Starting phenix.real_space_refine on Fri Jul 3 19:46:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzj_45069/07_2026/9bzj_45069_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzj_45069/07_2026/9bzj_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 { model { file = "/net/cci-nas-00/data/ceres_data/9bzj_45069/07_2026/9bzj_45069_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzj_45069/07_2026/9bzj_45069_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bzj_45069/07_2026/9bzj_45069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzj_45069/07_2026/9bzj_45069.map" } 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-dev-6108/lib/python3.11/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, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 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: 3.25, per 1000 atoms: 0.20 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: 1.26 Conformation dependent library (CDL) restraints added in 548.1 milliseconds 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: 0.43 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: 2.80 Time building geometry restraints manager: 1.67 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=" O3B TTP A 803 " pdb=" PG TTP A 803 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" O3B TTP B 801 " pdb=" PG TTP B 801 " ideal model delta sigma weight residual 1.748 1.610 0.138 2.00e-02 2.50e+03 4.78e+01 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=" O3A TTP A 803 " pdb=" PB TTP A 803 " ideal model delta sigma weight residual 1.675 1.606 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21527 2.09 - 4.18: 526 4.18 - 6.27: 64 6.27 - 8.36: 8 8.36 - 10.45: 9 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 - 25.05: 9088 25.05 - 50.09: 655 50.09 - 75.14: 127 75.14 - 100.18: 26 100.18 - 125.23: 2 Dihedral angle restraints: 9898 sinusoidal: 4140 harmonic: 5758 Sorted by residual: dihedral pdb=" O4' GDP A 802 " pdb=" C1' GDP A 802 " pdb=" N9 GDP A 802 " pdb=" C8 GDP A 802 " ideal model delta sinusoidal sigma weight residual 27.02 -98.21 125.23 1 2.00e+01 2.50e-03 3.78e+01 dihedral pdb=" O4' GDP B 804 " pdb=" C1' GDP B 804 " pdb=" N9 GDP B 804 " pdb=" C8 GDP B 804 " ideal model delta sinusoidal sigma weight residual 27.02 -95.59 122.61 1 2.00e+01 2.50e-03 3.69e+01 dihedral pdb=" C VAL C 125 " pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual -122.00 -134.28 12.28 0 2.50e+00 1.60e-01 2.41e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2137 0.094 - 0.187: 189 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 3.060 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 3.060 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 3.060 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.991 3.060 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.520 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 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 0.139 16386 Z= 0.334 Angle : 0.787 10.445 22134 Z= 0.471 Chirality : 0.058 0.468 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.680 125.230 6202 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 are 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/Z covalent geometry : bond 0.00596 / 0.33 (16386) covalent geometry : angle 0.78738 / 0.47 (22134) hydrogen bonds : bond 0.15420 / 9.51 ( 871) hydrogen bonds : angle 6.51774 / 4.65 ( 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 : 0.645 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: 0.7958 (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: 0.8076 (m-30) cc_final: 0.7579 (m-30) REVERT: A 152 SER cc_start: 0.8599 (p) cc_final: 0.8234 (p) REVERT: A 157 LEU cc_start: 0.9275 (tp) cc_final: 0.8868 (tp) REVERT: A 172 LEU cc_start: 0.9261 (mp) cc_final: 0.8973 (mp) REVERT: A 186 ILE cc_start: 0.9098 (mt) cc_final: 0.8889 (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: 0.5870 (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: 0.7546 (p0) REVERT: A 259 ASN cc_start: 0.8087 (m-40) cc_final: 0.7625 (m-40) REVERT: A 265 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8517 (mmmt) REVERT: A 322 MET cc_start: 0.7756 (mmp) cc_final: 0.6237 (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: 0.8434 (p) REVERT: A 373 ILE cc_start: 0.9100 (mt) cc_final: 0.8790 (mt) REVERT: A 377 LYS cc_start: 0.8839 (mttt) cc_final: 0.8498 (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: 0.7707 (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: 0.7810 (m-40) REVERT: A 480 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7749 (mt-10) REVERT: A 490 THR cc_start: 0.8511 (m) cc_final: 0.8189 (m) REVERT: A 500 ILE cc_start: 0.9187 (mt) cc_final: 0.8965 (mt) REVERT: A 546 LEU cc_start: 0.9075 (mt) cc_final: 0.8845 (mt) REVERT: A 550 MET cc_start: 0.7295 (mtm) cc_final: 0.7030 (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: 0.8395 (pt) REVERT: A 644 ILE cc_start: 0.8381 (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: 0.8659 (mp) REVERT: B 51 LEU cc_start: 0.8137 (tp) cc_final: 0.7883 (tp) REVERT: B 147 GLN cc_start: 0.7969 (mt0) cc_final: 0.7603 (mt0) REVERT: B 175 VAL cc_start: 0.8898 (t) cc_final: 0.8629 (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: 0.7938 (mmmt) REVERT: B 286 ASP cc_start: 0.6400 (OUTLIER) cc_final: 0.6147 (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: 0.8071 (m-10) REVERT: B 362 ASP cc_start: 0.6386 (m-30) cc_final: 0.5896 (m-30) REVERT: B 366 LYS cc_start: 0.8586 (ptpp) cc_final: 0.8325 (ptpp) REVERT: B 373 ILE cc_start: 0.9116 (mt) cc_final: 0.8850 (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: 0.8518 (mt) REVERT: B 467 ASN cc_start: 0.8197 (t0) cc_final: 0.7932 (t0) REVERT: B 494 MET cc_start: 0.7579 (mtp) cc_final: 0.7125 (mtp) REVERT: B 496 ASN cc_start: 0.7642 (t0) cc_final: 0.7390 (t0) REVERT: B 500 ILE cc_start: 0.9131 (mt) cc_final: 0.8901 (mt) REVERT: B 561 LEU cc_start: 0.8484 (tp) cc_final: 0.8126 (tp) REVERT: B 570 MET cc_start: 0.6811 (mtm) cc_final: 0.6474 (mtm) REVERT: B 605 THR cc_start: 0.7613 (m) cc_final: 0.6861 (m) REVERT: B 640 MET cc_start: 0.7912 (tpp) cc_final: 0.7137 (tpp) REVERT: B 644 ILE cc_start: 0.8666 (mt) cc_final: 0.8260 (mt) REVERT: C 43 THR cc_start: 0.4801 (p) cc_final: 0.4479 (m) REVERT: C 92 PHE cc_start: 0.6653 (t80) cc_final: 0.6164 (t80) REVERT: C 96 MET cc_start: 0.4835 (mmm) cc_final: 0.4397 (mmm) REVERT: C 169 TYR cc_start: 0.4145 (m-80) cc_final: 0.3718 (m-80) REVERT: C 185 MET cc_start: 0.3037 (mtp) cc_final: 0.2623 (ptt) REVERT: C 195 LEU cc_start: 0.7441 (tt) cc_final: 0.7197 (tt) REVERT: D 95 MET cc_start: 0.1774 (tmm) cc_final: 0.1062 (tmm) REVERT: D 151 ILE cc_start: 0.5937 (mm) cc_final: 0.5187 (mm) REVERT: D 178 PHE cc_start: 0.4551 (m-80) cc_final: 0.4122 (m-80) REVERT: D 194 ILE cc_start: 0.6906 (mt) cc_final: 0.6620 (mt) REVERT: D 286 VAL cc_start: 0.2691 (t) cc_final: 0.1562 (p) outliers start: 23 outliers final: 6 residues processed: 1010 average time/residue: 0.1306 time to fit residues: 191.9021 Evaluate side-chains 678 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 670 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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: 0.9990 chunk 149 optimal weight: 9.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN A 232 ASN A 242 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** 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 201 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 69 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 136 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN D 249 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.133630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.097760 restraints weight = 37100.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.100874 restraints weight = 20187.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.103078 restraints weight = 13257.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.104391 restraints weight = 9755.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.105260 restraints weight = 7788.821| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 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 = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 13 (19 function evaluations) r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 16386 Z= 0.283 Angle : 0.724 8.709 22134 Z= 0.388 Chirality : 0.047 0.331 2360 Planarity : 0.005 0.078 2818 Dihedral : 9.750 133.171 2290 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.12 % Allowed : 3.38 % 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 are not related in a simple way. whole: 0.96 (0.18), residues: 1932 helix: 1.04 (0.15), residues: 1133 sheet: -0.30 (0.40), residues: 150 loop : 0.40 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 225 TYR 0.019 0.002 TYR D 262 PHE 0.029 0.003 PHE D 320 TRP 0.048 0.003 TRP D 124 HIS 0.009 0.002 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.28 (16386) covalent geometry : angle 0.72391 / 0.39 (22134) hydrogen bonds : bond 0.04810 / 3.05 ( 871) hydrogen bonds : angle 5.14272 / 3.67 ( 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 758 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 756 time to evaluate : 0.475 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 27 ASP cc_start: 0.9303 (p0) cc_final: 0.9078 (p0) REVERT: A 31 GLU cc_start: 0.9310 (mm-30) cc_final: 0.9034 (mp0) REVERT: A 99 LYS cc_start: 0.9348 (mmtp) cc_final: 0.9069 (mmtp) REVERT: A 117 ARG cc_start: 0.9095 (mtp85) cc_final: 0.8802 (mtp85) REVERT: A 118 TYR cc_start: 0.9173 (t80) cc_final: 0.8960 (t80) REVERT: A 144 MET cc_start: 0.9157 (mtm) cc_final: 0.8804 (mtm) REVERT: