Starting phenix.real_space_refine on Sun Aug 24 01:06:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzk_45070/08_2025/9bzk_45070_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzk_45070/08_2025/9bzk_45070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bzk_45070/08_2025/9bzk_45070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzk_45070/08_2025/9bzk_45070.map" model { file = "/net/cci-nas-00/data/ceres_data/9bzk_45070/08_2025/9bzk_45070_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzk_45070/08_2025/9bzk_45070_neut.cif" } resolution = 4.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.60, per 1000 atoms: 0.22 Number of scatterers: 16038 At special positions: 0 Unit cell: (94.302, 132.834, 129.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 503.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.104A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.985A 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: 3.664A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.949A 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: 3.575A 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: 3.693A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.393A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.627A 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: 4.018A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.074A 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: 3.878A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.872A 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: 5.118A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A 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: 4.068A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A 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: 4.936A 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: 3.567A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.668A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.876A 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: 6.359A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.478A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.394A 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: 7.799A 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: 7.501A 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: 5.660A 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: 4.049A 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: 6.564A 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: 6.549A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.02 Time building geometry restraints manager: 1.76 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: 4852 1.34 - 1.46: 3050 1.46 - 1.58: 8303 1.58 - 1.70: 25 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 2.35e+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 1.03e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.033 1.08e-02 8.57e+03 9.06e+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 7.29e+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 6.76e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21576 2.09 - 4.18: 515 4.18 - 6.27: 37 6.27 - 8.36: 2 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 110.54 116.65 -6.11 1.36e+00 5.41e-01 2.02e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.17 -4.46 1.15e+00 7.56e-01 1.50e+01 angle pdb=" N SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.24 -3.96 1.09e+00 8.42e-01 1.32e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.86 -4.36 1.23e+00 6.61e-01 1.25e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.71 -4.00 1.15e+00 7.56e-01 1.21e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 9469 35.80 - 71.61: 338 71.61 - 107.41: 37 107.41 - 143.22: 3 143.22 - 179.02: 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 -179.02 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 31.94 148.04 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: 2146 0.094 - 0.187: 181 0.187 - 0.281: 28 0.281 - 0.375: 3 0.375 - 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 4.63e+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 2.97e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " -0.017 2.00e-02 2.50e+03 1.12e-02 2.21e+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 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.010 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 9.72e-03 1.89e+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 " -0.002 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 " 0.008 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 128 2.51 - 3.11: 11559 3.11 - 3.70: 27043 3.70 - 4.30: 41517 4.30 - 4.90: 65395 Nonbonded interactions: 145642 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 1.965 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.013 3.040 ... (remaining 145637 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.180 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 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 : 0.741 10.450 22134 Z= 0.463 Chirality : 0.058 0.468 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.952 179.023 6154 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.40 % Allowed : 15.21 % Favored : 83.39 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.18), residues: 1932 helix: 0.58 (0.14), residues: 1151 sheet: 0.47 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 196 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE D 92 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.74064 (22134) hydrogen bonds : bond 0.15423 ( 871) hydrogen bonds : angle 6.51778 ( 2571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 913 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 37 PHE cc_start: 0.7508 (m-80) cc_final: 0.7149 (m-80) REVERT: A 41 ILE cc_start: 0.8408 (mm) cc_final: 0.8169 (mm) REVERT: A 99 LYS cc_start: 0.8803 (mmtt) cc_final: 0.8386 (mmtm) REVERT: A 106 LEU cc_start: 0.8446 (tp) cc_final: 0.8063 (tp) REVERT: A 118 TYR cc_start: 0.7505 (t80) cc_final: 0.7186 (t80) REVERT: A 119 GLU cc_start: 0.7086 (mp0) cc_final: 0.6854 (mp0) REVERT: A 144 MET cc_start: 0.6928 (mtm) cc_final: 0.6686 (mtm) REVERT: A 172 LEU cc_start: 0.9353 (mp) cc_final: 0.9134 (mp) REVERT: A 179 LEU cc_start: 0.8735 (tp) cc_final: 0.8522 (tp) REVERT: A 188 ILE cc_start: 0.9062 (mt) cc_final: 0.8732 (mt) REVERT: A 192 LEU cc_start: 0.9304 (mt) cc_final: 0.8857 (mt) REVERT: A 202 ASN cc_start: 0.9213 (t0) cc_final: 0.8927 (t0) REVERT: A 236 TYR cc_start: 0.8422 (t80) cc_final: 0.8003 (t80) REVERT: A 264 THR cc_start: 0.8918 (p) cc_final: 0.8550 (m) REVERT: A 275 VAL cc_start: 0.8957 (m) cc_final: 0.8568 (m) REVERT: A 278 LEU cc_start: 0.8110 (tp) cc_final: 0.7832 (tp) REVERT: A 322 MET cc_start: 0.7414 (mmp) cc_final: 0.6527 (mmm) REVERT: A 326 PHE cc_start: 0.8335 (m-10) cc_final: 0.7960 (m-80) REVERT: A 332 VAL cc_start: 0.8552 (t) cc_final: 0.8343 (t) REVERT: A 362 ASP cc_start: 0.6343 (m-30) cc_final: 0.5928 (m-30) REVERT: A 407 ILE cc_start: 0.8739 (mt) cc_final: 0.8083 (mt) REVERT: A 441 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6594 (mt-10) REVERT: A 493 MET cc_start: 0.8030 (tmm) cc_final: 0.7757 (tmm) REVERT: A 521 THR cc_start: 0.8394 (p) cc_final: 0.8122 (t) REVERT: A 550 MET cc_start: 0.6605 (mtm) cc_final: 0.5850 (mtp) REVERT: A 587 VAL cc_start: 0.8823 (t) cc_final: 0.8594 (t) REVERT: A 594 VAL cc_start: 0.9069 (m) cc_final: 0.8866 (m) REVERT: A 644 ILE cc_start: 0.8778 (mt) cc_final: 0.8332 (mt) REVERT: A 652 ILE cc_start: 0.8933 (mt) cc_final: 0.8612 (mt) REVERT: B 58 LEU cc_start: 0.8920 (mt) cc_final: 0.8696 (mt) REVERT: B 119 GLU cc_start: 0.7782 (mp0) cc_final: 0.7507 (mp0) REVERT: B 190 MET cc_start: 0.8079 (mtm) cc_final: 0.7837 (mtm) REVERT: B 191 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8098 (mm-40) REVERT: B 205 LYS cc_start: 0.8288 (mttp) cc_final: 0.7898 (mtmm) REVERT: B 211 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6898 (mm-30) REVERT: B 265 LYS cc_start: 0.8841 (mmtt) cc_final: 0.7992 (mmmt) REVERT: B 278 LEU cc_start: 0.8720 (tp) cc_final: 0.8328 (tp) REVERT: B 322 MET cc_start: 0.7656 (mmm) cc_final: 0.6056 (mmm) REVERT: B 345 LYS cc_start: 0.8415 (tttt) cc_final: 0.8107 (ttpt) REVERT: B 355 TYR cc_start: 0.7499 (m-80) cc_final: 0.7134 (m-80) REVERT: B 362 ASP cc_start: 0.6438 (m-30) cc_final: 0.6075 (m-30) REVERT: B 387 GLN cc_start: 0.7521 (mt0) cc_final: 0.6809 (mt0) REVERT: B 430 LYS cc_start: 0.8025 (mttt) cc_final: 0.7733 (mtmm) REVERT: B 492 PHE cc_start: 0.7730 (m-80) cc_final: 0.7475 (m-80) REVERT: B 561 LEU cc_start: 0.8223 (tp) cc_final: 0.8011 (tp) REVERT: B 570 MET cc_start: 0.6973 (mtm) cc_final: 0.6041 (mtm) REVERT: B 574 TYR cc_start: 0.7964 (m-80) cc_final: 0.7614 (m-80) REVERT: B 585 SER cc_start: 0.8561 (p) cc_final: 0.7971 (p) REVERT: B 631 ASP cc_start: 0.7624 (m-30) cc_final: 0.7289 (m-30) REVERT: B 644 ILE cc_start: 0.8728 (mt) cc_final: 0.8482 (mt) REVERT: C 89 VAL cc_start: 0.5211 (t) cc_final: 0.3782 (t) REVERT: C 90 LEU cc_start: 0.5607 (mt) cc_final: 0.5081 (mt) REVERT: D 112 LEU cc_start: 0.7301 (mt) cc_final: 0.6470 (mt) REVERT: D 256 VAL cc_start: 0.5192 (t) cc_final: 0.4842 (t) REVERT: D 286 VAL cc_start: 0.5978 (t) cc_final: 0.5600 (p) outliers start: 24 outliers final: 8 residues processed: 928 average time/residue: 0.1432 time to fit residues: 192.0464 Evaluate side-chains 656 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 648 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.0770 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN B 61 ASN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN C 23 ASN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN D 71 ASN D 80 HIS ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.145687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.102930 restraints weight = 38287.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.106837 restraints weight = 21722.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.109494 restraints weight = 14191.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.111330 restraints weight = 10185.