Starting phenix.real_space_refine on Thu Sep 18 10:04:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzj_45069/09_2025/9bzj_45069_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzj_45069/09_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_45069/09_2025/9bzj_45069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzj_45069/09_2025/9bzj_45069.map" model { file = "/net/cci-nas-00/data/ceres_data/9bzj_45069/09_2025/9bzj_45069_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzj_45069/09_2025/9bzj_45069_neut.cif" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 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: 4.30, per 1000 atoms: 0.27 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: 1.49 Conformation dependent library (CDL) restraints added in 809.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 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: 3.24 Time building geometry restraints manager: 1.80 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: 1.160 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.900 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.310 ------------------------------------------------------------------------------- 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 : 8.25 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG D 225 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.73993 (22134) hydrogen bonds : bond 0.15420 ( 871) hydrogen bonds : angle 6.51774 ( 2571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 999 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8162 (p) cc_final: 0.7957 (m) REVERT: A 12 LEU cc_start: 0.8765 (mt) cc_final: 0.8508 (mp) REVERT: A 55 LEU cc_start: 0.8884 (mt) cc_final: 0.8609 (mt) REVERT: A 76 ASP cc_start: 0.8075 (m-30) cc_final: 0.7579 (m-30) REVERT: A 152 SER cc_start: 0.8599 (p) cc_final: 0.8233 (p) REVERT: A 157 LEU cc_start: 0.9274 (tp) cc_final: 0.8868 (tp) REVERT: A 172 LEU cc_start: 0.9261 (mp) cc_final: 0.8972 (mp) REVERT: A 186 ILE cc_start: 0.9098 (mt) cc_final: 0.8890 (mt) REVERT: A 188 ILE cc_start: 0.9093 (mt) cc_final: 0.8806 (mt) REVERT: A 192 LEU cc_start: 0.9318 (mt) cc_final: 0.8866 (mt) REVERT: A 211 GLU cc_start: 0.6249 (mt-10) cc_final: 0.5871 (tp30) REVERT: A 236 TYR cc_start: 0.7661 (t80) cc_final: 0.7385 (t80) REVERT: A 238 ASP cc_start: 0.7874 (p0) cc_final: 0.7545 (p0) REVERT: A 259 ASN cc_start: 0.8087 (m-40) cc_final: 0.7626 (m-40) REVERT: A 265 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8518 (mmmt) REVERT: A 322 MET cc_start: 0.7756 (mmp) cc_final: 0.6239 (mmm) REVERT: A 326 PHE cc_start: 0.8518 (m-10) cc_final: 0.7947 (m-80) REVERT: A 355 TYR cc_start: 0.7427 (m-80) cc_final: 0.7214 (m-80) REVERT: A 367 VAL cc_start: 0.8652 (m) cc_final: 0.8435 (p) REVERT: A 373 ILE cc_start: 0.9100 (mt) cc_final: 0.8789 (mt) REVERT: A 377 LYS cc_start: 0.8839 (mttt) cc_final: 0.8497 (mttm) REVERT: A 407 ILE cc_start: 0.8904 (mt) cc_final: 0.8460 (mt) REVERT: A 415 ASN cc_start: 0.8025 (t0) cc_final: 0.7708 (t0) REVERT: A 417 LEU cc_start: 0.8059 (tt) cc_final: 0.7706 (tt) REVERT: A 418 ASN cc_start: 0.8250 (m-40) cc_final: 0.7391 (m110) REVERT: A 435 SER cc_start: 0.9330 (p) cc_final: 0.8992 (t) REVERT: A 447 ASN cc_start: 0.8127 (m-40) cc_final: 0.7811 (m-40) REVERT: A 480 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7749 (mt-10) REVERT: A 490 THR cc_start: 0.8511 (m) cc_final: 0.8188 (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: 0.7028 (mtm) REVERT: A 594 VAL cc_start: 0.8906 (m) cc_final: 0.8577 (t) REVERT: A 597 ILE cc_start: 0.8719 (pt) cc_final: 0.8393 (pt) REVERT: A 644 ILE cc_start: 0.8380 (mt) cc_final: 0.7912 (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: 0.8661 (mp) REVERT: B 51 LEU cc_start: 0.8137 (tp) cc_final: 0.7882 (tp) REVERT: B 147 GLN cc_start: 0.7969 (mt0) cc_final: 0.7601 (mt0) REVERT: B 175 VAL cc_start: 0.8898 (t) cc_final: 0.8630 (t) REVERT: B 204 SER cc_start: 0.8988 (m) cc_final: 0.7912 (t) REVERT: B 261 PHE cc_start: 0.8606 (t80) cc_final: 0.8317 (t80) REVERT: B 265 LYS cc_start: 0.8801 (mmtt) cc_final: 0.7941 (mmmt) REVERT: B 286 ASP cc_start: 0.6400 (OUTLIER) cc_final: 0.6150 (m-30) REVERT: B 315 ASP cc_start: 0.8332 (p0) cc_final: 0.7901 (p0) REVERT: B 326 PHE cc_start: 0.8294 (m-10) cc_final: 0.8068 (m-10) REVERT: B 362 ASP cc_start: 0.6385 (m-30) cc_final: 0.5898 (m-30) REVERT: B 366 LYS cc_start: 0.8586 (ptpp) cc_final: 0.8324 (ptpp) REVERT: B 373 ILE cc_start: 0.9115 (mt) cc_final: 0.8849 (mt) REVERT: B 384 GLU cc_start: 0.9052 (pm20) cc_final: 0.8320 (pm20) REVERT: B 387 GLN cc_start: 0.7898 (mt0) cc_final: 0.7607 (mt0) 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: 0.7932 (t0) REVERT: B 494 MET cc_start: 0.7580 (mtp) cc_final: 0.7126 (mtp) REVERT: B 496 ASN cc_start: 0.7643 (t0) cc_final: 0.7392 (t0) REVERT: B 500 ILE cc_start: 0.9131 (mt) cc_final: 0.8901 (mt) REVERT: B 561 LEU cc_start: 0.8483 (tp) cc_final: 0.8126 (tp) REVERT: B 570 MET cc_start: 0.6811 (mtm) cc_final: 0.6472 (mtm) REVERT: B 605 THR cc_start: 0.7613 (m) cc_final: 0.6865 (m) REVERT: B 640 MET cc_start: 0.7912 (tpp) cc_final: 0.7137 (tpp) REVERT: B 644 ILE cc_start: 0.8665 (mt) cc_final: 0.8258 (mt) REVERT: C 43 THR cc_start: 0.4801 (p) cc_final: 0.4481 (m) REVERT: C 92 PHE cc_start: 0.6653 (t80) cc_final: 0.6167 (t80) REVERT: C 96 MET cc_start: 0.4835 (mmm) cc_final: 0.4402 (mmm) REVERT: C 169 TYR cc_start: 0.4145 (m-80) cc_final: 0.3717 (m-80) REVERT: C 185 MET cc_start: 0.3037 (mtp) cc_final: 0.2625 (ptt) REVERT: C 195 LEU cc_start: 0.7441 (tt) cc_final: 0.7188 (tt) REVERT: D 95 MET cc_start: 0.1773 (tmm) cc_final: 0.0973 (tmm) REVERT: D 151 ILE cc_start: 0.5937 (mm) cc_final: 0.5202 (mm) REVERT: D 178 PHE cc_start: 0.4551 (m-80) cc_final: 0.4120 (m-80) REVERT: D 194 ILE cc_start: 0.6907 (mt) cc_final: 0.6615 (mt) REVERT: D 286 VAL cc_start: 0.2691 (t) cc_final: 0.1557 (p) outliers start: 23 outliers final: 6 residues processed: 1010 average time/residue: 0.1499 time to fit residues: 218.3672 Evaluate side-chains 677 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 669 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.0970 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 9.9990 overall best weight: 3.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 232 ASN A 242 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 387 GLN 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 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 GLN D 233 ASN D 249 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.132299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.093586 restraints weight = 39939.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.097221 restraints weight = 20985.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.099629 restraints weight = 13010.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.101256 restraints weight = 9024.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.102373 restraints weight = 6805.536| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16386 Z= 0.285 Angle : 0.729 8.869 22134 Z= 0.392 Chirality : 0.047 0.317 2360 Planarity : 0.004 0.072 2818 Dihedral : 11.447 178.522 2242 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.17 % Allowed : 3.32 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.18), residues: 1932 helix: 1.02 (0.15), residues: 1130 sheet: -0.31 (0.40), residues: 150 loop : 0.39 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 225 TYR 0.019 0.002 TYR D 236 PHE 0.029 0.003 PHE D 320 TRP 0.045 0.003 TRP D 124 HIS 0.011 0.002 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00596 (16386) covalent geometry : angle 0.72893 (22134) hydrogen bonds : bond 0.04698 ( 871) hydrogen bonds : angle 5.13112 ( 2571) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 757 time to evaluate : 0.606 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: A 8 LYS cc_start: 0.9290 (tttt) cc_final: 0.9070 (tttm) REVERT: A 27 ASP cc_start: 0.9378 (p0) cc_final: 0.9086 (p0) REVERT: A 31 GLU cc_start: 0.9385 (mm-30) cc_final: 0.9051 (mp0) REVERT: A 117 ARG cc_start: 0.9146 (mtp85) cc_final: 0.8839 (mtp85) REVERT: A 118 TYR cc_start: 0.9191 (t80) cc_final: 0.8969 (t80) REVERT: A 144 MET cc_start: 0.9121 (mtm) cc_final: 0.8769 (mtm) REVERT: A 147 GLN cc_start: 0.9039 (mt0) cc_final: 0.8387 (mt0) REVERT: A 157 LEU cc_start: 0.9262 (tp) cc_final: 0.9054 (tp) REVERT: A 172 LEU cc_start: 0.9663 (mp) cc_final: 0.9403 (mp) REVERT: A 236 TYR cc_start: 0.9182 (t80) cc_final: 0.8380 (t80) REVERT: A 274 ARG cc_start: 0.8464 (ttp80) cc_final: 0.8245 (ttp80) REVERT: A 276 LYS cc_start: 0.9248 (ptpp) cc_final: 0.8895 (mppt) REVERT: A 322 MET cc_start: 0.8743 (mmp) cc_final: 0.7743 (tpp) REVERT: A 326 PHE cc_start: 0.9626 (m-10) cc_final: 0.8851 (m-80) REVERT: A 333 LYS cc_start: 0.9103 (tmtt) cc_final: 0.8607 (tptt) REVERT: A 344 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8255 (mp0) REVERT: A 355 TYR cc_start: 0.9125 (m-80) cc_final: 0.8739 (m-80) REVERT: A 407 ILE cc_start: 0.9315 (mt) cc_final: 0.8882 (mt) REVERT: A 428 THR cc_start: 0.9584 (m) cc_final: 0.9237 (m) REVERT: A 456 LYS cc_start: 0.9095 (mtmt) cc_final: 0.8836 (ptpt) REVERT: A 505 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8292 (mt-10) REVERT: A 515 ASP cc_start: 0.8814 (m-30) cc_final: 0.8587 (m-30) REVERT: A 550 MET cc_start: 0.7687 (mtm) cc_final: 0.7213 (mtm) REVERT: A 604 ARG cc_start: 0.8716 (mmp80) cc_final: 0.8406 (mmp80) REVERT: A 606 TYR cc_start: 0.7683 (m-80) cc_final: 0.7313 (m-80) REVERT: A 611 THR cc_start: 0.9220 (p) cc_final: 0.8188 (p) REVERT: A 632 