A 147 GLN cc_start: 0.8983 (mt0) cc_final: 0.8321 (mt0) REVERT: A 172 LEU cc_start: 0.9620 (mp) cc_final: 0.9377 (mp) REVERT: A 204 SER cc_start: 0.9585 (m) cc_final: 0.9382 (t) REVERT: A 217 GLU cc_start: 0.9259 (mm-30) cc_final: 0.9036 (tp30) REVERT: A 236 TYR cc_start: 0.9211 (t80) cc_final: 0.8356 (t80) REVERT: A 274 ARG cc_start: 0.8468 (ttp80) cc_final: 0.8224 (ttp80) REVERT: A 276 LYS cc_start: 0.9226 (ptpp) cc_final: 0.8893 (mppt) REVERT: A 322 MET cc_start: 0.8710 (mmp) cc_final: 0.7675 (tpp) REVERT: A 326 PHE cc_start: 0.9612 (m-10) cc_final: 0.8853 (m-80) REVERT: A 333 LYS cc_start: 0.9145 (tmtt) cc_final: 0.8875 (tmtt) REVERT: A 344 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8286 (mp0) REVERT: A 355 TYR cc_start: 0.9124 (m-80) cc_final: 0.8730 (m-80) REVERT: A 375 LYS cc_start: 0.9291 (mttm) cc_final: 0.8828 (mtpp) REVERT: A 407 ILE cc_start: 0.9279 (mt) cc_final: 0.8833 (mt) REVERT: A 428 THR cc_start: 0.9582 (m) cc_final: 0.9221 (m) REVERT: A 456 LYS cc_start: 0.9052 (mtmt) cc_final: 0.8804 (ptpt) REVERT: A 505 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8309 (mt-10) REVERT: A 508 LYS cc_start: 0.9598 (tttm) cc_final: 0.9355 (ttpp) REVERT: A 515 ASP cc_start: 0.8860 (m-30) cc_final: 0.8636 (m-30) REVERT: A 550 MET cc_start: 0.7681 (mtm) cc_final: 0.7208 (mtm) REVERT: A 604 ARG cc_start: 0.8702 (mmp80) cc_final: 0.8385 (mmp80) REVERT: A 606 TYR cc_start: 0.7649 (m-80) cc_final: 0.7317 (m-80) REVERT: A 611 THR cc_start: 0.9183 (p) cc_final: 0.8294 (p) REVERT: A 632 MET cc_start: 0.8876 (mtp) cc_final: 0.8655 (mtp) REVERT: A 639 ASP cc_start: 0.8904 (m-30) cc_final: 0.8684 (m-30) REVERT: A 649 ASP cc_start: 0.8620 (p0) cc_final: 0.8410 (p0) REVERT: A 668 ASN cc_start: 0.9425 (m-40) cc_final: 0.9160 (m110) REVERT: B 40 TYR cc_start: 0.9210 (t80) cc_final: 0.9005 (t80) REVERT: B 51 LEU cc_start: 0.9411 (tp) cc_final: 0.9067 (tp) REVERT: B 71 LEU cc_start: 0.9481 (mm) cc_final: 0.9202 (mm) REVERT: B 95 MET cc_start: 0.9242 (tpp) cc_final: 0.8952 (tpp) REVERT: B 119 GLU cc_start: 0.9331 (mp0) cc_final: 0.9073 (mp0) REVERT: B 128 PHE cc_start: 0.9566 (t80) cc_final: 0.9325 (t80) REVERT: B 149 TYR cc_start: 0.9242 (t80) cc_final: 0.8852 (t80) REVERT: B 162 LYS cc_start: 0.9600 (tppt) cc_final: 0.9218 (mmmm) REVERT: B 172 LEU cc_start: 0.9339 (mp) cc_final: 0.8924 (mp) REVERT: B 173 LEU cc_start: 0.9648 (mt) cc_final: 0.9348 (mt) REVERT: B 186 ILE cc_start: 0.9757 (mt) cc_final: 0.9405 (mt) REVERT: B 190 MET cc_start: 0.9535 (mtm) cc_final: 0.9048 (mtm) REVERT: B 191 GLN cc_start: 0.9075 (mm-40) cc_final: 0.8821 (mm-40) REVERT: B 211 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8317 (mm-30) REVERT: B 223 VAL cc_start: 0.9413 (m) cc_final: 0.9075 (m) REVERT: B 227 MET cc_start: 0.9161 (mtt) cc_final: 0.8712 (mtt) REVERT: B 286 ASP cc_start: 0.8523 (m-30) cc_final: 0.7559 (m-30) REVERT: B 312 GLN cc_start: 0.9005 (pm20) cc_final: 0.8795 (pm20) REVERT: B 319 MET cc_start: 0.9122 (tpp) cc_final: 0.8771 (tpp) REVERT: B 362 ASP cc_start: 0.8727 (m-30) cc_final: 0.7715 (m-30) REVERT: B 370 ASN cc_start: 0.9505 (m-40) cc_final: 0.9000 (m-40) REVERT: B 390 GLN cc_start: 0.9133 (mt0) cc_final: 0.8881 (mm110) REVERT: B 393 SER cc_start: 0.9574 (t) cc_final: 0.9310 (p) REVERT: B 398 ASP cc_start: 0.8840 (t0) cc_final: 0.8607 (t70) REVERT: B 406 ASP cc_start: 0.8023 (m-30) cc_final: 0.7616 (m-30) REVERT: B 410 ASN cc_start: 0.8923 (m110) cc_final: 0.8643 (m110) REVERT: B 413 SER cc_start: 0.9579 (m) cc_final: 0.9181 (t) REVERT: B 415 ASN cc_start: 0.9565 (t0) cc_final: 0.9153 (t0) REVERT: B 416 ILE cc_start: 0.9642 (mt) cc_final: 0.9439 (mt) REVERT: B 446 ARG cc_start: 0.8377 (mtp85) cc_final: 0.8033 (mmm-85) REVERT: B 447 ASN cc_start: 0.8658 (m-40) cc_final: 0.7663 (m-40) REVERT: B 458 MET cc_start: 0.9465 (mmm) cc_final: 0.8866 (mmm) REVERT: B 467 ASN cc_start: 0.9218 (t0) cc_final: 0.9015 (t0) REVERT: B 494 MET cc_start: 0.9437 (mtp) cc_final: 0.9068 (mtp) REVERT: B 558 TRP cc_start: 0.9274 (m100) cc_final: 0.8578 (m100) REVERT: B 574 TYR cc_start: 0.8657 (m-80) cc_final: 0.8294 (m-80) REVERT: B 602 GLU cc_start: 0.8226 (pt0) cc_final: 0.7909 (pt0) REVERT: B 615 MET cc_start: 0.9173 (mmp) cc_final: 0.8903 (mmp) REVERT: B 627 LYS cc_start: 0.9360 (tttp) cc_final: 0.8798 (tttp) REVERT: B 632 MET cc_start: 0.9096 (mtm) cc_final: 0.8367 (mtm) REVERT: B 636 LYS cc_start: 0.9698 (mmmm) cc_final: 0.9422 (mmmm) REVERT: B 640 MET cc_start: 0.9561 (tpp) cc_final: 0.8664 (tpp) REVERT: B 644 ILE cc_start: 0.9737 (mt) cc_final: 0.9495 (mt) REVERT: B 648 ILE cc_start: 0.9394 (mm) cc_final: 0.9089 (mm) REVERT: B 682 ILE cc_start: 0.9723 (mt) cc_final: 0.9365 (mt) REVERT: C 196 ARG cc_start: 0.8594 (ptp-110) cc_final: 0.8098 (ttm110) REVERT: C 233 ASN cc_start: 0.9088 (m110) cc_final: 0.8880 (m110) REVERT: D 69 GLN cc_start: 0.7261 (mm-40) cc_final: 0.6868 (mm-40) REVERT: D 137 MET cc_start: 0.6611 (mtm) cc_final: 0.6035 (mmp) REVERT: D 149 ASP cc_start: 0.9087 (m-30) cc_final: 0.8774 (m-30) REVERT: D 151 ILE cc_start: 0.7314 (mm) cc_final: 0.6804 (mm) REVERT: D 244 GLU cc_start: 0.9265 (tp30) cc_final: 0.9063 (tp30) outliers start: 2 outliers final: 0 residues processed: 756 average time/residue: 0.1229 time to fit residues: 138.6283 Evaluate side-chains 631 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 631 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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: 5.9990 chunk 28 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.133484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.093886 restraints weight = 39977.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.097638 restraints weight = 21098.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.100109 restraints weight = 13068.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.101727 restraints weight = 9168.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.102819 restraints weight = 7004.181| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.5494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16386 Z= 0.161 Angle : 0.592 11.257 22134 Z= 0.320 Chirality : 0.043 0.198 2360 Planarity : 0.004 0.041 2818 Dihedral : 9.278 133.054 2290 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.29 % Allowed : 2.21 % Favored : 97.49 % 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 are not related in a simple way. whole: 1.01 (0.18), residues: 1932 helix: 1.09 (0.15), residues: 1128 sheet: 0.38 (0.44), residues: 110 loop : 0.22 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 669 TYR 0.026 0.002 TYR C 174 PHE 0.037 0.002 PHE D 168 TRP 0.031 0.002 TRP D 124 HIS 0.016 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (16386) covalent geometry : angle 0.59211 / 0.32 (22134) hydrogen bonds : bond 0.04218 / 2.69 ( 871) hydrogen bonds : angle 4.94008 / 3.52 ( 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 726 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 721 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9333 (mmm) cc_final: 0.8788 (tpp) REVERT: A 99 LYS cc_start: 0.9376 (mmtp) cc_final: 0.9029 (mmtp) REVERT: A 117 ARG cc_start: 0.9071 (mtp85) cc_final: 0.8723 (mtp85) REVERT: A 139 GLU cc_start: 0.9450 (mm-30) cc_final: 0.9108 (tp30) REVERT: A 144 MET cc_start: 0.9148 (mtm) cc_final: 0.8726 (mtm) REVERT: A 147 GLN cc_start: 0.8983 (mt0) cc_final: 0.8273 (mt0) REVERT: A 172 LEU cc_start: 0.9624 (mp) cc_final: 0.9293 (mp) REVERT: A 204 SER cc_start: 0.9524 (m) cc_final: 0.9083 (t) REVERT: A 227 MET cc_start: 0.9382 (mtp) cc_final: 0.8994 (mtp) REVERT: A 251 LEU cc_start: 0.9382 (tp) cc_final: 0.9140 (tp) REVERT: A 317 MET cc_start: 0.8972 (ptm) cc_final: 0.8301 (ptm) REVERT: A 318 ASP cc_start: 0.9318 (t0) cc_final: 0.9116 (t0) REVERT: A 322 MET cc_start: 0.8996 (mmp) cc_final: 0.8070 (tpp) REVERT: A 326 PHE cc_start: 0.9673 (m-10) cc_final: 0.8829 (m-80) REVERT: A 333 LYS cc_start: 0.9147 (tmtt) cc_final: 0.8643 (tptp) REVERT: A 344 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8356 (mp0) REVERT: A 348 MET cc_start: 0.9036 (ptp) cc_final: 0.8714 (ptp) REVERT: A 361 GLN cc_start: 0.8947 (tp40) cc_final: 0.8392 (tp40) REVERT: A 376 VAL cc_start: 0.9118 (t) cc_final: 0.8663 (t) REVERT: A 403 ILE cc_start: 0.9417 (mm) cc_final: 0.8923 (mm) REVERT: A 405 LEU cc_start: 0.9001 (mt) cc_final: 0.8620 (mt) REVERT: A 407 ILE cc_start: 0.9311 (mt) cc_final: 0.8757 (mt) REVERT: A 428 THR cc_start: 0.9603 (m) cc_final: 0.9282 (m) REVERT: A 447 ASN cc_start: 0.8690 (m110) cc_final: 0.8458 (m-40) REVERT: A 456 LYS cc_start: 0.9107 (mtmt) cc_final: 0.8813 (ptpt) REVERT: A 505 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8558 (mt-10) REVERT: A 550 MET cc_start: 0.8082 (mtm) cc_final: 0.7687 (mtm) REVERT: A 606 TYR cc_start: 0.7738 (m-80) cc_final: 0.7379 (m-80) REVERT: A 611 THR cc_start: 0.9079 (p) cc_final: 0.8147 (p) REVERT: A 615 MET cc_start: 0.9220 (mmp) cc_final: 0.8702 (mmp) REVERT: A 668 ASN cc_start: 0.9395 (m-40) cc_final: 0.9187 (m-40) REVERT: B 40 TYR cc_start: 0.9343 (t80) cc_final: 0.9004 (t80) REVERT: B 51 LEU cc_start: 0.9423 (tp) cc_final: 0.9047 (tp) REVERT: B 55 LEU cc_start: 0.9791 (mt) cc_final: 0.9571 (mt) REVERT: B 71 LEU cc_start: 0.9474 (mm) cc_final: 0.9215 (mm) REVERT: B 95 MET cc_start: 0.9169 (tpp) cc_final: 0.8611 (tpp) REVERT: B 116 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8130 (mt-10) REVERT: B 119 GLU cc_start: 0.9254 (mp0) cc_final: 0.8986 (mp0) REVERT: B 139 GLU cc_start: 0.9346 (mm-30) cc_final: 0.9131 (mm-30) REVERT: B 149 TYR cc_start: 0.9198 (t80) cc_final: 0.8790 (t80) REVERT: B 162 LYS cc_start: 0.9590 (tppt) cc_final: 0.8570 (mmmt) REVERT: B 172 LEU cc_start: 0.9308 (mp) cc_final: 0.8973 (mp) REVERT: B 173 LEU cc_start: 0.9667 (mt) cc_final: 0.9314 (mt) REVERT: B 191 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8641 (mm-40) REVERT: B 209 LYS cc_start: 0.9070 (tppt) cc_final: 0.8828 (tppt) REVERT: B 211 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8264 (mm-30) REVERT: B 223 VAL cc_start: 0.9431 (m) cc_final: 0.9155 (m) REVERT: B 227 MET cc_start: 0.8961 (mtt) cc_final: 0.8535 (mtt) REVERT: B 250 TYR cc_start: 0.9155 (m-80) cc_final: 0.8853 (m-80) REVERT: B 257 ASP cc_start: 0.8786 (m-30) cc_final: 0.8376 (m-30) REVERT: B 261 PHE cc_start: 0.9354 (t80) cc_final: 0.9021 (t80) REVERT: B 263 ASP cc_start: 0.9178 (m-30) cc_final: 0.8869 (m-30) REVERT: B 266 LYS cc_start: 0.9471 (mtpp) cc_final: 0.9104 (mttp) REVERT: B 286 ASP cc_start: 0.8550 (m-30) cc_final: 0.7616 (m-30) REVERT: B 321 GLU cc_start: 0.8796 (pp20) cc_final: 0.8547 (pp20) REVERT: B 349 LEU cc_start: 0.9664 (mp) cc_final: 0.9457 (mp) REVERT: B 362 ASP cc_start: 0.8596 (m-30) cc_final: 0.7589 (m-30) REVERT: B 370 ASN cc_start: 0.9452 (m-40) cc_final: 0.8898 (m-40) REVERT: B 379 SER cc_start: 0.9244 (t) cc_final: 0.8745 (t) REVERT: B 387 GLN cc_start: 0.9148 (mt0) cc_final: 0.8933 (mt0) REVERT: B 390 GLN cc_start: 0.9177 (mt0) cc_final: 0.8825 (mm110) REVERT: B 393 SER cc_start: 0.9604 (t) cc_final: 0.9355 (p) REVERT: B 398 ASP cc_start: 0.8615 (t0) cc_final: 0.8403 (t70) REVERT: B 402 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8882 (mm-30) REVERT: B 406 ASP cc_start: 0.8055 (m-30) cc_final: 0.7599 (m-30) REVERT: B 410 ASN cc_start: 0.8939 (m110) cc_final: 0.8664 (m110) REVERT: B 413 SER cc_start: 0.9609 (m) cc_final: 0.9253 (t) REVERT: B 415 ASN cc_start: 0.9650 (t0) cc_final: 0.9123 (t0) REVERT: B 447 ASN cc_start: 0.8579 (m-40) cc_final: 0.7279 (m-40) REVERT: B 467 ASN cc_start: 0.9216 (t0) cc_final: 0.8952 (t0) REVERT: B 505 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8494 (mt-10) REVERT: B 516 GLN cc_start: 0.9034 (tp-100) cc_final: 0.8776 (tp-100) REVERT: B 561 LEU cc_start: 0.9678 (tp) cc_final: 0.9393 (tp) REVERT: B 574 TYR cc_start: 0.8502 (m-80) cc_final: 0.8123 (m-80) REVERT: B 586 TYR cc_start: 0.9305 (m-80) cc_final: 0.9009 (m-80) REVERT: B 599 GLU cc_start: 0.8765 (pt0) cc_final: 0.8562 (pt0) REVERT: B 602 GLU cc_start: 0.8582 (pt0) cc_final: 0.7934 (pt0) REVERT: B 610 LYS cc_start: 0.9248 (ttpp) cc_final: 0.9040 (tttm) REVERT: B 615 MET cc_start: 0.9263 (mmp) cc_final: 0.8982 (mmp) REVERT: B 627 LYS cc_start: 0.9377 (tttp) cc_final: 0.8767 (tttp) REVERT: B 628 GLU cc_start: 0.8568 (mm-30) cc_final: 0.7801 (mm-30) REVERT: B 632 MET cc_start: 0.8696 (mtm) cc_final: 0.8460 (mtm) REVERT: B 640 MET cc_start: 0.9607 (tpp) cc_final: 0.8844 (tpp) REVERT: B 648 ILE cc_start: 0.9410 (mm) cc_final: 0.9165 (mm) REVERT: B 667 LEU cc_start: 0.9603 (tp) cc_final: 0.9224 (tp) REVERT: B 682 ILE cc_start: 0.9656 (mt) cc_final: 0.9365 (mt) REVERT: C 93 MET cc_start: 0.9160 (mtp) cc_final: 0.8838 (mtp) REVERT: C 233 ASN cc_start: 0.9349 (m110) cc_final: 0.9119 (m110) REVERT: D 59 LEU cc_start: 0.6902 (mm) cc_final: 0.6340 (tt) REVERT: D 79 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8709 (pt0) REVERT: D 137 MET cc_start: 0.6734 (mtm) cc_final: 0.5993 (mmp) REVERT: D 151 ILE cc_start: 0.6821 (mm) cc_final: 0.6542 (mm) REVERT: D 212 ILE cc_start: 0.7641 (pt) cc_final: 0.7413 (pt) REVERT: D 235 LEU cc_start: 0.8970 (mt) cc_final: 0.8525 (pp) REVERT: D 263 ASN cc_start: 0.8678 (m-40) cc_final: 0.8317 (m-40) outliers start: 5 outliers final: 1 residues processed: 722 average time/residue: 0.1166 time to fit residues: 126.6244 Evaluate side-chains 630 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 629 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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: 5.9990 chunk 157 optimal weight: 7.9990 chunk 168 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 127 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 191 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN A 44 ASN A 242 GLN A 365 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 387 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN B 588 GLN B 645 GLN C 28 GLN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 127 GLN D 128 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.126414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.089799 restraints weight = 41419.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.093201 restraints weight = 21947.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.095349 restraints weight = 13679.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.096900 restraints weight = 9650.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.097899 restraints weight = 7387.792| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.6353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 16386 Z= 0.366 Angle : 0.759 11.610 22134 Z= 0.405 Chirality : 0.046 0.222 2360 Planarity : 0.005 0.074 2818 Dihedral : 9.497 139.389 2290 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.12 % Allowed : 2.80 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.18), residues: 1932 helix: 0.82 (0.15), residues: 1138 sheet: -0.69 (0.38), residues: 152 loop : -0.00 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 665 TYR 0.022 0.002 TYR C 174 PHE 0.034 0.003 PHE D 178 TRP 0.019 0.002 TRP D 124 HIS 0.018 0.002 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00760 / 0.37 (16386) covalent geometry : angle 0.75892 / 0.40 (22134) hydrogen bonds : bond 0.04550 / 2.90 ( 871) hydrogen bonds : angle 5.22780 / 3.73 ( 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 669 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 667 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.9602 (mm) cc_final: 0.9370 (mm) REVERT: A 14 ASN cc_start: 0.9370 (m-40) cc_final: 0.9081 (m110) REVERT: A 144 MET cc_start: 0.9093 (mtm) cc_final: 0.8756 (mtm) REVERT: A 147 GLN cc_start: 0.9067 (mt0) cc_final: 0.8419 (mt0) REVERT: A 172 LEU cc_start: 0.9718 (mp) cc_final: 0.9343 (mp) REVERT: A 227 MET cc_start: 0.9339 (mtp) cc_final: 0.8940 (mtp) REVERT: A 236 TYR cc_start: 0.9335 (t80) cc_final: 0.8643 (t80) REVERT: A 257 ASP cc_start: 0.9192 (m-30) cc_final: 0.8929 (m-30) REVERT: A 290 GLU cc_start: 0.8827 (tp30) cc_final: 0.8489 (tp30) REVERT: A 315 ASP cc_start: 0.9197 (p0) cc_final: 0.8904 (p0) REVERT: A 317 MET cc_start: 0.8938 (ptm) cc_final: 0.8515 (ptm) REVERT: A 322 MET cc_start: 0.8808 (mmp) cc_final: 0.8566 (mmm) REVERT: A 333 LYS cc_start: 0.9136 (tmtt) cc_final: 0.8713 (tptp) REVERT: A 348 MET cc_start: 0.9053 (ptp) cc_final: 0.8601 (ptp) REVERT: A 361 GLN cc_start: 0.9074 (tp40) cc_final: 0.8847 (tp40) REVERT: A 381 LEU cc_start: 0.9324 (tp) cc_final: 0.9114 (tp) REVERT: A 402 GLU cc_start: 0.8835 (tp30) cc_final: 0.8566 (tp30) REVERT: A 403 ILE cc_start: 0.9494 (mm) cc_final: 0.9028 (mm) REVERT: A 405 LEU cc_start: 0.8908 (mt) cc_final: 0.8573 (mt) REVERT: A 407 ILE cc_start: 0.9318 (mt) cc_final: 0.8840 (mt) REVERT: A 443 THR cc_start: 0.9424 (m) cc_final: 0.9219 (t) REVERT: A 458 MET cc_start: 0.9168 (mmp) cc_final: 0.8564 (mmp) REVERT: A 505 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8186 (mt-10) REVERT: A 562 LYS cc_start: 0.9754 (tttm) cc_final: 0.9549 (ttmm) REVERT: A 604 ARG cc_start: 0.8903 (mmp80) cc_final: 0.8643 (mmp80) REVERT: A 615 MET cc_start: 0.9137 (mmp) cc_final: 0.8827 (mmp) REVERT: A 640 MET cc_start: 0.9307 (tpp) cc_final: 0.8998 (tpp) REVERT: B 51 LEU cc_start: 0.9513 (tp) cc_final: 0.9165 (tp) REVERT: B 55 LEU cc_start: 0.9833 (mt) cc_final: 0.9588 (mt) REVERT: B 67 GLU cc_start: 0.9291 (tm-30) cc_final: 0.8928 (tm-30) REVERT: B 71 LEU cc_start: 0.9497 (mm) cc_final: 0.9217 (mm) REVERT: B 95 MET cc_start: 0.9136 (tpp) cc_final: 0.8900 (tpp) REVERT: B 115 LEU cc_start: 0.9571 (mp) cc_final: 0.9356 (mp) REVERT: B 116 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8655 (mt-10) REVERT: B 119 GLU cc_start: 0.9364 (mp0) cc_final: 0.8964 (mp0) REVERT: B 149 TYR cc_start: 0.9375 (t80) cc_final: 0.9058 (t80) REVERT: B 172 LEU cc_start: 0.9354 (mp) cc_final: 0.9104 (mp) REVERT: B 211 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8358 (mm-30) REVERT: B 227 MET cc_start: 0.9029 (mtt) cc_final: 0.8784 (mtt) REVERT: B 250 TYR cc_start: 0.9114 (m-80) cc_final: 0.8744 (m-80) REVERT: B 258 ILE cc_start: 0.9495 (tp) cc_final: 0.9211 (tp) REVERT: B 263 ASP cc_start: 0.9224 (m-30) cc_final: 0.8883 (m-30) REVERT: B 266 LYS cc_start: 0.9504 (mtpp) cc_final: 0.9181 (mtmm) REVERT: B 286 ASP cc_start: 0.8580 (m-30) cc_final: 0.7654 (m-30) REVERT: B 321 GLU cc_start: 0.8920 (pp20) cc_final: 0.8288 (pp20) REVERT: B 322 MET cc_start: 0.9399 (tpt) cc_final: 0.8994 (mmm) REVERT: B 362 ASP cc_start: 0.8685 (m-30) cc_final: 0.7559 (m-30) REVERT: B 370 ASN cc_start: 0.9582 (m-40) cc_final: 0.9013 (m110) REVERT: B 373 ILE cc_start: 0.9648 (mt) cc_final: 0.9393 (tp) REVERT: B 379 SER cc_start: 0.9149 (t) cc_final: 0.8827 (t) REVERT: B 393 SER cc_start: 0.9650 (t) cc_final: 0.9322 (p) REVERT: B 398 ASP cc_start: 0.8693 (t0) cc_final: 0.8493 (t70) REVERT: B 407 ILE cc_start: 0.9503 (mt) cc_final: 0.9277 (mt) REVERT: B 410 ASN cc_start: 0.9084 (m110) cc_final: 0.8732 (m110) REVERT: B 413 SER cc_start: 0.9564 (m) cc_final: 0.9191 (t) REVERT: B 415 ASN cc_start: 0.9642 (t0) cc_final: 0.9029 (t0) REVERT: B 602 GLU cc_start: 0.8353 (pt0) cc_final: 0.8146 (pt0) REVERT: B 610 LYS cc_start: 0.9143 (ttpp) cc_final: 0.8858 (ttpp) REVERT: B 615 MET cc_start: 0.9243 (mmp) cc_final: 0.8862 (mmp) REVERT: B 627 LYS cc_start: 0.9421 (tttp) cc_final: 0.8970 (tttp) REVERT: B 628 GLU cc_start: 0.8684 (mm-30) cc_final: 0.7491 (mm-30) REVERT: B 640 MET cc_start: 