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.112768 restraints weight = 7850.312| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16386 Z= 0.206 Angle : 0.640 11.745 22134 Z= 0.342 Chirality : 0.044 0.275 2360 Planarity : 0.004 0.074 2818 Dihedral : 11.243 175.899 2242 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.17 % Allowed : 2.45 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.19), residues: 1932 helix: 1.32 (0.15), residues: 1126 sheet: -0.01 (0.41), residues: 134 loop : 0.54 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 235 TYR 0.026 0.002 TYR A 498 PHE 0.028 0.002 PHE D 172 TRP 0.015 0.002 TRP B 558 HIS 0.008 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00433 (16386) covalent geometry : angle 0.63997 (22134) hydrogen bonds : bond 0.04692 ( 871) hydrogen bonds : angle 5.06279 ( 2571) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 727 time to evaluate : 0.434 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 29 ASP cc_start: 0.9263 (t0) cc_final: 0.8817 (t70) REVERT: A 91 PHE cc_start: 0.9641 (m-80) cc_final: 0.9397 (m-80) REVERT: A 118 TYR cc_start: 0.9019 (t80) cc_final: 0.8578 (t80) REVERT: A 119 GLU cc_start: 0.8915 (mp0) cc_final: 0.8368 (mp0) REVERT: A 143 LEU cc_start: 0.9278 (tp) cc_final: 0.8970 (tp) REVERT: A 147 GLN cc_start: 0.9112 (mt0) cc_final: 0.8253 (mm-40) REVERT: A 148 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8501 (mt-10) REVERT: A 150 GLN cc_start: 0.9308 (tp40) cc_final: 0.9036 (tp40) REVERT: A 172 LEU cc_start: 0.9504 (mp) cc_final: 0.8887 (mp) REVERT: A 173 LEU cc_start: 0.9548 (mt) cc_final: 0.9095 (mt) REVERT: A 176 ASN cc_start: 0.8719 (t0) cc_final: 0.8388 (t0) REVERT: A 187 ASP cc_start: 0.9419 (t70) cc_final: 0.8698 (t0) REVERT: A 188 ILE cc_start: 0.9702 (mt) cc_final: 0.9412 (mt) REVERT: A 191 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8302 (mp10) REVERT: A 195 LEU cc_start: 0.9574 (mt) cc_final: 0.9326 (mt) REVERT: A 202 ASN cc_start: 0.9376 (t0) cc_final: 0.9108 (t0) REVERT: A 214 LYS cc_start: 0.9044 (tppt) cc_final: 0.8752 (mmtt) REVERT: A 223 VAL cc_start: 0.9607 (m) cc_final: 0.9167 (p) REVERT: A 243 ARG cc_start: 0.6833 (tmt-80) cc_final: 0.6570 (tpt-90) REVERT: A 257 ASP cc_start: 0.9290 (m-30) cc_final: 0.8984 (m-30) REVERT: A 270 ASP cc_start: 0.7932 (t70) cc_final: 0.7388 (t70) REVERT: A 314 MET cc_start: 0.9310 (ttt) cc_final: 0.9099 (ttt) REVERT: A 335 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8604 (mm-30) REVERT: A 348 MET cc_start: 0.8776 (tpt) cc_final: 0.7635 (tpp) REVERT: A 355 TYR cc_start: 0.9009 (m-10) cc_final: 0.8739 (m-10) REVERT: A 357 TYR cc_start: 0.9022 (m-10) cc_final: 0.8597 (m-10) REVERT: A 366 LYS cc_start: 0.9515 (mtmt) cc_final: 0.9219 (mtmm) REVERT: A 377 LYS cc_start: 0.9001 (mttt) cc_final: 0.8729 (mtmm) REVERT: A 406 ASP cc_start: 0.8110 (m-30) cc_final: 0.7402 (m-30) REVERT: A 407 ILE cc_start: 0.9113 (mt) cc_final: 0.8875 (mt) REVERT: A 418 ASN cc_start: 0.9410 (m-40) cc_final: 0.9105 (m-40) REVERT: A 421 GLU cc_start: 0.8739 (pp20) cc_final: 0.8312 (pp20) REVERT: A 444 ASP cc_start: 0.8244 (t0) cc_final: 0.7993 (t0) REVERT: A 446 ARG cc_start: 0.7564 (mmt180) cc_final: 0.7112 (mmt180) REVERT: A 493 MET cc_start: 0.8946 (tmm) cc_final: 0.8565 (tmm) REVERT: A 550 MET cc_start: 0.7257 (mtm) cc_final: 0.6909 (mtp) REVERT: A 583 SER cc_start: 0.9492 (m) cc_final: 0.8991 (p) REVERT: A 595 MET cc_start: 0.9316 (mmp) cc_final: 0.9053 (mmp) REVERT: A 615 MET cc_start: 0.8826 (mmp) cc_final: 0.8354 (mmp) REVERT: A 649 ASP cc_start: 0.9121 (p0) cc_final: 0.8903 (p0) REVERT: A 668 ASN cc_start: 0.9196 (m110) cc_final: 0.8863 (m110) REVERT: A 684 TYR cc_start: 0.7766 (m-10) cc_final: 0.7102 (m-80) REVERT: B 51 LEU cc_start: 0.9042 (tp) cc_final: 0.8700 (tp) REVERT: B 87 LYS cc_start: 0.9344 (tptp) cc_final: 0.9050 (tptp) REVERT: B 95 MET cc_start: 0.9239 (tpp) cc_final: 0.8955 (tpp) REVERT: B 99 LYS cc_start: 0.9550 (mmmt) cc_final: 0.9140 (mmmt) REVERT: B 119 GLU cc_start: 0.8990 (mp0) cc_final: 0.8763 (mp0) REVERT: B 133 ASP cc_start: 0.8778 (t0) cc_final: 0.8461 (t0) REVERT: B 136 LYS cc_start: 0.9567 (mmmm) cc_final: 0.9308 (mtpp) REVERT: B 147 GLN cc_start: 0.8934 (mt0) cc_final: 0.8533 (mm-40) REVERT: B 211 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8141 (mm-30) REVERT: B 236 TYR cc_start: 0.9061 (t80) cc_final: 0.8534 (t80) REVERT: B 250 TYR cc_start: 0.9195 (m-80) cc_final: 0.8777 (m-80) REVERT: B 286 ASP cc_start: 0.8186 (m-30) cc_final: 0.7739 (m-30) REVERT: B 308 LYS cc_start: 0.9481 (mtmt) cc_final: 0.9252 (ptpp) REVERT: B 322 MET cc_start: 0.9041 (mmm) cc_final: 0.8208 (mmm) REVERT: B 326 PHE cc_start: 0.9112 (m-80) cc_final: 0.8495 (m-80) REVERT: B 333 LYS cc_start: 0.9295 (tptm) cc_final: 0.8928 (tttm) REVERT: B 335 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7856 (mt-10) REVERT: B 348 MET cc_start: 0.8994 (ptp) cc_final: 0.8498 (ptt) REVERT: B 352 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8706 (mt-10) REVERT: B 355 TYR cc_start: 0.8991 (m-80) cc_final: 0.8523 (m-80) REVERT: B 362 ASP cc_start: 0.8548 (m-30) cc_final: 0.7709 (m-30) REVERT: B 410 ASN cc_start: 0.8853 (m110) cc_final: 0.8637 (m110) REVERT: B 415 ASN cc_start: 0.9580 (t0) cc_final: 0.9282 (t0) REVERT: B 458 MET cc_start: 0.9470 (mmm) cc_final: 0.9194 (mmm) REVERT: B 493 MET cc_start: 0.9589 (tmm) cc_final: 0.9353 (tmm) REVERT: B 515 ASP cc_start: 0.9239 (m-30) cc_final: 0.8911 (m-30) REVERT: B 522 TYR cc_start: 0.8932 (m-10) cc_final: 0.8425 (m-10) REVERT: B 558 TRP cc_start: 0.9259 (m100) cc_final: 0.8596 (m100) REVERT: B 599 GLU cc_start: 0.8551 (pt0) cc_final: 0.8284 (pt0) REVERT: B 601 ILE cc_start: 0.9538 (mm) cc_final: 0.9204 (tp) REVERT: B 604 ARG cc_start: 0.9360 (tpp80) cc_final: 0.9117 (tpp80) REVERT: B 615 MET cc_start: 0.9262 (mmp) cc_final: 0.8771 (mmp) REVERT: B 632 MET cc_start: 0.8799 (mpp) cc_final: 0.8334 (mpp) REVERT: B 640 MET cc_start: 0.9095 (tpp) cc_final: 0.8858 (tpp) REVERT: B 657 PHE cc_start: 0.8947 (m-80) cc_final: 0.8434 (m-80) REVERT: B 664 THR cc_start: 0.9162 (p) cc_final: 0.8934 (p) REVERT: B 667 LEU cc_start: 0.9268 (tp) cc_final: 0.9010 (tp) REVERT: B 684 TYR cc_start: 0.7616 (m-10) cc_final: 0.6404 (m-10) REVERT: C 17 PHE cc_start: 0.8549 (p90) cc_final: 0.7549 (p90) REVERT: C 21 PHE cc_start: 0.9038 (m-10) cc_final: 0.8125 (m-10) REVERT: C 87 LYS cc_start: 0.8911 (mtmm) cc_final: 0.8621 (mtmt) REVERT: C 204 TYR cc_start: 0.9191 (t80) cc_final: 0.8789 (t80) REVERT: D 20 MET cc_start: 0.8151 (ttp) cc_final: 0.7802 (ptm) REVERT: D 45 LYS cc_start: 0.8498 (pttt) cc_final: 0.8105 (pttt) REVERT: D 46 TYR cc_start: 0.8564 (m-80) cc_final: 0.8156 (m-80) REVERT: D 105 TYR cc_start: 0.8949 (m-10) cc_final: 0.8430 (m-10) REVERT: D 169 TYR cc_start: 0.8810 (m-80) cc_final: 0.8379 (m-80) REVERT: D 194 ILE cc_start: 0.9826 (mt) cc_final: 0.9610 (mm) REVERT: D 197 ASP cc_start: 0.9073 (m-30) cc_final: 0.8774 (m-30) REVERT: D 204 TYR cc_start: 0.9591 (t80) cc_final: 0.9288 (t80) outliers start: 3 outliers final: 0 residues processed: 728 average time/residue: 0.1164 time to fit residues: 125.4074 Evaluate side-chains 605 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 605 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 182 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 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** B 418 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 HIS C 98 ASN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 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 = 0.3790 r_free = 0.3790 target = 0.137392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.096883 restraints weight = 39838.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.100688 restraints weight = 22095.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.103199 restraints weight = 14262.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.104948 restraints weight = 10159.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106229 restraints weight = 7741.712| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16386 Z= 0.183 Angle : 0.604 9.317 22134 Z= 0.319 Chirality : 0.043 0.207 2360 Planarity : 0.004 0.045 2818 Dihedral : 10.963 176.612 2242 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.06 % Allowed : 2.45 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.19), residues: 1932 helix: 1.33 (0.15), residues: 1119 sheet: 0.17 (0.43), residues: 134 loop : 0.33 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 121 TYR 0.023 0.002 TYR B 574 PHE 0.026 0.002 PHE A 171 TRP 0.019 0.002 TRP D 124 HIS 0.006 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00388 (16386) covalent geometry : angle 0.60406 (22134) hydrogen bonds : bond 0.04196 ( 871) hydrogen bonds : angle 4.85109 ( 2571) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 687 time to evaluate : 0.578 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 29 ASP cc_start: 0.9214 (t0) cc_final: 0.8726 (t70) REVERT: A 118 TYR cc_start: 0.8714 (t80) cc_final: 0.8005 (t80) REVERT: A 119 GLU cc_start: 0.8909 (mp0) cc_final: 0.8356 (mp0) REVERT: A 125 VAL cc_start: 0.9426 (t) cc_final: 0.9212 (t) REVERT: A 150 GLN cc_start: 0.9308 (tp40) cc_final: 0.8873 (tp40) REVERT: A 172 LEU cc_start: 0.9468 (mp) cc_final: 0.8914 (mp) REVERT: A 173 LEU cc_start: 0.9593 (mt) cc_final: 0.9353 (mt) REVERT: A 181 ASP cc_start: 0.9182 (m-30) cc_final: 0.8767 (m-30) REVERT: A 214 LYS cc_start: 0.9090 (tppt) cc_final: 0.8714 (mmtt) REVERT: A 221 LYS cc_start: 0.8826 (mmtp) cc_final: 0.8437 (mmtp) REVERT: A 223 VAL cc_start: 0.9508 (m) cc_final: 0.9207 (p) REVERT: A 239 GLN cc_start: 0.8280 (mt0) cc_final: 0.7835 (tm-30) REVERT: A 257 ASP cc_start: 0.9291 (m-30) cc_final: 0.8768 (m-30) REVERT: A 270 ASP cc_start: 0.8112 (t70) cc_final: 0.7540 (t70) REVERT: A 277 THR cc_start: 0.8803 (p) cc_final: 0.8578 (p) REVERT: A 290 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8712 (tm-30) REVERT: A 295 ASP cc_start: 0.8647 (t70) cc_final: 0.8356 (t70) REVERT: A 355 TYR cc_start: 0.9015 (m-10) cc_final: 0.8795 (m-10) REVERT: A 366 LYS cc_start: 0.9511 (mtmt) cc_final: 0.9185 (mtmm) REVERT: A 406 ASP cc_start: 0.8220 (m-30) cc_final: 0.8003 (m-30) REVERT: A 407 ILE cc_start: 0.9233 (mt) cc_final: 0.9011 (mt) REVERT: A 421 GLU cc_start: 0.8831 (pp20) cc_final: 0.8555 (pp20) REVERT: A 493 MET cc_start: 0.8852 (tmm) cc_final: 0.8361 (tmm) REVERT: A 515 ASP cc_start: 0.8966 (m-30) cc_final: 0.8615 (m-30) REVERT: A 528 PHE cc_start: 0.8996 (m-80) cc_final: 0.8444 (m-10) REVERT: A 550 MET cc_start: 0.7155 (mtm) cc_final: 0.6578 (mtp) REVERT: A 561 LEU cc_start: 0.9516 (tp) cc_final: 0.9233 (tp) REVERT: A 583 SER cc_start: 0.9471 (m) cc_final: 0.9056 (p) REVERT: A 598 MET cc_start: 0.8336 (mtp) cc_final: 0.7757 (mtp) REVERT: A 602 GLU cc_start: 0.7481 (pp20) cc_final: 0.7228 (tm-30) REVERT: A 615 MET cc_start: 0.9178 (mmp) cc_final: 0.8757 (mmp) REVERT: A 639 ASP cc_start: 0.9219 (m-30) cc_final: 