Starting phenix.real_space_refine on Sat May 17 16:46:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzj_45069/05_2025/9bzj_45069_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzj_45069/05_2025/9bzj_45069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bzj_45069/05_2025/9bzj_45069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzj_45069/05_2025/9bzj_45069.map" model { file = "/net/cci-nas-00/data/ceres_data/9bzj_45069/05_2025/9bzj_45069_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzj_45069/05_2025/9bzj_45069_neut.cif" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 11.16, per 1000 atoms: 0.70 Number of scatterers: 16038 At special positions: 0 Unit cell: (93.288, 128.778, 130.806, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.45 Conformation dependent library (CDL) restraints added in 2.0 seconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 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: 4.84 Time building geometry restraints manager: 5.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4752 1.34 - 1.46: 3107 1.46 - 1.58: 8345 1.58 - 1.70: 26 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.061 1.25e-02 6.40e+03 2.39e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.039 1.20e-02 6.94e+03 1.04e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.032 1.08e-02 8.57e+03 8.79e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.569 -0.032 1.17e-02 7.31e+03 7.31e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.573 -0.033 1.25e-02 6.40e+03 6.81e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21576 2.09 - 4.18: 516 4.18 - 6.27: 37 6.27 - 8.36: 1 8.36 - 10.45: 4 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.59 -6.05 1.36e+00 5.41e-01 1.98e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.14 -4.43 1.15e+00 7.56e-01 1.48e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.82 -4.32 1.23e+00 6.61e-01 1.23e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.68 -3.97 1.15e+00 7.56e-01 1.19e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.54 3.65 1.06e+00 8.90e-01 1.18e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 9468 35.81 - 71.61: 339 71.61 - 107.42: 37 107.42 - 143.22: 3 143.22 - 179.03: 3 Dihedral angle restraints: 9850 sinusoidal: 4092 harmonic: 5758 Sorted by residual: dihedral pdb=" C2 TTP A 803 " pdb=" C1' TTP A 803 " pdb=" N1 TTP A 803 " pdb=" O4' TTP A 803 " ideal model delta sinusoidal sigma weight residual -58.32 120.71 -179.03 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 TTP B 801 " pdb=" C1' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " ideal model delta sinusoidal sigma weight residual 301.68 151.19 150.50 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" C5' TTP A 803 " pdb=" O5' TTP A 803 " pdb=" PA TTP A 803 " pdb=" O3A TTP A 803 " ideal model delta sinusoidal sigma weight residual 179.97 31.92 148.05 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 9847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2142 0.094 - 0.187: 184 0.187 - 0.281: 29 0.281 - 0.374: 3 0.374 - 0.468: 2 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.48e+00 chirality pdb=" CA TYR C 169 " pdb=" N TYR C 169 " pdb=" C TYR C 169 " pdb=" CB TYR C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.70e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " -0.018 2.00e-02 2.50e+03 1.13e-02 2.23e+00 pdb=" CG PHE D 92 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 169 " 0.017 2.00e-02 2.50e+03 9.83e-03 1.93e+00 pdb=" CG TYR C 169 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 169 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 169 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 169 " 0.009 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 130 2.51 - 3.11: 11553 3.11 - 3.70: 27047 3.70 - 4.30: 41558 4.30 - 4.90: 65430 Nonbonded interactions: 145718 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.991 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.013 3.040 ... (remaining 145713 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 39.090 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16386 Z= 0.315 Angle : 0.740 10.445 22134 Z= 0.463 Chirality : 0.058 0.468 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.952 179.028 6154 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.34 % Allowed : 15.38 % Favored : 83.28 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.18), residues: 1932 helix: 0.58 (0.14), residues: 1151 sheet: 0.46 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 PHE 0.021 0.002 PHE C 227 TYR 0.020 0.002 TYR D 179 ARG 0.003 0.000 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.15420 ( 871) hydrogen bonds : angle 6.51774 ( 2571) covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.73993 (22134) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 999 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.8765 (mt) cc_final: 0.8500 (mp) REVERT: A 55 LEU cc_start: 0.8884 (mt) cc_final: 0.8613 (mt) REVERT: A 76 ASP cc_start: 0.8075 (m-30) cc_final: 0.7584 (m-30) REVERT: A 152 SER cc_start: 0.8599 (p) cc_final: 0.8239 (p) REVERT: A 157 LEU cc_start: 0.9274 (tp) cc_final: 0.8862 (tp) REVERT: A 172 LEU cc_start: 0.9261 (mp) cc_final: 0.8971 (mp) REVERT: A 188 ILE cc_start: 0.9093 (mt) cc_final: 0.8802 (mt) REVERT: A 192 LEU cc_start: 0.9318 (mt) cc_final: 0.8863 (mt) REVERT: A 211 GLU cc_start: 0.6249 (mt-10) cc_final: 0.5867 (tp30) REVERT: A 236 TYR cc_start: 0.7661 (t80) cc_final: 0.7361 (t80) REVERT: A 238 ASP cc_start: 0.7874 (p0) cc_final: 0.7554 (p0) REVERT: A 259 ASN cc_start: 0.8087 (m-40) cc_final: 0.7612 (m-40) REVERT: A 265 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8517 (mmmt) REVERT: A 308 LYS cc_start: 0.8783 (mtmm) cc_final: 0.8522 (mtmm) REVERT: A 322 MET cc_start: 0.7756 (mmp) cc_final: 0.6265 (mmm) REVERT: A 326 PHE cc_start: 0.8518 (m-10) cc_final: 0.7921 (m-80) REVERT: A 355 TYR cc_start: 0.7427 (m-80) cc_final: 0.7205 (m-80) REVERT: A 367 VAL cc_start: 0.8652 (m) cc_final: 0.8449 (p) REVERT: A 373 ILE cc_start: 0.9100 (mt) cc_final: 0.8794 (mt) REVERT: A 377 LYS cc_start: 0.8839 (mttt) cc_final: 0.8499 (mttm) REVERT: A 407 ILE cc_start: 0.8904 (mt) cc_final: 0.8462 (mt) REVERT: A 415 ASN cc_start: 0.8025 (t0) cc_final: 0.7711 (t0) REVERT: A 417 LEU cc_start: 0.8059 (tt) cc_final: 0.7704 (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: 0.8990 (t) REVERT: A 447 ASN cc_start: 0.8127 (m-40) cc_final: 0.7799 (m-40) REVERT: A 480 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7745 (mt-10) REVERT: A 490 THR cc_start: 0.8511 (m) cc_final: 0.8183 (m) REVERT: A 500 ILE cc_start: 0.9186 (mt) cc_final: 0.8967 (mt) REVERT: A 546 LEU cc_start: 0.9075 (mt) cc_final: 0.8846 (mt) REVERT: A 550 MET cc_start: 0.7294 (mtm) cc_final: 0.7026 (mtm) REVERT: A 594 VAL cc_start: 0.8906 (m) cc_final: 0.8580 (t) REVERT: A 597 ILE cc_start: 0.8719 (pt) cc_final: 0.8369 (pt) REVERT: A 611 THR cc_start: 0.7322 (t) cc_final: 0.7085 (p) REVERT: A 644 ILE cc_start: 0.8380 (mt) cc_final: 0.7909 (mt) REVERT: A 653 SER cc_start: 0.9125 (OUTLIER) cc_final: 0.8843 (p) REVERT: B 12 LEU cc_start: 0.8951 (mt) cc_final: 0.8660 (mp) REVERT: B 51 LEU cc_start: 0.8137 (tp) cc_final: 0.7887 (tp) REVERT: B 147 GLN cc_start: 0.7969 (mt0) cc_final: 0.7604 (mt0) REVERT: B 175 VAL cc_start: 0.8898 (t) cc_final: 0.8637 (t) REVERT: B 204 SER cc_start: 0.8988 (m) cc_final: 0.7894 (t) REVERT: B 261 PHE cc_start: 0.8606 (t80) cc_final: 0.8322 (t80) REVERT: B 265 LYS cc_start: 0.8801 (mmtt) cc_final: 0.7939 (mmmt) REVERT: B 286 ASP cc_start: 0.6400 (OUTLIER) cc_final: 0.6144 (m-30) REVERT: B 315 ASP cc_start: 0.8332 (p0) cc_final: 0.7908 (p0) REVERT: B 326 PHE cc_start: 0.8294 (m-10) cc_final: 0.8073 (m-10) REVERT: B 362 ASP cc_start: 0.6385 (m-30) cc_final: 0.5903 (m-30) REVERT: B 366 LYS cc_start: 0.8586 (ptpp) cc_final: 0.8328 (ptpp) REVERT: B 373 ILE cc_start: 0.9115 (mt) cc_final: 0.8851 (mt) REVERT: B 384 GLU cc_start: 0.9052 (pm20) cc_final: 0.8311 (pm20) REVERT: B 425 ILE cc_start: 0.8783 (mt) cc_final: 0.8517 (mt) REVERT: B 467 ASN cc_start: 0.8197 (t0) cc_final: 0.7927 (t0) REVERT: B 494 MET cc_start: 0.7580 (mtp) cc_final: 0.7129 (mtp) REVERT: B 496 ASN cc_start: 0.7643 (t0) cc_final: 0.7393 (t0) REVERT: B 500 ILE cc_start: 0.9131 (mt) cc_final: 0.8905 (mt) REVERT: B 561 LEU cc_start: 0.8483 (tp) cc_final: 0.8128 (tp) REVERT: B 570 MET cc_start: 0.6811 (mtm) cc_final: 0.6470 (mtm) REVERT: B 605 THR cc_start: 0.7613 (m) cc_final: 0.6870 (m) REVERT: B 640 MET cc_start: 0.7912 (tpp) cc_final: 0.7138 (tpp) REVERT: B 644 ILE cc_start: 0.8665 (mt) cc_final: 0.8272 (mt) REVERT: C 43 THR cc_start: 0.4801 (p) cc_final: 0.4513 (m) REVERT: C 92 PHE cc_start: 0.6653 (t80) cc_final: 0.6162 (t80) REVERT: C 96 MET cc_start: 0.4835 (mmm) cc_final: 0.4378 (mmm) REVERT: C 169 TYR cc_start: 0.4145 (m-80) cc_final: 0.3723 (m-80) REVERT: C 185 MET cc_start: 0.3037 (mtp) cc_final: 0.2614 (ptt) REVERT: C 195 LEU cc_start: 0.7441 (tt) cc_final: 0.7165 (tt) REVERT: D 95 MET cc_start: 0.1773 (tmm) cc_final: 0.0989 (tmm) REVERT: D 151 ILE cc_start: 0.5937 (mm) cc_final: 0.5205 (mm) REVERT: D 178 PHE cc_start: 0.4551 (m-80) cc_final: 0.4118 (m-80) REVERT: D 194 ILE cc_start: 0.6907 (mt) cc_final: 0.6641 (mt) REVERT: D 286 VAL cc_start: 0.2691 (t) cc_final: 0.1560 (p) outliers start: 23 outliers final: 5 residues processed: 1010 average time/residue: 0.3002 time to fit residues: 433.3136 Evaluate side-chains 673 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 666 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 0.3980 chunk 98 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 174 optimal weight: 0.9980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 232 ASN A 242 GLN A 361 GLN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN B 676 HIS C 249 GLN C 263 ASN D 71 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 128 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.142517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.101001 restraints weight = 38425.