0.9494 (tpp) cc_final: 0.9105 (tpp) REVERT: B 655 THR cc_start: 0.9621 (m) cc_final: 0.9355 (t) REVERT: B 667 LEU cc_start: 0.9652 (tp) cc_final: 0.9361 (tp) REVERT: B 668 ASN cc_start: 0.9522 (m-40) cc_final: 0.9201 (m110) REVERT: B 671 ASP cc_start: 0.8864 (m-30) cc_final: 0.8621 (m-30) REVERT: C 55 TYR cc_start: 0.8514 (t80) cc_final: 0.8079 (t80) REVERT: C 93 MET cc_start: 0.9346 (mtp) cc_final: 0.9101 (mtp) REVERT: C 183 LYS cc_start: 0.5118 (mppt) cc_final: 0.4605 (ptmt) REVERT: C 196 ARG cc_start: 0.8628 (ptm160) cc_final: 0.8418 (ptm-80) REVERT: C 233 ASN cc_start: 0.9275 (m110) cc_final: 0.9070 (m-40) REVERT: D 74 MET cc_start: 0.5289 (tmm) cc_final: 0.4856 (tmm) REVERT: D 117 THR cc_start: 0.8105 (t) cc_final: 0.7841 (t) REVERT: D 151 ILE cc_start: 0.7243 (mm) cc_final: 0.6960 (mm) REVERT: D 212 ILE cc_start: 0.8012 (pt) cc_final: 0.7805 (pt) REVERT: D 230 ASP cc_start: 0.8833 (t0) cc_final: 0.8540 (t0) REVERT: D 233 ASN cc_start: 0.8540 (m110) cc_final: 0.8178 (m110) outliers start: 2 outliers final: 0 residues processed: 668 average time/residue: 0.1166 time to fit residues: 116.8155 Evaluate side-chains 582 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 582 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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: 0.9990 chunk 120 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 129 optimal weight: 0.2980 chunk 32 optimal weight: 0.7980 chunk 122 optimal weight: 0.0060 chunk 115 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN A 242 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 HIS ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 249 GLN D 28 GLN D 69 GLN D 127 GLN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.132640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.094167 restraints weight = 39654.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.097853 restraints weight = 20541.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.100277 restraints weight = 12623.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.101939 restraints weight = 8794.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.102991 restraints weight = 6659.118| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.6609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16386 Z= 0.136 Angle : 0.603 15.805 22134 Z= 0.322 Chirality : 0.043 0.203 2360 Planarity : 0.004 0.051 2818 Dihedral : 8.863 135.663 2290 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.12 % Allowed : 1.86 % Favored : 98.02 % 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 are not related in a simple way. whole: 0.67 (0.18), residues: 1932 helix: 0.93 (0.15), residues: 1132 sheet: -0.55 (0.39), residues: 146 loop : 0.03 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 184 TYR 0.030 0.002 TYR B 574 PHE 0.034 0.002 PHE D 227 TRP 0.012 0.001 TRP D 124 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (16386) covalent geometry : angle 0.60253 / 0.32 (22134) hydrogen bonds : bond 0.03976 / 2.54 ( 871) hydrogen bonds : angle 4.94949 / 3.53 ( 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 701 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 699 time to evaluate : 0.584 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: 0.9562 (mm) cc_final: 0.9307 (mm) REVERT: A 14 ASN cc_start: 0.9382 (m-40) cc_final: 0.9020 (m110) REVERT: A 27 ASP cc_start: 0.9250 (p0) cc_final: 0.8782 (p0) REVERT: A 31 GLU cc_start: 0.8996 (mp0) cc_final: 0.8378 (mp0) REVERT: A 99 LYS cc_start: 0.9459 (mmtp) cc_final: 0.9016 (mmtp) REVERT: A 147 GLN cc_start: 0.9003 (mt0) cc_final: 0.8379 (mt0) REVERT: A 172 LEU cc_start: 0.9629 (mp) cc_final: 0.9267 (mp) REVERT: A 204 SER cc_start: 0.9531 (t) cc_final: 0.9301 (p) REVERT: A 227 MET cc_start: 0.9301 (mtp) cc_final: 0.8940 (mtp) REVERT: A 251 LEU cc_start: 0.9425 (tp) cc_final: 0.9185 (tp) REVERT: A 276 LYS cc_start: 0.9298 (ptpt) cc_final: 0.8980 (ptpp) REVERT: A 290 GLU cc_start: 0.8862 (tp30) cc_final: 0.8524 (tp30) REVERT: A 315 ASP cc_start: 0.8899 (p0) cc_final: 0.8272 (p0) REVERT: A 317 MET cc_start: 0.8730 (ptm) cc_final: 0.8290 (ptm) REVERT: A 320 ASN cc_start: 0.8962 (t0) cc_final: 0.8641 (t0) REVERT: A 333 LYS cc_start: 0.9210 (tmtt) cc_final: 0.8781 (tptp) REVERT: A 348 MET cc_start: 0.9064 (ptp) cc_final: 0.8527 (ptp) REVERT: A 361 GLN cc_start: 0.8991 (tp40) cc_final: 0.8563 (tp-100) REVERT: A 395 THR cc_start: 0.9596 (p) cc_final: 0.9393 (p) REVERT: A 405 LEU cc_start: 0.8983 (mt) cc_final: 0.8687 (mt) REVERT: A 407 ILE cc_start: 0.9250 (mt) cc_final: 0.8833 (mt) REVERT: A 413 SER cc_start: 0.9432 (m) cc_final: 0.9197 (m) REVERT: A 458 MET cc_start: 0.9056 (mmp) cc_final: 0.8448 (mmp) REVERT: A 501 GLN cc_start: 0.9422 (tt0) cc_final: 0.8670 (tm-30) REVERT: A 505 GLU cc_start: 0.8896 (mt-10) cc_final: 0.7932 (mt-10) REVERT: A 515 ASP cc_start: 0.8805 (m-30) cc_final: 0.8561 (m-30) REVERT: A 604 ARG cc_start: 0.8918 (mmp80) cc_final: 0.8616 (mmp80) REVERT: A 606 TYR cc_start: 0.7908 (m-80) cc_final: 0.7485 (m-80) REVERT: A 611 THR cc_start: 0.9169 (p) cc_final: 0.8278 (t) REVERT: A 632 MET cc_start: 0.8616 (mtp) cc_final: 0.7862 (mtp) REVERT: A 640 MET cc_start: 0.9345 (tpp) cc_final: 0.9059 (tpp) REVERT: A 672 LEU cc_start: 0.9422 (mt) cc_final: 0.9163 (mt) REVERT: B 15 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8690 (tm-30) REVERT: B 18 ILE cc_start: 0.9674 (pt) cc_final: 0.9383 (pt) REVERT: B 51 LEU cc_start: 0.9350 (tp) cc_final: 0.8978 (tp) REVERT: B 55 LEU cc_start: 0.9833 (mt) cc_final: 0.9592 (mt) REVERT: B 65 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8212 (tm-30) REVERT: B 67 GLU cc_start: 0.9296 (tm-30) cc_final: 0.8955 (tm-30) REVERT: B 95 MET cc_start: 0.9026 (tpp) cc_final: 0.8383 (tpp) REVERT: B 116 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8493 (mt-10) REVERT: B 119 GLU cc_start: 0.9238 (mp0) cc_final: 0.8891 (mp0) REVERT: B 149 TYR cc_start: 0.9230 (t80) cc_final: 0.8702 (t80) REVERT: B 187 ASP cc_start: 0.9299 (t0) cc_final: 0.9083 (t0) REVERT: B 211 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8294 (mm-30) REVERT: B 223 VAL cc_start: 0.9553 (m) cc_final: 0.9329 (m) REVERT: B 235 ARG cc_start: 0.9110 (tpp80) cc_final: 0.8875 (mtt-85) REVERT: B 266 LYS cc_start: 0.9444 (mtpp) cc_final: 0.9177 (mtpp) REVERT: B 286 ASP cc_start: 0.8475 (m-30) cc_final: 0.7652 (m-30) REVERT: B 321 GLU cc_start: 0.8747 (pp20) cc_final: 0.8328 (pp20) REVERT: B 322 MET cc_start: 0.9337 (tpt) cc_final: 0.9016 (mmm) REVERT: B 362 ASP cc_start: 0.8690 (m-30) cc_final: 0.7719 (m-30) REVERT: B 373 ILE cc_start: 0.9532 (mt) cc_final: 0.8921 (tp) REVERT: B 386 LEU cc_start: 0.9403 (mt) cc_final: 0.8832 (mt) REVERT: B 390 GLN cc_start: 0.9148 (mt0) cc_final: 0.8641 (mm110) REVERT: B 393 SER cc_start: 0.9594 (t) cc_final: 0.9334 (p) REVERT: B 398 ASP cc_start: 0.8651 (t0) cc_final: 0.8416 (t70) REVERT: B 403 ILE cc_start: 0.9519 (mp) cc_final: 0.9195 (tp) REVERT: B 413 SER cc_start: 0.9562 (m) cc_final: 0.9277 (t) REVERT: B 415 ASN cc_start: 0.9617 (t0) cc_final: 0.8928 (t0) REVERT: B 445 ILE cc_start: 0.9309 (mp) cc_final: 0.9076 (mp) REVERT: B 460 SER cc_start: 0.9473 (t) cc_final: 0.8931 (t) REVERT: B 467 ASN cc_start: 0.9022 (t0) cc_final: 0.8769 (t0) REVERT: B 505 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8218 (mt-10) REVERT: B 601 ILE cc_start: 0.9246 (mm) cc_final: 0.9031 (mm) REVERT: B 610 LYS cc_start: 0.9193 (ttpp) cc_final: 0.8830 (tttm) REVERT: B 615 MET cc_start: 0.9219 (mmp) cc_final: 0.8841 (mmm) REVERT: B 627 LYS cc_start: 0.9357 (tttp) cc_final: 0.8973 (tttp) REVERT: B 628 GLU cc_start: 0.8491 (mm-30) cc_final: 0.7842 (mm-30) REVERT: B 640 MET cc_start: 0.9572 (tpp) cc_final: 0.9199 (tpp) REVERT: B 650 GLN cc_start: 0.8484 (mt0) cc_final: 0.7815 (mm-40) REVERT: B 655 THR cc_start: 0.9572 (m) cc_final: 0.9314 (t) REVERT: B 667 LEU cc_start: 0.9548 (tp) cc_final: 0.9249 (tp) REVERT: B 668 ASN cc_start: 0.9406 (m-40) cc_final: 0.9161 (m110) REVERT: B 671 ASP cc_start: 0.8807 (m-30) cc_final: 0.8576 (m-30) REVERT: C 55 TYR cc_start: 0.8311 (t80) cc_final: 0.7688 (t80) REVERT: C 110 MET cc_start: 0.7853 (mtm) cc_final: 0.7602 (mtm) REVERT: C 183 LYS cc_start: 0.5003 (mppt) cc_final: 0.4532 (ptmt) REVERT: C 196 ARG cc_start: 0.8618 (ptm160) cc_final: 0.8214 (ttp-110) REVERT: C 233 ASN cc_start: 0.9349 (m110) cc_final: 0.9140 (m-40) REVERT: D 149 ASP cc_start: 0.9080 (m-30) cc_final: 0.8848 (m-30) REVERT: D 151 ILE cc_start: 0.7098 (mm) cc_final: 0.6842 (mm) REVERT: D 162 TYR cc_start: 0.9227 (m-10) cc_final: 0.8707 (m-10) REVERT: D 211 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8500 (tm-30) REVERT: D 212 ILE cc_start: 0.8339 (pt) cc_final: 0.8001 (pt) outliers start: 2 outliers final: 1 residues processed: 700 average time/residue: 0.1228 time to fit residues: 127.8077 Evaluate side-chains 612 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 611 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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: 7.9990 chunk 183 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 172 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 136 optimal weight: 20.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN A 158 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 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN C 91 ASN C 249 GLN C 263 ASN D 119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.127356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.090885 restraints weight = 41205.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.094232 restraints weight = 21461.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.096385 restraints weight = 13380.