0.8994 (m-30) REVERT: A 647 HIS cc_start: 0.9268 (m-70) cc_final: 0.8863 (m90) REVERT: A 672 LEU cc_start: 0.9286 (mt) cc_final: 0.9007 (mt) REVERT: B 12 LEU cc_start: 0.9376 (mt) cc_final: 0.9082 (mp) REVERT: B 51 LEU cc_start: 0.9190 (tp) cc_final: 0.8982 (tp) REVERT: B 52 LYS cc_start: 0.9342 (tptp) cc_final: 0.9106 (tppt) REVERT: B 54 LYS cc_start: 0.9675 (ttmt) cc_final: 0.9440 (ttmm) REVERT: B 67 GLU cc_start: 0.8990 (mp0) cc_final: 0.8787 (mp0) REVERT: B 87 LYS cc_start: 0.9324 (tptp) cc_final: 0.9087 (tptp) REVERT: B 95 MET cc_start: 0.9231 (tpp) cc_final: 0.9022 (tpp) REVERT: B 99 LYS cc_start: 0.9565 (mmmt) cc_final: 0.9276 (mmmt) REVERT: B 119 GLU cc_start: 0.9080 (mp0) cc_final: 0.8791 (mp0) REVERT: B 127 LEU cc_start: 0.9508 (mm) cc_final: 0.9217 (mm) REVERT: B 133 ASP cc_start: 0.8987 (t0) cc_final: 0.8729 (t0) REVERT: B 136 LYS cc_start: 0.9597 (mmmm) cc_final: 0.9364 (mtpp) REVERT: B 147 GLN cc_start: 0.9102 (mt0) cc_final: 0.8532 (mm-40) REVERT: B 205 LYS cc_start: 0.8888 (mttp) cc_final: 0.8644 (mmtp) REVERT: B 211 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8417 (mm-30) REVERT: B 236 TYR cc_start: 0.8996 (t80) cc_final: 0.8228 (t80) REVERT: B 250 TYR cc_start: 0.9201 (m-80) cc_final: 0.8811 (m-80) REVERT: B 286 ASP cc_start: 0.8243 (m-30) cc_final: 0.7891 (m-30) REVERT: B 290 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8308 (tm-30) REVERT: B 294 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8791 (mp0) REVERT: B 308 LYS cc_start: 0.9484 (mtmt) cc_final: 0.9236 (ptpp) REVERT: B 322 MET cc_start: 0.8785 (mmm) cc_final: 0.7788 (mmm) REVERT: B 326 PHE cc_start: 0.9242 (m-80) cc_final: 0.8522 (m-80) REVERT: B 333 LYS cc_start: 0.9429 (tptm) cc_final: 0.9083 (ttmm) REVERT: B 355 TYR cc_start: 0.9083 (m-80) cc_final: 0.8570 (m-80) REVERT: B 362 ASP cc_start: 0.8691 (m-30) cc_final: 0.7926 (m-30) REVERT: B 393 SER cc_start: 0.9605 (m) cc_final: 0.9168 (t) REVERT: B 402 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8291 (tm-30) REVERT: B 410 ASN cc_start: 0.8917 (m110) cc_final: 0.8617 (m110) REVERT: B 441 GLU cc_start: 0.9117 (pt0) cc_final: 0.8807 (pt0) REVERT: B 459 LYS cc_start: 0.9147 (mttp) cc_final: 0.8352 (mtpt) REVERT: B 515 ASP cc_start: 0.9251 (m-30) cc_final: 0.8932 (m-30) REVERT: B 522 TYR cc_start: 0.9114 (m-10) cc_final: 0.8834 (m-10) REVERT: B 558 TRP cc_start: 0.9276 (m100) cc_final: 0.8598 (m100) REVERT: B 588 GLN cc_start: 0.9258 (mm-40) cc_final: 0.8712 (mm-40) REVERT: B 598 MET cc_start: 0.8770 (mtp) cc_final: 0.8515 (mtp) REVERT: B 599 GLU cc_start: 0.8693 (pt0) cc_final: 0.8128 (pt0) REVERT: B 604 ARG cc_start: 0.9188 (tpp80) cc_final: 0.8780 (tpp80) REVERT: B 610 LYS cc_start: 0.9020 (ttpp) cc_final: 0.8802 (ttpp) REVERT: B 615 MET cc_start: 0.9203 (mmp) cc_final: 0.8840 (mmp) REVERT: B 628 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8483 (mm-30) REVERT: B 632 MET cc_start: 0.8583 (mpp) cc_final: 0.8274 (mpp) REVERT: B 640 MET cc_start: 0.9208 (tpp) cc_final: 0.8863 (tpp) REVERT: B 645 GLN cc_start: 0.9318 (tp40) cc_final: 0.8951 (tp-100) REVERT: B 664 THR cc_start: 0.9150 (p) cc_final: 0.8944 (p) REVERT: B 668 ASN cc_start: 0.9353 (m-40) cc_final: 0.9092 (m110) REVERT: B 677 ARG cc_start: 0.9171 (mmm-85) cc_final: 0.8729 (mmm-85) REVERT: C 17 PHE cc_start: 0.8422 (p90) cc_final: 0.7599 (p90) REVERT: C 21 PHE cc_start: 0.8979 (m-10) cc_final: 0.8108 (m-80) REVERT: C 74 MET cc_start: 0.8733 (mmp) cc_final: 0.8532 (mmp) REVERT: C 204 TYR cc_start: 0.9179 (t80) cc_final: 0.8897 (t80) REVERT: D 20 MET cc_start: 0.8190 (ttp) cc_final: 0.7957 (ptm) REVERT: D 23 ASN cc_start: 0.9591 (m110) cc_final: 0.9386 (m110) REVERT: D 46 TYR cc_start: 0.8527 (m-80) cc_final: 0.8186 (m-80) REVERT: D 96 MET cc_start: 0.8480 (tpt) cc_final: 0.8241 (tpp) REVERT: D 105 TYR cc_start: 0.9109 (m-10) cc_final: 0.8480 (m-10) REVERT: D 169 TYR cc_start: 0.8943 (m-80) cc_final: 0.8511 (m-80) REVERT: D 172 PHE cc_start: 0.8776 (m-80) cc_final: 0.8561 (m-80) REVERT: D 204 TYR cc_start: 0.9630 (t80) cc_final: 0.9243 (t80) outliers start: 1 outliers final: 0 residues processed: 687 average time/residue: 0.1214 time to fit residues: 123.2245 Evaluate side-chains 614 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 614 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 0.8980 chunk 157 optimal weight: 20.0000 chunk 168 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 185 optimal weight: 6.9990 chunk 191 optimal weight: 9.9990 chunk 159 optimal weight: 20.0000 chunk 182 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 147 GLN A 370 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN A 645 GLN ** A 650 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** B 568 HIS C 23 ASN C 25 ASN ** D 210 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 = 0.3808 r_free = 0.3808 target = 0.139982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.098509 restraints weight = 39760.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.102374 restraints weight = 22302.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.104944 restraints weight = 14223.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.106751 restraints weight = 10145.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.107977 restraints weight = 7741.066| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.5657 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= 0.151 Angle : 0.582 10.678 22134 Z= 0.304 Chirality : 0.044 0.623 2360 Planarity : 0.003 0.052 2818 Dihedral : 10.702 179.303 2242 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.12 % Allowed : 1.75 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.19), residues: 1932 helix: 1.37 (0.16), residues: 1119 sheet: 0.06 (0.42), residues: 132 loop : 0.25 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 604 TYR 0.023 0.001 TYR B 574 PHE 0.023 0.002 PHE C 92 TRP 0.007 0.001 TRP B 9 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00332 (16386) covalent geometry : angle 0.58175 (22134) hydrogen bonds : bond 0.03935 ( 871) hydrogen bonds : angle 4.80504 ( 2571) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 670 time to evaluate : 0.618 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 29 ASP cc_start: 0.9150 (t0) cc_final: 0.8946 (t70) REVERT: A 31 GLU cc_start: 0.9083 (mp0) cc_final: 0.8739 (mp0) REVERT: A 65 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8444 (mm-30) REVERT: A 106 LEU cc_start: 0.9426 (tp) cc_final: 0.9212 (tp) REVERT: A 116 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8444 (mt-10) REVERT: A 118 TYR cc_start: 0.8563 (t80) cc_final: 0.8337 (t80) REVERT: A 119 GLU cc_start: 0.8838 (mp0) cc_final: 0.8311 (mp0) REVERT: A 143 LEU cc_start: 0.9280 (tp) cc_final: 0.9008 (tp) REVERT: A 148 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8545 (mt-10) REVERT: A 150 GLN cc_start: 0.9153 (tp40) cc_final: 0.8790 (tp40) REVERT: A 172 LEU cc_start: 0.9443 (mp) cc_final: 0.8879 (mp) REVERT: A 173 LEU cc_start: 0.9651 (mt) cc_final: 0.9190 (mt) REVERT: A 181 ASP cc_start: 0.9153 (m-30) cc_final: 0.8688 (m-30) REVERT: A 214 LYS cc_start: 0.9091 (tppt) cc_final: 0.8740 (mmtt) REVERT: A 223 VAL cc_start: 0.9543 (m) cc_final: 0.9199 (p) REVERT: A 239 GLN cc_start: 0.8169 (mt0) cc_final: 0.7820 (tm-30) REVERT: A 252 ASN cc_start: 0.9414 (t0) cc_final: 0.8863 (t0) REVERT: A 326 PHE cc_start: 0.9640 (m-10) cc_final: 0.8986 (m-80) REVERT: A 335 GLU cc_start: 0.8134 (mp0) cc_final: 0.7792 (mp0) REVERT: A 355 TYR cc_start: 0.8784 (m-10) cc_final: 0.8565 (m-10) REVERT: A 366 LYS cc_start: 0.9521 (mtmt) cc_final: 0.9174 (mtmm) REVERT: A 396 ASP cc_start: 0.8781 (m-30) cc_final: 0.8362 (m-30) REVERT: A 406 ASP cc_start: 0.8228 (m-30) cc_final: 0.7553 (m-30) REVERT: A 418 ASN cc_start: 0.9264 (m110) cc_final: 0.9015 (m-40) REVERT: A 421 GLU cc_start: 0.8851 (pp20) cc_final: 0.8490 (pp20) REVERT: A 446 ARG cc_start: 0.7279 (mmm-85) cc_final: 0.7050 (mmm-85) REVERT: A 493 MET cc_start: 0.8816 (tmm) cc_final: 0.8383 (tmm) REVERT: A 515 ASP cc_start: 0.8901 (m-30) cc_final: 0.8643 (m-30) REVERT: A 528 PHE cc_start: 0.9028 (m-80) cc_final: 0.8458 (m-10) REVERT: A 550 MET cc_start: 0.7252 (mtm) cc_final: 0.6735 (mtp) REVERT: A 561 LEU cc_start: 0.9429 (tp) cc_final: 0.9196 (tp) REVERT: A 583 SER cc_start: 0.9443 (m) cc_final: 0.9084 (p) REVERT: A 615 MET cc_start: 0.9248 (mmp) cc_final: 0.8765 (mmp) REVERT: A 639 ASP cc_start: 0.9199 (m-30) cc_final: 0.8971 (m-30) REVERT: A 645 GLN cc_start: 0.8779 (tp40) cc_final: 0.7906 (tp40) REVERT: A 672 LEU cc_start: 0.9235 (mt) cc_final: 0.8972 (mt) REVERT: A 680 LYS cc_start: 0.9151 (mttt) cc_final: 0.8796 (mttt) REVERT: B 52 LYS cc_start: 0.9433 (tptp) cc_final: 0.9153 (tppt) REVERT: B 87 LYS cc_start: 0.9322 (tptp) cc_final: 0.8906 (tptp) REVERT: B 95 MET cc_start: 0.9228 (tpp) cc_final: 0.8988 (tpp) REVERT: B 99 LYS cc_start: 0.9589 (mmmt) cc_final: 0.9266 (mmmt) REVERT: B 119 GLU cc_start: 0.9031 (mp0) cc_final: 0.8763 (mp0) REVERT: B 127 LEU cc_start: 0.9493 (mm) cc_final: 0.9166 (mm) REVERT: B 147 GLN cc_start: 0.8947 (mt0) cc_final: 0.8591 (mm-40) REVERT: B 184 ARG cc_start: 0.9339 (tpp80) cc_final: 0.9112 (tpp80) REVERT: B 211 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8389 (mm-30) REVERT: B 223 VAL cc_start: 0.9229 (m) cc_final: 0.8736 (m) REVERT: B 250 TYR cc_start: 0.9187 (m-80) cc_final: 0.8798 (m-80) REVERT: B 308 LYS cc_start: 0.9456 (mtmt) cc_final: 0.9247 (ptpp) REVERT: B 322 MET cc_start: 0.8705 (mmm) cc_final: 0.7750 (mmm) REVERT: B 333 LYS cc_start: 0.9508 (tptm) cc_final: 0.9196 (ttmm) REVERT: B 348 MET cc_start: 0.9149 (ptt) cc_final: 0.8578 (ptp) REVERT: B 355 TYR cc_start: 0.9088 (m-80) cc_final: 0.8572 (m-80) REVERT: B 362 ASP cc_start: 0.8757 (m-30) cc_final: 0.8107 (m-30) REVERT: B 393 SER cc_start: 0.9575 (m) cc_final: 0.9185 (t) REVERT: B 402 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8309 (tm-30) REVERT: B 410 ASN cc_start: 0.8890 (m110) cc_final: 0.8577 (m110) REVERT: B 415 ASN cc_start: 0.9431 (t0) cc_final: 0.9176 (t0) REVERT: B 441 GLU cc_start: 0.9012 (pt0) cc_final: 0.8756 (pt0) REVERT: B 459 LYS cc_start: 0.9140 (mttp) cc_final: 0.8428 (mtpt) REVERT: B 471 TYR cc_start: 0.9545 (t80) cc_final: 0.9290 (t80) REVERT: B 515 ASP cc_start: 0.9237 (m-30) cc_final: 0.8884 (m-30) REVERT: B 597 ILE cc_start: 0.9595 (pt) cc_final: 0.9390 (pt) REVERT: B 599 GLU cc_start: 0.8656 (pt0) cc_final: 0.8067 (pt0) REVERT: B 601 ILE cc_start: 0.9457 (mm) cc_final: 0.8956 (tp) REVERT: B 610 LYS cc_start: 0.9015 (ttpp) cc_final: 0.8736 (tptt) REVERT: B 