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.104944 restraints weight = 20061.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.107527 restraints weight = 12587.812| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16386 Z= 0.193 Angle : 0.652 8.532 22134 Z= 0.348 Chirality : 0.045 0.326 2360 Planarity : 0.004 0.061 2818 Dihedral : 11.315 177.088 2242 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.17 % Allowed : 2.68 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.18), residues: 1932 helix: 1.28 (0.15), residues: 1123 sheet: -0.10 (0.40), residues: 140 loop : 0.38 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP D 124 HIS 0.009 0.001 HIS A 304 PHE 0.030 0.002 PHE D 320 TYR 0.022 0.002 TYR D 262 ARG 0.005 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04924 ( 871) hydrogen bonds : angle 5.04405 ( 2571) covalent geometry : bond 0.00420 (16386) covalent geometry : angle 0.65193 (22134) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 776 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9281 (tttt) cc_final: 0.9001 (tttm) REVERT: A 27 ASP cc_start: 0.9424 (p0) cc_final: 0.9136 (p0) REVERT: A 31 GLU cc_start: 0.9417 (mm-30) cc_final: 0.9018 (mp0) REVERT: A 41 ILE cc_start: 0.9497 (mm) cc_final: 0.9232 (mm) REVERT: A 118 TYR cc_start: 0.8977 (t80) cc_final: 0.8467 (t80) REVERT: A 139 GLU cc_start: 0.9453 (mm-30) cc_final: 0.9164 (tp30) REVERT: A 172 LEU cc_start: 0.9655 (mp) cc_final: 0.8973 (mp) REVERT: A 173 LEU cc_start: 0.9589 (mt) cc_final: 0.9315 (mt) REVERT: A 204 SER cc_start: 0.9586 (m) cc_final: 0.9226 (t) REVERT: A 236 TYR cc_start: 0.9042 (t80) cc_final: 0.8179 (t80) REVERT: A 315 ASP cc_start: 0.8704 (p0) cc_final: 0.8386 (p0) REVERT: A 322 MET cc_start: 0.8535 (mmp) cc_final: 0.7557 (tpp) REVERT: A 326 PHE cc_start: 0.9637 (m-10) cc_final: 0.9019 (m-80) REVERT: A 333 LYS cc_start: 0.8940 (tmtt) cc_final: 0.8694 (tptt) REVERT: A 355 TYR cc_start: 0.9107 (m-80) cc_final: 0.8509 (m-80) REVERT: A 357 TYR cc_start: 0.8885 (m-10) cc_final: 0.8364 (m-10) REVERT: A 406 ASP cc_start: 0.8760 (m-30) cc_final: 0.8098 (m-30) REVERT: A 407 ILE cc_start: 0.9285 (mt) cc_final: 0.8786 (mt) REVERT: A 435 SER cc_start: 0.9571 (p) cc_final: 0.9304 (t) REVERT: A 456 LYS cc_start: 0.9078 (mtmt) cc_final: 0.8865 (ptpt) REVERT: A 505 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8539 (mt-10) REVERT: A 508 LYS cc_start: 0.9515 (tttm) cc_final: 0.9312 (ttpp) REVERT: A 515 ASP cc_start: 0.8870 (m-30) cc_final: 0.8582 (m-30) REVERT: A 550 MET cc_start: 0.7511 (mtm) cc_final: 0.6414 (mtm) REVERT: A 615 MET cc_start: 0.9108 (mmp) cc_final: 0.8873 (mmp) REVERT: A 632 MET cc_start: 0.8799 (mtp) cc_final: 0.8557 (mtp) REVERT: A 640 MET cc_start: 0.9351 (tpp) cc_final: 0.8930 (tpp) REVERT: A 672 LEU cc_start: 0.9309 (mt) cc_final: 0.9053 (mt) REVERT: B 51 LEU cc_start: 0.9434 (tp) cc_final: 0.8889 (tp) REVERT: B 71 LEU cc_start: 0.9443 (mm) cc_final: 0.8977 (mm) REVERT: B 81 PHE cc_start: 0.9521 (m-80) cc_final: 0.9267 (m-80) REVERT: B 87 LYS cc_start: 0.9402 (tptm) cc_final: 0.9153 (tptm) REVERT: B 95 MET cc_start: 0.9207 (tpp) cc_final: 0.8901 (tpp) REVERT: B 119 GLU cc_start: 0.9193 (mp0) cc_final: 0.8984 (mp0) REVERT: B 162 LYS cc_start: 0.9547 (tppt) cc_final: 0.9230 (mmmm) REVERT: B 186 ILE cc_start: 0.9752 (mt) cc_final: 0.9504 (mt) REVERT: B 191 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8721 (mm-40) REVERT: B 211 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8247 (mm-30) REVERT: B 223 VAL cc_start: 0.9367 (m) cc_final: 0.9023 (m) REVERT: B 227 MET cc_start: 0.9155 (mtt) cc_final: 0.8653 (mtt) REVERT: B 257 ASP cc_start: 0.8799 (m-30) cc_final: 0.8572 (m-30) REVERT: B 312 GLN cc_start: 0.8932 (pm20) cc_final: 0.8728 (pm20) REVERT: B 333 LYS cc_start: 0.9208 (tptt) cc_final: 0.8945 (ttmm) REVERT: B 362 ASP cc_start: 0.8638 (m-30) cc_final: 0.8354 (m-30) REVERT: B 370 ASN cc_start: 0.9443 (m-40) cc_final: 0.8852 (m-40) REVERT: B 390 GLN cc_start: 0.9118 (mt0) cc_final: 0.8851 (mm110) REVERT: B 398 ASP cc_start: 0.8652 (t0) cc_final: 0.8421 (t70) REVERT: B 410 ASN cc_start: 0.8741 (m110) cc_final: 0.8468 (m110) REVERT: B 413 SER cc_start: 0.9609 (m) cc_final: 0.9273 (t) REVERT: B 415 ASN cc_start: 0.9513 (t0) cc_final: 0.9148 (t0) REVERT: B 446 ARG cc_start: 0.8330 (mtp85) cc_final: 0.7914 (mmm-85) REVERT: B 447 ASN cc_start: 0.8562 (m-40) cc_final: 0.7469 (m-40) REVERT: B 458 MET cc_start: 0.9405 (mmm) cc_final: 0.8962 (mmm) REVERT: B 467 ASN cc_start: 0.9178 (t0) cc_final: 0.8864 (t0) REVERT: B 493 MET cc_start: 0.9587 (tmm) cc_final: 0.9378 (tmm) REVERT: B 494 MET cc_start: 0.9460 (mtp) cc_final: 0.9086 (mtp) REVERT: B 496 ASN cc_start: 0.9740 (t0) cc_final: 0.9396 (t0) REVERT: B 499 SER cc_start: 0.9883 (t) cc_final: 0.9627 (p) REVERT: B 561 LEU cc_start: 0.9645 (tp) cc_final: 0.9412 (tp) REVERT: B 574 TYR cc_start: 0.8522 (m-80) cc_final: 0.8135 (m-80) REVERT: B 602 GLU cc_start: 0.8302 (pt0) cc_final: 0.8030 (pt0) REVERT: B 627 LYS cc_start: 0.9027 (tttt) cc_final: 0.8463 (tttm) REVERT: B 632 MET cc_start: 0.9101 (mtm) cc_final: 0.8427 (mtm) REVERT: B 636 LYS cc_start: 0.9676 (mmmm) cc_final: 0.9414 (mmmm) REVERT: B 640 MET cc_start: 0.9584 (tpp) cc_final: 0.9283 (tpp) REVERT: B 682 ILE cc_start: 0.9717 (mt) cc_final: 0.9471 (mt) REVERT: C 91 ASN cc_start: 0.8659 (m-40) cc_final: 0.8309 (m-40) REVERT: C 92 PHE cc_start: 0.8822 (t80) cc_final: 0.7347 (t80) REVERT: C 95 MET cc_start: 0.8230 (tmm) cc_final: 0.7777 (tmm) REVERT: C 96 MET cc_start: 0.7560 (mmm) cc_final: 0.6618 (mmm) REVERT: C 118 ILE cc_start: 0.8247 (mm) cc_final: 0.8012 (mm) REVERT: C 196 ARG cc_start: 0.8407 (ptp-110) cc_final: 0.7990 (ttm110) REVERT: D 95 MET cc_start: 0.4103 (tmm) cc_final: 0.3389 (tmm) REVERT: D 137 MET cc_start: 0.6656 (mtm) cc_final: 0.6305 (mmp) REVERT: D 149 ASP cc_start: 0.9095 (m-30) cc_final: 0.8849 (m-30) REVERT: D 151 ILE cc_start: 0.6995 (mm) cc_final: 0.6495 (mm) REVERT: D 233 ASN cc_start: 0.8610 (m110) cc_final: 0.8378 (m110) REVERT: D 318 ASP cc_start: 0.8771 (m-30) cc_final: 0.8507 (m-30) outliers start: 3 outliers final: 0 residues processed: 777 average time/residue: 0.2768 time to fit residues: 314.9450 Evaluate side-chains 642 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 642 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 175 optimal weight: 0.0370 chunk 34 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 191 optimal weight: 20.0000 chunk 57 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 171 optimal weight: 0.9980 chunk 189 optimal weight: 0.0060 chunk 141 optimal weight: 9.9990 overall best weight: 0.6076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** 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 69 GLN D 127 GLN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.139353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.099577 restraints weight = 38876.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.103487 restraints weight = 20441.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.106010 restraints weight = 12672.271| |-----------------------------------------------------------------------------| 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) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.5153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16386 Z= 0.135 Angle : 0.589 10.190 22134 Z= 0.313 Chirality : 0.042 0.170 2360 Planarity : 0.003 0.039 2818 Dihedral : 11.036 177.212 2242 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.17 % Allowed : 1.98 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.18), residues: 1932 helix: 1.20 (0.15), residues: 1110 sheet: -0.29 (0.40), residues: 138 loop : 0.23 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 124 HIS 0.005 0.001 HIS A 438 PHE 0.025 0.002 PHE D 166 TYR 0.018 0.001 TYR C 174 ARG 0.005 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.04070 ( 871) hydrogen bonds : angle 4.90902 ( 2571) covalent geometry : bond 0.00296 (16386) covalent geometry : angle 0.58867 (22134) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 724 time to evaluate : 1.883 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 8 LYS cc_start: 0.9321 (tttt) cc_final: 0.9112 (tttm) REVERT: A 31 GLU cc_start: 0.9330 (mm-30) cc_final: 0.9112 (mm-30) REVERT: A 139 GLU cc_start: 0.9418 (mm-30) cc_final: 0.9211 (tp30) REVERT: A 144 MET cc_start: 0.9050 (mtm) cc_final: 0.8526 (mtm) REVERT: A 147 GLN cc_start: 0.8760 (mt0) cc_final: 0.8291 (mt0) REVERT: A 172 LEU cc_start: 0.9600 (mp) cc_final: 0.8890 (mp) REVERT: A 173 LEU cc_start: 0.9526 (mt) cc_final: 0.9258 (mt) REVERT: A 204 SER cc_start: 0.9529 (m) cc_final: 0.9156 (t) REVERT: A 227 MET cc_start: 0.9369 (mtp) cc_final: 0.8999 (mtp) REVERT: A 236 TYR cc_start: 0.8964 (t80) cc_final: 0.8207 (t80) REVERT: A 251 LEU cc_start: 0.9317 (tp) cc_final: 0.9106 (tp) REVERT: A 267 ILE cc_start: 0.9445 (mm) cc_final: 0.9220 (mm) REVERT: A 278 LEU cc_start: 0.9366 (tp) cc_final: 0.9111 (tp) REVERT: A 286 ASP cc_start: 0.8367 (p0) cc_final: 0.7283 (p0) REVERT: A 317 MET cc_start: 0.8744 (ptm) cc_final: 0.8216 (ptp) REVERT: A 320 ASN cc_start: 0.9154 (t0) cc_final: 0.8696 (t0) REVERT: A 322 MET cc_start: 0.8937 (mmp) cc_final: 0.8020 (tpp) REVERT: A 326 PHE cc_start: 0.9661 (m-10) cc_final: 0.8942 (m-80) REVERT: A 333 LYS cc_start: 0.9087 (tmtt) cc_final: 0.8580 (tptp) REVERT: A 357 TYR cc_start: 0.8819 (m-10) cc_final: 0.8417 (m-10) REVERT: A 375 LYS cc_start: 0.9231 (mttm) cc_final: 0.8643 (mtpp) REVERT: A 406 ASP cc_start: 0.8781 (m-30) cc_final: 0.8163 (m-30) REVERT: A 407 ILE cc_start: 0.9259 (mt) cc_final: 0.8748 (mt) REVERT: A 447 ASN cc_start: 0.8355 (m110) cc_final: 0.8123 (m-40) REVERT: A 456 LYS cc_start: 0.9079 (mtmt) cc_final: 0.8847 (ptpt) REVERT: A 458 MET cc_start: 0.9059 (mmp) cc_final: 0.8589 (mmp) REVERT: A 461 ILE cc_start: 0.9062 (pt) cc_final: 0.8860 (pt) REVERT: A 479 TYR cc_start: 0.8855 (t80) cc_final: 0.8627 (t80) REVERT: A 501 GLN cc_start: 0.9419 (tt0) cc_final: 0.9201 (tt0) REVERT: A 505 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8475 (mt-10) REVERT: A 508 LYS cc_start: 0.9532 (tttm) cc_final: 0.9296 (ttpp) REVERT: A 515 ASP cc_start: 0.8830 (m-30) cc_final: 0.8493 (m-30) REVERT: A 604 ARG cc_start: 0.8979 (mmp80) cc_final: 0.8468 (mmp80) REVERT: A 615 MET cc_start: 0.9206 (mmp) cc_final: 0.8983 (mmp) REVERT: A 640 MET cc_start: 0.9290 (tpp) cc_final: 0.8948 (tpp) REVERT: A 650 GLN cc_start: 0.8618 (mt0) cc_final: 0.8261 (mt0) REVERT: B 51 LEU cc_start: 0.9374 (tp) cc_final: 0.8831 (tp) REVERT: B 71 LEU cc_start: 0.9426 (mm) cc_final: 0.8991 (mt) REVERT: B 95 MET cc_start: 0.9213 (tpp) cc_final: 0.8655 (tpp) REVERT: B 119 GLU cc_start: 0.8994 (mp0) cc_final: 0.8781 (mp0) REVERT: B 162 LYS cc_start: 0.9546 (tppt) cc_final: 0.8741 (tppp) REVERT: B 168 VAL cc_start: 0.9193 (t) cc_final: 0.8784 (t) REVERT: B 191 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8492 (mt0) REVERT: B 211 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8099 (mm-30) REVERT: B 223 VAL cc_start: 0.9311 (m) cc_final: 0.9100 (m) REVERT: B 227 MET cc_start: 0.9118 (mtt) cc_final: 0.8638 (mtt) REVERT: B 257 ASP cc_start: 0.8744 (m-30) cc_final: 0.8366 (m-30) REVERT: B 266 LYS cc_start: 0.9455 (mtpp) cc_final: 0.9035 (mttp) REVERT: B 286 ASP cc_start: 0.8485 (m-30) cc_final: 0.7498 (m-30) REVERT: B 312 GLN cc_start: 0.8515 (pm20) cc_final: 0.8311 (pm20) REVERT: B 321 GLU cc_start: 0.8708 (pp20) cc_final: 0.8453 (pp20) REVERT: B 333 LYS cc_start: 0.9257 (tptt) cc_final: 0.9045 (ttmm) REVERT: B 362 ASP cc_start: 0.8535 (m-30) cc_final: 0.7544 (m-30) REVERT: B 370 ASN cc_start: 0.9353 (m-40) cc_final: 0.8650 (m-40) REVERT: B 392 SER cc_start: 0.9188 (m) cc_final: 0.8859 (m) REVERT: B 398 ASP cc_start: 0.8622 (t0) cc_final: 0.8370 (t70) REVERT: B 403 ILE cc_start: 0.9529 (mp) cc_final: 0.9249 (tp) REVERT: B 410 ASN cc_start: 0.8770 (m110) cc_final: 0.8398 (m110) REVERT: B 413 SER cc_start: 0.9618 (m) cc_final: 0.9265 (t) REVERT: B 415 ASN cc_start: 0.9625 (t0) cc_final: 0.9091 (t0) REVERT: B 447 ASN cc_start: 0.8415 (m-40) cc_final: 0.7036 (m-40) REVERT: B 458 MET cc_start: 0.9319 (mmm) cc_final: 0.8766 (mmm) REVERT: B 493 MET cc_start: 0.9554 (tmm) cc_final: 0.9350 (tmm) REVERT: B 494 MET cc_start: 0.9498 (mtp) cc_final: 0.9224 (mtp) REVERT: B 496 ASN cc_start: 0.9754 (t0) cc_final: 0.9354 (t0) REVERT: B 499 SER cc_start: 0.9895 (t) cc_final: 0.9631 (p) REVERT: B 505 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8481 (mt-10) REVERT: B 515 ASP cc_start: 0.9146 (t0) cc_final: 0.8907 (t0) REVERT: B 516 GLN cc_start: 0.9122 (tp-100) cc_final: 0.8864 (tp-100) REVERT: B 561 LEU cc_start: 0.9618 (tp) cc_final: 0.9356 (tp) REVERT: B 574 TYR cc_start: 0.8404 (m-80) cc_final: 0.8106 (m-10) REVERT: B 586 TYR cc_start: 0.9266 (m-80) cc_final: 0.9024 (m-80) REVERT: B 599 GLU cc_start: 0.8809 (pt0) cc_final: 0.8587 (pt0) REVERT: B 601 ILE cc_start: 0.9499 (mm) cc_final: 0.8751 (mm) REVERT: B 602 GLU cc_start: 0.8547 (pt0) cc_final: 0.8144 (pt0) REVERT: B 627 LYS cc_start: 0.9340 (tttt) cc_final: 0.8670 (tttm) REVERT: B 628 GLU cc_start: 0.8511 (mm-30) cc_final: 0.7937 (mm-30) REVERT: B 632 MET cc_start: 0.9018 (mtm) cc_final: 0.8524 (mtm) REVERT: B 636 LYS cc_start: 0.9683 (mmmm) cc_final: 0.9417 (mmmm) REVERT: B 640 MET cc_start: 0.9608 (tpp) cc_final: 0.8849 (tpp) REVERT: B 667 LEU cc_start: 0.9605 (tp) cc_final: 0.9169 (tp) REVERT: B 682 ILE cc_start: 0.9660 (mt) cc_final: 0.9396 (mt) REVERT: B 686 ARG cc_start: 0.8669 (ttm-80) cc_final: 0.8394 (tpt170) REVERT: C 92 PHE cc_start: 0.8826 (t80) cc_final: 0.8095 (t80) REVERT: D 79 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8679 (pt0) REVERT: D 95 MET cc_start: 0.3001 (tmm) cc_final: 0.2524 (tmm) REVERT: D 137 MET cc_start: 0.8228 (mtm) cc_final: 0.7748 (mmp) REVERT: D 149 ASP cc_start: 0.9007 (m-30) cc_final: 0.8807 (m-30) REVERT: D 151 ILE cc_start: 0.6218 (mm) cc_final: 0.5715 (mm) REVERT: D 211 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8632 (tm-30) REVERT: D 263 ASN cc_start: 0.8650 (m-40) cc_final: 0.8388 (m-40) outliers start: 3 outliers final: 0 residues processed: 725 average time/residue: 0.2680 time to fit residues: 287.5341 Evaluate side-chains 645 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 645 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 180 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 148 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN A 572 HIS ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN C 263 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.130284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.092838 restraints weight = 39543.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.096387 restraints weight = 20481.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.098731 restraints weight = 12723.956| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 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 = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16386 Z= 0.236 Angle : 0.641 8.924 22134 Z= 0.342 Chirality : 0.043 0.162 2360 Planarity : 0.004 0.052 2818 Dihedral : 11.017 179.879 2242 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.06 % Allowed : 2.62 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.18), residues: 1932 helix: 1.13 (0.15), residues: 1130 sheet: -0.53 (0.39), residues: 148 loop : 0.11 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 9 HIS 0.005 0.001 HIS A 368 PHE 0.024 0.002 PHE D 178 TYR 0.018 0.002 TYR A 394 ARG 0.005 0.001 ARG A 350 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 871) hydrogen bonds : angle 4.93421 ( 2571) covalent geometry : bond 0.00501 (16386) covalent geometry : angle 0.64102 (22134) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 690 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.9538 (OUTLIER) cc_final: 0.9252 (mm) REVERT: A 14 ASN cc_start: 0.9364 (m-40) cc_final: 0.9087 (m110) REVERT: A 31 GLU cc_start: 0.9358 (mm-30) cc_final: 0.9143 (mm-30) REVERT: A 69 LEU cc_start: 0.9556 (mt) cc_final: 0.9329 (pp) REVERT: A 95 MET cc_start: 0.9198 (mmm) cc_final: 0.8960 (tpp) REVERT: A 139 GLU cc_start: 0.9445 (mm-30) cc_final: 0.9203 (tp30) REVERT: A 144 MET cc_start: 0.9082 (mtm) cc_final: 0.8610 (mtm) REVERT: A 147 GLN cc_start: 0.8907 (mt0) cc_final: 0.8391 (mt0) REVERT: A 172 LEU cc_start: 0.9617 (mp) cc_final: 0.9314 (mp) REVERT: A 205 LYS cc_start: 0.8614 (mttp) cc_final: 0.8304 (mtpp) REVERT: A 227 MET cc_start: 0.9384 (mtp) cc_final: 0.8992 (mtp) REVERT: A 228 LYS cc_start: 0.9315 (mmmt) cc_final: 0.9100 (mmtm) REVERT: A 231 ASP cc_start: 0.9206 (t0) cc_final: 0.8980 (t0) REVERT: A 236 TYR cc_start: 0.9183 (t80) cc_final: 0.8511 (t80) REVERT: A 257 ASP cc_start: 0.9109 (m-30) cc_final: 0.8892 (m-30) REVERT: A 317 MET cc_start: 0.8771 (ptm) cc_final: 0.8001 (ptm) REVERT: A 318 ASP cc_start: 0.9247 (t0) cc_final: 0.9024 (t0) REVERT: A 322 MET cc_start: 0.8685 (mmp) cc_final: 0.7944 (tpp) REVERT: A 326 PHE cc_start: 0.9681 (m-10) cc_final: 0.8899 (m-80) REVERT: A 333 LYS cc_start: 0.9134 (tmtt) cc_final: 0.8615 (tptt) REVERT: A 348 MET cc_start: 0.9096 (ptp) cc_final: 0.8765 (ptp) REVERT: A 361 GLN cc_start: 0.8950 (tp-100) cc_final: 0.8444 (tp-100) REVERT: A 407 ILE cc_start: 0.9241 (mt) cc_final: 0.8742 (mt) REVERT: A 413 SER cc_start: 0.9394 (m) cc_final: 0.9189 (m) REVERT: A 447 ASN cc_start: 0.8427 (m-40) cc_final: 0.8120 (m-40) REVERT: A 456 LYS cc_start: 0.9134 (mtmt) cc_final: 0.8668 (ptpt) REVERT: A 458 MET cc_start: 0.9126 (mmp) cc_final: 0.8597 (mmp) REVERT: A 505 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8300 (mt-10) REVERT: A 515 ASP cc_start: 0.8858 (m-30) cc_final: 0.8503 (m-30) REVERT: A 562 LYS cc_start: 0.9795 (tttm) cc_final: 0.9456 (ttmm) REVERT: A 603 GLU cc_start: 0.8352 (pp20) cc_final: 0.8092 (tm-30) REVERT: A 632 MET cc_start: 0.8700 (mtp) cc_final: 0.8492 (mtp) REVERT: A 672 LEU cc_start: 0.9441 (mt) cc_final: 0.9196 (mt) REVERT: A 683 TYR cc_start: 0.8590 (t80) cc_final: 0.8388 (t80) REVERT: B 51 LEU cc_start: 0.9488 (tp) cc_final: 0.9124 (tp) REVERT: B 55 LEU cc_start: 0.9799 (mt) cc_final: 0.9589 (mt) REVERT: B 67 GLU cc_start: 0.9238 (tm-30) cc_final: 0.8786 (tm-30) REVERT: B 119 GLU cc_start: 0.9221 (mp0) cc_final: 0.8903 (mp0) REVERT: B 147 GLN cc_start: 0.9277 (mt0) cc_final: 0.8708 (mt0) REVERT: B 173 LEU cc_start: 0.9642 (mt) cc_final: 0.9400 (mt) REVERT: B 174 GLU cc_start: 0.7813 (tp30) cc_final: 0.7517 (tp30) REVERT: B 211 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8256 (mm-30) REVERT: B 227 MET cc_start: 0.9058 (mtt) cc_final: 0.8812 (mtt) REVERT: B 258 ILE cc_start: 0.9404 (tp) cc_final: 0.9180 (tp) REVERT: B 286 ASP cc_start: 0.8555 (m-30) cc_final: 0.7624 (m-30) REVERT: B 316 GLU cc_start: 0.9234 (tt0) cc_final: 0.8985 (tt0) REVERT: B 321 GLU cc_start: 0.8919 (pp20) cc_final: 0.8652 (pp20) REVERT: B 333 LYS cc_start: 0.9252 (tptt) cc_final: 0.8990 (ttmm) REVERT: B 362 ASP cc_start: 0.8588 (m-30) cc_final: 0.7567 (m-30) REVERT: B 370 ASN cc_start: 0.9525 (m-40) cc_final: 0.9088 (m-40) REVERT: B 398 ASP cc_start: 0.8734 (t0) cc_final: 0.8466 (t70) REVERT: B 403 ILE cc_start: 0.9569 (mp) cc_final: 0.9271 (tp) REVERT: B 406 ASP cc_start: 0.8051 (m-30) cc_final: 0.7749 (m-30) REVERT: B 410 ASN cc_start: 0.9012 (m110) cc_final: 0.8644 (m110) REVERT: B 413 SER cc_start: 0.9586 (m) cc_final: 0.9196 (t) REVERT: B 415 ASN cc_start: 0.9657 (t0) cc_final: 0.9011 (t0) REVERT: B 420 MET cc_start: 0.9555 (mmp) cc_final: 0.9342 (mmp) REVERT: B 425 ILE cc_start: 0.9386 (mt) cc_final: 0.8487 (mt) REVERT: B 445 ILE cc_start: 0.9070 (mm) cc_final: 0.8836 (mm) REVERT: B 493 MET cc_start: 0.9600 (tmm) cc_final: 0.9360 (tmm) REVERT: B 494 MET cc_start: 0.9475 (mtp) cc_final: 0.9076 (ttm) REVERT: B 599 GLU cc_start: 0.8891 (pt0) cc_final: 0.8574 (pt0) REVERT: B 601 ILE cc_start: 0.9538 (mm) cc_final: 0.8864 (mm) REVERT: B 615 MET cc_start: 0.9286 (mmm) cc_final: 0.9085 (mmp) REVERT: B 618 LEU cc_start: 0.9566 (tp) cc_final: 0.8995 (mt) REVERT: B 627 LYS cc_start: 0.9337 (tttt) cc_final: 0.8966 (tttm) REVERT: B 628 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8156 (mm-30) REVERT: B 636 LYS cc_start: 0.9677 (mmmm) cc_final: 0.9362 (mmmm) REVERT: B 640 MET cc_start: 0.9623 (tpp) cc_final: 0.8941 (tpp) REVERT: B 655 THR cc_start: 0.9501 (m) cc_final: 0.9181 (t) REVERT: B 667 LEU cc_start: 0.9584 (tp) cc_final: 0.9122 (tp) REVERT: C 110 MET cc_start: 0.7953 (mtm) cc_final: 0.7731 (mtm) REVERT: C 196 ARG cc_start: 0.8633 (ptm160) cc_final: 0.8381 (ptm-80) REVERT: C 233 ASN cc_start: 0.9246 (m110) cc_final: 0.9027 (m110) REVERT: D 137 MET cc_start: 0.8179 (mtm) cc_final: 0.7719 (mmp) REVERT: D 174 TYR cc_start: 0.8623 (t80) cc_final: 0.8417 (t80) REVERT: D 185 MET cc_start: 0.4705 (mmp) cc_final: 0.4345 (tpp) REVERT: D 211 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8660 (tm-30) REVERT: D 244 GLU cc_start: 0.9211 (tp30) cc_final: 0.8936 (tp30) outliers start: 1 outliers final: 0 residues processed: 690 average time/residue: 0.2755 time to fit residues: 283.7763 Evaluate side-chains 609 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 608 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN A 361 GLN A 365 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 249 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** 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 = 0.3667 r_free = 0.3667 target = 0.130870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.093306 restraints weight = 40036.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.096913 restraints weight = 20570.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.099262 restraints weight = 12750.988| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 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 = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.6295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16386 Z= 0.191 Angle : 0.598 7.861 22134 Z= 0.320 Chirality : 0.043 0.172 2360 Planarity : 0.004 0.049 2818 Dihedral : 10.894 173.903 2242 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.12 % Allowed : 2.10 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.18), residues: 1932 helix: 1.05 (0.15), residues: 1131 sheet: -0.61 (0.39), residues: 146 loop : 0.10 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 124 HIS 0.008 0.001 HIS B 368 PHE 0.025 0.002 PHE D 178 TYR 0.034 0.002 TYR B 574 ARG 0.005 0.001 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.03938 ( 871) hydrogen bonds : angle 4.83391 ( 2571) covalent geometry : bond 0.00410 (16386) covalent geometry : angle 0.59847 (22134) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 694 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.9541 (mp) cc_final: 0.9228 (mm) REVERT: A 14 ASN cc_start: 0.9445 (m-40) cc_final: 0.9166 (m110) REVERT: A 30 LYS cc_start: 0.9446 (tmmt) cc_final: 0.9244 (tptt) REVERT: A 54 LYS cc_start: 0.9625 (tttt) cc_final: 0.9421 (ttmm) REVERT: A 69 LEU cc_start: 0.9598 (mt) cc_final: 0.9348 (pp) REVERT: A 118 TYR cc_start: 0.9106 (t80) cc_final: 0.8891 (t80) REVERT: A 120 ASP cc_start: 0.9037 (m-30) cc_final: 0.8764 (m-30) REVERT: A 144 MET cc_start: 0.9025 (mtm) cc_final: 0.8550 (mtm) REVERT: A 172 LEU cc_start: 0.9669 (mp) cc_final: 0.9281 (mp) REVERT: A 227 MET cc_start: 0.9377 (mtp) cc_final: 0.8978 (mtp) REVERT: A 231 ASP cc_start: 0.9204 (t0) cc_final: 0.8972 (t0) REVERT: A 236 TYR cc_start: 0.9215 (t80) cc_final: 0.8623 (t80) REVERT: A 252 ASN cc_start: 0.9109 (t0) cc_final: 0.8829 (t0) REVERT: A 290 GLU cc_start: 0.9019 (tp30) cc_final: 0.8605 (tp30) REVERT: A 317 MET cc_start: 0.8699 (ptm) cc_final: 0.8060 (ptm) REVERT: A 318 ASP cc_start: 0.9098 (t0) cc_final: 0.8883 (t0) REVERT: A 322 MET cc_start: 0.8782 (mmp) cc_final: 0.8532 (mmm) REVERT: A 333 LYS cc_start: 0.9183 (tmtt) cc_final: 0.8614 (tptp) REVERT: A 348 MET cc_start: 0.9105 (ptp) cc_final: 0.8774 (ptp) REVERT: A 357 TYR cc_start: 0.8900 (m-10) cc_final: 0.8649 (m-10) REVERT: A 361 GLN cc_start: 0.9129 (tp40) cc_final: 0.8667 (tp-100) REVERT: A 395 THR cc_start: 0.9538 (p) cc_final: 0.9320 (p) REVERT: A 407 ILE cc_start: 0.9408 (mt) cc_final: 0.8846 (mt) REVERT: A 447 ASN cc_start: 0.8240 (m-40) cc_final: 0.7924 (m-40) REVERT: A 456 LYS cc_start: 0.9104 (mtmt) cc_final: 0.8704 (ptpt) REVERT: A 458 MET cc_start: 0.9147 (mmp) cc_final: 0.8608 (mmp) REVERT: A 505 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8330 (mt-10) REVERT: A 515 ASP cc_start: 0.8821 (m-30) cc_final: 0.8482 (m-30) REVERT: A 550 MET cc_start: 0.8065 (mtm) cc_final: 0.7819 (mtm) REVERT: A 562 LYS cc_start: 0.9825 (tttm) cc_final: 0.9524 (ttmm) REVERT: A 588 GLN cc_start: 0.9093 (mm-40) cc_final: 0.8754 (mm-40) REVERT: A 603 GLU cc_start: 0.8346 (pp20) cc_final: 0.8039 (tm-30) REVERT: A 604 ARG cc_start: 0.8982 (mmp80) cc_final: 0.8633 (mmp80) REVERT: A 615 MET cc_start: 0.9167 (mmp) cc_final: 0.8790 (mmp) REVERT: A 672 LEU cc_start: 0.9454 (mt) cc_final: 0.9225 (mt) REVERT: A 683 TYR cc_start: 0.8693 (t80) cc_final: 0.8232 (t80) REVERT: B 51 LEU cc_start: 0.9423 (tp) cc_final: 0.9040 (tp) REVERT: B 55 LEU cc_start: 0.9831 (mt) cc_final: 0.9599 (mt) REVERT: B 67 GLU cc_start: 0.9313 (tm-30) cc_final: 0.8866 (tm-30) REVERT: B 95 MET cc_start: 0.9304 (tpp) cc_final: 0.9007 (tpp) REVERT: B 106 LEU cc_start: 0.9632 (tp) cc_final: 0.9415 (tp) REVERT: B 115 LEU cc_start: 0.9583 (mp) cc_final: 0.9187 (mp) REVERT: B 119 GLU cc_start: 0.9210 (mp0) cc_final: 0.8845 (mp0) REVERT: B 173 LEU cc_start: 0.9640 (mt) cc_final: 0.9406 (mt) REVERT: B 211 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8274 (mm-30) REVERT: B 223 VAL cc_start: 0.9518 (m) cc_final: 0.9268 (m) REVERT: B 227 MET cc_start: 0.8891 (mtt) cc_final: 0.8685 (mtt) REVERT: B 235 ARG cc_start: 0.9213 (tpp80) cc_final: 0.8832 (mtt-85) REVERT: B 257 ASP cc_start: 0.8946 (m-30) cc_final: 0.8640 (m-30) REVERT: B 258 ILE cc_start: 0.9476 (tp) cc_final: 0.9257 (tp) REVERT: B 266 LYS cc_start: 0.9424 (mtpp) cc_final: 0.9219 (mtpp) REVERT: B 286 ASP cc_start: 0.8583 (m-30) cc_final: 0.7612 (m-30) REVERT: B 312 GLN cc_start: 0.8955 (pm20) cc_final: 0.8590 (pm20) REVERT: B 319 MET cc_start: 0.9027 (tpp) cc_final: 0.8815 (tpp) REVERT: B 321 GLU cc_start: 0.8946 (pp20) cc_final: 0.8628 (pp20) REVERT: B 333 LYS cc_start: 0.9276 (tptt) cc_final: 0.8969 (ttmm) REVERT: B 362 ASP cc_start: 0.8673 (m-30) cc_final: 0.7728 (m-30) REVERT: B 370 ASN cc_start: 0.9648 (m-40) cc_final: 0.9174 (m110) REVERT: B 373 ILE cc_start: 0.9507 (mt) cc_final: 0.9218 (tp) REVERT: B 386 LEU cc_start: 0.9396 (mt) cc_final: 0.9035 (mt) REVERT: B 398 ASP cc_start: 0.8794 (t0) cc_final: 0.8514 (t70) REVERT: B 403 ILE cc_start: 0.9552 (mp) cc_final: 0.9199 (tp) REVERT: B 406 ASP cc_start: 0.8093 (m-30) cc_final: 0.7803 (m-30) REVERT: B 410 ASN cc_start: 0.9057 (m110) cc_final: 0.8798 (m110) REVERT: B 413 SER cc_start: 0.9590 (m) cc_final: 0.9241 (t) REVERT: B 415 ASN cc_start: 0.9668 (t0) cc_final: 0.9011 (t0) REVERT: B 425 ILE cc_start: 0.9356 (mt) cc_final: 0.8601 (mt) REVERT: B 434 ASP cc_start: 0.9009 (m-30) cc_final: 0.8796 (m-30) REVERT: B 458 MET cc_start: 0.9332 (mmm) cc_final: 0.8819 (mmm) REVERT: B 467 ASN cc_start: 0.9108 (t0) cc_final: 0.8891 (t0) REVERT: B 493 MET cc_start: 0.9619 (tmm) cc_final: 0.9360 (tmm) REVERT: B 494 MET cc_start: 0.9471 (mtp) cc_final: 0.9167 (ttm) REVERT: B 548 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8367 (mm-30) REVERT: B 586 TYR cc_start: 0.9360 (m-80) cc_final: 0.9155 (m-10) REVERT: B 588 GLN cc_start: 0.9638 (mm110) cc_final: 0.9259 (mm110) REVERT: B 599 GLU cc_start: 0.8907 (pt0) cc_final: 0.8536 (pt0) REVERT: B 601 ILE cc_start: 0.9547 (mm) cc_final: 0.8801 (mm) REVERT: B 602 GLU cc_start: 0.8636 (pt0) cc_final: 0.8363 (pt0) REVERT: B 618 LEU cc_start: 0.9557 (tp) cc_final: 0.8976 (mt) REVERT: B 627 LYS cc_start: 0.9318 (tttt) cc_final: 0.8880 (tttt) REVERT: B 628 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8035 (mm-30) REVERT: B 640 MET cc_start: 0.9607 (tpp) cc_final: 0.9224 (tpp) REVERT: B 648 ILE cc_start: 0.9392 (mm) cc_final: 0.9119 (mm) REVERT: B 650 GLN cc_start: 0.8510 (mt0) cc_final: 0.7953 (mm-40) REVERT: B 655 THR cc_start: 0.9573 (m) cc_final: 0.9302 (t) REVERT: B 667 LEU cc_start: 0.9582 (tp) cc_final: 0.9118 (tp) REVERT: C 55 TYR cc_start: 0.8406 (t80) cc_final: 0.7870 (t80) REVERT: C 68 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7769 (pp20) REVERT: C 93 MET cc_start: 0.9155 (mtp) cc_final: 0.8794 (mtp) REVERT: C 110 MET cc_start: 0.7941 (mtm) cc_final: 0.7700 (mtm) REVERT: C 196 ARG cc_start: 0.8648 (ptm160) cc_final: 0.8379 (ptm-80) REVERT: C 233 ASN cc_start: 0.9287 (m110) cc_final: 0.9068 (m110) REVERT: C 241 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7816 (pm20) REVERT: D 74 MET cc_start: 0.4605 (tmm) cc_final: 0.4015 (tmm) REVERT: D 137 MET cc_start: 0.8241 (mtm) cc_final: 0.7729 (mmp) REVERT: D 189 GLU cc_start: 0.9014 (tt0) cc_final: 0.8797 (mp0) REVERT: D 211 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8740 (tm-30) REVERT: D 320 PHE cc_start: 0.8441 (m-10) cc_final: 0.8065 (m-10) outliers start: 2 outliers final: 0 residues processed: 696 average time/residue: 0.2701 time to fit residues: 278.7305 Evaluate side-chains 618 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 617 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 31 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 69 optimal weight: 0.0040 chunk 156 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 115 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 chunk 169 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 HIS B 645 GLN C 69 GLN C 249 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 ASN D 128 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.133901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.096330 restraints weight = 39759.