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.097918 restraints weight = 9364.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.098934 restraints weight = 7135.461| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.7046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 16386 Z= 0.271 Angle : 0.680 8.913 22134 Z= 0.366 Chirality : 0.045 0.192 2360 Planarity : 0.004 0.053 2818 Dihedral : 8.963 140.766 2290 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % 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 are not related in a simple way. whole: 0.50 (0.18), residues: 1932 helix: 0.80 (0.15), residues: 1129 sheet: -0.76 (0.39), residues: 148 loop : -0.00 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 575 TYR 0.029 0.002 TYR B 574 PHE 0.033 0.002 PHE A 254 TRP 0.010 0.002 TRP A 623 HIS 0.006 0.002 HIS C 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.27 (16386) covalent geometry : angle 0.67956 / 0.37 (22134) hydrogen bonds : bond 0.04133 / 2.61 ( 871) hydrogen bonds : angle 5.19655 / 3.73 ( 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 656 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 656 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.9616 (mm) cc_final: 0.9383 (mm) REVERT: A 14 ASN cc_start: 0.9510 (m-40) cc_final: 0.9190 (m110) REVERT: A 27 ASP cc_start: 0.9249 (p0) cc_final: 0.8878 (p0) REVERT: A 31 GLU cc_start: 0.8956 (mp0) cc_final: 0.8628 (mp0) REVERT: A 95 MET cc_start: 0.9166 (tpp) cc_final: 0.8744 (mmm) REVERT: A 99 LYS cc_start: 0.9553 (mmtp) cc_final: 0.8986 (mmtp) REVERT: A 119 GLU cc_start: 0.9004 (mp0) cc_final: 0.8590 (mp0) REVERT: A 120 ASP cc_start: 0.8982 (m-30) cc_final: 0.8698 (m-30) REVERT: A 122 ILE cc_start: 0.9670 (mp) cc_final: 0.9396 (mp) REVERT: A 144 MET cc_start: 0.9073 (mtm) cc_final: 0.8580 (mtm) REVERT: A 166 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8433 (mm-30) REVERT: A 168 VAL cc_start: 0.8849 (t) cc_final: 0.8580 (m) REVERT: A 172 LEU cc_start: 0.9676 (mp) cc_final: 0.9283 (mp) REVERT: A 218 ASN cc_start: 0.9369 (t0) cc_final: 0.9147 (m-40) REVERT: A 227 MET cc_start: 0.9335 (mtp) cc_final: 0.8906 (mtp) REVERT: A 276 LYS cc_start: 0.9289 (ptpt) cc_final: 0.8854 (ptpp) REVERT: A 291 LEU cc_start: 0.9533 (mp) cc_final: 0.9117 (mp) REVERT: A 318 ASP cc_start: 0.9319 (t0) cc_final: 0.9102 (t0) REVERT: A 322 MET cc_start: 0.9127 (tpt) cc_final: 0.8592 (tpp) REVERT: A 333 LYS cc_start: 0.9402 (tmtt) cc_final: 0.8919 (tptp) REVERT: A 348 MET cc_start: 0.9062 (ptp) cc_final: 0.8552 (ptp) REVERT: A 361 GLN cc_start: 0.9038 (tp40) cc_final: 0.8714 (tp-100) REVERT: A 402 GLU cc_start: 0.8804 (tp30) cc_final: 0.8543 (tp30) REVERT: A 403 ILE cc_start: 0.9479 (mm) cc_final: 0.9023 (mm) REVERT: A 407 ILE cc_start: 0.9333 (mt) cc_final: 0.8882 (mt) REVERT: A 458 MET cc_start: 0.9109 (mmp) cc_final: 0.8483 (mmp) REVERT: A 468 LEU cc_start: 0.9629 (tp) cc_final: 0.9409 (tp) REVERT: A 472 LEU cc_start: 0.9438 (mt) cc_final: 0.9188 (mp) REVERT: A 505 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8326 (mt-10) REVERT: A 515 ASP cc_start: 0.8789 (m-30) cc_final: 0.8531 (m-30) REVERT: A 550 MET cc_start: 0.8233 (mtm) cc_final: 0.7911 (mtm) REVERT: A 561 LEU cc_start: 0.9672 (tp) cc_final: 0.9466 (tp) REVERT: A 570 MET cc_start: 0.9257 (mtp) cc_final: 0.8891 (mtm) REVERT: A 640 MET cc_start: 0.9293 (tpp) cc_final: 0.9031 (tpp) REVERT: A 683 TYR cc_start: 0.8801 (t80) cc_final: 0.8542 (t80) REVERT: B 51 LEU cc_start: 0.9417 (tp) cc_final: 0.9073 (tp) REVERT: B 55 LEU cc_start: 0.9838 (mt) cc_final: 0.9586 (mt) REVERT: B 67 GLU cc_start: 0.9281 (tm-30) cc_final: 0.9014 (tm-30) REVERT: B 95 MET cc_start: 0.9079 (tpp) cc_final: 0.8691 (tpp) REVERT: B 98 PHE cc_start: 0.9596 (t80) cc_final: 0.9097 (t80) REVERT: B 116 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8583 (mt-10) REVERT: B 119 GLU cc_start: 0.9338 (mp0) cc_final: 0.8941 (mp0) REVERT: B 128 PHE cc_start: 0.9653 (t80) cc_final: 0.9450 (t80) REVERT: B 149 TYR cc_start: 0.9457 (t80) cc_final: 0.8764 (t80) REVERT: B 184 ARG cc_start: 0.9308 (tpp80) cc_final: 0.8959 (tpp80) REVERT: B 191 GLN cc_start: 0.8575 (mm110) cc_final: 0.8176 (mt0) REVERT: B 211 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8509 (mm-30) REVERT: B 258 ILE cc_start: 0.9497 (tp) cc_final: 0.9221 (tp) REVERT: B 266 LYS cc_start: 0.9469 (mtpp) cc_final: 0.9210 (mtpp) REVERT: B 286 ASP cc_start: 0.8438 (m-30) cc_final: 0.7567 (m-30) REVERT: B 290 GLU cc_start: 0.9206 (tp30) cc_final: 0.8952 (tp30) REVERT: B 316 GLU cc_start: 0.9073 (tt0) cc_final: 0.8869 (tt0) REVERT: B 322 MET cc_start: 0.9387 (tpt) cc_final: 0.9154 (mmm) REVERT: B 362 ASP cc_start: 0.8660 (m-30) cc_final: 0.7611 (m-30) REVERT: B 393 SER cc_start: 0.9626 (t) cc_final: 0.9305 (p) REVERT: B 398 ASP cc_start: 0.8657 (t0) cc_final: 0.8430 (t70) REVERT: B 403 ILE cc_start: 0.9564 (mp) cc_final: 0.9229 (tp) REVERT: B 413 SER cc_start: 0.9592 (m) cc_final: 0.9160 (t) REVERT: B 415 ASN cc_start: 0.9560 (t0) cc_final: 0.8929 (t0) REVERT: B 463 LEU cc_start: 0.9778 (tp) cc_final: 0.9560 (tp) REVERT: B 467 ASN cc_start: 0.9165 (t0) cc_final: 0.8924 (t0) REVERT: B 483 GLU cc_start: 0.9397 (pm20) cc_final: 0.9167 (pm20) REVERT: B 505 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8221 (mt-10) REVERT: B 610 LYS cc_start: 0.9153 (ttpp) cc_final: 0.8814 (ttpp) REVERT: B 615 MET cc_start: 0.9238 (mmp) cc_final: 0.8797 (mmm) REVERT: B 627 LYS cc_start: 0.9395 (tttp) cc_final: 0.9013 (tttp) REVERT: B 628 GLU cc_start: 0.8574 (mm-30) cc_final: 0.7745 (mm-30) REVERT: B 633 ASP cc_start: 0.8918 (t0) cc_final: 0.8453 (t0) REVERT: B 640 MET cc_start: 0.9487 (tpp) cc_final: 0.9123 (tpp) REVERT: B 667 LEU cc_start: 0.9589 (tp) cc_final: 0.9285 (tp) REVERT: B 668 ASN cc_start: 0.9479 (m-40) cc_final: 0.9179 (m110) REVERT: B 671 ASP cc_start: 0.8843 (m-30) cc_final: 0.8537 (m-30) REVERT: C 55 TYR cc_start: 0.8254 (t80) cc_final: 0.7760 (t80) REVERT: C 93 MET cc_start: 0.9408 (mtp) cc_final: 0.9162 (mtp) REVERT: C 110 MET cc_start: 0.7810 (mtm) cc_final: 0.7568 (mtm) REVERT: C 111 THR cc_start: 0.3603 (m) cc_final: 0.3337 (m) REVERT: C 183 LYS cc_start: 0.5448 (mppt) cc_final: 0.5002 (ptmt) REVERT: C 196 ARG cc_start: 0.8683 (ptm160) cc_final: 0.8370 (ptm-80) REVERT: C 233 ASN cc_start: 0.9332 (m110) cc_final: 0.9106 (m-40) REVERT: C 269 MET cc_start: 0.5965 (tmm) cc_final: 0.5593 (ppp) REVERT: D 20 MET cc_start: 0.9199 (tpt) cc_final: 0.8978 (tpt) REVERT: D 47 LEU cc_start: 0.7830 (mt) cc_final: 0.7145 (mt) REVERT: D 74 MET cc_start: 0.4940 (tmm) cc_final: 0.4504 (tmm) REVERT: D 151 ILE cc_start: 0.7343 (mm) cc_final: 0.7099 (mm) REVERT: D 174 TYR cc_start: 0.8597 (t80) cc_final: 0.8178 (t80) REVERT: D 276 TYR cc_start: 0.8404 (t80) cc_final: 0.8074 (t80) outliers start: 0 outliers final: 0 residues processed: 656 average time/residue: 0.1188 time to fit residues: 117.0723 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 : 0.599 ------------------------------------------------------------------------------- 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: 4.9990 chunk 51 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN ** B 147 GLN ** 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 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.127736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.090378 restraints weight = 41438.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.093786 restraints weight = 21852.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.096035 restraints weight = 13652.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.097523 restraints weight = 9569.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.098498 restraints weight = 7347.542| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.7317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 16386 Z= 0.235 Angle : 0.654 10.466 22134 Z= 0.350 Chirality : 0.045 0.241 2360 Planarity : 0.004 0.049 2818 Dihedral : 8.767 147.536 2290 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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 are not related in a simple way. whole: 0.51 (0.19), residues: 1932 helix: 0.75 (0.15), residues: 1128 sheet: -0.79 (0.39), residues: 148 loop : 0.13 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 446 TYR 0.032 0.002 TYR A 118 PHE 0.031 0.002 PHE B 98 TRP 0.013 0.002 TRP D 124 HIS 0.006 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.24 (16386) covalent geometry : angle 0.65365 / 0.35 (22134) hydrogen bonds : bond 0.04006 / 2.53 ( 871) hydrogen bonds : angle 5.14754 / 3.69 ( 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 660 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 660 time to evaluate : 0.622 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: 0.9616 (mm) cc_final: 0.9362 (mm) REVERT: A 14 ASN cc_start: 0.9447 (m-40) cc_final: 0.9168 (m110) REVERT: A 27 ASP cc_start: 0.9260 (p0) cc_final: 0.8706 (p0) REVERT: A 31 GLU cc_start: 0.8963 (mp0) cc_final: 0.8443 (mp0) REVERT: A 95 MET cc_start: 0.9122 (tpp) cc_final: 0.8798 (mmm) REVERT: A 99 LYS cc_start: 0.9564 (mmtp) cc_final: 0.8943 (mmtp) REVERT: A 119 GLU cc_start: 0.9031 (mp0) cc_final: 0.8608 (mp0) REVERT: A 139 GLU cc_start: 0.9406 (mm-30) cc_final: 0.9154 (tp30) REVERT: A 144 MET cc_start: 0.8965 (mtm) cc_final: 0.8376 (mtm) REVERT: A 158 ASN cc_start: 0.9632 (m110) cc_final: 0.9405 (m-40) REVERT: A 164 ARG cc_start: 0.8695 (ptm-80) cc_final: 0.8218 (ptt90) REVERT: A 172 LEU cc_start: 0.9676 (mp) cc_final: 0.9215 (mp) REVERT: A 173 LEU cc_start: 0.9620 (mt) cc_final: 0.9385 (mt) REVERT: A 204 SER cc_start: 0.9570 (t) cc_final: 0.9345 (p) REVERT: A 227 MET cc_start: 0.9308 (mtp) cc_final: 0.8912 (mtp) REVERT: A 276 LYS