MET cc_start: 0.8870 (mtp) cc_final: 0.8660 (mtp) REVERT: A 649 ASP cc_start: 0.8703 (p0) cc_final: 0.8477 (p0) REVERT: A 668 ASN cc_start: 0.9476 (m-40) cc_final: 0.9196 (m110) REVERT: B 51 LEU cc_start: 0.9444 (tp) cc_final: 0.9110 (tp) REVERT: B 71 LEU cc_start: 0.9499 (mm) cc_final: 0.9199 (mm) REVERT: B 119 GLU cc_start: 0.9330 (mp0) cc_final: 0.9032 (mp0) REVERT: B 128 PHE cc_start: 0.9583 (t80) cc_final: 0.9348 (t80) REVERT: B 149 TYR cc_start: 0.9257 (t80) cc_final: 0.8867 (t80) REVERT: B 162 LYS cc_start: 0.9603 (tppt) cc_final: 0.9217 (mmmm) REVERT: B 172 LEU cc_start: 0.9372 (mp) cc_final: 0.8950 (mp) REVERT: B 173 LEU cc_start: 0.9658 (mt) cc_final: 0.9351 (mt) REVERT: B 186 ILE cc_start: 0.9764 (mt) cc_final: 0.9419 (mt) REVERT: B 190 MET cc_start: 0.9524 (mtm) cc_final: 0.9040 (mtm) REVERT: B 191 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8847 (mm-40) REVERT: B 211 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8313 (mm-30) REVERT: B 223 VAL cc_start: 0.9435 (m) cc_final: 0.9170 (m) REVERT: B 227 MET cc_start: 0.9154 (mtt) cc_final: 0.8727 (mtt) REVERT: B 286 ASP cc_start: 0.8585 (m-30) cc_final: 0.7604 (m-30) REVERT: B 312 GLN cc_start: 0.9004 (pm20) cc_final: 0.8656 (pm20) REVERT: B 319 MET cc_start: 0.9111 (tpp) cc_final: 0.8753 (tpp) REVERT: B 362 ASP cc_start: 0.8713 (m-30) cc_final: 0.7672 (m-30) REVERT: B 370 ASN cc_start: 0.9494 (m-40) cc_final: 0.9033 (m-40) REVERT: B 390 GLN cc_start: 0.9138 (mt0) cc_final: 0.8896 (mm110) REVERT: B 393 SER cc_start: 0.9585 (t) cc_final: 0.9313 (p) REVERT: B 406 ASP cc_start: 0.8007 (m-30) cc_final: 0.7608 (m-30) REVERT: B 410 ASN cc_start: 0.8943 (m110) cc_final: 0.8628 (m110) REVERT: B 413 SER cc_start: 0.9581 (m) cc_final: 0.9205 (t) REVERT: B 415 ASN cc_start: 0.9576 (t0) cc_final: 0.9152 (t0) REVERT: B 416 ILE cc_start: 0.9639 (mt) cc_final: 0.9435 (mt) REVERT: B 446 ARG cc_start: 0.8339 (mtp85) cc_final: 0.8052 (mmm-85) REVERT: B 447 ASN cc_start: 0.8619 (m-40) cc_final: 0.7595 (m-40) REVERT: B 467 ASN cc_start: 0.9188 (t0) cc_final: 0.8984 (t0) REVERT: B 494 MET cc_start: 0.9496 (mtp) cc_final: 0.9143 (mtp) REVERT: B 574 TYR cc_start: 0.8665 (m-80) cc_final: 0.8340 (m-80) REVERT: B 602 GLU cc_start: 0.8308 (pt0) cc_final: 0.8022 (pt0) REVERT: B 615 MET cc_start: 0.9213 (mmp) cc_final: 0.8909 (mmp) REVERT: B 627 LYS cc_start: 0.9352 (tttp) cc_final: 0.8828 (tttp) REVERT: B 632 MET cc_start: 0.9122 (mtm) cc_final: 0.8397 (mtm) REVERT: B 636 LYS cc_start: 0.9701 (mmmm) cc_final: 0.9424 (mmmm) REVERT: B 640 MET cc_start: 0.9596 (tpp) cc_final: 0.8726 (tpp) REVERT: B 644 ILE cc_start: 0.9743 (mt) cc_final: 0.9502 (mt) REVERT: B 648 ILE cc_start: 0.9377 (mm) cc_final: 0.9066 (mm) REVERT: B 682 ILE cc_start: 0.9720 (mt) cc_final: 0.9369 (mt) REVERT: C 58 VAL cc_start: 0.7778 (OUTLIER) cc_final: 0.7173 (t) REVERT: C 196 ARG cc_start: 0.8494 (ptp-110) cc_final: 0.8079 (ttm110) REVERT: D 137 MET cc_start: 0.6547 (mtm) cc_final: 0.6001 (mmp) REVERT: D 151 ILE cc_start: 0.7257 (mm) cc_final: 0.6721 (mm) REVERT: D 194 ILE cc_start: 0.9326 (mt) cc_final: 0.9073 (mt) outliers start: 3 outliers final: 0 residues processed: 758 average time/residue: 0.1381 time to fit residues: 154.7608 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 : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 150 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 365 ASN A 645 GLN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN B 645 GLN C 132 GLN C 249 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 128 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.133957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.095041 restraints weight = 39728.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.098803 restraints weight = 20861.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.101253 restraints weight = 12843.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.102882 restraints weight = 8955.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.104036 restraints weight = 6784.653| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16386 Z= 0.154 Angle : 0.596 8.504 22134 Z= 0.320 Chirality : 0.043 0.186 2360 Planarity : 0.004 0.043 2818 Dihedral : 11.072 178.291 2242 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.29 % Allowed : 2.10 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.19), residues: 1932 helix: 1.11 (0.15), residues: 1124 sheet: -0.17 (0.40), residues: 132 loop : 0.30 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 669 TYR 0.026 0.001 TYR C 174 PHE 0.027 0.002 PHE D 227 TRP 0.034 0.002 TRP D 124 HIS 0.004 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00339 (16386) covalent geometry : angle 0.59555 (22134) hydrogen bonds : bond 0.04162 ( 871) hydrogen bonds : angle 4.88273 ( 2571) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 728 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ASN cc_start: 0.9244 (t0) cc_final: 0.8972 (t0) REVERT: A 95 MET cc_start: 0.9248 (mmm) cc_final: 0.8828 (tpp) REVERT: A 99 LYS cc_start: 0.9342 (mmtp) cc_final: 0.9048 (mmtp) REVERT: A 117 ARG cc_start: 0.9063 (mtp85) cc_final: 0.8701 (mtp85) REVERT: A 139 GLU cc_start: 0.9443 (mm-30) cc_final: 0.9176 (tp30) REVERT: A 144 MET cc_start: 0.9123 (mtm) cc_final: 0.8702 (mtm) REVERT: A 147 GLN cc_start: 0.8996 (mt0) cc_final: 0.8302 (mt0) REVERT: A 172 LEU cc_start: 0.9611 (mp) cc_final: 0.9256 (mp) REVERT: A 204 SER cc_start: 0.9591 (t) cc_final: 0.9267 (p) REVERT: A 227 MET cc_start: 0.9375 (mtp) cc_final: 0.8977 (mtp) REVERT: A 236 TYR cc_start: 0.9079 (t80) cc_final: 0.8333 (t80) REVERT: A 251 LEU cc_start: 0.9424 (tp) cc_final: 0.9164 (tp) REVERT: A 315 ASP cc_start: 0.8913 (p0) cc_final: 0.8628 (p0) REVERT: A 317 MET cc_start: 0.8908 (ptm) cc_final: 0.8405 (ptm) REVERT: A 320 ASN cc_start: 0.9112 (t0) cc_final: 0.8817 (t0) REVERT: A 322 MET cc_start: 0.8999 (mmp) cc_final: 0.7958 (tpp) REVERT: A 326 PHE cc_start: 0.9655 (m-10) cc_final: 0.8862 (m-80) REVERT: A 333 LYS cc_start: 0.9193 (tmtt) cc_final: 0.8716 (tptp) REVERT: A 348 MET cc_start: 0.9018 (ptp) cc_final: 0.8694 (ptp) REVERT: A 361 GLN cc_start: 0.8936 (tp40) cc_final: 0.8426 (tp40) REVERT: A 376 VAL cc_start: 0.9079 (t) cc_final: 0.8640 (t) REVERT: A 403 ILE cc_start: 0.9385 (mm) cc_final: 0.8904 (mm) REVERT: A 405 LEU cc_start: 0.9000 (mt) cc_final: 0.8683 (mt) REVERT: A 407 ILE cc_start: 0.9303 (mt) cc_final: 0.8858 (mt) REVERT: A 413 SER cc_start: 0.9360 (m) cc_final: 0.9160 (m) REVERT: A 428 THR cc_start: 0.9607 (m) cc_final: 0.9296 (m) REVERT: A 447 ASN cc_start: 0.8681 (m110) cc_final: 0.8475 (m-40) REVERT: A 456 LYS cc_start: 0.9113 (mtmt) cc_final: 0.8820 (ptpt) REVERT: A 501 GLN cc_start: 0.9411 (tt0) cc_final: 0.8642 (tm-30) REVERT: A 505 GLU cc_start: 0.8915 (mt-10) cc_final: 0.7939 (mt-10) REVERT: A 550 MET cc_start: 0.8104 (mtm) cc_final: 0.7710 (mtm) REVERT: A 606 TYR cc_start: 0.7730 (m-80) cc_final: 0.7394 (m-80) REVERT: A 611 THR cc_start: 0.9039 (p) cc_final: 0.8351 (t) REVERT: A 615 MET cc_start: 0.9212 (mmp) cc_final: 0.8764 (mmp) REVERT: B 51 LEU cc_start: 0.9396 (tp) cc_final: 0.9016 (tp) REVERT: B 55 LEU cc_start: 0.9785 (mt) cc_final: 0.9582 (mt) REVERT: B 71 LEU cc_start: 0.9476 (mm) cc_final: 0.9218 (mm) REVERT: B 95 MET cc_start: 0.9124 (tpp) cc_final: 0.8412 (tpp) REVERT: B 116 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8159 (mt-10) REVERT: B 119 GLU cc_start: 0.9240 (mp0) cc_final: 0.8972 (mp0) REVERT: B 139 GLU cc_start: 0.9326 (mm-30) cc_final: 0.9116 (mm-30) REVERT: B 149 TYR cc_start: 0.9214 (t80) cc_final: 0.8758 (t80) REVERT: B 172 LEU cc_start: 0.9292 (mp) cc_final: 0.8962 (mp) REVERT: B 173 LEU cc_start: 0.9674 (mt) cc_final: 0.9319 (mt) REVERT: B 191 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8694 (mm-40) REVERT: B 211 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8264 (mm-30) REVERT: B 214 LYS cc_start: 0.8152 (mmtm) cc_final: 0.7930 (mmtm) REVERT: B 223 VAL cc_start: 0.9427 (m) cc_final: 0.9142 (m) REVERT: B 227 MET cc_start: 0.8940 (mtt) cc_final: 0.8567 (mtt) REVERT: B 250 TYR cc_start: 0.9146 (m-80) cc_final: 0.8899 (m-80) REVERT: B 257 ASP cc_start: 0.8797 (m-30) cc_final: 0.8394 (m-30) REVERT: B 261 PHE cc_start: 0.9390 (t80) cc_final: 0.9074 (t80) REVERT: B 263 ASP cc_start: 0.9147 (m-30) cc_final: 0.8720 (m-30) REVERT: B 266 LYS cc_start: 0.9453 (mtpp) cc_final: 0.9252 (mtmm) REVERT: B 286 ASP cc_start: 0.8529 (m-30) cc_final: 0.7724 (m-30) REVERT: B 321 GLU cc_start: 0.8790 (pp20) cc_final: 0.8535 (pp20) REVERT: B 362 ASP cc_start: 0.8566 (m-30) cc_final: 0.7584 (m-30) REVERT: B 370 ASN cc_start: 0.9446 (m-40) cc_final: 0.8869 (m-40) REVERT: B 379 SER cc_start: 0.9238 (t) cc_final: 0.8719 (t) REVERT: B 387 GLN cc_start: 0.9151 (mt0) cc_final: 0.8927 (mt0) REVERT: B 390 GLN cc_start: 0.9180 (mt0) cc_final: 0.8830 (mm110) REVERT: B 393 SER cc_start: 0.9601 (t) cc_final: 0.9359 (p) REVERT: B 398 ASP cc_start: 0.8509 (t70) cc_final: 0.8288 (t70) REVERT: B 402 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8819 (mm-30) REVERT: B 403 ILE cc_start: 0.9553 (mp) cc_final: 0.9228 (tp) REVERT: B 406 ASP cc_start: 0.8060 (m-30) cc_final: 0.7623 (m-30) REVERT: B 410 ASN cc_start: 0.8956 (m110) cc_final: 0.8689 (m110) REVERT: B 413 SER cc_start: 0.9611 (m) cc_final: 0.9287 (t) REVERT: B 415 ASN cc_start: 0.9662 (t0) cc_final: 0.9171 (t0) REVERT: B 443 THR cc_start: 0.9403 (m) cc_final: 0.9152 (t) REVERT: B 447 ASN cc_start: 0.8616 (m-40) cc_final: 0.7288 (m-40) REVERT: B 493 MET cc_start: 0.9533 (tmm) cc_final: 0.9285 (tmm) REVERT: B 499 SER cc_start: 0.9894 (t) cc_final: 0.9644 (p) REVERT: B 505 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8473 (mt-10) REVERT: B 516 GLN cc_start: 0.9007 (tp-100) cc_final: 0.8769 (tp-100) REVERT: B 550 MET cc_start: 0.8106 (mtt) cc_final: 0.7354 (mtm) REVERT: B 574 TYR cc_start: 0.8497 (m-80) cc_final: 0.8137 (m-80) REVERT: B 586 TYR cc_start: 0.9323 (m-80) cc_final: 0.8918 (m-80) REVERT: B 604 ARG cc_start: 0.9373 (mmm-85) cc_final: 0.9121 (mmp80) REVERT: B 610 LYS cc_start: 0.9333 (tttm) cc_final: 0.9047 (tttm) REVERT: B 615 MET cc_start: 0.9256 (mmp) cc_final: 0.8961 (mmp) REVERT: B 627 LYS cc_start: 0.9404 (tttp) cc_final: 0.8820 (tttp) REVERT: B 628 GLU cc_start: 0.8541 (mm-30) cc_final: 0.7037 (mm-30) REVERT: B 640 MET cc_start: 0.9577 (tpp) cc_final: 0.8837 (tpp) REVERT: B 648 ILE cc_start: 0.9402 (mm) cc_final: 0.9163 (mm) REVERT: B 667 LEU cc_start: 0.9605 (tp) cc_final: 0.9224 (tp) REVERT: B 682 ILE cc_start: 0.9637 (mt) cc_final: 0.9300 (mt) REVERT: C 233 ASN cc_start: 0.9330 (m110) cc_final: 0.9081 (m110) REVERT: D 79 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8722 (pt0) REVERT: D 137 MET cc_start: 0.7015 (mtm) cc_final: 0.6271 (mmp) REVERT: D 149 ASP cc_start: 0.9019 (m-30) cc_final: 0.8742 (m-30) REVERT: D 151 ILE cc_start: 0.6636 (mm) cc_final: 0.6128 (mm) REVERT: D 185 MET cc_start: 0.4302 (mmp) cc_final: 0.3559 (tpp) REVERT: D 189 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: D 211 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8559 (tm-30) REVERT: D 235 LEU cc_start: 0.8990 (mt) cc_final: 0.8514 (pp) REVERT: D 263 ASN cc_start: 0.8745 (m-40) cc_final: 0.8426 (m-40) outliers start: 5 outliers final: 0 residues processed: 730 average time/residue: 0.1376 time to fit residues: 149.2035 Evaluate side-chains 634 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 633 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 7.9990 chunk 157 optimal weight: 9.9990 chunk 168 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 185 optimal weight: 7.9990 chunk 191 optimal weight: 20.0000 chunk 159 optimal weight: 20.0000 chunk 182 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 44 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 675 HIS ** 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 387 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN C 28 GLN C 249 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 119 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.126167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.089010 restraints weight = 41938.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.092360 restraints weight = 22097.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.094504 restraints weight = 13816.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.095977 restraints weight = 9725.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096980 restraints weight = 7462.197| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.6438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 16386 Z= 0.378 Angle : 0.778 12.299 22134 Z= 0.412 Chirality : 0.047 0.218 2360 Planarity : 0.005 0.078 2818 Dihedral : 11.357 176.976 2242 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.17 % Allowed : 2.56 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.18), residues: 1932 helix: 0.82 (0.15), residues: 1129 sheet: -0.27 (0.41), residues: 136 loop : -0.05 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 446 TYR 0.029 0.002 TYR D 130 PHE 0.033 0.003 PHE A 254 TRP 0.020 0.003 TRP D 124 HIS 0.008 0.002 HIS A 551 Details of bonding type rmsd covalent geometry : bond 0.00788 (16386) covalent geometry : angle 0.77786 (22134) hydrogen bonds : bond 0.04562 ( 871) hydrogen bonds : angle 5.27772 ( 2571) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 661 time to evaluate : 0.677 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: A 10 ILE cc_start: 0.9617 (mm) cc_final: 0.9407 (mm) REVERT: A 14 ASN cc_start: 0.9391 (m-40) cc_final: 0.9077 (m110) REVERT: A 65 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8665 (mp0) REVERT: A 95 MET cc_start: 0.9217 (mmm) cc_final: 0.8949 (tpp) REVERT: A 99 LYS cc_start: 0.9495 (mmtp) cc_final: 0.9177 (mmtp) REVERT: A 119 GLU cc_start: 0.9076 (mp0) cc_final: 0.8778 (mp0) REVERT: A 120 ASP cc_start: 0.8969 (m-30) cc_final: 0.8651 (m-30) REVERT: A 144 MET cc_start: 0.9065 (mtm) cc_final: 0.8767 (mtm) REVERT: A 147 GLN cc_start: 0.9094 (mt0) cc_final: 0.8471 (mt0) REVERT: A 166 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8598 (mm-30) REVERT: A 172 LEU cc_start: 0.9727 (mp) cc_final: 0.9374 (mp) REVERT: A 227 MET cc_start: 0.9350 (mtp) cc_final: 0.8964 (mtp) REVERT: A 236 TYR cc_start: 0.9330 (t80) cc_final: 0.8750 (t80) REVERT: A 317 MET cc_start: 0.8938 (ptm) cc_final: 0.8543 (ptm) REVERT: A 322 MET cc_start: 0.9086 (mmp) cc_final: 0.8615 (tpp) REVERT: A 333 LYS cc_start: 0.9154 (tmtt) cc_final: 0.8758 (tptp) REVERT: A 361 GLN cc_start: 0.9010 (tp40) cc_final: 0.8788 (tp-100) REVERT: A 381 LEU cc_start: 0.9333 (tp) cc_final: 0.9130 (tp) REVERT: A 402 GLU cc_start: 0.8849 (tp30) cc_final: 0.8581 (tp30) REVERT: A 403 ILE cc_start: 0.9505 (mm) cc_final: 0.9022 (mm) REVERT: A 407 ILE cc_start: 0.9301 (mt) cc_final: 0.8803 (mt) REVERT: A 458 MET cc_start: 0.9200 (mmp) cc_final: 0.8570 (mmp) REVERT: A 501 GLN cc_start: 0.9368 (tt0) cc_final: 0.9151 (tt0) REVERT: A 505 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8223 (mt-10) REVERT: A 604 ARG cc_start: 0.8894 (mmp80) cc_final: 0.8672 (mmp80) REVERT: A 615 MET cc_start: 0.9151 (mmp) cc_final: 0.8756 (mmp) REVERT: A 640 MET cc_start: 0.9456 (tpp) cc_final: 0.9163 (tpp) REVERT: B 51 LEU cc_start: 0.9499 (tp) cc_final: 0.9170 (tp) REVERT: B 55 LEU cc_start: 0.9828 (mt) cc_final: 0.9581 (mt) REVERT: B 67 GLU cc_start: 0.9311 (tm-30) cc_final: 0.8948 (tm-30) REVERT: B 71 LEU cc_start: 0.9530 (mm) cc_final: 0.9231 (mm) REVERT: B 95 MET cc_start: 0.9224 (tpp) cc_final: 0.8934 (tpp) REVERT: B 115 LEU cc_start: 0.9594 (mp) cc_final: 0.9376 (mp) REVERT: B 116 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8664 (mt-10) REVERT: B 119 GLU cc_start: 0.9363 (mp0) cc_final: 0.8975 (mp0) REVERT: B 147 GLN cc_start: 0.9373 (mt0) cc_final: 0.9055 (mt0) REVERT: B 149 TYR cc_start: 0.9431 (t80) cc_final: 0.8885 (t80) REVERT: B 172 LEU cc_start: 0.9333 (mp) cc_final: 0.9077 (mp) REVERT: B 184 ARG cc_start: 0.9212 (mmm-85) cc_final: 0.8999 (tpp80) REVERT: B 211 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8332 (mm-30) REVERT: B 227 MET cc_start: 0.8995 (mtt) cc_final: 0.8763 (mtt) REVERT: B 235 ARG cc_start: 0.9182 (tpp80) cc_final: 0.8832 (mtt-85) REVERT: B 250 TYR cc_start: 0.9121 (m-80) cc_final: 0.8802 (m-80) REVERT: B 258 ILE cc_start: 0.9532 (tp) cc_final: 0.9249 (tp) REVERT: B 263 ASP cc_start: 0.9218 (m-30) cc_final: 0.8786 (m-30) REVERT: B 266 LYS cc_start: 0.9500 (mtpp) cc_final: 0.9124 (mtmm) REVERT: B 282 VAL cc_start: 0.9782 (t) cc_final: 0.9481 (m) REVERT: B 286 ASP cc_start: 0.8560 (m-30) cc_final: 0.8254 (m-30) REVERT: B 319 MET cc_start: 0.9028 (tpp) cc_final: 0.8822 (tpp) REVERT: B 321 GLU cc_start: 0.8928 (pp20) cc_final: 0.8405 (pp20) REVERT: B 322 MET cc_start: 0.9418 (tpt) cc_final: 0.8946 (mmm) REVERT: B 362 ASP cc_start: 0.8680 (m-30) cc_final: 0.7932 (m-30) REVERT: B 370 ASN cc_start: 0.9590 (m-40) cc_final: 0.9200 (m110) REVERT: B 392 SER cc_start: 0.9410 (m) cc_final: 0.8987 (t) REVERT: B 393 SER cc_start: 0.9661 (t) cc_final: 0.9350 (p) REVERT: B 398 ASP cc_start: 0.8636 (t70) cc_final: 0.8422 (t70) REVERT: B 406 ASP cc_start: 0.8071 (m-30) cc_final: 0.7862 (m-30) REVERT: B 407 ILE cc_start: 0.9506 (mt) cc_final: 0.9284 (mt) REVERT: B 410 ASN cc_start: 0.9086 (m110) cc_final: 0.8727 (m110) REVERT: B 413 SER cc_start: 0.9595 (m) cc_final: 0.9252 (t) REVERT: B 415 ASN cc_start: 0.9631 (t0) cc_final: 0.9036 (t0) REVERT: B 493 MET cc_start: 0.9500 (tmm) cc_final: 0.9257 (tmm) REVERT: B 505 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8470 (mt-10) REVERT: B 610 LYS cc_start: 0.9074 (tttm) cc_final: 0.8804 (ttpp) REVERT: B 615 MET cc_start: 0.9175 (mmp) cc_final: 0.8788 (mmp) REVERT: B 627 LYS cc_start: 0.9409 (tttp) cc_final: 0.8874 (tttp) REVERT: B 628 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7269 (mm-30) REVERT: B 640 MET cc_start: 0.9461 (tpp) cc_final: 0.9096 (tpp) REVERT: B 655 THR cc_start: 0.9603 (m) cc_final: 0.9373 (t) REVERT: B 667 LEU cc_start: 0.9646 (tp) cc_final: 0.9365 (tp) REVERT: B 668 ASN cc_start: 0.9517 (m-40) cc_final: 0.9232 (m110) REVERT: B 671 ASP cc_start: 0.8847 (m-30) cc_final: 0.8537 (m-30) REVERT: C 55 TYR cc_start: 0.8524 (t80) cc_final: 0.8112 (t80) REVERT: C 183 LYS cc_start: 0.5114 (mppt) cc_final: 0.4604 (ptmt) REVERT: D 74 MET cc_start: 0.5179 (tmm) cc_final: 0.4716 (tmm) REVERT: D 137 MET cc_start: 0.7787 (mtp) cc_final: 0.7451 (mmp) REVERT: D 151 ILE cc_start: 0.7325 (mm) cc_final: 0.7003 (mm) REVERT: D 230 ASP cc_start: 0.8962 (t0) cc_final: 0.8608 (t70) REVERT: D 233 ASN cc_start: 0.8726 (m110) cc_final: 0.8423 (m110) REVERT: D 243 THR cc_start: 0.8987 (p) cc_final: 0.8668 (p) outliers start: 3 outliers final: 0 residues processed: 662 average time/residue: 0.1386 time to fit residues: 136.4402 Evaluate side-chains 579 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 579 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 32 optimal weight: 0.0030 chunk 122 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 168 optimal weight: 10.0000 chunk 157 optimal weight: 20.0000 overall best weight: 0.7794 ------------------------------------------------------------------------------- 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 B 25 GLN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 249 GLN D 24 GLN D 28 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.134055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.094816 restraints weight = 40149.