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.100028 restraints weight = 20469.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.102389 restraints weight = 12506.356| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.6590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16386 Z= 0.153 Angle : 0.604 7.533 22134 Z= 0.320 Chirality : 0.043 0.195 2360 Planarity : 0.004 0.053 2818 Dihedral : 10.825 178.634 2242 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.06 % Allowed : 1.52 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.18), residues: 1932 helix: 1.02 (0.15), residues: 1128 sheet: -0.64 (0.39), residues: 146 loop : 0.12 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 124 HIS 0.005 0.001 HIS C 80 PHE 0.030 0.002 PHE D 168 TYR 0.030 0.001 TYR B 574 ARG 0.006 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 871) hydrogen bonds : angle 4.85490 ( 2571) covalent geometry : bond 0.00338 (16386) covalent geometry : angle 0.60400 (22134) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 695 time to evaluate : 1.741 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: 0.9510 (mp) cc_final: 0.9119 (mp) REVERT: A 14 ASN cc_start: 0.9475 (m-40) cc_final: 0.9158 (m110) REVERT: A 30 LYS cc_start: 0.9490 (tmmt) cc_final: 0.9276 (tptt) REVERT: A 69 LEU cc_start: 0.9611 (mt) cc_final: 0.9329 (pp) REVERT: A 119 GLU cc_start: 0.8988 (mp0) cc_final: 0.8527 (mp0) REVERT: A 120 ASP cc_start: 0.8942 (m-30) cc_final: 0.8729 (m-30) REVERT: A 172 LEU cc_start: 0.9609 (mp) cc_final: 0.9285 (mp) REVERT: A 190 MET cc_start: 0.9015 (mtp) cc_final: 0.8679 (mtp) REVERT: A 227 MET cc_start: 0.9373 (mtp) cc_final: 0.8978 (mtp) REVERT: A 231 ASP cc_start: 0.9186 (t0) cc_final: 0.8956 (t0) REVERT: A 236 TYR cc_start: 0.9192 (t80) cc_final: 0.8223 (t80) REVERT: A 257 ASP cc_start: 0.9185 (m-30) cc_final: 0.8909 (m-30) REVERT: A 290 GLU cc_start: 0.8993 (tp30) cc_final: 0.8635 (tm-30) REVERT: A 317 MET cc_start: 0.8584 (ptm) cc_final: 0.7944 (ptm) REVERT: A 318 ASP cc_start: 0.9062 (t0) cc_final: 0.8803 (t0) REVERT: A 322 MET cc_start: 0.8753 (mmp) cc_final: 0.8524 (mmm) REVERT: A 333 LYS cc_start: 0.9181 (tmtt) cc_final: 0.8678 (tptp) REVERT: A 357 TYR cc_start: 0.8802 (m-10) cc_final: 0.8573 (m-10) REVERT: A 361 GLN cc_start: 0.9208 (tp40) cc_final: 0.8798 (tp-100) REVERT: A 394 TYR cc_start: 0.8983 (m-10) cc_final: 0.8679 (m-10) REVERT: A 407 ILE cc_start: 0.9308 (mt) cc_final: 0.8864 (mt) REVERT: A 447 ASN cc_start: 0.8191 (m-40) cc_final: 0.7920 (m-40) REVERT: A 458 MET cc_start: 0.9063 (mmp) cc_final: 0.8549 (mmp) REVERT: A 505 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8204 (mt-10) REVERT: A 515 ASP cc_start: 0.8776 (m-30) cc_final: 0.8455 (m-30) REVERT: A 562 LYS cc_start: 0.9812 (tttm) cc_final: 0.9520 (ttmm) REVERT: A 588 GLN cc_start: 0.9080 (mm-40) cc_final: 0.8792 (mm110) REVERT: A 603 GLU cc_start: 0.8322 (pp20) cc_final: 0.8075 (tm-30) REVERT: A 604 ARG cc_start: 0.8999 (mmp80) cc_final: 0.8448 (mmp80) REVERT: A 615 MET cc_start: 0.9201 (mmp) cc_final: 0.8811 (mmm) REVERT: A 672 LEU cc_start: 0.9453 (mt) cc_final: 0.9231 (mt) REVERT: A 683 TYR cc_start: 0.8957 (t80) cc_final: 0.8477 (t80) REVERT: B 51 LEU cc_start: 0.9395 (tp) cc_final: 0.9014 (tp) REVERT: B 55 LEU cc_start: 0.9829 (mt) cc_final: 0.9606 (mt) REVERT: B 67 GLU cc_start: 0.9324 (tm-30) cc_final: 0.8836 (tm-30) REVERT: B 95 MET cc_start: 0.9220 (tpp) cc_final: 0.8424 (tpp) REVERT: B 98 PHE cc_start: 0.9595 (t80) cc_final: 0.9108 (t80) REVERT: B 119 GLU cc_start: 0.9160 (mp0) cc_final: 0.8774 (mp0) REVERT: B 209 LYS cc_start: 0.9130 (tppt) cc_final: 0.8835 (tppp) REVERT: B 211 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8183 (mm-30) REVERT: B 223 VAL cc_start: 0.9539 (m) cc_final: 0.9285 (m) REVERT: B 235 ARG cc_start: 0.9243 (tpp80) cc_final: 0.8783 (mtm-85) REVERT: B 257 ASP cc_start: 0.8939 (m-30) cc_final: 0.8622 (m-30) REVERT: B 258 ILE cc_start: 0.9480 (tp) cc_final: 0.9280 (tp) REVERT: B 286 ASP cc_start: 0.8588 (m-30) cc_final: 0.7694 (m-30) REVERT: B 290 GLU cc_start: 0.9185 (tp30) cc_final: 0.8899 (tp30) REVERT: B 321 GLU cc_start: 0.8964 (pp20) cc_final: 0.8594 (pp20) REVERT: B 333 LYS cc_start: 0.9243 (tptt) cc_final: 0.8955 (ttmm) REVERT: B 362 ASP cc_start: 0.8658 (m-30) cc_final: 0.7731 (m-30) REVERT: B 370 ASN cc_start: 0.9609 (m-40) cc_final: 0.9070 (m110) REVERT: B 373 ILE cc_start: 0.9460 (mt) cc_final: 0.9208 (tp) REVERT: B 398 ASP cc_start: 0.8787 (t0) cc_final: 0.8479 (t70) REVERT: B 403 ILE cc_start: 0.9542 (mp) cc_final: 0.9206 (tp) REVERT: B 406 ASP cc_start: 0.8063 (m-30) cc_final: 0.7797 (m-30) REVERT: B 413 SER cc_start: 0.9639 (m) cc_final: 0.9288 (t) REVERT: B 415 ASN cc_start: 0.9666 (t0) cc_final: 0.8634 (t0) REVERT: B 418 ASN cc_start: 0.9331 (m-40) cc_final: 0.8887 (m110) REVERT: B 425 ILE cc_start: 0.9374 (mt) cc_final: 0.9110 (mt) REVERT: B 458 MET cc_start: 0.9263 (mmm) cc_final: 0.8777 (mmm) REVERT: B 467 ASN cc_start: 0.9162 (t0) cc_final: 0.8927 (t0) REVERT: B 505 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8256 (mt-10) REVERT: B 548 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8374 (mm-30) REVERT: B 586 TYR cc_start: 0.9349 (m-80) cc_final: 0.8942 (m-80) REVERT: B 599 GLU cc_start: 0.8880 (pt0) cc_final: 0.8610 (pt0) REVERT: B 601 ILE cc_start: 0.9568 (mm) cc_final: 0.8800 (mm) REVERT: B 602 GLU cc_start: 0.8700 (pt0) cc_final: 0.8141 (pt0) REVERT: B 618 LEU cc_start: 0.9546 (tp) cc_final: 0.8925 (mt) REVERT: B 627 LYS cc_start: 0.9346 (tttt) cc_final: 0.8827 (tttp) REVERT: B 628 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8345 (mm-30) REVERT: B 632 MET cc_start: 0.9034 (mtp) cc_final: 0.8712 (mtp) REVERT: B 633 ASP cc_start: 0.8950 (t0) cc_final: 0.8440 (t0) REVERT: B 636 LYS cc_start: 0.9622 (mmmm) cc_final: 0.9382 (mmtp) REVERT: B 640 MET cc_start: 0.9608 (tpp) cc_final: 0.9201 (tpp) REVERT: B 655 THR cc_start: 0.9524 (m) cc_final: 0.9245 (t) REVERT: B 667 LEU cc_start: 0.9585 (tp) cc_final: 0.9107 (tp) REVERT: C 55 TYR cc_start: 0.8311 (t80) cc_final: 0.7718 (t80) REVERT: C 68 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7745 (pp20) REVERT: C 93 MET cc_start: 0.9227 (mtp) cc_final: 0.8847 (mtp) REVERT: C 110 MET cc_start: 0.7853 (mtm) cc_final: 0.7624 (mtm) REVERT: C 196 ARG cc_start: 0.8679 (ptm160) cc_final: 0.8395 (ptm-80) REVERT: C 233 ASN cc_start: 0.9295 (m110) cc_final: 0.9080 (m110) REVERT: D 74 MET cc_start: 0.4589 (tmm) cc_final: 0.4275 (tmm) REVERT: D 137 MET cc_start: 0.8207 (mtm) cc_final: 0.7574 (mmp) REVERT: D 149 ASP cc_start: 0.9042 (m-30) cc_final: 0.8772 (m-30) REVERT: D 174 TYR cc_start: 0.8604 (t80) cc_final: 0.8181 (t80) REVERT: D 189 GLU cc_start: 0.9071 (tt0) cc_final: 0.8839 (mp0) REVERT: D 315 LEU cc_start: 0.8656 (tp) cc_final: 0.8423 (tt) outliers start: 1 outliers final: 0 residues processed: 696 average time/residue: 0.2619 time to fit residues: 271.0797 Evaluate side-chains 613 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 613 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 39 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 chunk 23 optimal weight: 0.0040 chunk 40 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 184 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN A 645 GLN ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN B 588 GLN B 645 GLN C 69 GLN C 249 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.133239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.095995 restraints weight = 39667.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.099662 restraints weight = 20574.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.101987 restraints weight = 12669.414| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.6857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16386 Z= 0.138 Angle : 0.596 7.753 22134 Z= 0.314 Chirality : 0.042 0.188 2360 Planarity : 0.004 0.054 2818 Dihedral : 10.760 178.857 2242 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.06 % Allowed : 0.99 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.19), residues: 1932 helix: 1.12 (0.15), residues: 1113 sheet: -0.67 (0.39), residues: 150 loop : 0.12 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 124 HIS 0.005 0.001 HIS B 313 PHE 0.035 0.002 PHE D 109 TYR 0.024 0.001 TYR A 394 ARG 0.006 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.03818 ( 871) hydrogen bonds : angle 4.79967 ( 2571) covalent geometry : bond 0.00306 (16386) covalent geometry : angle 0.59552 (22134) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 692 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.9514 (m-40) cc_final: 0.9178 (m110) REVERT: A 30 LYS cc_start: 0.9489 (tmmt) cc_final: 0.9285 (tptt) REVERT: A 69 LEU cc_start: 0.9632 (mt) cc_final: 0.9334 (pp) REVERT: A 119 GLU cc_start: 0.8984 (mp0) cc_final: 0.8515 (mp0) REVERT: A 147 GLN cc_start: 0.8956 (mt0) cc_final: 0.8321 (mt0) REVERT: A 172 LEU cc_start: 0.9620 (mp) cc_final: 0.9259 (mp) REVERT: A 190 MET cc_start: 0.8984 (mtp) cc_final: 0.8746 (mtp) REVERT: A 227 MET cc_start: 0.9378 (mtp) cc_final: 0.8950 (mtp) REVERT: A 231 ASP cc_start: 0.9180 (t0) cc_final: 0.8961 (t0) REVERT: A 236 TYR cc_start: 0.9196 (t80) cc_final: 0.8216 (t80) REVERT: A 257 ASP cc_start: 0.9227 (m-30) cc_final: 0.8981 (m-30) REVERT: A 290 GLU cc_start: 0.8962 (tp30) cc_final: 0.8534 (tp30) REVERT: A 318 ASP cc_start: 0.8936 (t0) cc_final: 0.8626 (t0) REVERT: A 322 MET cc_start: 0.8718 (mmp) cc_final: 0.8498 (tpp) REVERT: A 333 LYS cc_start: 0.9415 (tmtt) cc_final: 0.8865 (tptp) REVERT: A 357 TYR cc_start: 0.8879 (m-10) cc_final: 0.8547 (m-10) REVERT: A 394 TYR cc_start: 0.8971 (m-10) cc_final: 0.8516 (m-10) REVERT: A 405 LEU cc_start: 0.8807 (mt) cc_final: 0.8540 (mt) REVERT: A 407 ILE cc_start: 0.9346 (mt) cc_final: 0.8908 (mt) REVERT: A 410 ASN cc_start: 0.8974 (OUTLIER) cc_final: 0.8462 (t160) REVERT: A 447 ASN cc_start: 0.8131 (m-40) cc_final: 0.7870 (m-40) REVERT: A 458 MET cc_start: 0.9061 (mmp) cc_final: 0.8622 (mmp) REVERT: A 505 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8301 (mt-10) REVERT: A 515 ASP cc_start: 0.8763 (m-30) cc_final: 0.8344 (m-30) REVERT: A 561 LEU cc_start: 0.9567 (tp) cc_final: 0.9365 (tp) REVERT: A 562 LYS cc_start: 0.9819 (tttm) cc_final: 0.9529 (ttmm) REVERT: A 603 GLU cc_start: 0.8341 (pp20) cc_final: 0.8071 (tm-30) REVERT: A 604 ARG cc_start: 0.9014 (mmp80) cc_final: 0.8612 (mmp80) REVERT: A 615 MET cc_start: 0.9195 (mmp) cc_final: 0.8868 (mmp) REVERT: A 632 MET cc_start: 0.8770 (mtp) cc_final: 0.8536 (mtp) REVERT: A 672 LEU cc_start: 0.9466 (mt) cc_final: 0.9238 (mt) REVERT: A 683 TYR cc_start: 0.8872 (t80) cc_final: 0.8272 (t80) REVERT: A 686 ARG cc_start: 0.6512 (tpt170) cc_final: 0.5831 (tpt170) REVERT: B 51 LEU cc_start: 0.9353 (tp) cc_final: 0.8980 (tp) REVERT: B 55 LEU cc_start: 0.9834 (mt) cc_final: 0.9600 (mt) REVERT: B 67 GLU cc_start: 0.9308 (tm-30) cc_final: 0.8799 (tm-30) REVERT: B 95 MET cc_start: 0.9148 (tpp) cc_final: 0.8365 (tpp) REVERT: B 98 PHE cc_start: 0.9551 (t80) cc_final: 0.9011 (t80) REVERT: B 106 LEU cc_start: 0.9531 (tp) cc_final: 0.9329 (tp) REVERT: B 115 LEU cc_start: 0.9326 (mp) cc_final: 0.9052 (mp) REVERT: B 116 GLU cc_start: 0.8413 (mp0) cc_final: 0.8195 (mp0) REVERT: B 119 GLU cc_start: 0.9165 (mp0) cc_final: 0.8793 (mp0) REVERT: B 147 GLN cc_start: 0.9326 (mt0) cc_final: 0.8799 (mt0) REVERT: B 209 LYS cc_start: 0.9085 (tppt) cc_final: 0.8821 (tppp) REVERT: B 211 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8132 (mm-30) REVERT: B 235 ARG cc_start: 0.9243 (tpp80) cc_final: 0.8754 (mtm-85) REVERT: B 257 ASP cc_start: 0.8944 (m-30) cc_final: 0.8643 (m-30) REVERT: B 258 ILE cc_start: 0.9492 (tp) cc_final: 0.9280 (tp) REVERT: B 286 ASP cc_start: 0.8593 (m-30) cc_final: 0.7733 (m-30) REVERT: B 290 GLU cc_start: 0.9258 (tp30) cc_final: 0.8923 (tp30) REVERT: B 333 LYS cc_start: 0.9239 (tptt) cc_final: 0.8954 (ttmm) REVERT: B 362 ASP cc_start: 0.8658 (m-30) cc_final: 0.7772 (m-30) REVERT: B 373 ILE cc_start: 0.9436 (mt) cc_final: 0.9158 (tp) REVERT: B 398 ASP cc_start: 0.8767 (t0) cc_final: 0.8437 (t70) REVERT: B 403 ILE cc_start: 0.9507 (mp) cc_final: 0.9164 (tp) REVERT: B 413 SER cc_start: 0.9643 (m) cc_final: 0.9227 (t) REVERT: B 415 ASN cc_start: 0.9636 (t0) cc_final: 0.8484 (t0) REVERT: B 418 ASN cc_start: 0.9285 (m-40) cc_final: 0.8885 (m-40) REVERT: B 434 ASP cc_start: 0.9010 (m-30) cc_final: 0.8766 (m-30) REVERT: B 458 MET cc_start: 0.9273 (mmm) cc_final: 0.8732 (mmm) REVERT: B 505 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8218 (mt-10) REVERT: B 548 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8395 (mm-30) REVERT: B 586 TYR cc_start: 0.9185 (m-80) cc_final: 0.8970 (m-80) REVERT: B 598 MET cc_start: 0.9134 (mtm) cc_final: 0.8884 (mtm) REVERT: B 599 GLU cc_start: 0.8918 (pt0) cc_final: 0.8513 (pt0) REVERT: B 601 ILE cc_start: 0.9545 (mm) cc_final: 0.8780 (mm) REVERT: B 602 GLU cc_start: 0.8631 (pt0) cc_final: 0.8176 (pt0) REVERT: B 610 LYS cc_start: 0.9117 (tmtt) cc_final: 0.8808 (tmtt) REVERT: B 618 LEU cc_start: 0.9544 (tp) cc_final: 0.8931 (mt) REVERT: B 627 LYS cc_start: 0.9340 (tttt) cc_final: 0.8815 (tttp) REVERT: B 628 GLU cc_start: 0.8633 (mm-30) cc_final: 0.7727 (mm-30) REVERT: B 632 MET cc_start: 0.9027 (mtp) cc_final: 0.8722 (mtp) REVERT: B 633 ASP cc_start: 0.8813 (t0) cc_final: 0.8484 (t0) REVERT: B 640 MET cc_start: 0.9591 (tpp) cc_final: 0.9240 (tpp) REVERT: B 646 GLN cc_start: 0.9227 (pt0) cc_final: 0.8975 (pt0) REVERT: B 650 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8188 (mm-40) REVERT: B 655 THR cc_start: 0.9527 (m) cc_final: 0.9252 (t) REVERT: B 667 LEU cc_start: 0.9590 (tp) cc_final: 0.9120 (tp) REVERT: B 668 ASN cc_start: 0.9364 (m-40) cc_final: 0.9126 (m110) REVERT: C 55 TYR cc_start: 0.8180 (t80) cc_final: 0.7659 (t80) REVERT: C 68 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7716 (pp20) REVERT: C 93 MET cc_start: 0.9312 (mtp) cc_final: 0.8992 (mtp) REVERT: C 110 MET cc_start: 0.7817 (mtm) cc_final: 0.7579 (mtm) REVERT: C 196 ARG cc_start: 0.8684 (ptm160) cc_final: 0.8403 (ptm-80) REVERT: C 233 ASN cc_start: 0.9274 (m110) cc_final: 0.9059 (m110) REVERT: D 74 MET cc_start: 0.4508 (tmm) cc_final: 0.4101 (tmm) REVERT: D 137 MET cc_start: 0.8259 (mtm) cc_final: 0.7491 (mmp) REVERT: D 149 ASP cc_start: 0.9001 (m-30) cc_final: 0.8738 (m-30) REVERT: D 174 TYR cc_start: 0.8627 (t80) cc_final: 0.8257 (t80) REVERT: D 189 GLU cc_start: 0.9120 (tt0) cc_final: 0.8835 (mp0) outliers start: 1 outliers final: 0 residues processed: 693 average time/residue: 0.2737 time to fit residues: 282.3037 Evaluate side-chains 604 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 603 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 180 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN D 28 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.133353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.096303 restraints weight = 39642.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.099892 restraints weight = 20859.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.102225 restraints weight = 12953.858| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.7066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16386 Z= 0.141 Angle : 0.616 7.448 22134 Z= 0.325 Chirality : 0.043 0.271 2360 Planarity : 0.004 0.056 2818 Dihedral : 10.709 178.264 2242 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.19), residues: 1932 helix: 1.10 (0.15), residues: 1113 sheet: -0.72 (0.39), residues: 148 loop : 0.08 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 124 HIS 0.003 0.001 HIS B 255 PHE 0.032 0.002 PHE D 109 TYR 0.024 0.001 TYR B 574 ARG 0.007 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.03783 ( 871) hydrogen bonds : angle 4.80962 ( 2571) covalent geometry : bond 0.00315 (16386) covalent geometry : angle 0.61571 (22134) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 684 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.9551 (m-40) cc_final: 0.9199 (m110) REVERT: A 27 ASP cc_start: 0.9421 (p0) cc_final: 0.9216 (p0) REVERT: A 30 LYS cc_start: 0.9501 (tmmt) cc_final: 0.9279 (tptt) REVERT: A 69 LEU cc_start: 0.9620 (mt) cc_final: 0.9329 (pp) REVERT: A 95 MET cc_start: 0.9069 (mmm) cc_final: 0.8861 (tpp) REVERT: A 147 GLN cc_start: 0.8976 (mt0) cc_final: 0.8373 (mt0) REVERT: A 172 LEU cc_start: 0.9652 (mp) cc_final: 0.9313 (mp) REVERT: A 190 MET cc_start: 0.9008 (mtp) cc_final: 0.8769 (mtp) REVERT: A 227 MET cc_start: 0.9380 (mtp) cc_final: 0.8934 (mtp) REVERT: A 236 TYR cc_start: 0.9184 (t80) cc_final: 0.8281 (t80) REVERT: A 257 ASP cc_start: 0.9172 (m-30) cc_final: 0.8935 (m-30) REVERT: A 259 ASN cc_start: 0.9187 (m-40) cc_final: 0.8863 (m-40) REVERT: A 317 MET cc_start: 0.8569 (ptm) cc_final: 0.8368 (ptm) REVERT: A 318 ASP cc_start: 0.8563 (t0) cc_final: 0.8135 (t0) REVERT: A 333 LYS cc_start: 0.9389 (tmtt) cc_final: 0.8883 (tptp) REVERT: A 345 LYS cc_start: 0.9535 (tttt) cc_final: 0.9302 (ttpt) REVERT: A 357 TYR cc_start: 0.8863 (m-10) cc_final: 0.8498 (m-10) REVERT: A 393 SER cc_start: 0.8532 (p) cc_final: 0.7911 (p) REVERT: A 405 LEU cc_start: 0.8911 (mt) cc_final: 0.8440 (mt) REVERT: A 407 ILE cc_start: 0.9295 (mt) cc_final: 0.8887 (mt) REVERT: A 447 ASN cc_start: 0.8090 (m-40) cc_final: 0.7865 (m-40) REVERT: A 458 MET cc_start: 0.9012 (mmp) cc_final: 0.8569 (mmp) REVERT: A 501 GLN cc_start: 0.9439 (tt0) cc_final: 0.8796 (tm-30) REVERT: A 505 GLU cc_start: 0.8934 (mt-10) cc_final: 0.7882 (mt-10) REVERT: A 515 ASP cc_start: 0.8753 (m-30) cc_final: 0.8353 (m-30) REVERT: A 562 LYS cc_start: 0.9817 (tttm) cc_final: 0.9549 (ttmm) REVERT: A 603 GLU cc_start: 0.8301 (pp20) cc_final: 0.8056 (tm-30) REVERT: A 604 ARG cc_start: 0.9020 (mmp80) cc_final: 0.8583 (mmp80) REVERT: A 606 TYR cc_start: 0.8076 (m-80) cc_final: 0.7865 (m-80) REVERT: A 615 MET cc_start: 0.9192 (mmp) cc_final: 0.8875 (mmp) REVERT: A 632 MET cc_start: 0.8708 (mtp) cc_final: 0.8471 (mtp) REVERT: A 683 TYR cc_start: 0.8725 (t80) cc_final: 0.7996 (t80) REVERT: B 51 LEU cc_start: 0.9345 (tp) cc_final: 0.8990 (tp) REVERT: B 55 LEU cc_start: 0.9836 (mt) cc_final: 0.9614 (mt) REVERT: B 67 GLU cc_start: 0.9291 (tm-30) cc_final: 0.8832 (tm-30) REVERT: B 71 LEU cc_start: 0.9545 (mm) cc_final: 0.9269 (mp) REVERT: B 95 MET cc_start: 0.9099 (tpp) cc_final: 0.8061 (tpp) REVERT: B 98 PHE cc_start: 0.9548 (t80) cc_final: 0.8988 (t80) REVERT: B 106 LEU cc_start: 0.9540 (tp) cc_final: 0.9314 (tp) REVERT: B 115 LEU cc_start: 0.9395 (mp) cc_final: 0.9141 (mp) REVERT: B 116 GLU cc_start: 0.8343 (mp0) cc_final: 0.8114 (mp0) REVERT: B 119 GLU cc_start: 0.9156 (mp0) cc_final: 0.8754 (mp0) REVERT: B 147 GLN cc_start: 0.9322 (mt0) cc_final: 0.8934 (mt0) REVERT: B 209 LYS cc_start: 0.9114 (tppt) cc_final: 0.8905 (tptp) REVERT: B 211 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8077 (mm-30) REVERT: B 257 ASP cc_start: 0.8919 (m-30) cc_final: 0.8634 (m-30) REVERT: B 258 ILE cc_start: 0.9502 (tp) cc_final: 0.9297 (tp) REVERT: B 276 LYS cc_start: 0.9438 (mmpt) cc_final: 0.9207 (mmmt) REVERT: B 286 ASP cc_start: 0.8607 (m-30) cc_final: 0.7749 (m-30) REVERT: B 290 GLU cc_start: 0.9246 (tp30) cc_final: 0.8908 (tp30) REVERT: B 322 MET cc_start: 