Starting phenix.real_space_refine on Thu Aug 6 15:10:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzk_45070/08_2026/9bzk_45070_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzk_45070/08_2026/9bzk_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 { model { file = "/net/cci-nas-00/data/ceres_data/9bzk_45070/08_2026/9bzk_45070_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzk_45070/08_2026/9bzk_45070_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bzk_45070/08_2026/9bzk_45070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzk_45070/08_2026/9bzk_45070.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 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: 3.25, per 1000 atoms: 0.20 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: 1.40 Conformation dependent library (CDL) restraints added in 650.5 milliseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.104A 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: 2.81 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 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=" O3B TTP A 803 " pdb=" PG TTP A 803 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" O3B TTP B 801 " pdb=" PG TTP B 801 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.061 1.25e-02 6.40e+03 2.35e+01 bond pdb=" O3A TTP A 803 " pdb=" PB TTP A 803 " ideal model delta sigma weight residual 1.675 1.606 0.069 2.00e-02 2.50e+03 1.21e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.608 0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21527 2.09 - 4.18: 525 4.18 - 6.27: 64 6.27 - 8.36: 9 8.36 - 10.45: 9 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.65 -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 - 25.05: 9088 25.05 - 50.10: 656 50.10 - 75.15: 126 75.15 - 100.20: 26 100.20 - 125.26: 2 Dihedral angle restraints: 9898 sinusoidal: 4140 harmonic: 5758 Sorted by residual: dihedral pdb=" O4' GDP A 802 " pdb=" C1' GDP A 802 " pdb=" N9 GDP A 802 " pdb=" C8 GDP A 802 " ideal model delta sinusoidal sigma weight residual 27.02 -98.23 125.26 1 2.00e+01 2.50e-03 3.79e+01 dihedral pdb=" O4' GDP B 804 " pdb=" C1' GDP B 804 " pdb=" N9 GDP B 804 " pdb=" C8 GDP B 804 " ideal model delta sinusoidal sigma weight residual 27.02 -95.56 122.59 1 2.00e+01 2.50e-03 3.69e+01 dihedral pdb=" C VAL C 125 " pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual -122.00 -134.34 12.34 0 2.50e+00 1.60e-01 2.43e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2141 0.094 - 0.187: 186 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: 1.070 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.680 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6054 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.139 16386 Z= 0.334 Angle : 0.788 10.450 22134 Z= 0.472 Chirality : 0.058 0.468 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.680 125.256 6202 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 are 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/Z covalent geometry : bond 0.00596 / 0.33 (16386) covalent geometry : angle 0.78802 / 0.47 (22134) hydrogen bonds : bond 0.15423 / 9.51 ( 871) hydrogen bonds : angle 6.51778 / 4.65 ( 2571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 913 time to evaluate : 0.609 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: 0.7833 (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: 0.7961 (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: 0.6811 (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: 0.8711 (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: 0.6437 (m-30) cc_final: 0.6074 (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: 0.7972 (p) REVERT: B 631 ASP cc_start: 0.7625 (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: 0.1306 time to fit residues: 176.8053 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 : 0.593 ------------------------------------------------------------------------------- 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: 0.9980 chunk 149 optimal weight: 4.