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.098506 restraints weight = 20952.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.100919 restraints weight = 13003.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.102494 restraints weight = 9085.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.103546 restraints weight = 6939.581| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 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 = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.6676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16386 Z= 0.139 Angle : 0.605 8.266 22134 Z= 0.324 Chirality : 0.043 0.202 2360 Planarity : 0.004 0.053 2818 Dihedral : 10.990 178.391 2242 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.17 % Allowed : 2.39 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.18), residues: 1932 helix: 1.00 (0.15), residues: 1130 sheet: 0.17 (0.43), residues: 112 loop : -0.03 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 184 TYR 0.031 0.002 TYR B 574 PHE 0.032 0.002 PHE D 227 TRP 0.014 0.001 TRP D 124 HIS 0.006 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00301 (16386) covalent geometry : angle 0.60537 (22134) hydrogen bonds : bond 0.04029 ( 871) hydrogen bonds : angle 4.96149 ( 2571) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 699 time to evaluate : 0.637 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: A 10 ILE cc_start: 0.9561 (mm) cc_final: 0.9303 (mm) REVERT: A 14 ASN cc_start: 0.9406 (m-40) cc_final: 0.9049 (m110) REVERT: A 27 ASP cc_start: 0.9232 (p0) cc_final: 0.8783 (p0) REVERT: A 31 GLU cc_start: 0.8996 (mp0) cc_final: 0.8672 (mp0) REVERT: A 95 MET cc_start: 0.9227 (mmm) cc_final: 0.8875 (tpp) REVERT: A 99 LYS cc_start: 0.9480 (mmtp) cc_final: 0.9172 (mmtp) REVERT: A 117 ARG cc_start: 0.9200 (mtp85) cc_final: 0.8546 (mtp85) REVERT: A 150 GLN cc_start: 0.9239 (tm-30) cc_final: 0.8733 (tm-30) REVERT: A 172 LEU cc_start: 0.9634 (mp) cc_final: 0.9297 (mp) REVERT: A 190 MET cc_start: 0.8954 (mtp) cc_final: 0.8633 (mtp) REVERT: A 227 MET cc_start: 0.9340 (mtp) cc_final: 0.8933 (mtp) REVERT: A 236 TYR cc_start: 0.9177 (t80) cc_final: 0.8093 (t80) REVERT: A 264 THR cc_start: 0.9315 (p) cc_final: 0.8920 (p) REVERT: A 290 GLU cc_start: 0.8859 (tp30) cc_final: 0.8527 (tp30) REVERT: A 333 LYS cc_start: 0.9217 (tmtt) cc_final: 0.8698 (tptp) REVERT: A 361 GLN cc_start: 0.8972 (tp40) cc_final: 0.8564 (tp-100) REVERT: A 395 THR cc_start: 0.9592 (p) cc_final: 0.9391 (p) REVERT: A 407 ILE cc_start: 0.9270 (mt) cc_final: 0.8881 (mt) REVERT: A 413 SER cc_start: 0.9413 (m) cc_final: 0.9134 (m) REVERT: A 501 GLN cc_start: 0.9427 (tt0) cc_final: 0.8838 (tm-30) REVERT: A 505 GLU cc_start: 0.8934 (mt-10) cc_final: 0.7847 (mt-10) REVERT: A 570 MET cc_start: 0.9251 (mtp) cc_final: 0.9034 (mtp) REVERT: A 604 ARG cc_start: 0.8937 (mmp80) cc_final: 0.8655 (mmp80) REVERT: A 606 TYR cc_start: 0.8035 (m-80) cc_final: 0.7564 (m-80) REVERT: A 611 THR cc_start: 0.9163 (p) cc_final: 0.8416 (t) REVERT: A 615 MET cc_start: 0.9257 (mmp) cc_final: 0.8978 (mmp) REVERT: A 630 TYR cc_start: 0.8095 (m-80) cc_final: 0.7501 (m-80) REVERT: A 640 MET cc_start: 0.9457 (tpp) cc_final: 0.9153 (tpp) REVERT: A 672 LEU cc_start: 0.9432 (mt) cc_final: 0.9219 (mt) REVERT: B 25 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8400 (pm20) REVERT: B 51 LEU cc_start: 0.9381 (tp) cc_final: 0.9021 (tp) REVERT: B 55 LEU cc_start: 0.9835 (mt) cc_final: 0.9594 (mt) REVERT: B 67 GLU cc_start: 0.9249 (tm-30) cc_final: 0.8850 (tm-30) REVERT: B 71 LEU cc_start: 0.9556 (mm) cc_final: 0.9353 (mm) REVERT: B 95 MET cc_start: 0.8850 (tpp) cc_final: 0.8108 (tpp) REVERT: B 98 PHE cc_start: 0.9559 (t80) cc_final: 0.9183 (t80) REVERT: B 119 GLU cc_start: 0.9266 (mp0) cc_final: 0.8899 (mp0) REVERT: B 149 TYR cc_start: 0.9357 (t80) cc_final: 0.8750 (t80) REVERT: B 172 LEU cc_start: 0.9306 (mp) cc_final: 0.9042 (mp) REVERT: B 173 LEU cc_start: 0.9623 (mt) cc_final: 0.9370 (mt) REVERT: B 174 GLU cc_start: 0.7699 (tp30) cc_final: 0.7399 (tp30) REVERT: B 184 ARG cc_start: 0.9227 (mmm-85) cc_final: 0.8995 (tpp80) REVERT: B 187 ASP cc_start: 0.9261 (t0) cc_final: 0.9060 (t0) REVERT: B 211 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8271 (mm-30) REVERT: B 223 VAL cc_start: 0.9536 (m) cc_final: 0.9299 (m) REVERT: B 235 ARG cc_start: 0.9216 (tpp80) cc_final: 0.8863 (mtt-85) REVERT: B 257 ASP cc_start: 0.8919 (m-30) cc_final: 0.8644 (m-30) REVERT: B 286 ASP cc_start: 0.8468 (m-30) cc_final: 0.7540 (m-30) REVERT: B 319 MET cc_start: 0.8908 (tpp) cc_final: 0.8558 (tpp) REVERT: B 321 GLU cc_start: 0.8922 (pp20) cc_final: 0.8301 (pp20) REVERT: B 322 MET cc_start: 0.9387 (tpt) cc_final: 0.8924 (mmm) REVERT: B 362 ASP cc_start: 0.8683 (m-30) cc_final: 0.7740 (m-30) REVERT: B 386 LEU cc_start: 0.9351 (mt) cc_final: 0.8952 (mt) REVERT: B 393 SER cc_start: 0.9606 (t) cc_final: 0.9362 (p) REVERT: B 398 ASP cc_start: 0.8578 (t70) cc_final: 0.8369 (t70) REVERT: B 403 ILE cc_start: 0.9507 (mp) cc_final: 0.9165 (tp) REVERT: B 406 ASP cc_start: 0.8128 (m-30) cc_final: 0.7728 (m-30) REVERT: B 413 SER cc_start: 0.9584 (m) cc_final: 0.9303 (t) REVERT: B 415 ASN cc_start: 0.9625 (t0) cc_final: 0.8625 (t0) REVERT: B 418 ASN cc_start: 0.9298 (m-40) cc_final: 0.8876 (m-40) REVERT: B 423 LYS cc_start: 0.8805 (mmmt) cc_final: 0.7838 (mmmt) REVERT: B 460 SER cc_start: 0.9497 (t) cc_final: 0.8970 (t) REVERT: B 467 ASN cc_start: 0.9017 (t0) cc_final: 0.8736 (t0) REVERT: B 493 MET cc_start: 0.9522 (tmm) cc_final: 0.9216 (tmm) REVERT: B 505 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8484 (mt-10) REVERT: B 550 MET cc_start: 0.7672 (mtt) cc_final: 0.6198 (mtt) REVERT: B 610 LYS cc_start: 0.9208 (tttm) cc_final: 0.8972 (ttpp) REVERT: B 615 MET cc_start: 0.9168 (mmp) cc_final: 0.8921 (mmp) REVERT: B 627 LYS cc_start: 0.9409 (tttp) cc_final: 0.8948 (tttp) REVERT: B 628 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7526 (mm-30) REVERT: B 640 MET cc_start: 0.9509 (tpp) cc_final: 0.9028 (tpp) REVERT: B 650 GLN cc_start: 0.8504 (mt0) cc_final: 0.7743 (mm-40) REVERT: B 655 THR cc_start: 0.9680 (m) cc_final: 0.9380 (t) REVERT: B 667 LEU cc_start: 0.9529 (tp) cc_final: 0.9235 (tp) REVERT: B 668 ASN cc_start: 0.9394 (m-40) cc_final: 0.9149 (m110) REVERT: B 671 ASP cc_start: 0.8748 (m-30) cc_final: 0.8535 (m-30) REVERT: C 55 TYR cc_start: 0.8262 (t80) cc_final: 0.7650 (t80) REVERT: C 108 ILE cc_start: 0.8775 (pt) cc_final: 0.8563 (pt) REVERT: C 110 MET cc_start: 0.7983 (mtm) cc_final: 0.7727 (mtm) REVERT: C 183 LYS cc_start: 0.5130 (mppt) cc_final: 0.4638 (ptmt) REVERT: C 198 GLU cc_start: 0.9346 (mm-30) cc_final: 0.9106 (mm-30) REVERT: C 233 ASN cc_start: 0.9376 (m110) cc_final: 0.9147 (m110) REVERT: D 117 THR cc_start: 0.7903 (t) cc_final: 0.7632 (t) REVERT: D 137 MET cc_start: 0.8562 (mtp) cc_final: 0.8262 (mmp) REVERT: D 151 ILE cc_start: 0.7092 (mm) cc_final: 0.6766 (mm) REVERT: D 194 ILE cc_start: 0.9239 (mt) cc_final: 0.8916 (mt) outliers start: 3 outliers final: 1 residues processed: 702 average time/residue: 0.1364 time to fit residues: 142.2061 Evaluate side-chains 612 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 610 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 52 optimal weight: 0.0670 chunk 28 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 136 optimal weight: 20.0000 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 44 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** B 418 ASN B 501 GLN B 645 GLN C 249 GLN C 263 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 119 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.133030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.094130 restraints weight = 40192.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.097740 restraints weight = 21175.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.100100 restraints weight = 13114.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.101710 restraints weight = 9185.