cc_start: 0.9268 (ptpt) cc_final: 0.8834 (ptpp) REVERT: A 317 MET cc_start: 0.8794 (ptm) cc_final: 0.8537 (ptm) REVERT: A 318 ASP cc_start: 0.9152 (t0) cc_final: 0.8863 (t0) REVERT: A 322 MET cc_start: 0.8970 (tpt) cc_final: 0.8402 (tpp) REVERT: A 333 LYS cc_start: 0.9369 (tmtt) cc_final: 0.8932 (tptp) REVERT: A 348 MET cc_start: 0.9074 (ptp) cc_final: 0.8567 (ptp) REVERT: A 361 GLN cc_start: 0.8972 (tp40) cc_final: 0.8650 (tp-100) REVERT: A 402 GLU cc_start: 0.8847 (tp30) cc_final: 0.8574 (tp30) REVERT: A 403 ILE cc_start: 0.9485 (mm) cc_final: 0.9007 (mm) REVERT: A 407 ILE cc_start: 0.9315 (mt) cc_final: 0.8836 (mt) REVERT: A 447 ASN cc_start: 0.8648 (m-40) cc_final: 0.8246 (m-40) REVERT: A 458 MET cc_start: 0.9138 (mmp) cc_final: 0.8520 (mmp) REVERT: A 472 LEU cc_start: 0.9459 (mt) cc_final: 0.9233 (mp) REVERT: A 505 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8336 (mt-10) REVERT: A 515 ASP cc_start: 0.8785 (m-30) cc_final: 0.8477 (m-30) REVERT: A 550 MET cc_start: 0.8333 (mtm) cc_final: 0.8118 (mtm) REVERT: A 561 LEU cc_start: 0.9677 (tp) cc_final: 0.9471 (tp) REVERT: A 586 TYR cc_start: 0.9060 (m-80) cc_final: 0.8532 (m-80) REVERT: A 588 GLN cc_start: 0.9103 (mm-40) cc_final: 0.8732 (mm-40) REVERT: A 602 GLU cc_start: 0.7885 (pt0) cc_final: 0.6394 (pt0) REVERT: A 615 MET cc_start: 0.9182 (mmp) cc_final: 0.8825 (mmp) REVERT: A 640 MET cc_start: 0.9285 (tpp) cc_final: 0.9056 (tpp) REVERT: B 51 LEU cc_start: 0.9410 (tp) cc_final: 0.9062 (tp) REVERT: B 55 LEU cc_start: 0.9841 (mt) cc_final: 0.9575 (mt) REVERT: B 67 GLU cc_start: 0.9316 (tm-30) cc_final: 0.8963 (tm-30) REVERT: B 107 LYS cc_start: 0.9337 (mttp) cc_final: 0.8937 (mmmt) REVERT: B 119 GLU cc_start: 0.9323 (mp0) cc_final: 0.8925 (mp0) REVERT: B 128 PHE cc_start: 0.9647 (t80) cc_final: 0.9439 (t80) REVERT: B 147 GLN cc_start: 0.9244 (mt0) cc_final: 0.8932 (mt0) REVERT: B 149 TYR cc_start: 0.9470 (t80) cc_final: 0.8819 (t80) REVERT: B 174 GLU cc_start: 0.7993 (tp30) cc_final: 0.7782 (tp30) REVERT: B 184 ARG cc_start: 0.9297 (tpp80) cc_final: 0.8854 (tpp80) REVERT: B 211 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8471 (mm-30) REVERT: B 258 ILE cc_start: 0.9501 (tp) cc_final: 0.9285 (tp) REVERT: B 286 ASP cc_start: 0.8500 (m-30) cc_final: 0.7651 (m-30) REVERT: B 290 GLU cc_start: 0.9171 (tp30) cc_final: 0.8933 (tp30) REVERT: B 322 MET cc_start: 0.9436 (tpt) cc_final: 0.9152 (mmm) REVERT: B 362 ASP cc_start: 0.8657 (m-30) cc_final: 0.7596 (m-30) REVERT: B 393 SER cc_start: 0.9583 (t) cc_final: 0.9315 (p) REVERT: B 398 ASP cc_start: 0.8667 (t0) cc_final: 0.8436 (t70) REVERT: B 403 ILE cc_start: 0.9532 (mp) cc_final: 0.9209 (tp) REVERT: B 413 SER cc_start: 0.9501 (m) cc_final: 0.9128 (t) REVERT: B 415 ASN cc_start: 0.9564 (t0) cc_final: 0.8857 (t0) REVERT: B 434 ASP cc_start: 0.8954 (m-30) cc_final: 0.8746 (m-30) REVERT: B 435 SER cc_start: 0.9643 (p) cc_final: 0.9392 (t) REVERT: B 463 LEU cc_start: 0.9774 (tp) cc_final: 0.9538 (tp) REVERT: B 467 ASN cc_start: 0.9183 (t0) cc_final: 0.8835 (t0) REVERT: B 501 GLN cc_start: 0.9416 (tt0) cc_final: 0.9134 (tt0) REVERT: B 505 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8408 (mt-10) REVERT: B 610 LYS cc_start: 0.9158 (ttpp) cc_final: 0.8767 (tttm) REVERT: B 615 MET cc_start: 0.9306 (mmp) cc_final: 0.8847 (mmm) REVERT: B 627 LYS cc_start: 0.9410 (tttp) cc_final: 0.8947 (tttp) REVERT: B 628 GLU cc_start: 0.8654 (mm-30) cc_final: 0.7866 (mm-30) REVERT: B 633 ASP cc_start: 0.8991 (t0) cc_final: 0.8594 (t0) REVERT: B 640 MET cc_start: 0.9417 (tpp) cc_final: 0.9044 (tpp) REVERT: B 667 LEU cc_start: 0.9566 (tp) cc_final: 0.9265 (tp) REVERT: B 668 ASN cc_start: 0.9476 (m-40) cc_final: 0.9182 (m110) REVERT: B 671 ASP cc_start: 0.8795 (m-30) cc_final: 0.8476 (m-30) REVERT: C 110 MET cc_start: 0.7883 (mtm) cc_final: 0.7666 (mtm) REVERT: C 183 LYS cc_start: 0.5302 (mppt) cc_final: 0.4817 (ptmt) REVERT: C 196 ARG cc_start: 0.8629 (ptm160) cc_final: 0.8303 (ptm-80) REVERT: C 233 ASN cc_start: 0.9287 (m110) cc_final: 0.9066 (m-40) REVERT: C 269 MET cc_start: 0.5896 (tmm) cc_final: 0.5642 (ppp) REVERT: D 74 MET cc_start: 0.4871 (tmm) cc_final: 0.4301 (tmm) REVERT: D 151 ILE cc_start: 0.7541 (mm) cc_final: 0.7234 (mm) REVERT: D 174 TYR cc_start: 0.8580 (t80) cc_final: 0.8182 (t80) REVERT: D 212 ILE cc_start: 0.8532 (pt) cc_final: 0.8146 (pt) REVERT: D 216 GLN cc_start: 0.7435 (mm-40) cc_final: 0.7079 (mp10) outliers start: 0 outliers final: 0 residues processed: 660 average time/residue: 0.1123 time to fit residues: 111.0468 Evaluate side-chains 583 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 583 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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: 0.9990 chunk 99 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 153 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN ** 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 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.129289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.091424 restraints weight = 41043.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.094870 restraints weight = 21270.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.097171 restraints weight = 13158.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.098695 restraints weight = 9193.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.099746 restraints weight = 7037.309| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.7492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16386 Z= 0.164 Angle : 0.617 7.347 22134 Z= 0.333 Chirality : 0.044 0.217 2360 Planarity : 0.004 0.053 2818 Dihedral : 8.444 147.844 2290 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.06 % Allowed : 0.93 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.19), residues: 1932 helix: 0.84 (0.15), residues: 1126 sheet: -0.74 (0.39), residues: 144 loop : 0.22 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 446 TYR 0.027 0.001 TYR B 574 PHE 0.025 0.002 PHE D 178 TRP 0.012 0.001 TRP D 124 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (16386) covalent geometry : angle 0.61664 / 0.33 (22134) hydrogen bonds : bond 0.03857 / 2.45 ( 871) hydrogen bonds : angle 5.08861 / 3.66 ( 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 658 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 657 time to evaluate : 0.657 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: 0.9638 (mm) cc_final: 0.9345 (mm) REVERT: A 14 ASN cc_start: 0.9473 (m-40) cc_final: 0.9235 (m110) REVERT: A 27 ASP cc_start: 0.9217 (p0) cc_final: 0.8726 (p0) REVERT: A 31 GLU cc_start: 0.8963 (mp0) cc_final: 0.8588 (mp0) REVERT: A 119 GLU cc_start: 0.8914 (mp0) cc_final: 0.8488 (mp0) REVERT: A 128 PHE cc_start: 0.9508 (t80) cc_final: 0.9307 (t80) REVERT: A 144 MET cc_start: 0.8975 (mtm) cc_final: 0.8375 (mtm) REVERT: A 168 VAL cc_start: 0.8798 (t) cc_final: 0.8595 (m) REVERT: A 172 LEU cc_start: 0.9660 (mp) cc_final: 0.9161 (mp) REVERT: A 173 LEU cc_start: 0.9565 (mt) cc_final: 0.9335 (mt) REVERT: A 174 GLU cc_start: 0.8515 (pt0) cc_final: 0.8301 (pt0) REVERT: A 204 SER cc_start: 0.9549 (t) cc_final: 0.9313 (p) REVERT: A 227 MET cc_start: 0.9340 (mtp) cc_final: 0.8891 (mtp) REVERT: A 322 MET cc_start: 0.8858 (tpt) cc_final: 0.8300 (tpp) REVERT: A 333 LYS cc_start: 0.9391 (tmtt) cc_final: 0.8924 (tptp) REVERT: A 348 MET cc_start: 0.9090 (ptp) cc_final: 0.8539 (ptp) REVERT: A 361 GLN cc_start: 0.8974 (tp40) cc_final: 0.8710 (tp-100) REVERT: A 405 LEU cc_start: 0.9064 (mt) cc_final: 0.8705 (mt) REVERT: A 407 ILE cc_start: 0.9287 (mt) cc_final: 0.8856 (mt) REVERT: A 447 ASN cc_start: 0.8342 (m-40) cc_final: 0.7863 (m-40) REVERT: A 472 LEU cc_start: 0.9484 (mt) cc_final: 0.9254 (mp) REVERT: A 501 GLN cc_start: 0.9428 (tt0) cc_final: 0.8816 (tm-30) REVERT: A 505 GLU cc_start: 0.8866 (mt-10) cc_final: 0.7759 (mt-10) REVERT: A 515 ASP cc_start: 0.8752 (m-30) cc_final: 0.8402 (m-30) REVERT: A 588 GLN cc_start: 0.9123 (mm-40) cc_final: 0.8913 (mm-40) REVERT: A 615 MET cc_start: 0.9208 (mmp) cc_final: 0.8833 (mmm) REVERT: B 25 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8309 (pm20) REVERT: B 51 LEU cc_start: 0.9389 (tp) cc_final: 0.9049 (tp) REVERT: B 55 LEU cc_start: 0.9840 (mt) cc_final: 0.9555 (mt) REVERT: B 67 GLU cc_start: 0.9263 (tm-30) cc_final: 0.8920 (tm-30) REVERT: B 82 LYS cc_start: 0.9494 (mmmm) cc_final: 0.9194 (mmtt) REVERT: B 98 PHE cc_start: 0.9590 (t80) cc_final: 0.9258 (t80) REVERT: B 107 LYS cc_start: 0.9365 (mttp) cc_final: 0.9043 (mmmm) REVERT: B 119 GLU cc_start: 0.9302 (mp0) cc_final: 0.8934 (mp0) REVERT: B 147 GLN cc_start: 0.9226 (mt0) cc_final: 0.8878 (mt0) REVERT: B 149 TYR cc_start: 0.9464 (t80) cc_final: 0.8757 (t80) REVERT: B 174 GLU cc_start: 0.8057 (tp30) cc_final: 0.7786 (tp30) REVERT: B 184 ARG cc_start: 0.9291 (tpp80) cc_final: 0.8846 (tpp80) REVERT: B 211 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8440 (mm-30) REVERT: B 232 ASN cc_start: 0.8890 (m110) cc_final: 0.8230 (m110) REVERT: B 286 ASP cc_start: 0.8544 (m-30) cc_final: 0.7701 (m-30) REVERT: B 290 GLU cc_start: 0.9172 (tp30) cc_final: 0.8875 (tp30) REVERT: B 291 LEU cc_start: 0.9761 (mt) cc_final: 0.9560 (mt) REVERT: B 318 ASP cc_start: 0.8711 (t0) cc_final: 0.8301 (t0) REVERT: B 322 MET cc_start: 0.9467 (tpt) cc_final: 0.9130 (mmm) REVERT: B 362 ASP cc_start: 0.8595 (m-30) cc_final: 0.7537 (m-30) REVERT: B 393 SER cc_start: 0.9571 (t) cc_final: 0.9334 (p) REVERT: B 398 ASP cc_start: 0.8655 (t0) cc_final: 0.8395 (t70) REVERT: B 403 ILE cc_start: 0.9524 (mp) cc_final: 0.9245 (tp) REVERT: B 413 SER cc_start: 0.9566 (m) cc_final: 0.9129 (t) REVERT: B 415 ASN cc_start: 0.9563 (t0) cc_final: 0.8850 (t0) REVERT: B 434 ASP cc_start: 0.8996 (m-30) cc_final: 0.8771 (m-30) REVERT: B 463 LEU cc_start: 0.9768 (tp) cc_final: 0.9521 (tp) REVERT: B 467 ASN cc_start: 0.9164 (t0) cc_final: 0.8951 (t0) REVERT: B 505 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8243 (mt-10) REVERT: B 610 LYS cc_start: 0.9233 (ttpp) cc_final: 0.8816 (tttm) REVERT: B 615 MET cc_start: 0.9331 (mmp) cc_final: 0.9017 (mmm) REVERT: B 618 LEU cc_start: 0.9260 (mt) cc_final: 0.8860 (mt) REVERT: B 627 LYS cc_start: 0.9354 (tttp) cc_final: 0.8946 (tttp) REVERT: B 628 GLU cc_start: 0.8578 (mm-30) cc_final: 0.7655 (mm-30) REVERT: B 633 ASP cc_start: 0.8748 (t0) cc_final: 0.8374 (t0) REVERT: B 640 MET cc_start: 0.9446 (tpp) cc_final: 0.9095 (tpp) REVERT: B 667 LEU cc_start: 0.9596 (tp) cc_final: 0.9299 (tp) REVERT: B 668 ASN cc_start: 0.9451 (m-40) cc_final: 0.9143 (m110) REVERT: B 671 ASP cc_start: 0.8797 (m-30) cc_final: 0.8484 (m-30) REVERT: C 110 MET cc_start: 0.7736 (mtm) cc_final: 0.7495 (mtm) REVERT: C 196 ARG cc_start: 0.8621 (ptm160) cc_final: 0.8288 (ptm-80) REVERT: D 74 MET cc_start: 0.4789 (tmm) cc_final: 0.4361 (tmm) REVERT: D 96 MET cc_start: 0.0074 (mmt) cc_final: -0.0520 (mmt) REVERT: D 151 ILE cc_start: 0.7399 (mm) cc_final: 0.7092 (mm) REVERT: D 174 TYR cc_start: 0.8571 (t80) cc_final: 0.8340 (t80) REVERT: D 185 MET cc_start: 0.5898 (mmp) cc_final: 0.5646 (mmp) REVERT: D 212 ILE cc_start: 0.8545 (pt) cc_final: 0.8267 (pt) REVERT: D 216 GLN cc_start: 0.7454 (mm-40) cc_final: 0.7139 (mp10) outliers start: 1 outliers final: 0 residues processed: 658 average time/residue: 0.1142 time to fit residues: 113.4190 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 : 0.557 ------------------------------------------------------------------------------- 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: 5.9990 chunk 133 optimal weight: 0.5980 chunk 149 optimal weight: 0.2980 chunk 16 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 447 ASN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN C 249 GLN C 263 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.134520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.096367 restraints weight = 40309.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.099953 restraints weight = 20700.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.102310 restraints weight = 12773.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.103860 restraints weight = 8891.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.104948 restraints weight = 6791.664| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.7686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16386 Z= 0.134 Angle : 0.616 8.024 22134 Z= 0.331 Chirality : 0.044 0.205 2360 Planarity : 0.004 0.049 2818 Dihedral : 8.194 147.339 2290 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.18), residues: 1932 helix: 0.86 (0.15), residues: 1127 sheet: -0.84 (0.38), residues: 144 loop : 0.23 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 225 TYR 0.024 0.001 TYR B 574 PHE 0.023 0.002 PHE B 171 TRP 0.015 0.001 TRP D 124 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (16386) covalent geometry : angle 0.61574 / 0.33 (22134) hydrogen bonds : bond 0.03815 / 2.42 ( 871) hydrogen bonds : angle 5.07590 / 3.66 ( 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: 0 poor density : 648 time to evaluate : 0.610 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: 0.9633 (mm) cc_final: 0.9312 (mm) REVERT: A 14 ASN cc_start: 0.9449 (m-40) cc_final: 0.9248 (m-40) REVERT: A 27 ASP cc_start: 0.9181 (p0) cc_final: 0.8687 (p0) REVERT: A 31 GLU cc_start: 0.8987 (mp0) cc_final: 0.8610 (mp0) REVERT: A 119 GLU cc_start: 0.8848 (mp0) cc_final: 0.8417 (mp0) REVERT: A 122 ILE cc_start: 0.9652 (mp) cc_final: 0.9426 (mp) REVERT: A 144 MET cc_start: 0.8972 (mtm) cc_final: 0.8373 (mtm) REVERT: A 147 GLN cc_start: 0.8973 (mt0) cc_final: 0.8623 (mt0) REVERT: A 150 GLN cc_start: 0.9206 (tm-30) cc_final: 0.8648 (tm-30) REVERT: A 172 LEU cc_start: 0.9625 (mp) cc_final: 0.9187 (mp) REVERT: A 204 SER cc_start: 0.9554 (t) cc_final: 0.9233 (p) REVERT: A 227 MET cc_start: 0.9298 (mtp) cc_final: 0.8876 (mtp) REVERT: A 251 LEU cc_start: 0.9423 (tp) cc_final: 0.9132 (tp) REVERT: A 259 ASN cc_start: 0.9104 (m-40) cc_final: 0.8746 (m-40) REVERT: A 276 LYS cc_start: 0.9172 (ptpt) cc_final: 0.8769 (ptpp) REVERT: A 318 ASP cc_start: 0.9003 (t0) cc_final: 0.8799 (t0) REVERT: A 322 MET cc_start: 0.8759 (tpt) cc_final: 0.8547 (tpp) REVERT: A 333 LYS cc_start: 0.9380 (tmtt) cc_final: 0.8935 (tptp) REVERT: A 345 LYS cc_start: 0.9539 (tttt) cc_final: 0.9220 (ttpt) REVERT: A 348 MET cc_start: 0.9106 (ptp) cc_final: 0.8626 (ptp) REVERT: A 357 TYR cc_start: 0.8909 (m-10) cc_final: 0.8633 (m-10) REVERT: A 361 GLN cc_start: 0.8910 (tp40) cc_final: 0.8644 (tp-100) REVERT: A 405 LEU cc_start: 0.9041 (mt) cc_final: 0.8792 (mt) REVERT: A 407 ILE cc_start: 0.9151 (mt) cc_final: 0.8860 (mt) REVERT: A 413 SER cc_start: 0.9349 (m) cc_final: 0.9086 (m) REVERT: A 447 ASN cc_start: 0.8271 (m-40) cc_final: 0.7891 (m-40) REVERT: A 458 MET cc_start: 0.9020 (mmp) cc_final: 0.8573 (mmp) REVERT: A 472 LEU cc_start: 0.9477 (mt) cc_final: 0.9267 (mt) REVERT: A 505 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8277 (mt-10) REVERT: A 515 ASP cc_start: 0.8745 (m-30) cc_final: 0.8346 (m-30) REVERT: A 615 MET cc_start: 0.9168 (mmp) cc_final: 0.8855 (mmp) REVERT: B 18 ILE cc_start: 0.9638 (pt) cc_final: 0.9295 (pt) REVERT: B 51 LEU cc_start: 0.9312 (tp) cc_final: 0.8998 (tp) REVERT: B 55 LEU cc_start: 0.9835 (mt) cc_final: 0.9559 (mt) REVERT: B 65 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8177 (tm-30) REVERT: B 67 GLU cc_start: 0.9330 (tm-30) cc_final: 0.8984 (tm-30) REVERT: B 71 LEU cc_start: 0.9543 (mm) cc_final: 0.9331 (mp) REVERT: B 82 LYS cc_start: 0.9513 (mmmm) cc_final: 0.9168 (mmtt) REVERT: B 107 LYS cc_start: 0.9448 (mttp) cc_final: 0.9128 (mmmm) REVERT: B 115 LEU cc_start: 0.9611 (mp) cc_final: 0.9348 (mp) REVERT: B 116 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8744 (mp0) REVERT: B 119 GLU cc_start: 0.9272 (mp0) cc_final: 0.8909 (mp0) REVERT: B 149 TYR cc_start: 0.9439 (t80) cc_final: 0.8642 (t80) REVERT: B 164 ARG cc_start: 0.8935 (ttp80) cc_final: 0.8714 (tmm-80) REVERT: B 174 GLU cc_start: 0.7968 (tp30) cc_final: 0.7745 (tp30) REVERT: B 184 ARG cc_start: 0.9262 (tpp80) cc_final: 0.8817 (tpp80) REVERT: B 211 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8395 (mm-30) REVERT: B 227 MET cc_start: 0.9258 (mtt) cc_final: 0.8877 (mtt) REVERT: B 251 LEU cc_start: 0.9553 (tp) cc_final: 0.9178 (tp) REVERT: B 286 ASP cc_start: 0.8451 (m-30) cc_final: 0.7710 (m-30) REVERT: B 290 GLU cc_start: 0.9175 (tp30) cc_final: 0.8762 (tp30) REVERT: B 291 LEU cc_start: 0.9754 (mt) cc_final: 0.9397 (mt) REVERT: B 318 ASP cc_start: 0.8778 (t0) cc_final: 0.8357 (t0) REVERT: B 322 MET cc_start: 0.9471 (tpt) cc_final: 0.9138 (mmm) REVERT: B 362 ASP cc_start: 0.8589 (m-30) cc_final: 0.7493 (m-30) REVERT: B 398 ASP cc_start: 0.8576 (t0) cc_final: 0.8214 (t0) REVERT: B 403 ILE cc_start: 0.9519 (mp) cc_final: 0.9252 (tp) REVERT: B 413 SER cc_start: 0.9582 (m) cc_final: 0.9278 (t) REVERT: B 415 ASN cc_start: 0.9585 (t0) cc_final: 0.8975 (t0) REVERT: B 434 ASP cc_start: 0.9000 (m-30) cc_final: 0.8789 (m-30) REVERT: B 505 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8246 (mt-10) REVERT: B 550 MET cc_start: 0.7730 (mtp) cc_final: 0.7363 (mtp) REVERT: B 610 LYS cc_start: 0.9231 (ttpp) cc_final: 0.8785 (tmtt) REVERT: B 615 MET cc_start: 0.9335 (mmp) cc_final: 0.8999 (mmm) REVERT: B 618 LEU cc_start: 0.9302 (mt) cc_final: 0.8850 (mt) REVERT: B 627 LYS cc_start: 0.9409 (tttp) cc_final: 0.8924 (tttp) REVERT: B 633 ASP cc_start: 0.8767 (t0) cc_final: 0.7549 (t0) REVERT: B 636 LYS cc_start: 0.9636 (mmtp) cc_final: 0.9155 (mttm) REVERT: B 640 MET cc_start: 0.9467 (tpp) cc_final: 0.9042 (tpp) REVERT: B 667 LEU cc_start: 0.9579 (tp) cc_final: 0.9238 (tp) REVERT: B 668 ASN cc_start: 0.9392 (m-40) cc_final: 0.9113 (m110) REVERT: B 671 ASP cc_start: 0.8766 (m-30) cc_final: 0.8476 (m-30) REVERT: B 686 ARG cc_start: 0.8630 (ttm-80) cc_final: 0.8395 (tpt170) REVERT: C 74 MET cc_start: 0.7923 (mtm) cc_final: 0.5764 (mtm) REVERT: C 110 MET cc_start: 0.7745 (mtm) cc_final: 0.7482 (mtm) REVERT: C 196 ARG cc_start: 0.8443 (ptm160) cc_final: 0.8081 (ptm-80) REVERT: D 137 MET cc_start: 0.8702 (mmp) cc_final: 0.8264 (ptp) REVERT: D 151 ILE cc_start: 0.7197 (mm) cc_final: 0.6866 (mm) REVERT: D 174 TYR cc_start: 0.8548 (t80) cc_final: 0.8314 (t80) REVERT: D 185 MET cc_start: 0.5734 (mmp) cc_final: 0.5491 (mmp) REVERT: D 216 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7229 (mp10) REVERT: D 233 ASN cc_start: 0.8992 (m110) cc_final: 0.8782 (m110) REVERT: D 243 THR cc_start: 0.8994 (p) cc_final: 0.8691 (p) outliers start: 0 outliers final: 0 residues processed: 648 average time/residue: 0.1185 time to fit residues: 115.2660 Evaluate side-chains 580 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 580 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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: 0.7980 chunk 62 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 165 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 54 optimal weight: 0.1980 chunk 132 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 365 ASN B 467 ASN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN C 91 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 = 0.3767 r_free = 0.3767 target = 0.134286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.095962 restraints weight = 40419.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.099628 restraints weight = 21016.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.102019 restraints weight = 13029.