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** 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 23 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN D 71 ASN D 80 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.149210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.105776 restraints weight = 37743.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.109845 restraints weight = 21448.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.112595 restraints weight = 14002.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.114551 restraints weight = 10047.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.115903 restraints weight = 7720.058| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 11 (16 function evaluations) r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.4203 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= 0.166 Angle : 0.622 11.260 22134 Z= 0.333 Chirality : 0.043 0.249 2360 Planarity : 0.004 0.076 2818 Dihedral : 9.303 129.281 2290 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.12 % Allowed : 2.62 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.18), residues: 1932 helix: 1.29 (0.15), residues: 1126 sheet: -0.04 (0.41), residues: 134 loop : 0.51 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 235 TYR 0.027 0.002 TYR A 498 PHE 0.030 0.002 PHE D 259 TRP 0.011 0.002 TRP B 558 HIS 0.007 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (16386) covalent geometry : angle 0.62193 / 0.33 (22134) hydrogen bonds : bond 0.04596 / 2.90 ( 871) hydrogen bonds : angle 5.02878 / 3.57 ( 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 742 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 740 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.9445 (mp) cc_final: 0.9235 (mt) REVERT: A 29 ASP cc_start: 0.9282 (t0) cc_final: 0.8758 (t70) REVERT: A 82 LYS cc_start: 0.9685 (mtpp) cc_final: 0.9426 (mmtp) REVERT: A 118 TYR cc_start: 0.8905 (t80) cc_final: 0.8469 (t80) REVERT: A 119 GLU cc_start: 0.8841 (mp0) cc_final: 0.8291 (mp0) REVERT: A 143 LEU cc_start: 0.9237 (tp) cc_final: 0.8932 (tp) REVERT: A 147 GLN cc_start: 0.9055 (mt0) cc_final: 0.7513 (mt0) REVERT: A 148 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8510 (mt-10) REVERT: A 150 GLN cc_start: 0.9292 (tp40) cc_final: 0.9022 (tp40) REVERT: A 176 ASN cc_start: 0.8762 (t0) cc_final: 0.8447 (t0) REVERT: A 187 ASP cc_start: 0.9411 (t70) cc_final: 0.8701 (t0) REVERT: A 188 ILE cc_start: 0.9695 (mt) cc_final: 0.9404 (mt) REVERT: A 191 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8343 (mp10) REVERT: A 195 LEU cc_start: 0.9573 (mt) cc_final: 0.9335 (mt) REVERT: A 202 ASN cc_start: 0.9274 (t0) cc_final: 0.8884 (t0) REVERT: A 214 LYS cc_start: 0.8933 (tppt) cc_final: 0.8599 (mmtt) REVERT: A 221 LYS cc_start: 0.8931 (mmtp) cc_final: 0.8524 (mmtp) REVERT: A 223 VAL cc_start: 0.9573 (m) cc_final: 0.9106 (p) REVERT: A 243 ARG cc_start: 0.6873 (tmt-80) cc_final: 0.6610 (tpt-90) REVERT: A 257 ASP cc_start: 0.9243 (m-30) cc_final: 0.8952 (m-30) REVERT: A 270 ASP cc_start: 0.7940 (t70) cc_final: 0.7395 (t70) REVERT: A 319 MET cc_start: 0.9085 (tpp) cc_final: 0.8858 (tpp) REVERT: A 322 MET cc_start: 0.8508 (mmp) cc_final: 0.7704 (mmm) REVERT: A 326 PHE cc_start: 0.9599 (m-10) cc_final: 0.8898 (m-80) REVERT: A 335 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8402 (mm-30) REVERT: A 348 MET cc_start: 0.8813 (tpt) cc_final: 0.8437 (tpp) REVERT: A 355 TYR cc_start: 0.9016 (m-10) cc_final: 0.8766 (m-10) REVERT: A 357 TYR cc_start: 0.8878 (m-10) cc_final: 0.8564 (m-80) REVERT: A 366 LYS cc_start: 0.9521 (mtmt) cc_final: 0.9245 (mtmm) REVERT: A 385 VAL cc_start: 0.9431 (t) cc_final: 0.9227 (t) REVERT: A 407 ILE cc_start: 0.9058 (mt) cc_final: 0.8823 (mt) REVERT: A 418 ASN cc_start: 0.9423 (m-40) cc_final: 0.9064 (m-40) REVERT: A 421 GLU cc_start: 0.8687 (pp20) cc_final: 0.8263 (pp20) REVERT: A 493 MET cc_start: 0.8958 (tmm) cc_final: 0.8617 (tmm) REVERT: A 515 ASP cc_start: 0.8964 (m-30) cc_final: 0.8738 (m-30) REVERT: A 550 MET cc_start: 0.7202 (mtm) cc_final: 0.6896 (mtp) REVERT: A 583 SER cc_start: 0.9438 (m) cc_final: 0.8854 (p) REVERT: A 588 GLN cc_start: 0.8986 (mm-40) cc_final: 0.8060 (mm-40) REVERT: A 595 MET cc_start: 0.9249 (mmp) cc_final: 0.9035 (mmt) REVERT: A 598 MET cc_start: 0.8392 (mtm) cc_final: 0.7872 (mtm) REVERT: A 615 MET cc_start: 0.8816 (mmp) cc_final: 0.8298 (mmp) REVERT: A 634 MET cc_start: 0.8994 (mmm) cc_final: 0.8784 (mmm) REVERT: A 668 ASN cc_start: 0.9163 (m110) cc_final: 0.8820 (m110) REVERT: A 684 TYR cc_start: 0.7772 (m-10) cc_final: 0.7135 (m-80) REVERT: B 12 LEU cc_start: 0.9298 (mp) cc_final: 0.8790 (mt) REVERT: B 15 GLU cc_start: 0.9404 (mt-10) cc_final: 0.9130 (mt-10) REVERT: B 51 LEU cc_start: 0.8921 (tp) cc_final: 0.8572 (tp) REVERT: B 87 LYS cc_start: 0.9301 (tptp) cc_final: 0.9025 (tptp) REVERT: B 99 LYS cc_start: 0.9534 (mmmt) cc_final: 0.9199 (mmmt) REVERT: B 107 LYS cc_start: 0.9387 (mttt) cc_final: 0.9168 (mptt) REVERT: B 147 GLN cc_start: 0.8871 (mt0) cc_final: 0.8618 (mm-40) REVERT: B 211 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8069 (mm-30) REVERT: B 236 TYR cc_start: 0.8941 (t80) cc_final: 0.8542 (t80) REVERT: B 250 TYR cc_start: 0.9173 (m-80) cc_final: 0.8797 (m-80) REVERT: B 308 LYS cc_start: 0.9464 (mtmt) cc_final: 0.9245 (ptpp) REVERT: B 322 MET cc_start: 0.8993 (mmm) cc_final: 0.8173 (mmm) REVERT: B 326 PHE cc_start: 0.9067 (m-80) cc_final: 0.8448 (m-80) REVERT: B 333 LYS cc_start: 0.9255 (tptm) cc_final: 0.8884 (tttm) REVERT: B 348 MET cc_start: 0.8978 (ptp) cc_final: 0.8450 (ptt) REVERT: B 352 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8700 (mt-10) REVERT: B 355 TYR cc_start: 0.8987 (m-80) cc_final: 0.8450 (m-80) REVERT: B 362 ASP cc_start: 0.8571 (m-30) cc_final: 0.7745 (m-30) REVERT: B 386 LEU cc_start: 0.9273 (mt) cc_final: 0.8651 (mt) REVERT: B 393 SER cc_start: 0.9554 (m) cc_final: 0.9319 (p) REVERT: B 403 ILE cc_start: 0.9461 (mp) cc_final: 0.9221 (tp) REVERT: B 415 ASN cc_start: 0.9544 (t0) cc_final: 0.9290 (t0) REVERT: B 416 ILE cc_start: 0.9589 (mt) cc_final: 0.9372 (mt) REVERT: B 458 MET cc_start: 0.9468 (mmm) cc_final: 0.9187 (mmm) REVERT: B 468 LEU cc_start: 0.9605 (tp) cc_final: 0.9295 (tp) REVERT: B 493 MET cc_start: 0.9575 (tmm) cc_final: 0.9311 (tmm) REVERT: B 515 ASP cc_start: 0.9225 (m-30) cc_final: 0.8890 (m-30) REVERT: B 558 TRP cc_start: 0.9184 (m100) cc_final: 0.8485 (m100) REVERT: B 571 TYR cc_start: 0.9135 (t80) cc_final: 0.8503 (t80) REVERT: B 599 GLU cc_start: 0.8530 (pt0) cc_final: 0.8291 (pt0) REVERT: B 601 ILE cc_start: 0.9527 (mm) cc_final: 0.9172 (tp) REVERT: B 632 MET cc_start: 0.8779 (mpp) cc_final: 0.8187 (mpp) REVERT: B 640 MET cc_start: 0.9115 (tpp) cc_final: 0.8846 (tpp) REVERT: B 650 GLN cc_start: 0.8638 (mt0) cc_final: 0.7799 (mm-40) REVERT: B 657 PHE cc_start: 0.8887 (m-80) cc_final: 0.8351 (m-80) REVERT: B 664 THR cc_start: 0.9118 (p) cc_final: 0.8877 (p) REVERT: B 668 ASN cc_start: 0.9318 (m-40) cc_final: 0.9109 (m110) REVERT: B 684 TYR cc_start: 0.7531 (m-10) cc_final: 0.6559 (m-10) REVERT: C 17 PHE cc_start: 0.8575 (p90) cc_final: 0.7748 (p90) REVERT: C 20 MET cc_start: 0.8760 (ppp) cc_final: 0.8546 (ppp) REVERT: C 21 PHE cc_start: 0.9047 (m-10) cc_final: 0.8248 (m-80) REVERT: C 87 LYS cc_start: 0.8770 (mtmm) cc_final: 0.8473 (mtmt) REVERT: C 204 TYR cc_start: 0.9193 (t80) cc_final: 0.8826 (t80) REVERT: C 283 ASN cc_start: 0.2209 (p0) cc_final: 0.1929 (p0) REVERT: D 20 MET cc_start: 0.8103 (ttp) cc_final: 0.7772 (ptm) REVERT: D 45 LYS cc_start: 0.8471 (pttt) cc_final: 0.8068 (pttt) REVERT: D 46 TYR cc_start: 0.8589 (m-80) cc_final: 0.8182 (m-80) REVERT: D 105 TYR cc_start: 0.8915 (m-10) cc_final: 0.8448 (m-10) REVERT: D 197 ASP cc_start: 0.9062 (m-30) cc_final: 0.8770 (m-30) REVERT: D 204 TYR cc_start: 0.9568 (t80) cc_final: 0.9262 (t80) outliers start: 2 outliers final: 0 residues processed: 740 average time/residue: 0.1302 time to fit residues: 143.8620 Evaluate side-chains 609 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 609 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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: 1.9990 chunk 131 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 182 optimal weight: 9.9990 chunk 159 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 158 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN ** A 147 GLN ** 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** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 HIS C 25 ASN C 98 ASN C 201 HIS ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.136107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.095452 restraints weight = 40883.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.099216 restraints weight = 22858.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.101750 restraints weight = 14486.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.103532 restraints weight = 10226.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.104820 restraints weight = 7746.504| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16386 Z= 0.221 Angle : 0.637 12.910 22134 Z= 0.337 Chirality : 0.046 0.795 2360 Planarity : 0.004 0.045 2818 Dihedral : 9.038 136.816 2290 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.23 % Allowed : 2.16 % 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 are not related in a simple way. whole: 1.09 (0.18), residues: 1932 helix: 1.15 (0.15), residues: 1133 sheet: 0.00 (0.41), residues: 134 loop : 0.34 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 121 TYR 0.031 0.002 TYR B 574 PHE 0.028 0.002 PHE A 171 TRP 0.025 0.002 TRP D 124 HIS 0.006 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.22 (16386) covalent geometry : angle 0.63650 / 0.34 (22134) hydrogen bonds : bond 0.04274 / 2.68 ( 871) hydrogen bonds : angle 4.87617 / 3.45 ( 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 674 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 670 time to evaluate : 0.605 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: 0.9163 (t0) cc_final: 0.8730 (t70) REVERT: A 118 TYR cc_start: 0.8901 (t80) cc_final: 0.8617 (t80) REVERT: A 119 GLU cc_start: 0.8951 (mp0) cc_final: 0.8453 (mp0) REVERT: A 136 LYS cc_start: 0.9500 (tttp) cc_final: 0.9266 (tttp) REVERT: A 139 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8937 (mt-10) REVERT: A 150 GLN cc_start: 0.9347 (tp40) cc_final: 0.9065 (tp40) REVERT: A 172 LEU cc_start: 0.9578 (mp) cc_final: 0.9044 (mp) REVERT: A 173 LEU cc_start: 0.9615 (mt) cc_final: 0.9158 (mt) REVERT: A 181 ASP cc_start: 0.9150 (m-30) cc_final: 0.8694 (m-30) REVERT: A 202 ASN cc_start: 0.9225 (t0) cc_final: 0.8989 (t0) REVERT: A 223 VAL