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.102775 restraints weight = 6996.528| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.6961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16386 Z= 0.167 Angle : 0.610 7.479 22134 Z= 0.328 Chirality : 0.043 0.199 2360 Planarity : 0.004 0.051 2818 Dihedral : 10.784 179.978 2242 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.12 % Allowed : 2.16 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.19), residues: 1932 helix: 1.08 (0.15), residues: 1111 sheet: 0.16 (0.45), residues: 114 loop : 0.04 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 446 TYR 0.049 0.002 TYR D 130 PHE 0.026 0.002 PHE D 168 TRP 0.009 0.001 TRP D 124 HIS 0.004 0.001 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00366 (16386) covalent geometry : angle 0.60973 (22134) hydrogen bonds : bond 0.04017 ( 871) hydrogen bonds : angle 4.99484 ( 2571) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 669 time to evaluate : 0.767 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 10 ILE cc_start: 0.9583 (mm) cc_final: 0.9325 (mm) REVERT: A 14 ASN cc_start: 0.9491 (m-40) cc_final: 0.9139 (m110) REVERT: A 31 GLU cc_start: 0.8971 (mp0) cc_final: 0.8683 (mp0) REVERT: A 95 MET cc_start: 0.9247 (mmm) cc_final: 0.8859 (tpp) REVERT: A 99 LYS cc_start: 0.9507 (mmtp) cc_final: 0.9207 (mmtp) REVERT: A 172 LEU cc_start: 0.9654 (mp) cc_final: 0.9245 (mp) REVERT: A 227 MET cc_start: 0.9384 (mtp) cc_final: 0.8932 (mtp) REVERT: A 290 GLU cc_start: 0.8864 (tp30) cc_final: 0.8469 (tp30) REVERT: A 317 MET cc_start: 0.8699 (ptm) cc_final: 0.7928 (ptm) REVERT: A 318 ASP cc_start: 0.9108 (t0) cc_final: 0.8044 (t0) REVERT: A 319 MET cc_start: 0.8820 (ttp) cc_final: 0.8533 (ttp) REVERT: A 333 LYS cc_start: 0.9190 (tmtt) cc_final: 0.8742 (tptp) REVERT: A 361 GLN cc_start: 0.9046 (tp40) cc_final: 0.8714 (tp-100) REVERT: A 402 GLU cc_start: 0.8767 (tp30) cc_final: 0.8530 (tp30) REVERT: A 403 ILE cc_start: 0.9472 (mm) cc_final: 0.8909 (mm) REVERT: A 407 ILE cc_start: 0.9226 (mt) cc_final: 0.8830 (mt) REVERT: A 458 MET cc_start: 0.9053 (mmp) cc_final: 0.8524 (mmp) REVERT: A 468 LEU cc_start: 0.9582 (tp) cc_final: 0.9350 (tp) REVERT: A 472 LEU cc_start: 0.9456 (mt) cc_final: 0.9221 (mp) REVERT: A 501 GLN cc_start: 0.9427 (tt0) cc_final: 0.8838 (tm-30) REVERT: A 505 GLU cc_start: 0.8918 (mt-10) cc_final: 0.7814 (mt-10) REVERT: A 515 ASP cc_start: 0.8811 (m-30) cc_final: 0.8447 (m-30) REVERT: A 588 GLN cc_start: 0.9089 (mm-40) cc_final: 0.8706 (mm-40) REVERT: A 604 ARG cc_start: 0.8919 (mmp80) cc_final: 0.8641 (mmp80) REVERT: A 606 TYR cc_start: 0.8040 (m-80) cc_final: 0.7633 (m-80) REVERT: A 611 THR cc_start: 0.9128 (p) cc_final: 0.8425 (t) REVERT: A 615 MET cc_start: 0.9254 (mmp) cc_final: 0.8853 (mmp) REVERT: A 640 MET cc_start: 0.9463 (tpp) cc_final: 0.9256 (tpp) REVERT: B 18 ILE cc_start: 0.9656 (pt) cc_final: 0.9396 (pt) REVERT: B 51 LEU cc_start: 0.9391 (tp) cc_final: 0.9033 (tp) REVERT: B 55 LEU cc_start: 0.9836 (mt) cc_final: 0.9610 (mt) REVERT: B 65 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7850 (tm-30) REVERT: B 67 GLU cc_start: 0.9322 (tm-30) cc_final: 0.8962 (tm-30) REVERT: B 71 LEU cc_start: 0.9556 (mm) cc_final: 0.9294 (mt) REVERT: B 95 MET cc_start: 0.8935 (tpp) cc_final: 0.8692 (tpp) REVERT: B 119 GLU cc_start: 0.9290 (mp0) cc_final: 0.8905 (mp0) REVERT: B 149 TYR cc_start: 0.9421 (t80) cc_final: 0.8771 (t80) REVERT: B 174 GLU cc_start: 0.7838 (tp30) cc_final: 0.7439 (tp30) REVERT: B 184 ARG cc_start: 0.9310 (mmm-85) cc_final: 0.9013 (tpp80) REVERT: B 187 ASP cc_start: 0.9253 (t0) cc_final: 0.9051 (t0) REVERT: B 211 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8388 (mm-30) REVERT: B 235 ARG cc_start: 0.9208 (tpp80) cc_final: 0.8783 (mtt-85) REVERT: B 257 ASP cc_start: 0.8962 (m-30) cc_final: 0.8701 (m-30) REVERT: B 258 ILE cc_start: 0.9468 (tp) cc_final: 0.9212 (tp) REVERT: B 263 ASP cc_start: 0.8997 (m-30) cc_final: 0.8635 (m-30) REVERT: B 286 ASP cc_start: 0.8537 (m-30) cc_final: 0.7573 (m-30) REVERT: B 290 GLU cc_start: 0.9174 (tp30) cc_final: 0.8943 (tp30) REVERT: B 308 LYS cc_start: 0.9618 (mtpp) cc_final: 0.9361 (mtpp) REVERT: B 319 MET cc_start: 0.8929 (tpp) cc_final: 0.8647 (tpp) REVERT: B 321 GLU cc_start: 0.8913 (pp20) cc_final: 0.8281 (pp20) REVERT: B 322 MET cc_start: 0.9418 (tpt) cc_final: 0.8959 (mmm) REVERT: B 362 ASP cc_start: 0.8657 (m-30) cc_final: 0.7645 (m-30) REVERT: B 370 ASN cc_start: 0.9635 (m110) cc_final: 0.9184 (m-40) REVERT: B 373 ILE cc_start: 0.9400 (mt) cc_final: 0.9012 (tp) REVERT: B 386 LEU cc_start: 0.9524 (mt) cc_final: 0.9288 (mt) REVERT: B 390 GLN cc_start: 0.8896 (mm110) cc_final: 0.8565 (mm-40) REVERT: B 393 SER cc_start: 0.9615 (t) cc_final: 0.9354 (p) REVERT: B 398 ASP cc_start: 0.8589 (t70) cc_final: 0.8345 (t70) REVERT: B 403 ILE cc_start: 0.9526 (mp) cc_final: 0.9203 (tp) REVERT: B 413 SER cc_start: 0.9582 (m) cc_final: 0.9222 (t) REVERT: B 415 ASN cc_start: 0.9685 (t0) cc_final: 0.8997 (t0) REVERT: B 435 SER cc_start: 0.9653 (p) cc_final: 0.9426 (t) REVERT: B 467 ASN cc_start: 0.9143 (t0) cc_final: 0.8871 (t0) REVERT: B 493 MET cc_start: 0.9501 (tmm) cc_final: 0.9164 (tmm) REVERT: B 610 LYS cc_start: 0.9237 (tttm) cc_final: 0.8955 (tttm) REVERT: B 615 MET cc_start: 0.9244 (mmp) cc_final: 0.8922 (mmp) REVERT: B 618 LEU cc_start: 0.9555 (tp) cc_final: 0.8879 (mt) REVERT: B 627 LYS cc_start: 0.9377 (tttp) cc_final: 0.8871 (tttp) REVERT: B 628 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7470 (mm-30) REVERT: B 640 MET cc_start: 0.9479 (tpp) cc_final: 0.9057 (tpp) REVERT: B 655 THR cc_start: 0.9703 (m) cc_final: 0.9422 (t) REVERT: B 667 LEU cc_start: 0.9622 (tp) cc_final: 0.9350 (tp) REVERT: B 668 ASN cc_start: 0.9426 (m-40) cc_final: 0.9171 (m110) REVERT: B 671 ASP cc_start: 0.8745 (m-30) cc_final: 0.8446 (m-30) REVERT: C 21 PHE cc_start: 0.7102 (m-80) cc_final: 0.6885 (m-80) REVERT: C 55 TYR cc_start: 0.8251 (t80) cc_final: 0.7777 (t80) REVERT: C 96 MET cc_start: 0.7890 (mmm) cc_final: 0.6918 (mmm) REVERT: C 110 MET cc_start: 0.7912 (mtm) cc_final: 0.7683 (mtm) REVERT: C 183 LYS cc_start: 0.5298 (mppt) cc_final: 0.4807 (ptmt) REVERT: C 233 ASN cc_start: 0.9364 (m110) cc_final: 0.9125 (m110) REVERT: D 47 LEU cc_start: 0.7856 (mt) cc_final: 0.7232 (mt) REVERT: D 74 MET cc_start: 0.4901 (tmm) cc_final: 0.4164 (tmm) REVERT: D 137 MET cc_start: 0.8541 (mtp) cc_final: 0.8184 (mmp) REVERT: D 172 PHE cc_start: 0.9094 (m-80) cc_final: 0.8888 (m-80) REVERT: D 174 TYR cc_start: 0.8545 (t80) cc_final: 0.8128 (t80) REVERT: D 194 ILE cc_start: 0.8914 (mt) cc_final: 0.8703 (mt) outliers start: 2 outliers final: 1 residues processed: 671 average time/residue: 0.1352 time to fit residues: 135.3429 Evaluate side-chains 589 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 588 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 186 optimal weight: 9.9990 chunk 140 optimal weight: 8.9990 chunk 115 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 447 ASN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN B 147 GLN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN C 249 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.128760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.090431 restraints weight = 40789.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.093812 restraints weight = 21434.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.096064 restraints weight = 13470.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.097504 restraints weight = 9529.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.098599 restraints weight = 7389.575| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.7275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 16386 Z= 0.258 Angle : 0.686 8.621 22134 Z= 0.365 Chirality : 0.046 0.233 2360 Planarity : 0.004 0.049 2818 Dihedral : 10.804 173.994 2242 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.19), residues: 1932 helix: 0.82 (0.15), residues: 1136 sheet: -0.81 (0.38), residues: 152 loop : 0.12 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 446 TYR 0.056 0.002 TYR D 130 PHE 0.022 0.002 PHE D 259 TRP 0.012 0.002 TRP D 124 HIS 0.005 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00551 (16386) covalent geometry : angle 0.68553 (22134) hydrogen bonds : bond 0.04205 ( 871) hydrogen bonds : angle 5.12402 ( 2571) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 663 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.9629 (mm) cc_final: 0.9381 (mm) REVERT: A 14 ASN cc_start: 0.9464 (m-40) cc_final: 0.9191 (m110) REVERT: A 27 ASP cc_start: 0.9275 (p0) cc_final: 0.8672 (p0) REVERT: A 31 GLU cc_start: 0.8989 (mp0) cc_final: 0.8457 (mp0) REVERT: A 95 MET cc_start: 0.9207 (mmm) cc_final: 0.8840 (tpp) REVERT: A 99 LYS cc_start: 0.9537 (mmtp) cc_final: 0.9215 (mmtp) REVERT: A 119 GLU cc_start: 0.9011 (mp0) cc_final: 0.8610 (mp0) REVERT: A 120 ASP cc_start: 0.8909 (m-30) cc_final: 0.8704 (m-30) REVERT: A 122 ILE cc_start: 0.9684 (mp) cc_final: 0.9343 (mp) REVERT: A 144 MET cc_start: 0.9028 (mtm) cc_final: 0.8418 (mtm) REVERT: A 147 GLN cc_start: 0.9048 (mt0) cc_final: 0.8484 (mt0) REVERT: A 172 LEU cc_start: 0.9674 (mp) cc_final: 0.9237 (mp) REVERT: A 190 MET cc_start: 0.9059 (mtp) cc_final: 0.8785 (mtp) REVERT: A 227 MET cc_start: 0.9333 (mtp) cc_final: 0.8924 (mtp) REVERT: A 236 TYR cc_start: 0.9326 (t80) cc_final: 0.8250 (t80) REVERT: A 291 LEU cc_start: 0.9549 (mt) cc_final: 0.9270 (mt) REVERT: A 318 ASP cc_start: 0.8343 (t0) cc_final: 0.7764 (t0) REVERT: A 320 ASN cc_start: 0.8923 (t0) cc_final: 0.8572 (t0) REVERT: A 333 LYS cc_start: 0.9376 (tmtt) cc_final: 0.8942 (tptp) REVERT: A 361 GLN cc_start: 0.9034 (tp40) cc_final: 0.8696 (tp-100) REVERT: A 402 GLU cc_start: 0.8872 (tp30) cc_final: 0.8584 (tp30) REVERT: A 403 ILE cc_start: 0.9502 (mm) cc_final: 0.9017 (mm) REVERT: A 405 LEU cc_start: 0.8714 (mt) cc_final: 0.8361 (mt) REVERT: A 407 ILE cc_start: 0.9296 (mt) cc_final: 0.8841 (mt) REVERT: A 418 ASN cc_start: 0.9107 (m-40) cc_final: 0.8513 (m-40) REVERT: A 458 MET cc_start: 0.9118 (mmp) cc_final: 0.8573 (mmp) REVERT: A 505 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8299 (mt-10) REVERT: A 515 ASP cc_start: 0.8802 (m-30) cc_final: 0.8425 (m-30) REVERT: A 586 TYR cc_start: 0.9057 (m-80) cc_final: 0.8553 (m-80) REVERT: A 602 GLU cc_start: 0.7958 (pt0) cc_final: 0.6435 (pt0) REVERT: A 615 MET cc_start: 0.9191 (mmp) cc_final: 0.8784 (mmp) REVERT: A 664 THR cc_start: 0.9609 (p) cc_final: 0.9303 (p) REVERT: A 668 ASN cc_start: 0.9516 (m110) cc_final: 0.9243 (m-40) REVERT: B 51 LEU cc_start: 0.9433 (tp) cc_final: 0.9096 (tp) REVERT: B 55 LEU cc_start: 0.9837 (mt) cc_final: 0.9581 (mt) REVERT: B 67 GLU cc_start: 0.9369 (tm-30) cc_final: 0.9018 (tm-30) REVERT: B 82 LYS cc_start: 0.9514 (mmmm) cc_final: 0.9223 (mmtt) REVERT: B 95 MET cc_start: 0.9057 (tpp) cc_final: 0.8676 (tpp) REVERT: B 106 LEU cc_start: 0.9681 (tp) cc_final: 0.9221 (tp) REVERT: B 115 LEU cc_start: 