615 MET cc_start: 0.9201 (mmp) cc_final: 0.8664 (mmp) REVERT: B 618 LEU cc_start: 0.9302 (tp) cc_final: 0.9064 (tp) REVERT: B 626 TYR cc_start: 0.8668 (m-80) cc_final: 0.7808 (m-80) REVERT: B 628 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8528 (mm-30) REVERT: B 632 MET cc_start: 0.8556 (mpp) cc_final: 0.8092 (mpp) REVERT: B 636 LYS cc_start: 0.9503 (mmtm) cc_final: 0.9238 (mmmm) REVERT: B 640 MET cc_start: 0.9245 (tpp) cc_final: 0.8794 (tpp) REVERT: B 645 GLN cc_start: 0.9225 (tp40) cc_final: 0.8974 (tp-100) REVERT: B 648 ILE cc_start: 0.9379 (mm) cc_final: 0.9140 (mm) REVERT: B 664 THR cc_start: 0.9261 (p) cc_final: 0.9034 (p) REVERT: B 667 LEU cc_start: 0.9344 (tp) cc_final: 0.9011 (tp) REVERT: B 668 ASN cc_start: 0.9300 (m-40) cc_final: 0.9093 (m-40) REVERT: B 677 ARG cc_start: 0.9185 (mmm-85) cc_final: 0.8736 (mmm-85) REVERT: C 17 PHE cc_start: 0.8529 (p90) cc_final: 0.7823 (p90) REVERT: D 46 TYR cc_start: 0.8641 (m-80) cc_final: 0.8045 (m-80) REVERT: D 96 MET cc_start: 0.8584 (tpt) cc_final: 0.8348 (tpp) REVERT: D 105 TYR cc_start: 0.9126 (m-10) cc_final: 0.8376 (m-10) REVERT: D 169 TYR cc_start: 0.9086 (m-80) cc_final: 0.8659 (m-80) REVERT: D 172 PHE cc_start: 0.8832 (m-80) cc_final: 0.8524 (m-80) REVERT: D 197 ASP cc_start: 0.9260 (m-30) cc_final: 0.8867 (m-30) REVERT: D 204 TYR cc_start: 0.9637 (t80) cc_final: 0.9304 (t80) outliers start: 2 outliers final: 0 residues processed: 671 average time/residue: 0.1154 time to fit residues: 115.1622 Evaluate side-chains 593 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 593 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 475 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN C 201 HIS ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN D 249 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.137985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.097948 restraints weight = 40484.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.101724 restraints weight = 22480.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.104214 restraints weight = 14300.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.105976 restraints weight = 10143.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.107126 restraints weight = 7690.195| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.6209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16386 Z= 0.188 Angle : 0.612 9.865 22134 Z= 0.320 Chirality : 0.043 0.241 2360 Planarity : 0.003 0.042 2818 Dihedral : 10.662 176.296 2242 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.06 % Allowed : 2.33 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.19), residues: 1932 helix: 1.23 (0.15), residues: 1142 sheet: -0.15 (0.41), residues: 132 loop : 0.15 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 350 TYR 0.041 0.002 TYR A 683 PHE 0.026 0.002 PHE D 154 TRP 0.010 0.002 TRP D 124 HIS 0.006 0.001 HIS A 568 Details of bonding type rmsd covalent geometry : bond 0.00407 (16386) covalent geometry : angle 0.61241 (22134) hydrogen bonds : bond 0.03888 ( 871) hydrogen bonds : angle 4.88607 ( 2571) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 663 time to evaluate : 0.470 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 31 GLU cc_start: 0.9041 (mp0) cc_final: 0.8684 (mp0) REVERT: A 116 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8519 (mt-10) REVERT: A 119 GLU cc_start: 0.8880 (mp0) cc_final: 0.8379 (mp0) REVERT: A 143 LEU cc_start: 0.9272 (tp) cc_final: 0.9002 (tp) REVERT: A 147 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8574 (mm-40) REVERT: A 148 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8585 (mt-10) REVERT: A 150 GLN cc_start: 0.9471 (tp40) cc_final: 0.8802 (tm-30) REVERT: A 158 ASN cc_start: 0.9404 (m-40) cc_final: 0.9079 (m-40) REVERT: A 164 ARG cc_start: 0.8842 (ptt90) cc_final: 0.8605 (ptt90) REVERT: A 169 SER cc_start: 0.8496 (p) cc_final: 0.8163 (p) REVERT: A 172 LEU cc_start: 0.9488 (mp) cc_final: 0.9114 (mp) REVERT: A 173 LEU cc_start: 0.9630 (mt) cc_final: 0.9408 (mt) REVERT: A 181 ASP cc_start: 0.9095 (m-30) cc_final: 0.8796 (m-30) REVERT: A 214 LYS cc_start: 0.9122 (tppt) cc_final: 0.8822 (mmtm) REVERT: A 243 ARG cc_start: 0.6467 (tmt-80) cc_final: 0.6190 (tpt170) REVERT: A 255 HIS cc_start: 0.8586 (t-90) cc_final: 0.8272 (t-90) REVERT: A 277 THR cc_start: 0.8654 (p) cc_final: 0.8132 (t) REVERT: A 290 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8513 (tm-30) REVERT: A 300 VAL cc_start: 0.9606 (m) cc_final: 0.8870 (m) REVERT: A 335 GLU cc_start: 0.8022 (mp0) cc_final: 0.7502 (mp0) REVERT: A 355 TYR cc_start: 0.8998 (m-10) cc_final: 0.8738 (m-10) REVERT: A 366 LYS cc_start: 0.9506 (mtmt) cc_final: 0.9177 (mtmm) REVERT: A 390 GLN cc_start: 0.8841 (mt0) cc_final: 0.8600 (mt0) REVERT: A 396 ASP cc_start: 0.8708 (m-30) cc_final: 0.8310 (m-30) REVERT: A 407 ILE cc_start: 0.9213 (mt) cc_final: 0.9004 (mt) REVERT: A 421 GLU cc_start: 0.8901 (pp20) cc_final: 0.8510 (pp20) REVERT: A 446 ARG cc_start: 0.7474 (mmm-85) cc_final: 0.7194 (mmm-85) REVERT: A 458 MET cc_start: 0.8867 (mmp) cc_final: 0.8598 (mmm) REVERT: A 479 TYR cc_start: 0.9205 (t80) cc_final: 0.8935 (t80) REVERT: A 483 GLU cc_start: 0.9431 (mp0) cc_final: 0.9092 (mp0) REVERT: A 493 MET cc_start: 0.8755 (tmm) cc_final: 0.8250 (tmm) REVERT: A 515 ASP cc_start: 0.8983 (m-30) cc_final: 0.8761 (m-30) REVERT: A 583 SER cc_start: 0.9453 (m) cc_final: 0.9096 (p) REVERT: A 602 GLU cc_start: 0.7854 (pp20) cc_final: 0.7222 (tm-30) REVERT: A 615 MET cc_start: 0.9182 (mmp) cc_final: 0.8742 (mmp) REVERT: A 639 ASP cc_start: 0.9118 (m-30) cc_final: 0.8807 (m-30) REVERT: A 640 MET cc_start: 0.9088 (tpp) cc_final: 0.8808 (tpp) REVERT: A 645 GLN cc_start: 0.8791 (tp40) cc_final: 0.8526 (tp-100) REVERT: A 672 LEU cc_start: 0.9286 (mt) cc_final: 0.9038 (mt) REVERT: B 51 LEU cc_start: 0.9285 (tp) cc_final: 0.9072 (tp) REVERT: B 52 LYS cc_start: 0.9451 (tptp) cc_final: 0.9176 (tppt) REVERT: B 67 GLU cc_start: 0.9030 (mp0) cc_final: 0.8748 (pm20) REVERT: B 87 LYS cc_start: 0.9326 (tptp) cc_final: 0.8928 (tptp) REVERT: B 95 MET cc_start: 0.9216 (tpp) cc_final: 0.8819 (tpp) REVERT: B 119 GLU cc_start: 0.9098 (mp0) cc_final: 0.8801 (mp0) REVERT: B 127 LEU cc_start: 0.9549 (mm) cc_final: 0.9180 (mm) REVERT: B 184 ARG cc_start: 0.9374 (tpp80) cc_final: 0.9049 (tpp80) REVERT: B 205 LYS cc_start: 0.8848 (mmtp) cc_final: 0.8452 (mmtp) REVERT: B 223 VAL cc_start: 0.9278 (m) cc_final: 0.8764 (m) REVERT: B 250 TYR cc_start: 0.9177 (m-80) cc_final: 0.8740 (m-80) REVERT: B 252 ASN cc_start: 0.9007 (t0) cc_final: 0.8772 (t0) REVERT: B 283 VAL cc_start: 0.9635 (t) cc_final: 0.9386 (t) REVERT: B 308 LYS cc_start: 0.9447 (mtmt) cc_final: 0.9188 (ptpp) REVERT: B 317 MET cc_start: 0.8915 (ptm) cc_final: 0.7589 (ptm) REVERT: B 333 LYS cc_start: 0.9532 (tptm) cc_final: 0.9195 (ttmm) REVERT: B 348 MET cc_start: 0.8915 (ptt) cc_final: 0.8391 (ptp) REVERT: B 355 TYR cc_start: 0.9031 (m-80) cc_final: 0.8537 (m-80) REVERT: B 362 ASP cc_start: 0.8891 (m-30) cc_final: 0.8565 (m-30) REVERT: B 392 SER cc_start: 0.9088 (m) cc_final: 0.8355 (p) REVERT: B 393 SER cc_start: 0.9561 (m) cc_final: 0.9058 (p) REVERT: B 394 TYR cc_start: 0.8717 (m-80) cc_final: 0.8408 (m-80) REVERT: B 402 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8149 (tm-30) REVERT: B 407 ILE cc_start: 0.8984 (mt) cc_final: 0.8732 (mt) REVERT: B 410 ASN cc_start: 0.8911 (m110) cc_final: 0.8564 (m110) REVERT: B 415 ASN cc_start: 0.9472 (t0) cc_final: 0.9269 (t0) REVERT: B 441 GLU cc_start: 0.9010 (pt0) cc_final: 0.8727 (pt0) REVERT: B 459 LYS cc_start: 0.9168 (mttp) cc_final: 0.8548 (mtmt) REVERT: B 515 ASP cc_start: 0.9214 (m-30) cc_final: 0.8882 (m-30) REVERT: B 522 TYR cc_start: 0.8948 (m-10) cc_final: 0.8686 (m-10) REVERT: B 585 SER cc_start: 0.8955 (p) cc_final: 0.8240 (t) REVERT: B 599 GLU cc_start: 0.8642 (pt0) cc_final: 0.8083 (pt0) REVERT: B 601 ILE cc_start: 0.9369 (mm) cc_final: 0.9058 (mm) REVERT: B 610 LYS cc_start: 0.9187 (ttpp) cc_final: 0.8944 (ttpp) REVERT: B 615 MET cc_start: 0.9254 (mmp) cc_final: 0.8851 (mmp) REVERT: B 626 TYR cc_start: 0.8901 (m-80) cc_final: 0.8044 (m-80) REVERT: B 628 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8589 (mm-30) REVERT: B 632 MET cc_start: 0.8368 (mpp) cc_final: 0.8099 (mpp) REVERT: B 636 LYS cc_start: 0.9564 (mmtm) cc_final: 0.9251 (mmmm) REVERT: B 640 MET cc_start: 0.9254 (tpp) cc_final: 0.8817 (tpp) REVERT: B 645 GLN cc_start: 0.9242 (tp40) cc_final: 0.8985 (tp-100) REVERT: B 648 ILE cc_start: 0.9369 (mm) cc_final: 0.9117 (mm) REVERT: B 667 LEU cc_start: 0.9326 (tp) cc_final: 0.9049 (tp) REVERT: B 668 ASN cc_start: 0.9357 (m-40) cc_final: 0.9118 (m-40) REVERT: C 17 PHE cc_start: 0.8598 (p90) cc_final: 0.8397 (p90) REVERT: C 87 LYS cc_start: 0.9216 (mtmm) cc_final: 0.8994 (mttt) REVERT: C 154 PHE cc_start: 0.8112 (t80) cc_final: 0.7705 (t80) REVERT: D 23 ASN cc_start: 0.9588 (m110) cc_final: 0.9386 (m110) REVERT: D 46 TYR cc_start: 0.8593 (m-80) cc_final: 0.8043 (m-80) REVERT: D 96 MET cc_start: 0.8849 (tpt) cc_final: 0.8561 (tpp) REVERT: D 105 TYR cc_start: 0.9214 (m-10) cc_final: 0.8632 (m-10) REVERT: D 169 TYR cc_start: 0.9261 (m-80) cc_final: 0.8808 (m-80) REVERT: D 172 PHE cc_start: 0.8978 (m-80) cc_final: 0.8585 (m-80) REVERT: D 204 TYR cc_start: 0.9656 (t80) cc_final: 0.9433 (t80) outliers start: 1 outliers final: 1 residues processed: 664 average time/residue: 0.1092 time to fit residues: 108.1091 Evaluate side-chains 592 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 591 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 HIS ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 25 GLN B 304 HIS ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.136423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.096414 restraints weight = 41359.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.100151 restraints weight = 22704.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.102641 restraints weight = 14290.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.104333 restraints weight = 10100.