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.103569 restraints weight = 9120.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.104617 restraints weight = 6983.641| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.7937 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= 0.138 Angle : 0.645 20.862 22134 Z= 0.341 Chirality : 0.044 0.239 2360 Planarity : 0.004 0.055 2818 Dihedral : 8.063 146.750 2290 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.06 % Allowed : 0.47 % 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 are not related in a simple way. whole: 0.66 (0.19), residues: 1932 helix: 0.85 (0.15), residues: 1128 sheet: -0.66 (0.40), residues: 144 loop : 0.20 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 243 TYR 0.023 0.001 TYR B 574 PHE 0.029 0.002 PHE B 98 TRP 0.031 0.001 TRP D 124 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (16386) covalent geometry : angle 0.64533 / 0.34 (22134) hydrogen bonds : bond 0.03882 / 2.48 ( 871) hydrogen bonds : angle 5.06274 / 3.66 ( 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 669 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 668 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.9639 (mm) cc_final: 0.9324 (mm) REVERT: A 14 ASN cc_start: 0.9485 (m-40) cc_final: 0.9282 (m110) REVERT: A 27 ASP cc_start: 0.9139 (p0) cc_final: 0.8638 (p0) REVERT: A 31 GLU cc_start: 0.8981 (mp0) cc_final: 0.8615 (mp0) REVERT: A 99 LYS cc_start: 0.9424 (mmtp) cc_final: 0.9179 (mmtp) REVERT: A 119 GLU cc_start: 0.8841 (mp0) cc_final: 0.8431 (mp0) REVERT: A 147 GLN cc_start: 0.8958 (mt0) cc_final: 0.8599 (mt0) REVERT: A 172 LEU cc_start: 0.9607 (mp) cc_final: 0.9125 (mp) REVERT: A 173 LEU cc_start: 0.9525 (mt) cc_final: 0.9314 (mt) REVERT: A 174 GLU cc_start: 0.8800 (pt0) cc_final: 0.8400 (pt0) REVERT: A 204 SER cc_start: 0.9547 (t) cc_final: 0.9256 (p) REVERT: A 214 LYS cc_start: 0.8840 (mmtt) cc_final: 0.8628 (mmtt) REVERT: A 227 MET cc_start: 0.9303 (mtp) cc_final: 0.8867 (mtp) REVERT: A 251 LEU cc_start: 0.9423 (tp) cc_final: 0.9129 (tp) REVERT: A 259 ASN cc_start: 0.9072 (m-40) cc_final: 0.8755 (m-40) REVERT: A 291 LEU cc_start: 0.9521 (mt) cc_final: 0.9068 (mt) REVERT: A 317 MET cc_start: 0.8507 (ptm) cc_final: 0.8181 (ptp) REVERT: A 318 ASP cc_start: 0.8990 (t0) cc_final: 0.8738 (t0) REVERT: A 322 MET cc_start: 0.8729 (tpt) cc_final: 0.8492 (tpp) REVERT: A 333 LYS cc_start: 0.9391 (tmtt) cc_final: 0.8969 (tptp) REVERT: A 345 LYS cc_start: 0.9507 (tttt) cc_final: 0.9190 (ttpt) REVERT: A 348 MET cc_start: 0.9081 (ptp) cc_final: 0.8522 (ptp) REVERT: A 357 TYR cc_start: 0.8906 (m-10) cc_final: 0.8577 (m-10) REVERT: A 361 GLN cc_start: 0.8925 (tp40) cc_final: 0.8694 (tp-100) REVERT: A 405 LEU cc_start: 0.8976 (mt) cc_final: 0.8711 (mt) REVERT: A 407 ILE cc_start: 0.9167 (mt) cc_final: 0.8885 (mt) REVERT: A 458 MET cc_start: 0.8922 (mmp) cc_final: 0.8408 (mmp) REVERT: A 472 LEU cc_start: 0.9491 (mt) cc_final: 0.9256 (mt) REVERT: A 485 ARG cc_start: 0.9061 (mtm-85) cc_final: 0.8823 (mtm110) REVERT: A 501 GLN cc_start: 0.9469 (tt0) cc_final: 0.8804 (tm-30) REVERT: A 505 GLU cc_start: 0.8874 (mt-10) cc_final: 0.7921 (mt-10) REVERT: A 515 ASP cc_start: 0.8762 (m-30) cc_final: 0.8338 (m-30) REVERT: A 529 ASP cc_start: 0.8845 (m-30) cc_final: 0.8616 (m-30) REVERT: A 604 ARG cc_start: 0.9097 (mmm-85) cc_final: 0.8663 (mmp80) REVERT: A 615 MET cc_start: 0.9161 (mmp) cc_final: 0.8846 (mmm) REVERT: A 639 ASP cc_start: 0.8925 (m-30) cc_final: 0.8612 (m-30) REVERT: A 675 HIS cc_start: 0.9446 (t70) cc_final: 0.9006 (t-170) REVERT: B 18 ILE cc_start: 0.9639 (pt) cc_final: 0.9283 (pt) REVERT: B 51 LEU cc_start: 0.9304 (tp) cc_final: 0.8995 (tp) REVERT: B 55 LEU cc_start: 0.9837 (mt) cc_final: 0.9572 (mt) REVERT: B 67 GLU cc_start: 0.9375 (tm-30) cc_final: 0.9002 (tm-30) REVERT: B 71 LEU cc_start: 0.9542 (mm) cc_final: 0.9319 (mp) REVERT: B 82 LYS cc_start: 0.9498 (mmmm) cc_final: 0.9132 (mmtt) REVERT: B 98 PHE cc_start: 0.9555 (t80) cc_final: 0.9044 (t80) REVERT: B 99 LYS cc_start: 0.9618 (mmmt) cc_final: 0.9141 (mmmt) REVERT: B 107 LYS cc_start: 0.9386 (mttp) cc_final: 0.9104 (mmmm) REVERT: B 115 LEU cc_start: 0.9601 (mp) cc_final: 0.9327 (mp) REVERT: B 116 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8637 (mp0) REVERT: B 119 GLU cc_start: 0.9305 (mp0) cc_final: 0.8931 (mp0) REVERT: B 149 TYR cc_start: 0.9411 (t80) cc_final: 0.8615 (t80) REVERT: B 161 ARG cc_start: 0.8450 (mtp85) cc_final: 0.8189 (mtt180) REVERT: B 162 LYS cc_start: 0.9505 (tppt) cc_final: 0.9268 (tppp) REVERT: B 164 ARG cc_start: 0.8969 (ttp80) cc_final: 0.8742 (ttp80) REVERT: B 174 GLU cc_start: 0.8099 (tp30) cc_final: 0.7812 (tp30) REVERT: B 184 ARG cc_start: 0.9266 (tpp80) cc_final: 0.8893 (tpp80) REVERT: B 211 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8352 (mm-30) REVERT: B 251 LEU cc_start: 0.9549 (tp) cc_final: 0.8964 (tp) REVERT: B 286 ASP cc_start: 0.8424 (m-30) cc_final: 0.7674 (m-30) REVERT: B 290 GLU cc_start: 0.9136 (tp30) cc_final: 0.8782 (tp30) REVERT: B 308 LYS cc_start: 0.9631 (mtpp) cc_final: 0.9383 (mtmm) REVERT: B 318 ASP cc_start: 0.8876 (t0) cc_final: 0.8570 (t0) REVERT: B 322 MET cc_start: 0.9467 (tpt) cc_final: 0.9191 (mmm) REVERT: B 362 ASP cc_start: 0.8533 (m-30) cc_final: 0.7479 (m-30) REVERT: B 373 ILE cc_start: 0.9446 (mt) cc_final: 0.9069 (tp) REVERT: B 387 GLN cc_start: 0.8944 (mt0) cc_final: 0.8584 (mt0) REVERT: B 390 GLN cc_start: 0.8976 (mt0) cc_final: 0.8741 (mm110) REVERT: B 398 ASP cc_start: 0.8584 (t0) cc_final: 0.8220 (t0) REVERT: B 413 SER cc_start: 0.9602 (m) cc_final: 0.9265 (t) REVERT: B 415 ASN cc_start: 0.9579 (t0) cc_final: 0.8688 (t0) REVERT: B 417 LEU cc_start: 0.9654 (tt) cc_final: 0.9438 (tt) REVERT: B 418 ASN cc_start: 0.9158 (m110) cc_final: 0.8911 (m110) REVERT: B 445 ILE cc_start: 0.9249 (mp) cc_final: 0.8412 (mp) REVERT: B 460 SER cc_start: 0.9286 (p) cc_final: 0.9031 (p) REVERT: B 501 GLN cc_start: 0.9408 (tt0) cc_final: 0.9105 (tt0) REVERT: B 505 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8549 (mt-10) REVERT: B 610 LYS cc_start: 0.9204 (ttpp) cc_final: 0.8747 (tmtt) REVERT: B 615 MET cc_start: 0.9378 (mmp) cc_final: 0.8979 (mmm) REVERT: B 618 LEU cc_start: 0.9298 (mt) cc_final: 0.8903 (mt) REVERT: B 627 LYS cc_start: 0.9399 (tttp) cc_final: 0.8935 (tttp) REVERT: B 633 ASP cc_start: 0.8703 (t0) cc_final: 0.7474 (t0) REVERT: B 636 LYS cc_start: 0.9645 (mmtp) cc_final: 0.9187 (mmtm) REVERT: B 640 MET cc_start: 0.9458 (tpp) cc_final: 0.9079 (tpp) REVERT: B 667 LEU cc_start: 0.9570 (tp) cc_final: 0.9233 (tp) REVERT: B 668 ASN cc_start: 0.9369 (m-40) cc_final: 0.9108 (m110) REVERT: B 671 ASP cc_start: 0.8744 (m-30) cc_final: 0.8448 (m-30) REVERT: C 86 ARG cc_start: 0.8663 (mpp80) cc_final: 0.8443 (mmt180) REVERT: C 96 MET cc_start: 0.7695 (mmm) cc_final: 0.6340 (mmm) REVERT: C 110 MET cc_start: 0.7585 (mtm) cc_final: 0.7361 (mtm) REVERT: C 111 THR cc_start: 0.3290 (m) cc_final: 0.3020 (m) REVERT: C 183 LYS cc_start: 0.5509 (mppt) cc_final: 0.5019 (ptmt) REVERT: C 196 ARG cc_start: 0.8502 (ptm160) cc_final: 0.8246 (ptm-80) REVERT: D 74 MET cc_start: 0.4081 (tmm) cc_final: 0.3828 (tmm) REVERT: D 109 PHE cc_start: 0.8081 (m-80) cc_final: 0.7472 (m-80) REVERT: D 137 MET cc_start: 0.8753 (mmp) cc_final: 0.8275 (ptp) REVERT: D 151 ILE cc_start: 0.7079 (mm) cc_final: 0.6671 (mm) REVERT: D 164 GLU cc_start: 0.9361 (pm20) cc_final: 0.8960 (pm20) REVERT: D 197 ASP cc_start: 0.9336 (m-30) cc_final: 0.9105 (m-30) REVERT: D 201 HIS cc_start: 0.8357 (m170) cc_final: 0.7902 (m170) REVERT: D 216 GLN cc_start: 0.7486 (mm-40) cc_final: 0.7188 (mp10) outliers start: 1 outliers final: 0 residues processed: 668 average time/residue: 0.1208 time to fit residues: 121.1470 Evaluate side-chains 587 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 587 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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: 4.9990 chunk 1 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 125 optimal weight: 0.0030 chunk 28 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN A 44 ASN ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN A 668 ASN ** B 147 GLN ** 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 467 ASN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.137870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.099439 restraints weight = 40319.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.103126 restraints weight = 21284.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.105538 restraints weight = 13266.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.107157 restraints weight = 9313.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.108183 restraints weight = 7134.734| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.8101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16386 Z= 0.139 Angle : 0.646 18.149 22134 Z= 0.342 Chirality : 0.045 0.241 2360 Planarity : 0.004 0.050 2818 Dihedral : 7.990 147.494 2290 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.12 % Allowed : 0.29 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.19), residues: 1932 helix: 0.81 (0.15), residues: 1142 sheet: -0.63 (0.41), residues: 142 loop : 0.08 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 243 TYR 0.019 0.001 TYR B 574 PHE 0.036 0.002 PHE D 227 TRP 0.023 0.001 TRP D 124 HIS 0.012 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (16386) covalent geometry : angle 0.64559 / 0.34 (22134) hydrogen bonds : bond 0.03912 / 2.52 ( 871) hydrogen bonds : angle 5.04525 / 3.63 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3421.27 seconds wall clock time: 60 minutes 3.73 seconds (3603.73 seconds total)