0.9562 (mp) cc_final: 0.8959 (mp) REVERT: B 116 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8646 (mp0) REVERT: B 119 GLU cc_start: 0.9332 (mp0) cc_final: 0.8922 (mp0) REVERT: B 128 PHE cc_start: 0.9685 (t80) cc_final: 0.9417 (t80) REVERT: B 149 TYR cc_start: 0.9492 (t80) cc_final: 0.8850 (t80) REVERT: B 174 GLU cc_start: 0.8142 (tp30) cc_final: 0.7462 (tp30) REVERT: B 184 ARG cc_start: 0.9288 (mmm-85) cc_final: 0.9032 (tpp80) REVERT: B 211 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8312 (mm-30) REVERT: B 235 ARG cc_start: 0.9243 (tpp80) cc_final: 0.8810 (mtm-85) REVERT: B 257 ASP cc_start: 0.8949 (m-30) cc_final: 0.8633 (m-30) REVERT: B 258 ILE cc_start: 0.9512 (tp) cc_final: 0.9257 (tp) REVERT: B 263 ASP cc_start: 0.8843 (m-30) cc_final: 0.8627 (m-30) REVERT: B 286 ASP cc_start: 0.8563 (m-30) cc_final: 0.7582 (m-30) REVERT: B 316 GLU cc_start: 0.8996 (pt0) cc_final: 0.8773 (pt0) REVERT: B 319 MET cc_start: 0.8926 (tpp) cc_final: 0.8642 (tpp) REVERT: B 322 MET cc_start: 0.9420 (tpt) cc_final: 0.9131 (mmm) REVERT: B 362 ASP cc_start: 0.8697 (m-30) cc_final: 0.7579 (m-30) REVERT: B 373 ILE cc_start: 0.9490 (mt) cc_final: 0.9254 (tp) REVERT: B 398 ASP cc_start: 0.8629 (t70) cc_final: 0.8364 (t70) REVERT: B 403 ILE cc_start: 0.9556 (mp) cc_final: 0.9209 (tp) REVERT: B 413 SER cc_start: 0.9493 (m) cc_final: 0.9170 (t) REVERT: B 415 ASN cc_start: 0.9593 (t0) cc_final: 0.8852 (t0) REVERT: B 446 ARG cc_start: 0.8611 (mmm-85) cc_final: 0.8200 (mmm-85) REVERT: B 447 ASN cc_start: 0.7946 (t0) cc_final: 0.7706 (t0) REVERT: B 463 LEU cc_start: 0.9762 (tp) cc_final: 0.9530 (tp) REVERT: B 467 ASN cc_start: 0.9179 (t0) cc_final: 0.8903 (t0) REVERT: B 480 GLU cc_start: 0.8819 (mp0) cc_final: 0.8609 (mp0) REVERT: B 493 MET cc_start: 0.9535 (tmm) cc_final: 0.9153 (tmm) REVERT: B 505 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8449 (mt-10) REVERT: B 550 MET cc_start: 0.8183 (mtt) cc_final: 0.7729 (mtt) REVERT: B 610 LYS cc_start: 0.9181 (tttm) cc_final: 0.8920 (tttm) REVERT: B 615 MET cc_start: 0.9259 (mmp) cc_final: 0.8867 (mmp) REVERT: B 627 LYS cc_start: 0.9361 (tttp) cc_final: 0.8997 (ttpp) REVERT: B 628 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7426 (mm-30) REVERT: B 633 ASP cc_start: 0.8859 (t0) cc_final: 0.8471 (t0) REVERT: B 640 MET cc_start: 0.9371 (tpp) cc_final: 0.8983 (tpp) REVERT: B 667 LEU cc_start: 0.9572 (tp) cc_final: 0.9242 (tp) REVERT: B 668 ASN cc_start: 0.9493 (m-40) cc_final: 0.9166 (m110) REVERT: B 671 ASP cc_start: 0.8794 (m-30) cc_final: 0.8492 (m-30) REVERT: C 21 PHE cc_start: 0.7630 (m-80) cc_final: 0.7407 (m-80) REVERT: C 96 MET cc_start: 0.7960 (mmm) cc_final: 0.6937 (mmm) REVERT: C 110 MET cc_start: 0.7867 (mtm) cc_final: 0.7627 (mtm) REVERT: C 183 LYS cc_start: 0.5352 (mppt) cc_final: 0.4868 (ptmt) REVERT: D 74 MET cc_start: 0.5145 (tmm) cc_final: 0.4703 (tmm) REVERT: D 96 MET cc_start: -0.0910 (mmt) cc_final: -0.1304 (mmt) REVERT: D 117 THR cc_start: 0.8068 (t) cc_final: 0.7791 (t) REVERT: D 137 MET cc_start: 0.8666 (mtp) cc_final: 0.8106 (ptm) REVERT: D 151 ILE cc_start: 0.7106 (mm) cc_final: 0.6805 (mm) REVERT: D 172 PHE cc_start: 0.9352 (m-80) cc_final: 0.8932 (m-80) REVERT: D 174 TYR cc_start: 0.8611 (t80) cc_final: 0.8184 (t80) REVERT: D 211 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8770 (tm-30) outliers start: 0 outliers final: 0 residues processed: 663 average time/residue: 0.1308 time to fit residues: 129.5973 Evaluate side-chains 584 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 584 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 153 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 313 HIS ** 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 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.133016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.095070 restraints weight = 40848.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.098545 restraints weight = 21136.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.100908 restraints weight = 13084.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.102484 restraints weight = 9190.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.103539 restraints weight = 7005.642| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.7473 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= 0.164 Angle : 0.629 7.783 22134 Z= 0.336 Chirality : 0.045 0.220 2360 Planarity : 0.004 0.044 2818 Dihedral : 10.473 170.907 2242 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.06 % Allowed : 1.11 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.18), residues: 1932 helix: 0.89 (0.15), residues: 1136 sheet: -0.17 (0.43), residues: 110 loop : -0.01 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 446 TYR 0.047 0.002 TYR D 130 PHE 0.020 0.002 PHE B 156 TRP 0.013 0.001 TRP D 124 HIS 0.008 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00361 (16386) covalent geometry : angle 0.62886 (22134) hydrogen bonds : bond 0.04042 ( 871) hydrogen bonds : angle 5.01399 ( 2571) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 663 time to evaluate : 0.648 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 10 ILE cc_start: 0.9644 (mm) cc_final: 0.9335 (mm) REVERT: A 14 ASN cc_start: 0.9487 (m-40) cc_final: 0.9241 (m110) REVERT: A 27 ASP cc_start: 0.9222 (p0) cc_final: 0.8719 (p0) REVERT: A 31 GLU cc_start: 0.8949 (mp0) cc_final: 0.8563 (mp0) REVERT: A 95 MET cc_start: 0.9072 (mmm) cc_final: 0.8773 (tpp) REVERT: A 99 LYS cc_start: 0.9501 (mmtp) cc_final: 0.9105 (mmtp) REVERT: A 119 GLU cc_start: 0.8908 (mp0) cc_final: 0.8463 (mp0) REVERT: A 139 GLU cc_start: 0.9401 (mm-30) cc_final: 0.9152 (tp30) REVERT: A 144 MET cc_start: 0.8963 (mtm) cc_final: 0.8362 (mtm) REVERT: A 172 LEU cc_start: 0.9653 (mp) cc_final: 0.9284 (mp) REVERT: A 190 MET cc_start: 0.9018 (mtp) cc_final: 0.8718 (mtp) REVERT: A 227 MET cc_start: 0.9346 (mtp) cc_final: 0.8875 (mtp) REVERT: A 236 TYR cc_start: 0.9251 (t80) cc_final: 0.8137 (t80) REVERT: A 259 ASN cc_start: 0.9095 (m-40) cc_final: 0.8814 (m-40) REVERT: A 318 ASP cc_start: 0.8532 (t0) cc_final: 0.8095 (t0) REVERT: A 333 LYS cc_start: 0.9357 (tmtt) cc_final: 0.8951 (tptp) REVERT: A 348 MET cc_start: 0.9048 (ptp) cc_final: 0.8547 (ptp) REVERT: A 361 GLN cc_start: 0.8974 (tp40) cc_final: 0.8679 (tp-100) REVERT: A 376 VAL cc_start: 0.9060 (t) cc_final: 0.8803 (t) REVERT: A 403 ILE cc_start: 0.9486 (mm) cc_final: 0.9204 (mm) REVERT: A 405 LEU cc_start: 0.8817 (mt) cc_final: 0.8495 (mt) REVERT: A 407 ILE cc_start: 0.9256 (mt) cc_final: 0.8867 (mt) REVERT: A 413 SER cc_start: 0.9381 (m) cc_final: 0.9175 (m) REVERT: A 458 MET cc_start: 0.9079 (mmp) cc_final: 0.8570 (mmp) REVERT: A 501 GLN cc_start: 0.9416 (tt0) cc_final: 0.8837 (tm-30) REVERT: A 505 GLU cc_start: 0.8889 (mt-10) cc_final: 0.7799 (mt-10) REVERT: A 515 ASP cc_start: 0.8753 (m-30) cc_final: 0.8359 (m-30) REVERT: A 529 ASP cc_start: 0.8888 (m-30) cc_final: 0.8660 (m-30) REVERT: A 586 TYR cc_start: 0.8963 (m-80) cc_final: 0.8436 (m-80) REVERT: A 588 GLN cc_start: 0.9110 (mm-40) cc_final: 0.8882 (mm-40) REVERT: A 602 GLU cc_start: 0.7885 (pt0) cc_final: 0.6372 (pt0) REVERT: A 604 ARG cc_start: 0.8908 (tpp-160) cc_final: 0.8647 (mmp80) REVERT: A 615 MET cc_start: 0.9238 (mmp) cc_final: 0.8837 (mmp) REVERT: B 51 LEU cc_start: 0.9350 (tp) cc_final: 0.9000 (tp) REVERT: B 55 LEU cc_start: 0.9838 (mt) cc_final: 0.9565 (mt) REVERT: B 67 GLU cc_start: 0.9389 (tm-30) cc_final: 0.9082 (tm-30) REVERT: B 82 LYS cc_start: 0.9494 (mmmm) cc_final: 0.9178 (mmtt) REVERT: B 98 PHE cc_start: 0.9539 (t80) cc_final: 0.9188 (t80) REVERT: B 106 LEU cc_start: 0.9678 (tp) cc_final: 0.9407 (tp) REVERT: B 107 LYS cc_start: 0.9394 (mttp) cc_final: 0.9076 (mmmm) REVERT: B 115 LEU cc_start: 0.9574 (mp) cc_final: 0.9094 (mp) REVERT: B 116 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8713 (mp0) REVERT: B 119 GLU cc_start: 0.9307 (mp0) cc_final: 0.8921 (mp0) REVERT: B 128 PHE cc_start: 0.9667 (t80) cc_final: 0.9461 (t80) REVERT: B 147 GLN cc_start: 0.9119 (mt0) cc_final: 0.8659 (mt0) REVERT: B 149 TYR cc_start: 0.9453 (t80) cc_final: 0.8838 (t80) REVERT: B 163 ARG cc_start: 0.8601 (ttp80) cc_final: 0.8236 (ttp80) REVERT: B 174 GLU cc_start: 0.7856 (tp30) cc_final: 0.7515 (tp30) REVERT: B 187 ASP cc_start: 0.9350 (t0) cc_final: 0.9118 (t0) REVERT: B 211 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8332 (mm-30) REVERT: B 232 ASN cc_start: 0.8925 (m110) cc_final: 0.8225 (m110) REVERT: B 235 ARG cc_start: 0.9268 (tpp80) cc_final: 0.8893 (mtt-85) REVERT: B 257 ASP cc_start: 0.8927 (m-30) cc_final: 0.8630 (m-30) REVERT: B 263 ASP cc_start: 0.8764 (m-30) cc_final: 0.8526 (m-30) REVERT: B 286 ASP cc_start: 0.8559 (m-30) cc_final: 0.7604 (m-30) REVERT: B 290 GLU cc_start: 0.9176 (tp30) cc_final: 0.8933 (tp30) REVERT: B 312 GLN cc_start: 0.9037 (pm20) cc_final: 0.8834 (pm20) REVERT: B 319 MET cc_start: 0.8861 (tpp) cc_final: 0.8592 (tpp) REVERT: B 322 MET cc_start: 0.9480 (tpt) cc_final: 0.9166 (mmm) REVERT: B 362 ASP cc_start: 0.8668 (m-30) cc_final: 0.7606 (m-30) REVERT: B 373 ILE cc_start: 0.9446 (mt) cc_final: 0.9209 (tp) REVERT: B 390 GLN cc_start: 0.9014 (mm110) cc_final: 0.8711 (mm110) REVERT: B 393 SER cc_start: 0.9592 (t) cc_final: 0.9326 (p) REVERT: B 398 ASP cc_start: 0.8574 (t70) cc_final: 0.8292 (t70) REVERT: B 403 ILE cc_start: 0.9508 (mp) cc_final: 0.9287 (tp) REVERT: B 413 SER cc_start: 0.9559 (m) cc_final: 0.9223 (t) REVERT: B 415 ASN cc_start: 0.9613 (t0) cc_final: 0.9001 (t0) REVERT: B 425 ILE cc_start: 0.9254 (mt) cc_final: 0.8964 (mt) REVERT: B 446 ARG cc_start: 0.8471 (mmm-85) cc_final: 