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.105568 restraints weight = 7683.874| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.6688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16386 Z= 0.227 Angle : 0.657 10.065 22134 Z= 0.343 Chirality : 0.044 0.212 2360 Planarity : 0.004 0.053 2818 Dihedral : 10.725 172.344 2242 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.19), residues: 1932 helix: 0.97 (0.15), residues: 1164 sheet: -0.29 (0.42), residues: 136 loop : 0.12 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 350 TYR 0.025 0.002 TYR B 574 PHE 0.027 0.002 PHE B 171 TRP 0.009 0.002 TRP B 9 HIS 0.021 0.002 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00487 (16386) covalent geometry : angle 0.65662 (22134) hydrogen bonds : bond 0.03955 ( 871) hydrogen bonds : angle 5.01151 ( 2571) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 646 time to evaluate : 0.588 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 29 ASP cc_start: 0.9157 (t70) cc_final: 0.8789 (t70) REVERT: A 31 GLU cc_start: 0.9048 (mp0) cc_final: 0.8804 (mp0) REVERT: A 65 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8210 (mp0) REVERT: A 117 ARG cc_start: 0.8717 (mtp85) cc_final: 0.8499 (mmt180) REVERT: A 119 GLU cc_start: 0.8921 (mp0) cc_final: 0.8508 (mp0) REVERT: A 142 ASN cc_start: 0.9304 (m-40) cc_final: 0.8972 (m110) REVERT: A 147 GLN cc_start: 0.8997 (mm-40) cc_final: 0.8697 (mm-40) REVERT: A 150 GLN cc_start: 0.9511 (tp40) cc_final: 0.9278 (tp40) REVERT: A 158 ASN cc_start: 0.9332 (m-40) cc_final: 0.9119 (m-40) REVERT: A 172 LEU cc_start: 0.9491 (mp) cc_final: 0.9080 (mp) REVERT: A 181 ASP cc_start: 0.9052 (m-30) cc_final: 0.8772 (m-30) REVERT: A 232 ASN cc_start: 0.8733 (m110) cc_final: 0.8151 (m110) REVERT: A 243 ARG cc_start: 0.6642 (tmt-80) cc_final: 0.6176 (tpt90) REVERT: A 255 HIS cc_start: 0.8613 (t-90) cc_final: 0.7790 (t-90) REVERT: A 257 ASP cc_start: 0.9075 (m-30) cc_final: 0.8616 (m-30) REVERT: A 276 LYS cc_start: 0.9106 (mmtm) cc_final: 0.8891 (mmtt) REVERT: A 277 THR cc_start: 0.8638 (p) cc_final: 0.8176 (t) REVERT: A 286 ASP cc_start: 0.8886 (m-30) cc_final: 0.8551 (m-30) REVERT: A 290 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8459 (tm-30) REVERT: A 291 LEU cc_start: 0.9489 (mt) cc_final: 0.9267 (mt) REVERT: A 333 LYS cc_start: 0.9521 (tppp) cc_final: 0.9248 (tppp) REVERT: A 335 GLU cc_start: 0.8138 (mp0) cc_final: 0.7865 (mp0) REVERT: A 348 MET cc_start: 0.8767 (tmm) cc_final: 0.8476 (tmm) REVERT: A 352 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8419 (tm-30) REVERT: A 357 TYR cc_start: 0.8653 (m-80) cc_final: 0.7484 (m-80) REVERT: A 362 ASP cc_start: 0.8546 (m-30) cc_final: 0.8108 (m-30) REVERT: A 366 LYS cc_start: 0.9517 (mtmt) cc_final: 0.9162 (mtmm) REVERT: A 383 SER cc_start: 0.9185 (p) cc_final: 0.8481 (p) REVERT: A 385 VAL cc_start: 0.9526 (t) cc_final: 0.9278 (t) REVERT: A 396 ASP cc_start: 0.8785 (m-30) cc_final: 0.8374 (m-30) REVERT: A 407 ILE cc_start: 0.9296 (mt) cc_final: 0.9049 (mt) REVERT: A 421 GLU cc_start: 0.8833 (pp20) cc_final: 0.8474 (pp20) REVERT: A 427 LYS cc_start: 0.9302 (ttpt) cc_final: 0.9069 (ttpt) REVERT: A 446 ARG cc_start: 0.7624 (mmm-85) cc_final: 0.7341 (mmm-85) REVERT: A 458 MET cc_start: 0.8921 (mmp) cc_final: 0.8489 (mmp) REVERT: A 483 GLU cc_start: 0.9472 (mp0) cc_final: 0.9189 (mp0) REVERT: A 493 MET cc_start: 0.8777 (tmm) cc_final: 0.8185 (tmm) REVERT: A 515 ASP cc_start: 0.8996 (m-30) cc_final: 0.8791 (m-30) REVERT: A 583 SER cc_start: 0.9426 (m) cc_final: 0.9058 (t) REVERT: A 604 ARG cc_start: 0.8747 (tpp80) cc_final: 0.8497 (mmm160) REVERT: A 615 MET cc_start: 0.9228 (mmp) cc_final: 0.8838 (mmp) REVERT: A 639 ASP cc_start: 0.9107 (m-30) cc_final: 0.8869 (m-30) REVERT: A 640 MET cc_start: 0.9169 (tpp) cc_final: 0.8921 (tpp) REVERT: A 641 ILE cc_start: 0.9721 (mm) cc_final: 0.9503 (mm) REVERT: A 645 GLN cc_start: 0.8757 (tp40) cc_final: 0.8507 (tp-100) REVERT: A 672 LEU cc_start: 0.9361 (mt) cc_final: 0.9076 (mt) REVERT: B 20 LYS cc_start: 0.9590 (mtpt) cc_final: 0.9269 (ptpp) REVERT: B 51 LEU cc_start: 0.9305 (tp) cc_final: 0.9044 (tp) REVERT: B 67 GLU cc_start: 0.9047 (mp0) cc_final: 0.8778 (pm20) REVERT: B 75 GLU cc_start: 0.9277 (mp0) cc_final: 0.8959 (pm20) REVERT: B 87 LYS cc_start: 0.9355 (tptp) cc_final: 0.8986 (tptp) REVERT: B 89 PHE cc_start: 0.9235 (t80) cc_final: 0.8817 (t80) REVERT: B 95 MET cc_start: 0.9203 (tpp) cc_final: 0.8839 (tpp) REVERT: B 106 LEU cc_start: 0.9206 (tp) cc_final: 0.8997 (tp) REVERT: B 119 GLU cc_start: 0.9179 (mp0) cc_final: 0.8857 (mp0) REVERT: B 127 LEU cc_start: 0.9557 (mm) cc_final: 0.9182 (mm) REVERT: B 174 GLU cc_start: 0.7460 (tp30) cc_final: 0.7028 (tp30) REVERT: B 184 ARG cc_start: 0.9385 (tpp80) cc_final: 0.9014 (tpp80) REVERT: B 202 ASN cc_start: 0.9281 (t0) cc_final: 0.8309 (t0) REVERT: B 223 VAL cc_start: 0.9242 (m) cc_final: 0.8703 (m) REVERT: B 250 TYR cc_start: 0.9156 (m-80) cc_final: 0.8711 (m-80) REVERT: B 252 ASN cc_start: 0.9094 (t0) cc_final: 0.8837 (t0) REVERT: B 286 ASP cc_start: 0.8991 (m-30) cc_final: 0.8479 (m-30) REVERT: B 308 LYS cc_start: 0.9385 (mtmt) cc_final: 0.9146 (ptpp) REVERT: B 322 MET cc_start: 0.9132 (mtm) cc_final: 0.8752 (mtp) REVERT: B 333 LYS cc_start: 0.9547 (tptm) cc_final: 0.9134 (ttmm) REVERT: B 348 MET cc_start: 0.9176 (ptt) cc_final: 0.8236 (ptp) REVERT: B 355 TYR cc_start: 0.9033 (m-80) cc_final: 0.8562 (m-80) REVERT: B 362 ASP cc_start: 0.8892 (m-30) cc_final: 0.8210 (m-30) REVERT: B 375 LYS cc_start: 0.9160 (mmtm) cc_final: 0.8675 (mmtm) REVERT: B 391 VAL cc_start: 0.8949 (t) cc_final: 0.8450 (p) REVERT: B 392 SER cc_start: 0.8898 (m) cc_final: 0.8261 (p) REVERT: B 393 SER cc_start: 0.9549 (m) cc_final: 0.9200 (p) REVERT: B 402 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8171 (tm-30) REVERT: B 410 ASN cc_start: 0.8809 (m110) cc_final: 0.8534 (m110) REVERT: B 441 GLU cc_start: 0.9020 (pt0) cc_final: 0.8780 (pt0) REVERT: B 459 LYS cc_start: 0.9255 (mttp) cc_final: 0.8566 (mtpt) REVERT: B 515 ASP cc_start: 0.9245 (m-30) cc_final: 0.8900 (m-30) REVERT: B 522 TYR cc_start: 0.8916 (m-10) cc_final: 0.8638 (m-10) REVERT: B 585 SER cc_start: 0.8958 (p) cc_final: 0.8312 (t) REVERT: B 610 LYS cc_start: 0.9215 (ttpp) cc_final: 0.8934 (ttpp) REVERT: B 615 MET cc_start: 0.9327 (mmp) cc_final: 0.8976 (mmp) REVERT: B 626 TYR cc_start: 0.9019 (m-80) cc_final: 0.8389 (m-80) REVERT: B 628 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8653 (mt-10) REVERT: B 636 LYS cc_start: 0.9573 (mmtm) cc_final: 0.9345 (mmmm) REVERT: B 640 MET cc_start: 0.9166 (tpp) cc_final: 0.8803 (tpp) REVERT: B 645 GLN cc_start: 0.9277 (tp40) cc_final: 0.9014 (tp-100) REVERT: B 648 ILE cc_start: 0.9329 (mm) cc_final: 0.9076 (mm) REVERT: B 664 THR cc_start: 0.9318 (p) cc_final: 0.9091 (p) REVERT: B 668 ASN cc_start: 0.9362 (m-40) cc_final: 0.9112 (m-40) REVERT: B 677 ARG cc_start: 0.9282 (mmm-85) cc_final: 0.8845 (mmm-85) REVERT: C 17 PHE cc_start: 0.8700 (p90) cc_final: 0.8125 (p90) REVERT: C 21 PHE cc_start: 0.8790 (m-10) cc_final: 0.7974 (m-80) REVERT: C 154 PHE cc_start: 0.8266 (t80) cc_final: 0.7787 (t80) REVERT: D 45 LYS cc_start: 0.8667 (pttt) cc_final: 0.8223 (pttt) REVERT: D 46 TYR cc_start: 0.8635 (m-80) cc_final: 0.8065 (m-80) REVERT: D 96 MET cc_start: 0.8955 (tpt) cc_final: 0.8653 (tpp) REVERT: D 103 LYS cc_start: 0.8276 (pttp) cc_final: 0.7558 (mmmt) REVERT: D 105 TYR cc_start: 0.9335 (m-10) cc_final: 0.8605 (m-10) REVERT: D 169 TYR cc_start: 0.9345 (m-80) cc_final: 0.8850 (m-80) REVERT: D 172 PHE cc_start: 0.9111 (m-80) cc_final: 0.8708 (m-80) REVERT: D 259 PHE cc_start: 0.8344 (t80) cc_final: 0.8004 (t80) outliers start: 0 outliers final: 0 residues processed: 646 average time/residue: 0.1265 time to fit residues: 120.9782 Evaluate side-chains 570 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 570 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 186 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 156 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS D 28 GLN ** D 210 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 = 0.3760 r_free = 0.3760 target = 0.138443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.098888 restraints weight = 40561.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.102618 restraints weight = 22319.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.105154 restraints weight = 13968.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.106923 restraints weight = 9764.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.108125 restraints weight = 7333.227| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.6972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16386 Z= 0.183 Angle : 0.644 9.143 22134 Z= 0.335 Chirality : 0.044 0.205 2360 Planarity : 0.004 0.050 2818 Dihedral : 10.731 170.396 2242 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.19), residues: 1932 helix: 1.00 (0.15), residues: 1151 sheet: -0.26 (0.41), residues: 132 loop : 0.01 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 161 TYR 0.021 0.002 TYR D 236 PHE 0.025 0.002 PHE B 491 TRP 0.017 0.002 TRP A 9 HIS 0.021 0.002 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00403 (16386) covalent geometry : angle 0.64413 (22134) hydrogen bonds : bond 0.03822 ( 871) hydrogen bonds : angle 5.05411 ( 2571) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 650 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9079 (t70) cc_final: 0.8863 (t70) REVERT: A 31 GLU cc_start: 0.9102 (mp0) cc_final: 0.8731 (mp0) REVERT: A 65 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8457 (mp0) REVERT: A 119 GLU cc_start: 0.8790 (mp0) cc_final: 0.8436 (mp0) REVERT: A 136 LYS cc_start: 0.9522 (tttm) cc_final: 0.9293 (tptt) REVERT: A 142 ASN cc_start: 0.9258 (m-40) cc_final: 0.8861 (m110) REVERT: A 148 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8549 (mt-10) REVERT: A 150 GLN cc_start: 0.9535 (tp40) cc_final: 0.9291 (tp40) REVERT: A 158 ASN cc_start: 0.9338 (m-40) cc_final: 0.9123 (m-40) REVERT: A 172 LEU cc_start: 0.9474 (mp) cc_final: 0.9220 (mp) REVERT: A 181 ASP cc_start: 0.9045 (m-30) cc_final: 0.8764 (m-30) REVERT: A 257 ASP cc_start: 0.9072 (m-30) cc_final: 0.8662 (m-30) REVERT: A 277 THR cc_start: 0.8623 (p) cc_final: 0.8157 (t) REVERT: A 286 ASP cc_start: 0.8826 (m-30) cc_final: 0.8539 (m-30) REVERT: A 290 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8441 (tm-30) REVERT: A 291 LEU cc_start: 0.9480 (mt) cc_final: 0.9229 (mt) REVERT: A 333 LYS cc_start: 0.9525 (tppp) cc_final: 0.9214 (tppp) REVERT: A 335 GLU cc_start: 0.8272 (mp0) cc_final: 0.7699 (mp0) REVERT: A 352 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8373 (tm-30) REVERT: A 357 TYR cc_start: 0.8526 (m-80) cc_final: 0.7436 (m-80) REVERT: A 362 ASP cc_start: 0.8504 (m-30) cc_final: 0.8104 (m-30) REVERT: A 366 LYS cc_start: 0.9520 (mtmt) cc_final: 0.9157 (mtmm) REVERT: A 383 SER cc_start: 0.9066 (p) cc_final: 0.8426 (p) REVERT: A 396 ASP cc_start: 0.8830 (m-30) cc_final: 0.8431 (m-30) REVERT: A 421 GLU cc_start: 0.8746 (pp20) cc_final: 