0.9411 (tpt) cc_final: 0.9046 (mmm) REVERT: B 333 LYS cc_start: 0.9239 (tptt) cc_final: 0.8927 (ttmm) REVERT: B 362 ASP cc_start: 0.8635 (m-30) cc_final: 0.7699 (m-30) REVERT: B 373 ILE cc_start: 0.9402 (mt) cc_final: 0.9151 (tp) REVERT: B 393 SER cc_start: 0.9600 (t) cc_final: 0.9323 (p) REVERT: B 398 ASP cc_start: 0.8741 (t0) cc_final: 0.8393 (t70) REVERT: B 413 SER cc_start: 0.9654 (m) cc_final: 0.9256 (t) REVERT: B 415 ASN cc_start: 0.9611 (t0) cc_final: 0.8440 (t0) REVERT: B 417 LEU cc_start: 0.9602 (tt) cc_final: 0.9397 (tt) REVERT: B 418 ASN cc_start: 0.9259 (m-40) cc_final: 0.8830 (m-40) REVERT: B 458 MET cc_start: 0.9232 (mmm) cc_final: 0.8743 (mmm) REVERT: B 467 ASN cc_start: 0.9088 (t0) cc_final: 0.8870 (t0) REVERT: B 501 GLN cc_start: 0.9455 (tt0) cc_final: 0.9204 (tt0) REVERT: B 505 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8498 (mt-10) REVERT: B 548 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8346 (mm-30) REVERT: B 586 TYR cc_start: 0.9294 (m-80) cc_final: 0.8858 (m-80) REVERT: B 598 MET cc_start: 0.9117 (mtm) cc_final: 0.8855 (mtm) REVERT: B 599 GLU cc_start: 0.8903 (pt0) cc_final: 0.8494 (pt0) REVERT: B 601 ILE cc_start: 0.9482 (mm) cc_final: 0.8694 (mm) REVERT: B 610 LYS cc_start: 0.9098 (tmtt) cc_final: 0.8748 (tmtt) REVERT: B 613 TYR cc_start: 0.8927 (t80) cc_final: 0.8668 (t80) REVERT: B 618 LEU cc_start: 0.9527 (tp) cc_final: 0.8897 (mt) REVERT: B 627 LYS cc_start: 0.9388 (tttt) cc_final: 0.8911 (tttp) REVERT: B 628 GLU cc_start: 0.8691 (mm-30) cc_final: 0.7711 (mm-30) REVERT: B 632 MET cc_start: 0.9009 (mtp) cc_final: 0.8734 (mtp) REVERT: B 633 ASP cc_start: 0.8728 (t0) cc_final: 0.7434 (t0) REVERT: B 636 LYS cc_start: 0.9620 (mmtp) cc_final: 0.9253 (mmtm) REVERT: B 640 MET cc_start: 0.9584 (tpp) cc_final: 0.9228 (tpp) REVERT: B 646 GLN cc_start: 0.9154 (pt0) cc_final: 0.8933 (pt0) REVERT: B 650 GLN cc_start: 0.8456 (mm-40) cc_final: 0.8235 (mm-40) REVERT: B 655 THR cc_start: 0.9546 (m) cc_final: 0.9273 (t) REVERT: B 667 LEU cc_start: 0.9598 (tp) cc_final: 0.9121 (tp) REVERT: C 55 TYR cc_start: 0.8241 (t80) cc_final: 0.7785 (t80) REVERT: C 68 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7707 (pp20) REVERT: C 110 MET cc_start: 0.7828 (mtm) cc_final: 0.7564 (mtm) REVERT: C 118 ILE cc_start: 0.8343 (mm) cc_final: 0.8101 (mm) REVERT: C 196 ARG cc_start: 0.8664 (ptm160) cc_final: 0.8377 (ptm-80) REVERT: D 137 MET cc_start: 0.8130 (mtm) cc_final: 0.7289 (mmp) REVERT: D 174 TYR cc_start: 0.8537 (t80) cc_final: 0.8153 (t80) REVERT: D 189 GLU cc_start: 0.9166 (tt0) cc_final: 0.8919 (mp0) REVERT: D 278 GLU cc_start: 0.6350 (pm20) cc_final: 0.6099 (pp20) outliers start: 0 outliers final: 0 residues processed: 684 average time/residue: 0.2627 time to fit residues: 268.0187 Evaluate side-chains 591 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 591 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 111 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 182 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 188 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 242 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN C 91 ASN C 249 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 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 = 0.3792 r_free = 0.3792 target = 0.138857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.101334 restraints weight = 39646.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.105073 restraints weight = 20734.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107511 restraints weight = 12785.882| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3314 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.7269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16386 Z= 0.139 Angle : 0.628 9.301 22134 Z= 0.334 Chirality : 0.043 0.270 2360 Planarity : 0.004 0.056 2818 Dihedral : 10.595 175.397 2242 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.19), residues: 1932 helix: 1.06 (0.15), residues: 1121 sheet: -0.60 (0.40), residues: 142 loop : 0.11 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 124 HIS 0.006 0.001 HIS C 201 PHE 0.031 0.002 PHE D 109 TYR 0.040 0.001 TYR D 130 ARG 0.007 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 871) hydrogen bonds : angle 4.82181 ( 2571) covalent geometry : bond 0.00310 (16386) covalent geometry : angle 0.62849 (22134) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 669 time to evaluate : 2.042 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: A 14 ASN cc_start: 0.9555 (m-40) cc_final: 0.9219 (m110) REVERT: A 27 ASP cc_start: 0.9362 (p0) cc_final: 0.9141 (p0) REVERT: A 30 LYS cc_start: 0.9468 (tmmt) cc_final: 0.9251 (tptt) REVERT: A 69 LEU cc_start: 0.9627 (mt) cc_final: 0.9318 (pp) REVERT: A 99 LYS cc_start: 0.9442 (mmtp) cc_final: 0.9048 (mttt) REVERT: A 172 LEU cc_start: 0.9666 (mp) cc_final: 0.9323 (mp) REVERT: A 190 MET cc_start: 0.8935 (mtp) cc_final: 0.8735 (mtp) REVERT: A 227 MET cc_start: 0.9378 (mtp) cc_final: 0.8949 (mtp) REVERT: A 235 ARG cc_start: 0.9121 (ttm-80) cc_final: 0.8748 (mtp85) REVERT: A 236 TYR cc_start: 0.9155 (t80) cc_final: 0.8074 (t80) REVERT: A 257 ASP cc_start: 0.9137 (m-30) cc_final: 0.8906 (m-30) REVERT: A 259 ASN cc_start: 0.9180 (m-40) cc_final: 0.8880 (m-40) REVERT: A 290 GLU cc_start: 0.8933 (mp0) cc_final: 0.8685 (mp0) REVERT: A 318 ASP cc_start: 0.8554 (t0) cc_final: 0.8047 (t0) REVERT: A 333 LYS cc_start: 0.9440 (tmtt) cc_final: 0.9002 (tptp) REVERT: A 357 TYR cc_start: 0.8778 (m-10) cc_final: 0.8454 (m-10) REVERT: A 370 ASN cc_start: 0.9403 (m110) cc_final: 0.8948 (m110) REVERT: A 393 SER cc_start: 0.8638 (p) cc_final: 0.8146 (p) REVERT: A 394 TYR cc_start: 0.9047 (m-80) cc_final: 0.8539 (m-10) REVERT: A 407 ILE cc_start: 0.9315 (mt) cc_final: 0.8910 (mt) REVERT: A 447 ASN cc_start: 0.8117 (m-40) cc_final: 0.7883 (m-40) REVERT: A 458 MET cc_start: 0.8983 (mmp) cc_final: 0.8535 (mmp) REVERT: A 494 MET cc_start: 0.8867 (mmt) cc_final: 0.8465 (mmt) REVERT: A 501 GLN cc_start: 0.9443 (tt0) cc_final: 0.8810 (tm-30) REVERT: A 505 GLU cc_start: 0.8909 (mt-10) cc_final: 0.7820 (mt-10) REVERT: A 515 ASP cc_start: 0.8762 (m-30) cc_final: 0.8379 (m-30) REVERT: A 562 LYS cc_start: 0.9814 (tttm) cc_final: 0.9445 (tppt) REVERT: A 603 GLU cc_start: 0.8207 (pp20) cc_final: 0.7947 (tm-30) REVERT: A 604 ARG cc_start: 0.9005 (mmp80) cc_final: 0.8608 (mmp80) REVERT: A 615 MET cc_start: 0.9147 (mmp) cc_final: 0.8881 (mmp) REVERT: A 632 MET cc_start: 0.8658 (mtp) cc_final: 0.7721 (mtp) REVERT: A 675 HIS cc_start: 0.9346 (t-90) cc_final: 0.8639 (t-90) REVERT: B 51 LEU cc_start: 0.9292 (tp) cc_final: 0.8956 (tp) REVERT: B 55 LEU cc_start: 0.9836 (mt) cc_final: 0.9604 (mt) REVERT: B 67 GLU cc_start: 0.9293 (tm-30) cc_final: 0.8824 (tm-30) REVERT: B 71 LEU cc_start: 0.9531 (mm) cc_final: 0.9324 (mp) REVERT: B 95 MET cc_start: 0.9110 (tpp) cc_final: 0.8472 (tpp) REVERT: B 98 PHE cc_start: 0.9543 (t80) cc_final: 0.9076 (t80) REVERT: B 119 GLU cc_start: 0.9137 (mp0) cc_final: 0.8713 (mp0) REVERT: B 147 GLN cc_start: 0.9378 (mt0) cc_final: 0.9089 (mt0) REVERT: B 174 GLU cc_start: 0.7956 (tp30) cc_final: 0.7703 (tp30) REVERT: B 209 LYS cc_start: 0.9097 (tppt) cc_final: 0.8816 (tppp) REVERT: B 211 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8180 (mm-30) REVERT: B 251 LEU cc_start: 0.9349 (tp) cc_final: 0.9138 (tp) REVERT: B 257 ASP cc_start: 0.8917 (m-30) cc_final: 0.8643 (m-30) REVERT: B 258 ILE cc_start: 0.9503 (tp) cc_final: 0.9269 (tp) REVERT: B 276 LYS cc_start: 0.9390 (mmpt) cc_final: 0.9167 (mmmt) REVERT: B 286 ASP cc_start: 0.8558 (m-30) cc_final: 0.7721 (m-30) REVERT: B 290 GLU cc_start: 0.9209 (tp30) cc_final: 0.8855 (tp30) REVERT: B 312 GLN cc_start: 0.9076 (pm20) cc_final: 0.8836 (pm20) REVERT: B 333 LYS cc_start: 0.9241 (tptt) cc_final: 0.8960 (ttmm) REVERT: B 362 ASP cc_start: 0.8584 (m-30) cc_final: 0.7601 (m-30) REVERT: B 373 ILE cc_start: 0.9363 (mt) cc_final: 0.9117 (tp) REVERT: B 393 SER cc_start: 0.9578 (t) cc_final: 0.9284 (p) REVERT: B 398 ASP cc_start: 0.8632 (t0) cc_final: 0.8307 (t70) REVERT: B 403 ILE cc_start: 0.9451 (mp) cc_final: 0.9216 (tp) REVERT: B 413 SER cc_start: 0.9631 (m) cc_final: 0.9228 (t) REVERT: B 415 ASN cc_start: 0.9620 (t0) cc_final: 0.8670 (t0) REVERT: B 434 ASP cc_start: 0.8970 (m-30) cc_final: 0.8769 (m-30) REVERT: B 458 MET cc_start: 0.9192 (mmm) cc_final: 0.8692 (mmm) REVERT: B 467 ASN cc_start: 0.9136 (t0) cc_final: 0.8923 (t0) REVERT: B 501 GLN cc_start: 0.9422 (tt0) cc_final: 0.9156 (tt0) REVERT: B 505 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8502 (mt-10) REVERT: B 586 TYR cc_start: 0.9256 (m-80) cc_final: 0.8849 (m-80) REVERT: B 599 GLU cc_start: 0.8840 (pt0) cc_final: 0.8426 (pt0) REVERT: B 601 ILE cc_start: 0.9434 (mm) cc_final: 0.8607 (mm) REVERT: B 604 ARG cc_start: 0.9309 (mmm160) cc_final: 0.8964 (mmp80) REVERT: B 610 LYS cc_start: 0.9119 (tmtt) cc_final: 0.8777 (tmtt) REVERT: B 613 TYR cc_start: 0.8802 (t80) cc_final: 0.8598 (t80) REVERT: B 618 LEU cc_start: 0.9476 (tp) cc_final: 0.8895 (mt) REVERT: B 626 TYR cc_start: 0.8580 (m-80) cc_final: 0.8064 (m-80) REVERT: B 627 LYS cc_start: 0.9373 (tttt) cc_final: 0.8852 (tttp) REVERT: B 632 MET cc_start: 0.8887 (mtp) cc_final: 0.8665 (mtp) REVERT: B 633 ASP cc_start: 0.8591 (t0) cc_final: 0.7522 (t0) REVERT: B 636 LYS cc_start: 0.9628 (mmtp) cc_final: 0.9244 (mmtm) REVERT: B 640 MET cc_start: 0.9523 (tpp) cc_final: 0.9183 (tpp) REVERT: B 646 GLN cc_start: 0.9101 (pt0) cc_final: 0.8838 (pt0) REVERT: B 655 THR cc_start: 0.9751 (m) cc_final: 0.9539 (t) REVERT: B 667 LEU cc_start: 0.9585 (tp) cc_final: 0.9150 (tp) REVERT: C 55 TYR cc_start: 0.8232 (t80) cc_final: 0.7733 (t80) REVERT: C 68 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7704 (pp20) REVERT: C 118 ILE cc_start: 0.8279 (mm) cc_final: 0.8067 (mm) REVERT: C 196 ARG cc_start: 0.8673 (ptm160) cc_final: 0.8366 (ptm-80) REVERT: D 74 MET cc_start: 0.3841 (tmm) cc_final: 0.3541 (tmm) REVERT: D 137 MET cc_start: 0.8173 (mtm) cc_final: 0.7307 (mmp) REVERT: D 149 ASP cc_start: 0.8918 (m-30) cc_final: 0.8692 (m-30) REVERT: D 174 TYR cc_start: 0.8547 (t80) cc_final: 0.8182 (t80) REVERT: D 189 GLU cc_start: 0.9166 (tt0) cc_final: 0.8919 (mp0) REVERT: D 244 GLU cc_start: 0.9095 (tp30) cc_final: 0.8840 (tp30) outliers start: 0 outliers final: 0 residues processed: 669 average time/residue: 0.2659 time to fit residues: 266.6112 Evaluate side-chains 595 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 595 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 137 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 160 optimal weight: 20.0000 chunk 106 optimal weight: 0.0030 chunk 120 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 119 ASN ** D 132 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 = 0.3710 r_free = 0.3710 target = 0.133508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.096259 restraints weight = 40277.