0.8232 (mmm-85) REVERT: B 467 ASN cc_start: 0.9184 (t0) cc_final: 0.8854 (t0) REVERT: B 493 MET cc_start: 0.9502 (tmm) cc_final: 0.9111 (tmm) REVERT: B 505 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8069 (mt-10) REVERT: B 550 MET cc_start: 0.8172 (mtt) cc_final: 0.7772 (mtt) REVERT: B 601 ILE cc_start: 0.9520 (mm) cc_final: 0.9145 (mm) REVERT: B 610 LYS cc_start: 0.9190 (tttm) cc_final: 0.8892 (tttm) REVERT: B 615 MET cc_start: 0.9260 (mmp) cc_final: 0.8856 (mmp) REVERT: B 618 LEU cc_start: 0.9601 (tp) cc_final: 0.9373 (mt) REVERT: B 627 LYS cc_start: 0.9423 (tttp) cc_final: 0.9097 (ttpt) REVERT: B 640 MET cc_start: 0.9395 (tpp) cc_final: 0.9032 (tpp) REVERT: B 667 LEU cc_start: 0.9593 (tp) cc_final: 0.9284 (tp) REVERT: B 668 ASN cc_start: 0.9448 (m-40) cc_final: 0.9156 (m110) REVERT: B 671 ASP cc_start: 0.8808 (m-30) cc_final: 0.8502 (m-30) REVERT: C 96 MET cc_start: 0.7947 (mmm) cc_final: 0.6936 (mmm) REVERT: C 110 MET cc_start: 0.7761 (mtm) cc_final: 0.7521 (mtm) REVERT: C 233 ASN cc_start: 0.9339 (m110) cc_final: 0.9107 (m110) REVERT: D 137 MET cc_start: 0.8757 (mtp) cc_final: 0.8243 (ptm) REVERT: D 151 ILE cc_start: 0.7129 (mm) cc_final: 0.6839 (mm) REVERT: D 172 PHE cc_start: 0.9245 (m-80) cc_final: 0.9043 (m-80) REVERT: D 174 TYR cc_start: 0.8511 (t80) cc_final: 0.8179 (t80) REVERT: D 185 MET cc_start: 0.5986 (mmp) cc_final: 0.5681 (mmp) REVERT: D 194 ILE cc_start: 0.8997 (mt) cc_final: 0.8756 (mt) REVERT: D 212 ILE cc_start: 0.8293 (pt) cc_final: 0.7706 (pt) outliers start: 1 outliers final: 0 residues processed: 664 average time/residue: 0.1349 time to fit residues: 133.4226 Evaluate side-chains 575 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 575 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 chunk 149 optimal weight: 20.0000 chunk 16 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 86 optimal weight: 0.3980 chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.132821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.095022 restraints weight = 40572.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.098489 restraints weight = 20966.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.100821 restraints weight = 13026.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.102373 restraints weight = 9173.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.103452 restraints weight = 7032.784| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.7654 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= 0.183 Angle : 0.644 9.319 22134 Z= 0.344 Chirality : 0.045 0.225 2360 Planarity : 0.004 0.045 2818 Dihedral : 10.415 170.229 2242 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.06 % Allowed : 0.52 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.18), residues: 1932 helix: 0.86 (0.15), residues: 1138 sheet: -0.20 (0.44), residues: 110 loop : 0.06 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 243 TYR 0.048 0.002 TYR D 130 PHE 0.023 0.002 PHE A 360 TRP 0.014 0.001 TRP D 124 HIS 0.005 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00402 (16386) covalent geometry : angle 0.64363 (22134) hydrogen bonds : bond 0.04052 ( 871) hydrogen bonds : angle 5.06043 ( 2571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 647 time to evaluate : 0.629 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 10 ILE cc_start: 0.9648 (mm) cc_final: 0.9337 (mm) REVERT: A 27 ASP cc_start: 0.9200 (p0) cc_final: 0.8698 (p0) REVERT: A 31 GLU cc_start: 0.8972 (mp0) cc_final: 0.8583 (mp0) REVERT: A 95 MET cc_start: 0.9100 (mmm) cc_final: 0.8793 (tpp) REVERT: A 99 LYS cc_start: 0.9500 (mmtp) cc_final: 0.9181 (mmtp) REVERT: A 119 GLU cc_start: 0.8883 (mp0) cc_final: 0.8437 (mp0) REVERT: A 122 ILE cc_start: 0.9639 (mp) cc_final: 0.9436 (mp) REVERT: A 128 PHE cc_start: 0.9500 (t80) cc_final: 0.9276 (t80) REVERT: A 139 GLU cc_start: 0.9385 (mm-30) cc_final: 0.9143 (tp30) REVERT: A 144 MET cc_start: 0.8982 (mtm) cc_final: 0.8427 (mtm) REVERT: A 147 GLN cc_start: 0.9068 (mt0) cc_final: 0.8647 (mt0) REVERT: A 166 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8528 (mm-30) REVERT: A 172 LEU cc_start: 0.9622 (mp) cc_final: 0.9297 (mp) REVERT: A 190 MET cc_start: 0.9033 (mtp) cc_final: 0.8729 (mtp) REVERT: A 227 MET cc_start: 0.9261 (mtp) cc_final: 0.8913 (mtp) REVERT: A 236 TYR cc_start: 0.9265 (t80) cc_final: 0.8064 (t80) REVERT: A 278 LEU cc_start: 0.9246 (tp) cc_final: 0.8992 (tp) REVERT: A 290 GLU cc_start: 0.8968 (tp30) cc_final: 0.8622 (tm-30) REVERT: A 291 LEU cc_start: 0.9509 (mp) cc_final: 0.9252 (mt) REVERT: A 318 ASP cc_start: 0.8558 (t0) cc_final: 0.8106 (t0) REVERT: A 333 LYS cc_start: 0.9368 (tmtt) cc_final: 0.8959 (tptp) REVERT: A 348 MET cc_start: 0.9080 (ptp) cc_final: 0.8566 (ptp) REVERT: A 357 TYR cc_start: 0.8825 (m-10) cc_final: 0.8412 (m-80) REVERT: A 361 GLN cc_start: 0.9021 (tp40) cc_final: 0.8700 (tp-100) REVERT: A 376 VAL cc_start: 0.9037 (t) cc_final: 0.8787 (t) REVERT: A 402 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7830 (tm-30) REVERT: A 407 ILE cc_start: 0.9290 (mt) cc_final: 0.8878 (mt) REVERT: A 410 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8392 (t160) REVERT: A 413 SER cc_start: 0.9361 (m) cc_final: 0.9142 (m) REVERT: A 458 MET cc_start: 0.9091 (mmp) cc_final: 0.8598 (mmp) REVERT: A 501 GLN cc_start: 0.9419 (tt0) cc_final: 0.8839 (tm-30) REVERT: A 505 GLU cc_start: 0.8886 (mt-10) cc_final: 0.7767 (mt-10) REVERT: A 515 ASP cc_start: 0.8741 (m-30) cc_final: 0.8343 (m-30) REVERT: A 529 ASP cc_start: 0.8867 (m-30) cc_final: 0.8634 (m-30) REVERT: A 615 MET cc_start: 0.9227 (mmp) cc_final: 0.8829 (mmp) REVERT: B 51 LEU cc_start: 0.9367 (tp) cc_final: 0.9034 (tp) REVERT: B 55 LEU cc_start: 0.9837 (mt) cc_final: 0.9578 (mt) REVERT: B 67 GLU cc_start: 0.9433 (tm-30) cc_final: 0.9114 (tm-30) REVERT: B 82 LYS cc_start: 0.9493 (mmmm) cc_final: 0.9170 (mmtt) REVERT: B 95 MET cc_start: 0.8988 (tpp) cc_final: 0.8366 (tpp) REVERT: B 106 LEU cc_start: 0.9710 (tp) cc_final: 0.9466 (tp) REVERT: B 107 LYS cc_start: 0.9416 (mttp) cc_final: 0.9095 (mmmm) REVERT: B 115 LEU cc_start: 0.9574 (mp) cc_final: 0.9362 (mp) REVERT: B 119 GLU cc_start: 0.9323 (mp0) cc_final: 0.8951 (mp0) REVERT: B 143 LEU cc_start: 0.9520 (tp) cc_final: 0.9209 (tp) REVERT: B 174 GLU cc_start: 0.7652 (tp30) cc_final: 0.7446 (tp30) REVERT: B 211 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8325 (mm-30) REVERT: B 227 MET cc_start: 0.9129 (mtt) cc_final: 0.8785 (mtt) REVERT: B 232 ASN cc_start: 0.8868 (m110) cc_final: 0.8192 (m110) REVERT: B 235 ARG cc_start: 0.9248 (tpp80) cc_final: 0.8866 (mtt-85) REVERT: B 257 ASP cc_start: 0.8883 (m-30) cc_final: 0.8576 (m-30) REVERT: B 276 LYS cc_start: 0.9399 (mptt) cc_final: 0.9015 (mptt) REVERT: B 286 ASP cc_start: 0.8551 (m-30) cc_final: 0.7629 (m-30) REVERT: B 290 GLU cc_start: 0.9179 (tp30) cc_final: 0.8954 (tp30) REVERT: B 319 MET cc_start: 0.8923 (tpp) cc_final: 0.8590 (tpp) REVERT: B 322 MET cc_start: 0.9482 (tpt) cc_final: 0.9230 (mmm) REVERT: B 362 ASP cc_start: 0.8701 (m-30) cc_final: 0.7621 (m-30) REVERT: B 373 ILE cc_start: 0.9454 (mt) cc_final: 0.9188 (tp) REVERT: B 398 ASP cc_start: 0.8575 (t70) cc_final: 0.8288 (t70) REVERT: B 403 ILE cc_start: 0.9524 (mp) cc_final: 0.9305 (tp) REVERT: B 413 SER cc_start: 0.9504 (m) cc_final: 0.9276 (t) REVERT: B 415 ASN cc_start: 0.9599 (t0) cc_final: 0.8941 (t0) REVERT: B 467 ASN cc_start: 0.9208 (t0) cc_final: 0.8940 (t0) REVERT: B 493 MET cc_start: 0.9514 (tmm) cc_final: 0.9101 (tmm) REVERT: B 505 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8248 (mt-10) REVERT: B 586 TYR cc_start: 0.9161 (m-10) cc_final: 0.8864 (m-80) REVERT: B 610 LYS cc_start: 0.9204 (tttm) cc_final: 0.8910 (tttm) REVERT: B 615 MET cc_start: 0.9248 (mmp) cc_final: 0.8804 (mmp) REVERT: B 627 LYS cc_start: 0.9404 (tttp) cc_final: 0.8977 (tttt) REVERT: B 628 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7565 (mm-30) REVERT: B 633 ASP cc_start: 0.8803 (t0) cc_final: 0.7712 (t0) REVERT: B 636 LYS cc_start: 0.9672 (mmtp) cc_final: 0.9330 (mmtm) REVERT: B 640 MET cc_start: 0.9409 (tpp) cc_final: 0.9074 (tpp) REVERT: B 667 LEU cc_start: 0.9590 (tp) cc_final: 0.9268 (tp) REVERT: B 668 ASN cc_start: 0.9449 (m-40) cc_final: 0.9165 (m110) REVERT: B 671 ASP cc_start: 0.8823 (m-30) cc_final: 0.8531 (m-30) REVERT: C 96 MET cc_start: 0.7967 (mmm) cc_final: 0.6941 (mmm) REVERT: C 108 ILE cc_start: 0.8947 (mt) cc_final: 0.8687 (pt) REVERT: C 110 MET cc_start: 0.7699 (mtm) cc_final: 0.7458 (mtm) REVERT: C 197 ASP cc_start: 0.9096 (m-30) cc_final: 0.8889 (m-30) REVERT: C 233 ASN cc_start: 0.9324 (m110) cc_final: 0.9092 (m110) REVERT: D 137 MET cc_start: 0.8832 (mtp) cc_final: 0.8381 (ptm) REVERT: D 151 ILE cc_start: 0.7172 (mm) cc_final: 0.6822 (mm) REVERT: D 172 PHE cc_start: 0.9286 (m-80) cc_final: 0.8838 (m-80) REVERT: D 174 TYR cc_start: 0.8487 (t80) cc_final: 0.8146 (t80) REVERT: D 185 MET cc_start: 0.5925 (mmp) cc_final: 0.5638 (mmp) REVERT: D 212 ILE cc_start: 0.8341 (pt) cc_final: 0.7789 (pt) REVERT: D 233 ASN cc_start: 0.8694 (m110) cc_final: 0.8449 (m110) REVERT: D 247 TYR cc_start: 0.8698 (m-80) cc_final: 0.8270 (m-80) outliers start: 1 outliers final: 0 residues processed: 648 average time/residue: 0.1258 time to fit residues: 121.9046 Evaluate side-chains 593 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 592 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 189 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 165 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 chunk 54 optimal weight: 0.0170 chunk 132 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.136572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.098283 restraints weight = 40210.