0.8436 (pp20) REVERT: A 427 LYS cc_start: 0.9251 (ttpt) cc_final: 0.9037 (ttpt) REVERT: A 441 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8840 (mm-30) REVERT: A 446 ARG cc_start: 0.7686 (mmm-85) cc_final: 0.7382 (mmm-85) REVERT: A 458 MET cc_start: 0.8911 (mmp) cc_final: 0.8494 (mmp) REVERT: A 483 GLU cc_start: 0.9459 (mp0) cc_final: 0.9217 (mp0) REVERT: A 493 MET cc_start: 0.8682 (tmm) cc_final: 0.8203 (tmm) REVERT: A 515 ASP cc_start: 0.8957 (m-30) cc_final: 0.8737 (m-30) REVERT: A 583 SER cc_start: 0.9381 (m) cc_final: 0.8986 (t) REVERT: A 604 ARG cc_start: 0.8717 (tpp80) cc_final: 0.8470 (mmm160) REVERT: A 615 MET cc_start: 0.9214 (mmp) cc_final: 0.8839 (mmp) REVERT: A 632 MET cc_start: 0.8483 (mtp) cc_final: 0.8169 (mtp) REVERT: A 639 ASP cc_start: 0.9068 (m-30) cc_final: 0.8860 (m-30) REVERT: A 640 MET cc_start: 0.9155 (tpp) cc_final: 0.8887 (tpp) REVERT: A 645 GLN cc_start: 0.8834 (tp40) cc_final: 0.8570 (tp-100) REVERT: A 686 ARG cc_start: 0.8376 (mtp-110) cc_final: 0.7896 (mtp-110) REVERT: B 20 LYS cc_start: 0.9591 (mtpt) cc_final: 0.9309 (mtpp) REVERT: B 51 LEU cc_start: 0.9262 (tp) cc_final: 0.9034 (tp) REVERT: B 55 LEU cc_start: 0.9726 (mt) cc_final: 0.9525 (mt) REVERT: B 75 GLU cc_start: 0.9251 (mp0) cc_final: 0.8943 (pm20) REVERT: B 87 LYS cc_start: 0.9329 (tptp) cc_final: 0.8982 (tptp) REVERT: B 95 MET cc_start: 0.9202 (tpp) cc_final: 0.8849 (tpp) REVERT: B 119 GLU cc_start: 0.9120 (mp0) cc_final: 0.8801 (mp0) REVERT: B 127 LEU cc_start: 0.9558 (mm) cc_final: 0.9184 (mm) REVERT: B 174 GLU cc_start: 0.7546 (tp30) cc_final: 0.6912 (tp30) REVERT: B 184 ARG cc_start: 0.9346 (tpp80) cc_final: 0.8660 (tpp80) REVERT: B 202 ASN cc_start: 0.9283 (t0) cc_final: 0.8144 (t0) REVERT: B 223 VAL cc_start: 0.9231 (m) cc_final: 0.8728 (m) REVERT: B 250 TYR cc_start: 0.9133 (m-80) cc_final: 0.8563 (m-80) REVERT: B 308 LYS cc_start: 0.9402 (mtmt) cc_final: 0.9188 (ptpp) REVERT: B 322 MET cc_start: 0.8883 (mtm) cc_final: 0.8475 (mtm) REVERT: B 333 LYS cc_start: 0.9566 (tptm) cc_final: 0.9152 (ttmm) REVERT: B 344 GLU cc_start: 0.9304 (mt-10) cc_final: 0.8952 (mt-10) REVERT: B 355 TYR cc_start: 0.9052 (m-80) cc_final: 0.8479 (m-10) REVERT: B 375 LYS cc_start: 0.9100 (mmtm) cc_final: 0.8670 (mmtm) REVERT: B 378 PHE cc_start: 0.8975 (p90) cc_final: 0.8727 (p90) REVERT: B 391 VAL cc_start: 0.9116 (t) cc_final: 0.8640 (p) REVERT: B 392 SER cc_start: 0.8868 (m) cc_final: 0.8214 (p) REVERT: B 393 SER cc_start: 0.9477 (m) cc_final: 0.8989 (p) REVERT: B 402 GLU cc_start: 0.8537 (tm-30) cc_final: 0.7882 (tm-30) REVERT: B 410 ASN cc_start: 0.8768 (m110) cc_final: 0.8490 (m110) REVERT: B 427 LYS cc_start: 0.9464 (ptpp) cc_final: 0.9255 (ptpp) REVERT: B 434 ASP cc_start: 0.9065 (m-30) cc_final: 0.8811 (m-30) REVERT: B 459 LYS cc_start: 0.9226 (mttp) cc_final: 0.8508 (mtpt) REVERT: B 500 ILE cc_start: 0.9785 (mt) cc_final: 0.9571 (mt) REVERT: B 515 ASP cc_start: 0.9191 (m-30) cc_final: 0.8832 (m-30) REVERT: B 570 MET cc_start: 0.8400 (mtp) cc_final: 0.7865 (mtp) REVERT: B 585 SER cc_start: 0.8962 (p) cc_final: 0.8262 (t) REVERT: B 597 ILE cc_start: 0.9650 (pt) cc_final: 0.9432 (pt) REVERT: B 615 MET cc_start: 0.9299 (mmp) cc_final: 0.9089 (mmp) REVERT: B 626 TYR cc_start: 0.8924 (m-80) cc_final: 0.8084 (m-80) REVERT: B 628 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8721 (mt-10) REVERT: B 636 LYS cc_start: 0.9580 (mmtm) cc_final: 0.9333 (mmmm) REVERT: B 640 MET cc_start: 0.9125 (tpp) cc_final: 0.8725 (tpp) REVERT: B 645 GLN cc_start: 0.9257 (tp40) cc_final: 0.9006 (tp-100) REVERT: B 648 ILE cc_start: 0.9320 (mm) cc_final: 0.9084 (mm) REVERT: B 664 THR cc_start: 0.9362 (p) cc_final: 0.9093 (p) REVERT: B 668 ASN cc_start: 0.9355 (m-40) cc_final: 0.9112 (m-40) REVERT: B 677 ARG cc_start: 0.9263 (mmm-85) cc_final: 0.8816 (mmm-85) REVERT: C 21 PHE cc_start: 0.8803 (m-10) cc_final: 0.8149 (m-80) REVERT: C 87 LYS cc_start: 0.9085 (mtmm) cc_final: 0.8825 (mttt) REVERT: C 90 LEU cc_start: 0.7697 (mt) cc_final: 0.7458 (mt) REVERT: C 154 PHE cc_start: 0.8087 (t80) cc_final: 0.7725 (t80) REVERT: C 315 LEU cc_start: 0.9015 (tp) cc_final: 0.8783 (tp) REVERT: D 45 LYS cc_start: 0.8692 (pttt) cc_final: 0.8263 (pttt) REVERT: D 46 TYR cc_start: 0.8613 (m-80) cc_final: 0.8077 (m-80) REVERT: D 96 MET cc_start: 0.8914 (tpt) cc_final: 0.8588 (tpp) REVERT: D 105 TYR cc_start: 0.9354 (m-10) cc_final: 0.8592 (m-10) REVERT: D 169 TYR cc_start: 0.9373 (m-80) cc_final: 0.8918 (m-80) REVERT: D 172 PHE cc_start: 0.9141 (m-80) cc_final: 0.8794 (m-80) REVERT: D 259 PHE cc_start: 0.8270 (t80) cc_final: 0.7954 (t80) REVERT: D 269 MET cc_start: 0.9245 (mtm) cc_final: 0.9039 (mtm) outliers start: 0 outliers final: 0 residues processed: 650 average time/residue: 0.1342 time to fit residues: 129.1667 Evaluate side-chains 564 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 564 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 153 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 370 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN D 25 ASN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.137315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.097999 restraints weight = 41127.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.101629 restraints weight = 22332.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.104090 restraints weight = 14219.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.105819 restraints weight = 10026.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.107059 restraints weight = 7597.417| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.7229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16386 Z= 0.185 Angle : 0.661 9.583 22134 Z= 0.345 Chirality : 0.045 0.234 2360 Planarity : 0.004 0.046 2818 Dihedral : 10.652 168.342 2242 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.06 % Allowed : 0.87 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.19), residues: 1932 helix: 0.99 (0.15), residues: 1135 sheet: -0.36 (0.41), residues: 132 loop : -0.03 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 161 TYR 0.025 0.002 TYR D 236 PHE 0.031 0.002 PHE D 154 TRP 0.016 0.002 TRP C 30 HIS 0.019 0.002 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00408 (16386) covalent geometry : angle 0.66145 (22134) hydrogen bonds : bond 0.03827 ( 871) hydrogen bonds : angle 5.08840 ( 2571) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 645 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9144 (t70) cc_final: 0.8759 (t70) REVERT: A 31 GLU cc_start: 0.9102 (mp0) cc_final: 0.8849 (mp0) REVERT: A 65 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8316 (mp0) REVERT: A 103 ASP cc_start: 0.8941 (m-30) cc_final: 0.8725 (m-30) REVERT: A 106 LEU cc_start: 0.9460 (tp) cc_final: 0.9186 (tp) REVERT: A 116 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8383 (mt-10) REVERT: A 119 GLU cc_start: 0.8857 (mp0) cc_final: 0.8455 (mp0) REVERT: A 136 LYS cc_start: 0.9534 (tttm) cc_final: 0.9248 (tptt) REVERT: A 142 ASN cc_start: 0.9286 (m-40) cc_final: 0.8875 (m110) REVERT: A 148 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8617 (mt-10) REVERT: A 172 LEU cc_start: 0.9478 (mp) cc_final: 0.9258 (mp) REVERT: A 181 ASP cc_start: 0.8995 (m-30) cc_final: 0.8746 (m-30) REVERT: A 232 ASN cc_start: 0.8720 (m110) cc_final: 0.8193 (m110) REVERT: A 250 TYR cc_start: 0.7995 (m-10) cc_final: 0.7771 (m-10) REVERT: A 257 ASP cc_start: 0.9101 (m-30) cc_final: 0.8891 (m-30) REVERT: A 277 THR cc_start: 0.8693 (p) cc_final: 0.8239 (t) REVERT: A 286 ASP cc_start: 0.8873 (m-30) cc_final: 0.8565 (m-30) REVERT: A 290 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8469 (tm-30) REVERT: A 291 LEU cc_start: 0.9466 (mt) cc_final: 0.9214 (mt) REVERT: A 325 LYS cc_start: 0.9101 (mppt) cc_final: 0.8821 (mmtm) REVERT: A 333 LYS cc_start: 0.9538 (tppp) cc_final: 0.9244 (tppp) REVERT: A 335 GLU cc_start: 0.8279 (mp0) cc_final: 0.8024 (mp0) REVERT: A 345 LYS cc_start: 0.9457 (mmmt) cc_final: 0.9256 (tttt) REVERT: A 357 TYR cc_start: 0.8512 (m-80) cc_final: 0.7487 (m-80) REVERT: A 362 ASP cc_start: 0.8542 (m-30) cc_final: 0.8113 (m-30) REVERT: A 366 LYS cc_start: 0.9522 (mtmt) cc_final: 0.9191 (mtmm) REVERT: A 383 SER cc_start: 0.8977 (p) cc_final: 0.8324 (p) REVERT: A 396 ASP cc_start: 0.8759 (m-30) cc_final: 0.8352 (m-30) REVERT: A 421 GLU cc_start: 0.8714 (pp20) cc_final: 0.8407 (pp20) REVERT: A 441 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8855 (mm-30) REVERT: A 446 ARG cc_start: 0.7698 (mmm-85) cc_final: 0.7316 (mmm-85) REVERT: A 458 MET cc_start: 0.8878 (mmp) cc_final: 0.8615 (mmm) REVERT: A 483 GLU cc_start: 0.9480 (mp0) cc_final: 0.9244 (mp0) REVERT: A 493 MET cc_start: 0.8765 (tmm) cc_final: 0.8253 (tmm) REVERT: A 515 ASP cc_start: 0.8983 (m-30) cc_final: 0.8756 (m-30) REVERT: A 583 SER cc_start: 0.9377 (m) cc_final: 0.8931 (t) REVERT: A 591 THR cc_start: 0.9445 (p) cc_final: 0.9234 (p) REVERT: A 604 ARG cc_start: 0.8701 (tpp80) cc_final: 0.8494 (mmm-85) REVERT: A 615 MET cc_start: 0.9228 (mmp) cc_final: 0.8835 (mmp) REVERT: A 632 MET cc_start: 0.8473 (mtp) cc_final: 0.7933 (mtp) REVERT: A 639 ASP cc_start: 0.9029 (m-30) cc_final: 0.8822 (m-30) REVERT: A 640 MET cc_start: 0.9167 (tpp) cc_final: 0.8930 (tpp) REVERT: A 645 GLN cc_start: 0.8761 (tp40) cc_final: 0.8367 (tp-100) REVERT: A 686 ARG cc_start: 0.8853 (mtp-110) cc_final: 0.8191 (mtp-110) REVERT: B 20 LYS cc_start: 0.9611 (mtpt) cc_final: 0.9301 (mtpp) REVERT: B 52 LYS cc_start: 0.9455 (tptp) cc_final: 0.9127 (tppt) REVERT: B 56 ASP cc_start: 0.9191 (m-30) cc_final: 0.8458 (m-30) REVERT: B 75 GLU cc_start: 0.9278 (mp0) cc_final: 0.8976 (pm20) REVERT: B 87 LYS cc_start: 0.9355 (tptp) cc_final: 0.9029 (tptp) REVERT: B 95 MET cc_start: 0.9152 (tpp) cc_final: 0.8749 (tpp) REVERT: B 119 GLU cc_start: 0.9060 (mp0) cc_final: 0.8732 (mp0) REVERT: B 127 LEU cc_start: 0.9555 (mm) cc_final: 0.9172 (mm) REVERT: B 174 GLU cc_start: 0.7578 (tp30) cc_final: 0.6980 (tp30) REVERT: B 184 ARG cc_start: 0.9325 (tpp80) cc_final: 0.8867 (tpp80) REVERT: B 202 ASN cc_start: 0.9288 (t0) cc_final: 0.8096 (t0) REVERT: B 211 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7969 (mm-30) REVERT: B 223 VAL cc_start: 0.9224 (m) cc_final: 0.8727 (m) REVERT: B 250 TYR cc_start: 0.9181 (m-80) cc_final: 0.8777 (m-80) REVERT: B 283 VAL cc_start: 0.9582 (t) cc_final: 0.9364 (t) REVERT: B 286 ASP cc_start: 0.9252 (m-30) cc_final: 0.8659 (m-30) REVERT: B 308 LYS cc_start: 0.9392 (mtmt) cc_final: 0.9180 (ptpp) REVERT: B 333 LYS cc_start: 0.9536 (tptm) cc_final: 0.9055 (ttmm) REVERT: B 344 