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.099879 restraints weight = 20913.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.102243 restraints weight = 12756.300| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 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 = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.7409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16386 Z= 0.175 Angle : 0.652 9.834 22134 Z= 0.344 Chirality : 0.044 0.267 2360 Planarity : 0.004 0.058 2818 Dihedral : 10.582 171.969 2242 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.19), residues: 1932 helix: 1.03 (0.15), residues: 1127 sheet: -0.70 (0.40), residues: 144 loop : 0.09 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 124 HIS 0.005 0.001 HIS C 201 PHE 0.031 0.002 PHE D 109 TYR 0.029 0.002 TYR D 130 ARG 0.008 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 871) hydrogen bonds : angle 4.85749 ( 2571) covalent geometry : bond 0.00385 (16386) covalent geometry : angle 0.65211 (22134) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 669 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.9597 (m-40) cc_final: 0.9268 (m110) REVERT: A 27 ASP cc_start: 0.9413 (p0) cc_final: 0.9207 (p0) REVERT: A 30 LYS cc_start: 0.9511 (tmmt) cc_final: 0.9282 (tptt) REVERT: A 99 LYS cc_start: 0.9246 (mmtp) cc_final: 0.8947 (mttt) REVERT: A 119 GLU cc_start: 0.8990 (mp0) cc_final: 0.8542 (mp0) REVERT: A 120 ASP cc_start: 0.8999 (m-30) cc_final: 0.8723 (m-30) REVERT: A 147 GLN cc_start: 0.9091 (mt0) cc_final: 0.8814 (mt0) REVERT: A 166 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8312 (mm-30) REVERT: A 172 LEU cc_start: 0.9667 (mp) cc_final: 0.9314 (mp) REVERT: A 190 MET cc_start: 0.9034 (mtp) cc_final: 0.8675 (mtp) REVERT: A 227 MET cc_start: 0.9359 (mtp) cc_final: 0.8981 (mtp) REVERT: A 236 TYR cc_start: 0.9219 (t80) cc_final: 0.8150 (t80) REVERT: A 257 ASP cc_start: 0.9138 (m-30) cc_final: 0.8868 (m-30) REVERT: A 290 GLU cc_start: 0.8999 (mp0) cc_final: 0.8720 (mp0) REVERT: A 318 ASP cc_start: 0.8872 (t0) cc_final: 0.8580 (t0) REVERT: A 333 LYS cc_start: 0.9405 (tmtt) cc_final: 0.8982 (tptp) REVERT: A 370 ASN cc_start: 0.9427 (m110) cc_final: 0.8944 (m110) REVERT: A 407 ILE cc_start: 0.9311 (mt) cc_final: 0.8879 (mt) REVERT: A 447 ASN cc_start: 0.8150 (m-40) cc_final: 0.7865 (m-40) REVERT: A 458 MET cc_start: 0.9073 (mmp) cc_final: 0.8615 (mmp) REVERT: A 479 TYR cc_start: 0.9052 (t80) cc_final: 0.8767 (t80) REVERT: A 494 MET cc_start: 0.8932 (mmt) cc_final: 0.8489 (mmt) REVERT: A 501 GLN cc_start: 0.9455 (tt0) cc_final: 0.8839 (tm-30) REVERT: A 505 GLU cc_start: 0.8903 (mt-10) cc_final: 0.7791 (mt-10) REVERT: A 515 ASP cc_start: 0.8811 (m-30) cc_final: 0.8407 (m-30) REVERT: A 529 ASP cc_start: 0.8974 (m-30) cc_final: 0.8727 (m-30) REVERT: A 562 LYS cc_start: 0.9810 (tttm) cc_final: 0.9513 (ttmm) REVERT: A 603 GLU cc_start: 0.8282 (pp20) cc_final: 0.7986 (tm-30) REVERT: A 604 ARG cc_start: 0.9013 (mmp80) cc_final: 0.8332 (mmp80) REVERT: A 615 MET cc_start: 0.9274 (mmp) cc_final: 0.8846 (mmm) REVERT: A 634 MET cc_start: 0.8840 (mmm) cc_final: 0.8533 (mmt) REVERT: A 675 HIS cc_start: 0.9368 (t-90) cc_final: 0.8872 (t70) REVERT: A 683 TYR cc_start: 0.8532 (t80) cc_final: 0.7773 (t80) REVERT: B 51 LEU cc_start: 0.9404 (tp) cc_final: 0.9054 (tp) REVERT: B 55 LEU cc_start: 0.9842 (mt) cc_final: 0.9630 (mt) REVERT: B 65 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7859 (tm-30) REVERT: B 67 GLU cc_start: 0.9352 (tm-30) cc_final: 0.8766 (tm-30) REVERT: B 95 MET cc_start: 0.9216 (tpp) cc_final: 0.8191 (tpp) REVERT: B 98 PHE cc_start: 0.9569 (t80) cc_final: 0.9082 (t80) REVERT: B 103 ASP cc_start: 0.9529 (m-30) cc_final: 0.9325 (m-30) REVERT: B 119 GLU cc_start: 0.9217 (mp0) cc_final: 0.8773 (mp0) REVERT: B 147 GLN cc_start: 0.9209 (mt0) cc_final: 0.8763 (mt0) REVERT: B 174 GLU cc_start: 0.8016 (tp30) cc_final: 0.7813 (tp30) REVERT: B 209 LYS cc_start: 0.9133 (tppt) cc_final: 0.8911 (tptp) REVERT: B 211 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8295 (mm-30) REVERT: B 257 ASP cc_start: 0.8957 (m-30) cc_final: 0.8684 (m-30) REVERT: B 258 ILE cc_start: 0.9518 (tp) cc_final: 0.9312 (tp) REVERT: B 276 LYS cc_start: 0.9389 (mmpt) cc_final: 0.9152 (mmmt) REVERT: B 286 ASP cc_start: 0.8581 (m-30) cc_final: 0.7738 (m-30) REVERT: B 290 GLU cc_start: 0.9256 (tp30) cc_final: 0.8934 (tp30) REVERT: B 333 LYS cc_start: 0.9240 (tptt) cc_final: 0.8887 (ttmm) REVERT: B 362 ASP cc_start: 0.8637 (m-30) cc_final: 0.7647 (m-30) REVERT: B 373 ILE cc_start: 0.9455 (mt) cc_final: 0.9209 (tp) REVERT: B 379 SER cc_start: 0.8430 (t) cc_final: 0.8147 (t) REVERT: B 393 SER cc_start: 0.9582 (t) cc_final: 0.9288 (p) REVERT: B 398 ASP cc_start: 0.8745 (t0) cc_final: 0.8409 (t70) REVERT: B 403 ILE cc_start: 0.9523 (mp) cc_final: 0.9238 (tp) REVERT: B 413 SER cc_start: 0.9606 (m) cc_final: 0.9384 (t) REVERT: B 415 ASN cc_start: 0.9551 (t0) cc_final: 0.8906 (t0) REVERT: B 434 ASP cc_start: 0.8992 (m-30) cc_final: 0.8754 (m-30) REVERT: B 458 MET cc_start: 0.9302 (mmm) cc_final: 0.8787 (mmm) REVERT: B 460 SER cc_start: 0.9467 (p) cc_final: 0.9263 (p) REVERT: B 467 ASN cc_start: 0.9112 (t0) cc_final: 0.8907 (t0) REVERT: B 501 GLN cc_start: 0.9461 (tt0) cc_final: 0.9200 (tt0) REVERT: B 586 TYR cc_start: 0.9290 (m-80) cc_final: 0.8830 (m-80) REVERT: B 598 MET cc_start: 0.9101 (mtm) cc_final: 0.8861 (mtm) REVERT: B 599 GLU cc_start: 0.8825 (pt0) cc_final: 0.8460 (pt0) REVERT: B 601 ILE cc_start: 0.9485 (mm) cc_final: 0.8563 (mm) REVERT: B 604 ARG cc_start: 0.9342 (mmm160) cc_final: 0.9081 (mmm160) REVERT: B 610 LYS cc_start: 0.9119 (tmtt) cc_final: 0.8806 (tmtt) REVERT: B 613 TYR cc_start: 0.8968 (t80) cc_final: 0.8521 (t80) REVERT: B 618 LEU cc_start: 0.9558 (tp) cc_final: 0.8959 (mt) REVERT: B 626 TYR cc_start: 0.8823 (m-80) cc_final: 0.8338 (m-80) REVERT: B 627 LYS cc_start: 0.9412 (tttt) cc_final: 0.8893 (tttp) REVERT: B 628 GLU cc_start: 0.8717 (mm-30) cc_final: 0.7834 (mm-30) REVERT: B 632 MET cc_start: 0.8941 (mtp) cc_final: 0.8665 (mtp) REVERT: B 633 ASP cc_start: 0.8678 (t0) cc_final: 0.7513 (t0) REVERT: B 636 LYS cc_start: 0.9643 (mmtp) cc_final: 0.9228 (mmtm) REVERT: B 640 MET cc_start: 0.9541 (tpp) cc_final: 0.9169 (tpp) REVERT: B 646 GLN cc_start: 0.9120 (pt0) cc_final: 0.8872 (pt0) REVERT: B 655 THR cc_start: 0.9743 (m) cc_final: 0.9480 (t) REVERT: B 667 LEU cc_start: 0.9596 (tp) cc_final: 0.9115 (tp) REVERT: C 55 TYR cc_start: 0.8243 (t80) cc_final: 0.7764 (t80) REVERT: C 110 MET cc_start: 0.7724 (mtm) cc_final: 0.7472 (mtm) REVERT: C 118 ILE cc_start: 0.8304 (mm) cc_final: 0.8101 (mm) REVERT: C 196 ARG cc_start: 0.8678 (ptm160) cc_final: 0.8422 (ptm-80) REVERT: C 315 LEU cc_start: 0.8681 (mm) cc_final: 0.8456 (mm) REVERT: D 74 MET cc_start: 0.4092 (tmm) cc_final: 0.3724 (tmm) REVERT: D 137 MET cc_start: 0.8167 (mtm) cc_final: 0.7300 (mmp) REVERT: D 149 ASP cc_start: 0.8947 (m-30) cc_final: 0.8699 (m-30) REVERT: D 174 TYR cc_start: 0.8557 (t80) cc_final: 0.8179 (t80) REVERT: D 189 GLU cc_start: 0.9213 (tt0) cc_final: 0.8928 (mp0) outliers start: 0 outliers final: 0 residues processed: 669 average time/residue: 0.2778 time to fit residues: 276.2155 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 : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 81 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 190 optimal weight: 0.2980 chunk 58 optimal weight: 0.8980 chunk 180 optimal weight: 0.0770 chunk 108 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 370 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 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 = 0.3807 r_free = 0.3807 target = 0.136591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.099490 restraints weight = 40069.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.103082 restraints weight = 20862.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.105501 restraints weight = 12951.248| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.7681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16386 Z= 0.131 Angle : 0.637 8.600 22134 Z= 0.337 Chirality : 0.043 0.262 2360 Planarity : 0.004 0.059 2818 Dihedral : 10.332 167.845 2242 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.18), residues: 1932 helix: 1.04 (0.15), residues: 1129 sheet: -0.66 (0.39), residues: 144 loop : -0.01 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 124 HIS 0.006 0.001 HIS C 201 PHE 0.031 0.002 PHE D 109 TYR 0.022 0.001 TYR B 574 ARG 0.009 0.001 ARG B 575 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 871) hydrogen bonds : angle 4.82467 ( 2571) covalent geometry : bond 0.00289 (16386) covalent geometry : angle 0.63684 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6832.66 seconds wall clock time: 119 minutes 57.62 seconds (7197.62 seconds total)