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.101850 restraints weight = 21030.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.104260 restraints weight = 13034.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.105786 restraints weight = 9120.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.106919 restraints weight = 7003.968| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.7857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16386 Z= 0.141 Angle : 0.655 9.581 22134 Z= 0.350 Chirality : 0.045 0.218 2360 Planarity : 0.004 0.076 2818 Dihedral : 10.183 167.141 2242 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.19), residues: 1932 helix: 0.84 (0.15), residues: 1142 sheet: -0.23 (0.43), residues: 110 loop : 0.04 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 604 TYR 0.052 0.002 TYR D 130 PHE 0.027 0.002 PHE B 98 TRP 0.016 0.001 TRP D 124 HIS 0.005 0.001 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00313 (16386) covalent geometry : angle 0.65465 (22134) hydrogen bonds : bond 0.04105 ( 871) hydrogen bonds : angle 5.05719 ( 2571) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 666 time to evaluate : 0.640 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: A 16 ILE cc_start: 0.9284 (mm) cc_final: 0.9077 (mm) REVERT: A 27 ASP cc_start: 0.9157 (p0) cc_final: 0.8638 (p0) REVERT: A 31 GLU cc_start: 0.8963 (mp0) cc_final: 0.8575 (mp0) REVERT: A 95 MET cc_start: 0.9043 (mmm) cc_final: 0.8668 (tpp) REVERT: A 99 LYS cc_start: 0.9478 (mmtp) cc_final: 0.9184 (mmtp) REVERT: A 107 LYS cc_start: 0.8884 (mtpp) cc_final: 0.8377 (mmmt) REVERT: A 119 GLU cc_start: 0.8857 (mp0) cc_final: 0.8374 (mp0) REVERT: A 147 GLN cc_start: 0.9012 (mt0) cc_final: 0.8561 (mt0) REVERT: A 150 GLN cc_start: 0.9222 (tm-30) cc_final: 0.8779 (tm-30) REVERT: A 166 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8534 (mm-30) REVERT: A 172 LEU cc_start: 0.9585 (mp) cc_final: 0.9235 (mp) REVERT: A 190 MET cc_start: 0.8929 (mtp) cc_final: 0.8676 (mtp) REVERT: A 227 MET cc_start: 0.9265 (mtp) cc_final: 0.8916 (mtp) REVERT: A 236 TYR cc_start: 0.9182 (t80) cc_final: 0.8157 (t80) REVERT: A 251 LEU cc_start: 0.9424 (tp) cc_final: 0.9210 (tp) REVERT: A 290 GLU cc_start: 0.8927 (tp30) cc_final: 0.8525 (tp30) REVERT: A 318 ASP cc_start: 0.8489 (t0) cc_final: 0.7925 (t0) REVERT: A 333 LYS cc_start: 0.9360 (tmtt) cc_final: 0.8957 (tptp) REVERT: A 348 MET cc_start: 0.9060 (ptp) cc_final: 0.8509 (ptp) REVERT: A 357 TYR cc_start: 0.8769 (m-10) cc_final: 0.8335 (m-80) REVERT: A 361 GLN cc_start: 0.8938 (tp40) cc_final: 0.8686 (tp-100) REVERT: A 376 VAL cc_start: 0.9046 (t) cc_final: 0.8841 (t) REVERT: A 405 LEU cc_start: 0.8723 (mt) cc_final: 0.8491 (mt) REVERT: A 407 ILE cc_start: 0.9239 (mt) cc_final: 0.8805 (mt) REVERT: A 413 SER cc_start: 0.9373 (m) cc_final: 0.9062 (m) REVERT: A 447 ASN cc_start: 0.8481 (m110) cc_final: 0.8073 (t0) REVERT: A 458 MET cc_start: 0.9010 (mmp) cc_final: 0.8472 (mmp) REVERT: A 472 LEU cc_start: 0.9462 (mt) cc_final: 0.9197 (mp) REVERT: A 501 GLN cc_start: 0.9429 (tt0) cc_final: 0.8855 (tm-30) REVERT: A 505 GLU cc_start: 0.8871 (mt-10) cc_final: 0.7767 (mt-10) REVERT: A 515 ASP cc_start: 0.8723 (m-30) cc_final: 0.8299 (m-30) REVERT: A 529 ASP cc_start: 0.8854 (m-30) cc_final: 0.8576 (m-30) REVERT: A 604 ARG cc_start: 0.9027 (tpp-160) cc_final: 0.8746 (tpp80) REVERT: A 610 LYS cc_start: 0.8720 (ttmm) cc_final: 0.8288 (mmtt) REVERT: A 615 MET cc_start: 0.9232 (mmp) cc_final: 0.8805 (mmp) REVERT: A 675 HIS cc_start: 0.9404 (t70) cc_final: 0.9053 (t70) REVERT: B 51 LEU cc_start: 0.9286 (tp) cc_final: 0.8962 (tp) REVERT: B 55 LEU cc_start: 0.9837 (mt) cc_final: 0.9565 (mt) REVERT: B 67 GLU cc_start: 0.9390 (tm-30) cc_final: 0.9052 (tm-30) REVERT: B 71 LEU cc_start: 0.9505 (mm) cc_final: 0.9269 (mp) REVERT: B 82 LYS cc_start: 0.9489 (mmmm) cc_final: 0.9134 (mmtt) REVERT: B 98 PHE cc_start: 0.9644 (t80) cc_final: 0.8688 (t80) REVERT: B 103 ASP cc_start: 0.9491 (m-30) cc_final: 0.9170 (m-30) REVERT: B 106 LEU cc_start: 0.9593 (tp) cc_final: 0.9252 (tp) REVERT: B 107 LYS cc_start: 0.9396 (mttp) cc_final: 0.9108 (mmmm) REVERT: B 115 LEU cc_start: 0.9580 (mp) cc_final: 0.9366 (mp) REVERT: B 119 GLU cc_start: 0.9285 (mp0) cc_final: 0.8932 (mp0) REVERT: B 143 LEU cc_start: 0.9619 (tp) cc_final: 0.8854 (tp) REVERT: B 148 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8572 (mt-10) REVERT: B 174 GLU cc_start: 0.7700 (tp30) cc_final: 0.7427 (tp30) REVERT: B 211 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8343 (mm-30) REVERT: B 232 ASN cc_start: 0.8860 (m110) cc_final: 0.8132 (m110) REVERT: B 235 ARG cc_start: 0.9259 (tpp80) cc_final: 0.8805 (mtm-85) REVERT: B 257 ASP cc_start: 0.8855 (m-30) cc_final: 0.8574 (m-30) REVERT: B 276 LYS cc_start: 0.9357 (mptt) cc_final: 0.8909 (mptt) REVERT: B 286 ASP cc_start: 0.8564 (m-30) cc_final: 0.7661 (m-30) REVERT: B 290 GLU cc_start: 0.9167 (tp30) cc_final: 0.8897 (tp30) REVERT: B 313 HIS cc_start: 0.8681 (m-70) cc_final: 0.8481 (m-70) REVERT: B 317 MET cc_start: 0.9082 (mtm) cc_final: 0.8852 (mpp) REVERT: B 319 MET cc_start: 0.8882 (tpp) cc_final: 0.8551 (tpt) REVERT: B 322 MET cc_start: 0.9478 (tpt) cc_final: 0.9274 (mmm) REVERT: B 362 ASP cc_start: 0.8650 (m-30) cc_final: 0.7586 (m-30) REVERT: B 373 ILE cc_start: 0.9387 (mt) cc_final: 0.9125 (tp) REVERT: B 390 GLN cc_start: 0.8970 (mm110) cc_final: 0.8594 (mm110) REVERT: B 393 SER cc_start: 0.9553 (t) cc_final: 0.9288 (p) REVERT: B 398 ASP cc_start: 0.8478 (t70) cc_final: 0.8201 (t70) REVERT: B 413 SER cc_start: 0.9501 (m) cc_final: 0.9227 (t) REVERT: B 415 ASN cc_start: 0.9592 (t0) cc_final: 0.8958 (t0) REVERT: B 493 MET cc_start: 0.9426 (tmm) cc_final: 0.9090 (tmm) REVERT: B 505 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8218 (mt-10) REVERT: B 541 GLU cc_start: 0.8796 (pm20) cc_final: 0.8457 (pp20) REVERT: B 601 ILE cc_start: 0.9501 (mm) cc_final: 0.9051 (mm) REVERT: B 606 TYR cc_start: 0.8737 (m-80) cc_final: 0.8429 (m-80) REVERT: B 615 MET cc_start: 0.9307 (mmp) cc_final: 0.9002 (mmm) REVERT: B 618 LEU cc_start: 0.9213 (mt) cc_final: 0.8864 (mt) REVERT: B 627 LYS cc_start: 0.9433 (tttp) cc_final: 0.9013 (tttt) REVERT: B 628 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7969 (mm-30) REVERT: B 633 ASP cc_start: 0.8784 (t0) cc_final: 0.7787 (t0) REVERT: B 636 LYS cc_start: 0.9662 (mmtp) cc_final: 0.9326 (mmtm) REVERT: B 640 MET cc_start: 0.9413 (tpp) cc_final: 0.9042 (tpp) REVERT: B 650 GLN cc_start: 0.8298 (mm-40) cc_final: 0.8082 (mm-40) REVERT: B 667 LEU cc_start: 0.9575 (tp) cc_final: 0.9242 (tp) REVERT: B 668 ASN cc_start: 0.9421 (m-40) cc_final: 0.9111 (m110) REVERT: B 671 ASP cc_start: 0.8807 (m-30) cc_final: 0.8534 (m-30) REVERT: C 96 MET cc_start: 0.7811 (mmm) cc_final: 0.6839 (mmm) REVERT: C 197 ASP cc_start: 0.9142 (m-30) cc_final: 0.8941 (m-30) REVERT: C 233 ASN cc_start: 0.9344 (m110) cc_final: 0.9117 (m110) REVERT: D 95 MET cc_start: 0.5189 (tmm) cc_final: 0.3999 (tmm) REVERT: D 109 PHE cc_start: 0.8394 (m-80) cc_final: 0.7725 (m-80) REVERT: D 137 MET cc_start: 0.8670 (mtp) cc_final: 0.8274 (ptm) REVERT: D 151 ILE cc_start: 0.7061 (mm) cc_final: 0.6730 (mm) REVERT: D 172 PHE cc_start: 0.9253 (m-80) cc_final: 0.8827 (m-80) REVERT: D 174 TYR cc_start: 0.8470 (t80) cc_final: 0.8156 (t80) REVERT: D 183 LYS cc_start: 0.8169 (pptt) cc_final: 0.6913 (tmtt) REVERT: D 185 MET cc_start: 0.5805 (mmp) cc_final: 0.5441 (mmp) REVERT: D 212 ILE cc_start: 0.8288 (pt) cc_final: 0.7683 (pt) REVERT: D 247 TYR cc_start: 0.8623 (m-80) cc_final: 0.8205 (m-80) outliers start: 0 outliers final: 0 residues processed: 666 average time/residue: 0.1162 time to fit residues: 115.7620 Evaluate side-chains 589 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 589 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 48 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 29 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 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 467 ASN B 501 GLN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** 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 = 0.3746 r_free = 0.3746 target = 0.136014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.098817 restraints weight = 39877.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.102361 restraints weight = 20654.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.104575 restraints weight = 12731.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.106206 restraints weight = 8923.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.107292 restraints weight = 6773.353| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.8040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16386 Z= 0.148 Angle : 0.643 9.505 22134 Z= 0.346 Chirality : 0.045 0.193 2360 Planarity : 0.004 0.063 2818 Dihedral : 10.018 160.652 2242 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.12 % Allowed : 0.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.19), residues: 1932 helix: 0.82 (0.15), residues: 1143 sheet: -0.78 (0.39), residues: 144 loop : 0.13 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 485 TYR 0.040 0.001 TYR D 130 PHE 0.024 0.002 PHE D 92 TRP 0.015 0.001 TRP D 124 HIS 0.005 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00329 (16386) covalent geometry : angle 0.64349 (22134) hydrogen bonds : bond 0.04081 ( 871) hydrogen bonds : angle 5.06439 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3677.25 seconds wall clock time: 64 minutes 23.71 seconds (3863.71 seconds total)