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8995 (mt-10) REVERT: B 355 TYR cc_start: 0.9072 (m-80) cc_final: 0.8522 (m-10) REVERT: B 362 ASP cc_start: 0.9025 (m-30) cc_final: 0.8696 (m-30) REVERT: B 375 LYS cc_start: 0.9078 (mmtm) cc_final: 0.8659 (mmtm) REVERT: B 378 PHE cc_start: 0.9009 (p90) cc_final: 0.8774 (p90) REVERT: B 392 SER cc_start: 0.9007 (m) cc_final: 0.7747 (p) REVERT: B 410 ASN cc_start: 0.8834 (m110) cc_final: 0.8566 (m110) REVERT: B 459 LYS cc_start: 0.9210 (mttp) cc_final: 0.8504 (mtpt) REVERT: B 494 MET cc_start: 0.9308 (mmt) cc_final: 0.9098 (mmt) REVERT: B 515 ASP cc_start: 0.9211 (m-30) cc_final: 0.8846 (m-30) REVERT: B 585 SER cc_start: 0.8960 (p) cc_final: 0.8248 (t) REVERT: B 615 MET cc_start: 0.9343 (mmp) cc_final: 0.9120 (mmp) REVERT: B 626 TYR cc_start: 0.8943 (m-80) cc_final: 0.8200 (m-80) REVERT: B 636 LYS cc_start: 0.9592 (mmtm) cc_final: 0.9377 (mmmm) REVERT: B 640 MET cc_start: 0.9120 (tpp) cc_final: 0.8739 (tpp) REVERT: B 645 GLN cc_start: 0.9274 (tp40) cc_final: 0.8965 (tp-100) REVERT: B 648 ILE cc_start: 0.9323 (mm) cc_final: 0.9113 (mm) REVERT: B 664 THR cc_start: 0.9326 (p) cc_final: 0.9034 (p) REVERT: B 668 ASN cc_start: 0.9342 (m-40) cc_final: 0.9081 (m-40) REVERT: B 677 ARG cc_start: 0.9243 (mmm-85) cc_final: 0.8759 (mmm-85) REVERT: C 17 PHE cc_start: 0.8162 (p90) cc_final: 0.7602 (p90) REVERT: C 21 PHE cc_start: 0.8816 (m-10) cc_final: 0.8190 (m-80) REVERT: C 87 LYS cc_start: 0.9153 (mtmm) cc_final: 0.8907 (mttt) REVERT: C 90 LEU cc_start: 0.7683 (mt) cc_final: 0.7475 (mt) REVERT: C 315 LEU cc_start: 0.9152 (tp) cc_final: 0.8862 (tp) REVERT: D 45 LYS cc_start: 0.8690 (pttt) cc_final: 0.8245 (pttt) REVERT: D 46 TYR cc_start: 0.8616 (m-80) cc_final: 0.8065 (m-80) REVERT: D 49 LYS cc_start: 0.9271 (tptp) cc_final: 0.9061 (tptp) REVERT: D 56 MET cc_start: 0.8772 (ptp) cc_final: 0.8196 (ttt) REVERT: D 105 TYR cc_start: 0.9362 (m-10) cc_final: 0.8629 (m-10) REVERT: D 154 PHE cc_start: 0.7821 (m-80) cc_final: 0.7557 (m-80) REVERT: D 169 TYR cc_start: 0.9407 (m-80) cc_final: 0.8978 (m-80) REVERT: D 172 PHE cc_start: 0.9137 (m-80) cc_final: 0.8792 (m-80) REVERT: D 177 TYR cc_start: 0.9098 (t80) cc_final: 0.8795 (t80) REVERT: D 259 PHE cc_start: 0.8268 (t80) cc_final: 0.7911 (t80) REVERT: D 313 GLU cc_start: 0.8693 (mp0) cc_final: 0.8380 (mp0) outliers start: 1 outliers final: 1 residues processed: 645 average time/residue: 0.1307 time to fit residues: 126.9928 Evaluate side-chains 559 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 558 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 8.9990 chunk 133 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN D 25 ASN D 28 GLN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.139075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.099335 restraints weight = 40487.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.103090 restraints weight = 22284.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105623 restraints weight = 14098.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.107358 restraints weight = 9900.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.108570 restraints weight = 7488.769| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.7413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16386 Z= 0.157 Angle : 0.657 12.677 22134 Z= 0.341 Chirality : 0.044 0.228 2360 Planarity : 0.004 0.043 2818 Dihedral : 10.457 167.690 2242 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.19), residues: 1932 helix: 0.98 (0.15), residues: 1135 sheet: 0.62 (0.46), residues: 102 loop : -0.16 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 164 TYR 0.037 0.002 TYR D 130 PHE 0.027 0.002 PHE C 92 TRP 0.013 0.001 TRP A 9 HIS 0.019 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00354 (16386) covalent geometry : angle 0.65720 (22134) hydrogen bonds : bond 0.03832 ( 871) hydrogen bonds : angle 5.08084 ( 2571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 649 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9078 (t70) cc_final: 0.8857 (t70) REVERT: A 31 GLU cc_start: 0.9111 (mp0) cc_final: 0.8858 (mp0) REVERT: A 101 TYR cc_start: 0.9500 (m-80) cc_final: 0.9170 (m-10) REVERT: A 116 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8257 (mt-10) REVERT: A 119 GLU cc_start: 0.8732 (mp0) cc_final: 0.8405 (mp0) REVERT: A 136 LYS cc_start: 0.9552 (tttm) cc_final: 0.9317 (tptt) REVERT: A 142 ASN cc_start: 0.9185 (m-40) cc_final: 0.8801 (m110) REVERT: A 148 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8641 (mt-10) REVERT: A 150 GLN cc_start: 0.9416 (tp40) cc_final: 0.8443 (tm-30) REVERT: A 158 ASN cc_start: 0.9387 (m-40) cc_final: 0.9125 (m-40) REVERT: A 181 ASP cc_start: 0.8982 (m-30) cc_final: 0.8756 (m-30) REVERT: A 194 LYS cc_start: 0.9399 (ttpp) cc_final: 0.9158 (ttmm) REVERT: A 232 ASN cc_start: 0.8738 (m110) cc_final: 0.8335 (m110) REVERT: A 254 PHE cc_start: 0.8402 (m-80) cc_final: 0.8191 (m-10) REVERT: A 257 ASP cc_start: 0.9224 (m-30) cc_final: 0.9016 (m-30) REVERT: A 277 THR cc_start: 0.8724 (p) cc_final: 0.8296 (t) REVERT: A 290 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8469 (tm-30) REVERT: A 291 LEU cc_start: 0.9428 (mt) cc_final: 0.9126 (mt) REVERT: A 333 LYS cc_start: 0.9510 (tppp) cc_final: 0.9219 (tppp) REVERT: A 335 GLU cc_start: 0.8312 (mp0) cc_final: 0.8056 (mp0) REVERT: A 352 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8435 (tm-30) REVERT: A 357 TYR cc_start: 0.8461 (m-80) cc_final: 0.7414 (m-80) REVERT: A 366 LYS cc_start: 0.9511 (mtmt) cc_final: 0.9155 (mtmm) REVERT: A 383 SER cc_start: 0.8994 (p) cc_final: 0.8228 (p) REVERT: A 396 ASP cc_start: 0.8794 (m-30) cc_final: 0.8381 (m-30) REVERT: A 418 ASN cc_start: 0.9441 (m-40) cc_final: 0.8822 (m-40) REVERT: A 421 GLU cc_start: 0.8748 (pp20) cc_final: 0.8325 (pp20) REVERT: A 441 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8834 (mm-30) REVERT: A 446 ARG cc_start: 0.7725 (mmm-85) cc_final: 0.7309 (mmm-85) REVERT: A 458 MET cc_start: 0.8836 (mmp) cc_final: 0.8483 (mmm) REVERT: A 483 GLU cc_start: 0.9470 (mp0) cc_final: 0.9236 (mp0) REVERT: A 493 MET cc_start: 0.8698 (tmm) cc_final: 0.8137 (tmm) REVERT: A 583 SER cc_start: 0.9345 (m) cc_final: 0.8969 (t) REVERT: A 584 ILE cc_start: 0.9556 (pt) cc_final: 0.8921 (pt) REVERT: A 591 THR cc_start: 0.9461 (p) cc_final: 0.9260 (p) REVERT: A 615 MET cc_start: 0.9221 (mmp) cc_final: 0.8843 (mmp) REVERT: A 632 MET cc_start: 0.8385 (mtp) cc_final: 0.7654 (mtp) REVERT: A 639 ASP cc_start: 0.9088 (m-30) cc_final: 0.8814 (m-30) REVERT: A 640 MET cc_start: 0.9152 (tpp) cc_final: 0.8921 (tpp) REVERT: A 645 GLN cc_start: 0.8674 (tp40) cc_final: 0.8294 (tp-100) REVERT: A 658 LEU cc_start: 0.9542 (mt) cc_final: 0.9260 (mt) REVERT: A 686 ARG cc_start: 0.8670 (mtp-110) cc_final: 0.8128 (mtp-110) REVERT: B 20 LYS cc_start: 0.9597 (mtpt) cc_final: 0.9333 (mtpp) REVERT: B 52 LYS cc_start: 0.9446 (tptp) cc_final: 0.9152 (tppt) REVERT: B 55 LEU cc_start: 0.9742 (mt) cc_final: 0.9497 (mt) REVERT: B 56 ASP cc_start: 0.9211 (m-30) cc_final: 0.8649 (m-30) REVERT: B 75 GLU cc_start: 0.9255 (mp0) cc_final: 0.8944 (pm20) REVERT: B 87 LYS cc_start: 0.9323 (tptp) cc_final: 0.9019 (tptp) REVERT: B 95 MET cc_start: 0.9106 (tpp) cc_final: 0.8713 (tpp) REVERT: B 106 LEU cc_start: 0.9196 (tp) cc_final: 0.8995 (tt) REVERT: B 119 GLU cc_start: 0.9033 (mp0) cc_final: 0.8713 (mp0) REVERT: B 127 LEU cc_start: 0.9560 (mm) cc_final: 0.9170 (mm) REVERT: B 184 ARG cc_start: 0.9320 (tpp80) cc_final: 0.8967 (tpp80) REVERT: B 202 ASN cc_start: 0.9272 (t0) cc_final: 0.8758 (t0) REVERT: B 223 VAL cc_start: 0.9238 (m) cc_final: 0.8745 (m) REVERT: B 235 ARG cc_start: 0.9222 (ptp90) cc_final: 0.8666 (ptp90) REVERT: B 250 TYR cc_start: 0.9171 (m-80) cc_final: 0.8683 (m-80) REVERT: B 286 ASP cc_start: 0.9126 (m-30) cc_final: 0.8883 (m-30) REVERT: B 308 LYS cc_start: 0.9437 (mtmt) cc_final: 0.9146 (ptpp) REVERT: B 321 GLU cc_start: 0.8417 (pp20) cc_final: 0.8194 (pp20) REVERT: B 333 LYS cc_start: 0.9545 (tptm) cc_final: 0.9150 (ttmm) REVERT: B 344 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8908 (mt-10) REVERT: B 355 TYR cc_start: 0.9108 (m-80) cc_final: 0.8583 (m-80) REVERT: B 362 ASP cc_start: 0.8953 (m-30) cc_final: 0.8721 (m-30) REVERT: B 375 LYS cc_start: 0.9042 (mmtm) cc_final: 0.8635 (mmtm) REVERT: B 391 VAL cc_start: 0.9100 (t) cc_final: 0.8709 (p) REVERT: B 392 SER cc_start: 0.8777 (m) cc_final: 0.8092 (p) REVERT: B 402 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8148 (tm-30) REVERT: B 410 ASN cc_start: 0.8711 (m110) cc_final: 0.8477 (m110) REVERT: B 440 SER cc_start: 0.9601 (p) cc_final: 0.9326 (p) REVERT: B 459 LYS cc_start: 0.9144 (mttp) cc_final: 0.8384 (mtpt) REVERT: B 494 MET cc_start: 0.9281 (mmt) cc_final: 0.9070 (mmt) REVERT: B 515 ASP cc_start: 0.9198 (m-30) cc_final: 0.8830 (m-30) REVERT: B 522 TYR cc_start: 0.8765 (m-10) cc_final: 0.8535 (m-10) REVERT: B 585 SER cc_start: 0.8981 (p) cc_final: 0.8306 (t) REVERT: B 597 ILE cc_start: 0.9613 (pt) cc_final: 0.9329 (pt) REVERT: B 615 MET cc_start: 0.9312 (mmp) cc_final: 0.9064 (mmp) REVERT: B 626 TYR cc_start: 0.8666 (m-80) cc_final: 0.7854 (m-80) REVERT: B 628 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8696 (mm-30) REVERT: B 636 LYS cc_start: 0.9582 (mmtm) cc_final: 0.9354 (mmmm) REVERT: B 640 MET cc_start: 0.9108 (tpp) cc_final: 0.8665 (tpp) REVERT: B 645 GLN cc_start: 0.9229 (tp40) cc_final: 0.8965 (tp-100) REVERT: B 648 ILE cc_start: 0.9301 (mm) cc_final: 0.9098 (mm) REVERT: B 664 THR cc_start: 0.9301 (p) cc_final: 0.9004 (p) REVERT: B 667 LEU cc_start: 0.9454 (tp) cc_final: 0.9254 (tp) REVERT: B 668 ASN cc_start: 0.9294 (m-40) cc_final: 0.9074 (m-40) REVERT: B 677 ARG cc_start: 0.9225 (mmm-85) cc_final: 0.8734 (mmm-85) REVERT: C 17 PHE cc_start: 0.8139 (p90) cc_final: 0.7489 (p90) REVERT: C 21 PHE cc_start: 0.8816 (m-10) cc_final: 0.8223 (m-80) REVERT: C 87 LYS cc_start: 0.9089 (mtmm) cc_final: 0.8857 (mttt) REVERT: C 154 PHE cc_start: 0.8211 (t80) cc_final: 0.7629 (t80) REVERT: D 45 LYS cc_start: 0.8677 (pttt) cc_final: 0.8235 (pttt) REVERT: D 46 TYR cc_start: 0.8667 (m-80) cc_final: 0.8121 (m-80) REVERT: D 105 TYR cc_start: 0.9379 (m-10) cc_final: 0.8622 (m-10) REVERT: D 154 PHE cc_start: 0.7869 (m-80) cc_final: 0.7605 (m-80) REVERT: D 169 TYR cc_start: 0.9391 (m-80) cc_final: 0.8994 (m-80) REVERT: D 172 PHE cc_start: 0.9116 (m-80) cc_final: 0.8830 (m-80) REVERT: D 173 TYR cc_start: 0.8438 (t80) cc_final: 0.7767 (t80) REVERT: D 177 TYR cc_start: 0.9052 (t80) cc_final: 0.8767 (t80) REVERT: D 186 GLN cc_start: 0.9120 (mp10) cc_final: 0.8875 (mp10) REVERT: D 190 ILE cc_start: 0.8974 (mt) cc_final: 0.8710 (tp) REVERT: D 259 PHE cc_start: 0.8198 (t80) cc_final: 0.7784 (t80) outliers start: 0 outliers final: 0 residues processed: 649 average time/residue: 0.1298 time to fit residues: 126.6076 Evaluate side-chains 582 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 582 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 189 optimal weight: 5.9990 chunk 181 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 50 optimal weight: 0.0970 overall best weight: 1.1180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN B 320 ASN B 387 GLN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN D 25 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 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 = 0.3815 r_free = 0.3815 target = 0.140567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.100413 restraints weight = 40363.