_start: 0.9504 (mt) cc_final: 0.9254 (mt) REVERT: A 496 ASN cc_start: 0.9411 (t0) cc_final: 0.9165 (t0) REVERT: A 501 GLN cc_start: 0.9407 (tt0) cc_final: 0.8832 (tm-30) REVERT: A 505 GLU cc_start: 0.8897 (mt-10) cc_final: 0.7813 (mt-10) REVERT: A 515 ASP cc_start: 0.8776 (m-30) cc_final: 0.8424 (m-30) REVERT: A 529 ASP cc_start: 0.8972 (m-30) cc_final: 0.8586 (m-30) REVERT: A 561 LEU cc_start: 0.9648 (tp) cc_final: 0.9448 (tp) REVERT: A 562 LYS cc_start: 0.9798 (tttm) cc_final: 0.9509 (ttmm) REVERT: A 604 ARG cc_start: 0.8858 (mmp80) cc_final: 0.8476 (mmp80) REVERT: A 630 TYR cc_start: 0.8343 (m-80) cc_final: 0.7661 (m-80) REVERT: A 639 ASP cc_start: 0.9007 (m-30) cc_final: 0.8704 (m-30) REVERT: B 51 LEU cc_start: 0.9392 (tp) cc_final: 0.9052 (tp) REVERT: B 55 LEU cc_start: 0.9827 (mt) cc_final: 0.9559 (mt) REVERT: B 67 GLU cc_start: 0.9310 (tm-30) cc_final: 0.8913 (tm-30) REVERT: B 82 LYS cc_start: 0.9496 (mmmm) cc_final: 0.9189 (mmtt) REVERT: B 95 MET cc_start: 0.9015 (tpp) cc_final: 0.8665 (tpp) REVERT: B 119 GLU cc_start: 0.9198 (mp0) cc_final: 0.8745 (mp0) REVERT: B 147 GLN cc_start: 0.9420 (mt0) cc_final: 0.9025 (mt0) REVERT: B 166 GLU cc_start: 0.8857 (tp30) cc_final: 0.8594 (tp30) REVERT: B 174 GLU cc_start: 0.8023 (tp30) cc_final: 0.7767 (tp30) REVERT: B 232 ASN cc_start: 0.8893 (m110) cc_final: 0.8217 (m110) REVERT: B 257 ASP cc_start: 0.8893 (m-30) cc_final: 0.8663 (m-30) REVERT: B 258 ILE cc_start: 0.9514 (tp) cc_final: 0.9302 (tp) REVERT: B 286 ASP cc_start: 0.8567 (m-30) cc_final: 0.7676 (m-30) REVERT: B 290 GLU cc_start: 0.9235 (tp30) cc_final: 0.8964 (tp30) REVERT: B 333 LYS cc_start: 0.9181 (tptt) cc_final: 0.8829 (ttmm) REVERT: B 362 ASP cc_start: 0.8580 (m-30) cc_final: 0.7612 (m-30) REVERT: B 393 SER cc_start: 0.9581 (t) cc_final: 0.9292 (p) REVERT: B 398 ASP cc_start: 0.8675 (t0) cc_final: 0.8377 (t70) REVERT: B 413 SER cc_start: 0.9550 (m) cc_final: 0.9190 (t) REVERT: B 415 ASN cc_start: 0.9642 (t0) cc_final: 0.9036 (t0) REVERT: B 434 ASP cc_start: 0.8991 (m-30) cc_final: 0.8779 (m-30) REVERT: B 458 MET cc_start: 0.9258 (mmm) cc_final: 0.8739 (mmm) REVERT: B 467 ASN cc_start: 0.9130 (t0) cc_final: 0.8928 (t0) REVERT: B 501 GLN cc_start: 0.9453 (tt0) cc_final: 0.9213 (tt0) REVERT: B 505 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8170 (mt-10) REVERT: B 550 MET cc_start: 0.8534 (mtp) cc_final: 0.8142 (mtp) REVERT: B 598 MET cc_start: 0.9003 (mtm) cc_final: 0.8788 (mtm) REVERT: B 599 GLU cc_start: 0.8801 (pt0) cc_final: 0.8170 (pt0) REVERT: B 601 ILE cc_start: 0.9528 (mm) cc_final: 0.8786 (mm) REVERT: B 615 MET cc_start: 0.9289 (mmm) cc_final: 0.9072 (mmp) REVERT: B 627 LYS cc_start: 0.9336 (tttt) cc_final: 0.8835 (tttp) REVERT: B 628 GLU cc_start: 0.8770 (mm-30) cc_final: 0.7956 (mm-30) REVERT: B 633 ASP cc_start: 0.8611 (t0) cc_final: 0.7551 (t0) REVERT: B 636 LYS cc_start: 0.9650 (mmtp) cc_final: 0.9302 (mmtm) REVERT: B 640 MET cc_start: 0.9419 (tpp) cc_final: 0.9065 (tpp) REVERT: B 655 THR cc_start: 0.9615 (m) cc_final: 0.9336 (t) REVERT: B 667 LEU cc_start: 0.9595 (tp) cc_final: 0.9142 (tp) REVERT: B 668 ASN cc_start: 0.9303 (m-40) cc_final: 0.9099 (m110) REVERT: B 671 ASP cc_start: 0.8980 (m-30) cc_final: 0.8766 (m-30) REVERT: C 68 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6938 (pp20) REVERT: C 96 MET cc_start: 0.7863 (mmm) cc_final: 0.6856 (mmm) REVERT: C 110 MET cc_start: 0.7597 (mtm) cc_final: 0.7365 (mtm) REVERT: C 111 THR cc_start: 0.3396 (m) cc_final: 0.3059 (p) REVERT: C 197 ASP cc_start: 0.9165 (m-30) cc_final: 0.8863 (m-30) REVERT: C 233 ASN cc_start: 0.9276 (m110) cc_final: 0.9067 (m110) REVERT: D 109 PHE cc_start: 0.8283 (m-80) cc_final: 0.7871 (m-80) REVERT: D 137 MET cc_start: 0.8315 (mtm) cc_final: 0.7565 (mmp) REVERT: D 151 ILE cc_start: 0.6532 (mm) cc_final: 0.6086 (mm) REVERT: D 179 TYR cc_start: 0.7761 (t80) cc_final: 0.6751 (t80) REVERT: D 183 LYS cc_start: 0.8280 (pttm) cc_final: 0.7348 (tttp) REVERT: D 189 GLU cc_start: 0.9258 (tt0) cc_final: 0.8731 (mp0) REVERT: D 194 ILE cc_start: 0.8767 (mt) cc_final: 0.8430 (mt) outliers start: 0 outliers final: 0 residues processed: 668 average time/residue: 0.2915 time to fit residues: 290.6051 Evaluate side-chains 586 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 586 time to evaluate : 1.980 ------------------------------------------------------------------------------- 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: 0.6980 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 179 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 180 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.137454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.100403 restraints weight = 39629.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.104011 restraints weight = 20809.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.106387 restraints weight = 12870.174| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.7700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16386 Z= 0.147 Angle : 0.649 8.841 22134 Z= 0.347 Chirality : 0.044 0.218 2360 Planarity : 0.004 0.064 2818 Dihedral : 10.397 173.896 2242 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: 0.72 (0.19), residues: 1932 helix: 1.06 (0.15), residues: 1133 sheet: -0.63 (0.40), residues: 146 loop : -0.10 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 124 HIS 0.005 0.001 HIS C 201 PHE 0.031 0.002 PHE D 109 TYR 0.025 0.001 TYR B 574 ARG 0.008 0.001 ARG B 575 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 871) hydrogen bonds : angle 5.00926 ( 2571) covalent geometry : bond 0.00330 (16386) covalent geometry : angle 0.64891 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7129.96 seconds wall clock time: 124 minutes 23.27 seconds (7463.27 seconds total)