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.104178 restraints weight = 22147.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.106526 restraints weight = 14009.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108394 restraints weight = 10019.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109577 restraints weight = 7577.315| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.7630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16386 Z= 0.146 Angle : 0.660 12.696 22134 Z= 0.345 Chirality : 0.044 0.195 2360 Planarity : 0.004 0.045 2818 Dihedral : 10.250 164.273 2242 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.19), residues: 1932 helix: 0.95 (0.15), residues: 1133 sheet: 0.51 (0.47), residues: 102 loop : -0.17 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 604 TYR 0.027 0.002 TYR D 130 PHE 0.025 0.002 PHE D 178 TRP 0.013 0.001 TRP A 9 HIS 0.018 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00326 (16386) covalent geometry : angle 0.65988 (22134) hydrogen bonds : bond 0.03881 ( 871) hydrogen bonds : angle 5.08228 ( 2571) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 643 time to evaluate : 0.655 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 29 ASP cc_start: 0.9156 (t70) cc_final: 0.8759 (t70) REVERT: A 31 GLU cc_start: 0.9115 (mp0) cc_final: 0.8850 (mp0) REVERT: A 65 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8461 (mp0) REVERT: A 116 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8252 (mt-10) REVERT: A 119 GLU cc_start: 0.8741 (mp0) cc_final: 0.8375 (mp0) REVERT: A 136 LYS cc_start: 0.9567 (tttm) cc_final: 0.9222 (tptt) REVERT: A 147 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8401 (mm-40) REVERT: A 148 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8783 (mt-10) REVERT: A 150 GLN cc_start: 0.9350 (tp40) cc_final: 0.8435 (tm-30) REVERT: A 152 SER cc_start: 0.9421 (p) cc_final: 0.9182 (p) REVERT: A 158 ASN cc_start: 0.9380 (m-40) cc_final: 0.9112 (m-40) REVERT: A 172 LEU cc_start: 0.9555 (mp) cc_final: 0.9258 (mp) REVERT: A 181 ASP cc_start: 0.9106 (m-30) cc_final: 0.8744 (m-30) REVERT: A 194 LYS cc_start: 0.9423 (ttpp) cc_final: 0.9155 (ttmm) REVERT: A 227 MET cc_start: 0.8971 (mtm) cc_final: 0.8765 (mtm) REVERT: A 232 ASN cc_start: 0.8768 (m110) cc_final: 0.8223 (m110) REVERT: A 257 ASP cc_start: 0.9212 (m-30) cc_final: 0.8947 (m-30) REVERT: A 277 THR cc_start: 0.8704 (p) cc_final: 0.8271 (t) REVERT: A 290 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8361 (tm-30) REVERT: A 291 LEU cc_start: 0.9444 (mt) cc_final: 0.9137 (mt) REVERT: A 325 LYS cc_start: 0.9266 (mppt) cc_final: 0.8893 (mmtm) REVERT: A 333 LYS cc_start: 0.9503 (tppp) cc_final: 0.9204 (tppp) REVERT: A 335 GLU cc_start: 0.8321 (mp0) cc_final: 0.8086 (mp0) REVERT: A 348 MET cc_start: 0.8707 (tmm) cc_final: 0.8337 (tmm) REVERT: A 352 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8480 (tm-30) REVERT: A 366 LYS cc_start: 0.9522 (mtmt) cc_final: 0.9146 (mtmm) REVERT: A 379 SER cc_start: 0.7989 (t) cc_final: 0.7602 (t) REVERT: A 396 ASP cc_start: 0.8760 (m-30) cc_final: 0.8299 (m-30) REVERT: A 407 ILE cc_start: 0.9196 (mt) cc_final: 0.8931 (mt) REVERT: A 421 GLU cc_start: 0.8695 (pp20) cc_final: 0.8301 (pp20) REVERT: A 441 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8835 (mm-30) REVERT: A 458 MET cc_start: 0.8753 (mmp) cc_final: 0.8435 (mmm) REVERT: A 493 MET cc_start: 0.8644 (tmm) cc_final: 0.8241 (tmm) REVERT: A 583 SER cc_start: 0.9343 (m) cc_final: 0.8914 (t) REVERT: A 584 ILE cc_start: 0.9544 (pt) cc_final: 0.8919 (pt) REVERT: A 591 THR cc_start: 0.9465 (p) cc_final: 0.9242 (p) REVERT: A 595 MET cc_start: 0.8762 (mmm) cc_final: 0.8468 (mtt) REVERT: A 598 MET cc_start: 0.8140 (ttt) cc_final: 0.7939 (ttt) REVERT: A 615 MET cc_start: 0.9208 (mmp) cc_final: 0.8840 (mmp) REVERT: A 632 MET cc_start: 0.8182 (mtp) cc_final: 0.7898 (mtp) REVERT: A 639 ASP cc_start: 0.9039 (m-30) cc_final: 0.8766 (m-30) REVERT: A 640 MET cc_start: 0.9159 (tpp) cc_final: 0.8881 (tpp) REVERT: A 645 GLN cc_start: 0.8683 (tp40) cc_final: 0.8316 (tp-100) REVERT: A 686 ARG cc_start: 0.8839 (mtp-110) cc_final: 0.8132 (mtp-110) REVERT: B 20 LYS cc_start: 0.9614 (mtpt) cc_final: 0.9354 (mtpp) REVERT: B 51 LEU cc_start: 0.9200 (tp) cc_final: 0.8915 (tp) REVERT: B 52 LYS cc_start: 0.9439 (tptp) cc_final: 0.9118 (tppt) REVERT: B 56 ASP cc_start: 0.9206 (m-30) cc_final: 0.8609 (m-30) REVERT: B 75 GLU cc_start: 0.9260 (mp0) cc_final: 0.8949 (pm20) REVERT: B 87 LYS cc_start: 0.9310 (tptp) cc_final: 0.9016 (tptp) REVERT: B 89 PHE cc_start: 0.9266 (t80) cc_final: 0.8939 (t80) REVERT: B 95 MET cc_start: 0.9090 (tpp) cc_final: 0.8788 (tpp) REVERT: B 119 GLU cc_start: 0.9017 (mp0) cc_final: 0.8675 (mp0) REVERT: B 127 LEU cc_start: 0.9564 (mm) cc_final: 0.9181 (mm) REVERT: B 184 ARG cc_start: 0.9298 (tpp80) cc_final: 0.9023 (tpp80) REVERT: B 218 ASN cc_start: 0.9425 (m110) cc_final: 0.9218 (m110) REVERT: B 221 LYS cc_start: 0.8838 (mmtp) cc_final: 0.8549 (mmmm) REVERT: B 223 VAL cc_start: 0.9277 (m) cc_final: 0.8760 (m) REVERT: B 250 TYR cc_start: 0.9148 (m-80) cc_final: 0.8690 (m-80) REVERT: B 257 ASP cc_start: 0.9094 (m-30) cc_final: 0.8807 (m-30) REVERT: B 286 ASP cc_start: 0.9045 (m-30) cc_final: 0.8259 (m-30) REVERT: B 308 LYS cc_start: 0.9429 (mtmt) cc_final: 0.9144 (ptpp) REVERT: B 333 LYS cc_start: 0.9529 (tptm) cc_final: 0.9129 (ttmm) REVERT: B 344 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8912 (mt-10) REVERT: B 355 TYR cc_start: 0.9132 (m-80) cc_final: 0.8567 (m-80) REVERT: B 362 ASP cc_start: 0.8954 (m-30) cc_final: 0.8205 (m-30) REVERT: B 375 LYS cc_start: 0.8983 (mmtm) cc_final: 0.8619 (mmtm) REVERT: B 391 VAL cc_start: 0.9056 (t) cc_final: 0.8642 (t) REVERT: B 392 SER cc_start: 0.8801 (m) cc_final: 0.7518 (p) REVERT: B 410 ASN cc_start: 0.8741 (m110) cc_final: 0.8486 (m110) REVERT: B 456 LYS cc_start: 0.9557 (ttmm) cc_final: 0.9183 (ttpp) REVERT: B 459 LYS cc_start: 0.9210 (mttp) cc_final: 0.8643 (mptt) REVERT: B 494 MET cc_start: 0.9271 (mmt) cc_final: 0.9066 (mmt) REVERT: B 505 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8556 (mt-10) REVERT: B 515 ASP cc_start: 0.9183 (m-30) cc_final: 0.8697 (m-30) REVERT: B 570 MET cc_start: 0.8211 (mtp) cc_final: 0.7226 (mtt) REVERT: B 585 SER cc_start: 0.8976 (p) cc_final: 0.8294 (t) REVERT: B 597 ILE cc_start: 0.9494 (pt) cc_final: 0.9254 (pt) REVERT: B 615 MET cc_start: 0.9283 (mmp) cc_final: 0.9003 (mmp) REVERT: B 626 TYR cc_start: 0.8535 (m-80) cc_final: 0.7735 (m-80) REVERT: B 628 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8732 (mm-30) REVERT: B 636 LYS cc_start: 0.9592 (mmtm) cc_final: 0.9355 (mmmm) REVERT: B 640 MET cc_start: 0.9125 (tpp) cc_final: 0.8656 (tpp) REVERT: B 645 GLN cc_start: 0.9233 (tp40) cc_final: 0.8979 (tp-100) REVERT: B 648 ILE cc_start: 0.9275 (mm) cc_final: 0.9049 (mm) REVERT: C 17 PHE cc_start: 0.8124 (p90) cc_final: 0.7388 (p90) REVERT: C 21 PHE cc_start: 0.8736 (m-10) cc_final: 0.8123 (m-80) REVERT: C 154 PHE cc_start: 0.8122 (t80) cc_final: 0.7656 (t80) REVERT: D 17 PHE cc_start: 0.7982 (p90) cc_final: 0.7670 (m-80) REVERT: D 45 LYS cc_start: 0.8710 (pttt) cc_final: 0.8277 (pttt) REVERT: D 46 TYR cc_start: 0.8651 (m-80) cc_final: 0.8073 (m-80) REVERT: D 104 SER cc_start: 0.8751 (m) cc_final: 0.8522 (m) REVERT: D 105 TYR cc_start: 0.9368 (m-10) cc_final: 0.8653 (m-10) REVERT: D 123 GLU cc_start: 0.8709 (mp0) cc_final: 0.8388 (pm20) REVERT: D 154 PHE cc_start: 0.7883 (m-80) cc_final: 0.7628 (m-80) REVERT: D 164 GLU cc_start: 0.8960 (pt0) cc_final: 0.8413 (pt0) REVERT: D 169 TYR cc_start: 0.9451 (m-80) cc_final: 0.9158 (m-80) REVERT: D 186 GLN cc_start: 0.9170 (mp10) cc_final: 0.8962 (mp10) REVERT: D 208 LEU cc_start: 0.9484 (mt) cc_final: 0.9265 (mt) REVERT: D 259 PHE cc_start: 0.8201 (t80) cc_final: 0.7770 (t80) outliers start: 0 outliers final: 0 residues processed: 643 average time/residue: 0.1337 time to fit residues: 128.9000 Evaluate side-chains 575 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 575 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 148 optimal weight: 7.9990 chunk 125 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 313 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.143207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.102951 restraints weight = 40343.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.106815 restraints weight = 21987.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.109444 restraints weight = 13900.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.111274 restraints weight = 9779.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.112552 restraints weight = 7394.447| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.7788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16386 Z= 0.142 Angle : 0.661 10.348 22134 Z= 0.346 Chirality : 0.044 0.188 2360 Planarity : 0.004 0.045 2818 Dihedral : 10.030 162.265 2242 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.06 % Allowed : 0.17 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.19), residues: 1932 helix: 0.87 (0.15), residues: 1141 sheet: -0.20 (0.45), residues: 118 loop : -0.16 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 164 TYR 0.031 0.002 TYR D 130 PHE 0.032 0.002 PHE D 172 TRP 0.028 0.002 TRP D 30 HIS 0.018 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00319 (16386) covalent geometry : angle 0.66106 (22134) hydrogen bonds : bond 0.03862 ( 871) hydrogen bonds : angle 5.05804 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3387.78 seconds wall clock time: 59 minutes 26.00 seconds (3566.00 seconds total)