cc_start: 0.9484 (m) cc_final: 0.9209 (p) REVERT: A 239 GLN cc_start: 0.8132 (mt0) cc_final: 0.7765 (tm-30) REVERT: A 252 ASN cc_start: 0.9178 (t0) cc_final: 0.8931 (t0) REVERT: A 257 ASP cc_start: 0.9355 (m-30) cc_final: 0.8906 (m-30) REVERT: A 277 THR cc_start: 0.8780 (p) cc_final: 0.8572 (p) REVERT: A 295 ASP cc_start: 0.8619 (t0) cc_final: 0.8312 (t0) REVERT: A 355 TYR cc_start: 0.8972 (m-10) cc_final: 0.8743 (m-10) REVERT: A 366 LYS cc_start: 0.9500 (mtmt) cc_final: 0.9141 (mtmm) REVERT: A 406 ASP cc_start: 0.8297 (m-30) cc_final: 0.7668 (m-30) REVERT: A 407 ILE cc_start: 0.9270 (mt) cc_final: 0.9025 (mt) REVERT: A 413 SER cc_start: 0.8952 (t) cc_final: 0.8752 (t) REVERT: A 421 GLU cc_start: 0.8822 (pp20) cc_final: 0.8558 (pp20) REVERT: A 444 ASP cc_start: 0.8280 (t0) cc_final: 0.7587 (t0) REVERT: A 446 ARG cc_start: 0.7930 (mmt90) cc_final: 0.7631 (mmm-85) REVERT: A 458 MET cc_start: 0.8949 (mmp) cc_final: 0.8557 (mmp) REVERT: A 493 MET cc_start: 0.8853 (tmm) cc_final: 0.8437 (tmm) REVERT: A 515 ASP cc_start: 0.9086 (m-30) cc_final: 0.8826 (m-30) REVERT: A 528 PHE cc_start: 0.9138 (m-80) cc_final: 0.8540 (m-10) REVERT: A 550 MET cc_start: 0.7363 (mtm) cc_final: 0.7085 (mtp) REVERT: A 561 LEU cc_start: 0.9457 (tp) cc_final: 0.9231 (tp) REVERT: A 583 SER cc_start: 0.9473 (m) cc_final: 0.9133 (p) REVERT: A 595 MET cc_start: 0.9317 (mmp) cc_final: 0.8945 (mmt) REVERT: A 615 MET cc_start: 0.9188 (mmp) cc_final: 0.8784 (mmp) REVERT: A 639 ASP cc_start: 0.9233 (m-30) cc_final: 0.9028 (m-30) REVERT: A 645 GLN cc_start: 0.8548 (tp40) cc_final: 0.8268 (tp-100) REVERT: A 647 HIS cc_start: 0.9289 (m-70) cc_final: 0.8948 (m90) REVERT: A 672 LEU cc_start: 0.9278 (mt) cc_final: 0.9000 (mt) REVERT: B 51 LEU cc_start: 0.9191 (tp) cc_final: 0.8900 (tp) REVERT: B 52 LYS cc_start: 0.9374 (tptp) cc_final: 0.9131 (tppt) REVERT: B 87 LYS cc_start: 0.9324 (tptp) cc_final: 0.9070 (tptp) REVERT: B 99 LYS cc_start: 0.9565 (mmmt) cc_final: 0.9276 (mmmt) REVERT: B 119 GLU cc_start: 0.9252 (mp0) cc_final: 0.8819 (mp0) REVERT: B 147 GLN cc_start: 0.9181 (mt0) cc_final: 0.8734 (mm-40) REVERT: B 235 ARG cc_start: 0.9101 (ptp-110) cc_final: 0.8536 (ptp90) REVERT: B 250 TYR cc_start: 0.9211 (m-80) cc_final: 0.8836 (m-80) REVERT: B 274 ARG cc_start: 0.8756 (tpp80) cc_final: 0.8499 (tpp80) REVERT: B 322 MET cc_start: 0.8802 (mmm) cc_final: 0.7928 (mmm) REVERT: B 333 LYS cc_start: 0.9517 (tptm) cc_final: 0.9284 (ttmm) REVERT: B 355 TYR cc_start: 0.8991 (m-80) cc_final: 0.8521 (m-80) REVERT: B 393 SER cc_start: 0.9623 (m) cc_final: 0.8883 (p) REVERT: B 410 ASN cc_start: 0.8990 (m110) cc_final: 0.8657 (m110) REVERT: B 415 ASN cc_start: 0.9589 (t0) cc_final: 0.9261 (t0) REVERT: B 416 ILE cc_start: 0.9656 (mt) cc_final: 0.9426 (mt) REVERT: B 420 MET cc_start: 0.9230 (mmm) cc_final: 0.8982 (mmm) REVERT: B 441 GLU cc_start: 0.9096 (pt0) cc_final: 0.8810 (pt0) REVERT: B 459 LYS cc_start: 0.9155 (mttp) cc_final: 0.8386 (mtpt) REVERT: B 487 PHE cc_start: 0.9770 (t80) cc_final: 0.9541 (t80) REVERT: B 515 ASP cc_start: 0.9221 (m-30) cc_final: 0.8906 (m-30) REVERT: B 599 GLU cc_start: 0.8624 (pt0) cc_final: 0.8108 (pt0) REVERT: B 601 ILE cc_start: 0.9487 (mm) cc_final: 0.9016 (tp) REVERT: B 628 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8526 (mm-30) REVERT: B 632 MET cc_start: 0.8610 (mpp) cc_final: 0.8276 (mpp) REVERT: B 640 MET cc_start: 0.9222 (tpp) cc_final: 0.8850 (tpp) REVERT: B 645 GLN cc_start: 0.9302 (tp40) cc_final: 0.8474 (tp-100) REVERT: B 664 THR cc_start: 0.9123 (p) cc_final: 0.8904 (p) REVERT: B 667 LEU cc_start: 0.9287 (tp) cc_final: 0.9063 (tp) REVERT: B 668 ASN cc_start: 0.9347 (m-40) cc_final: 0.9092 (m110) REVERT: B 677 ARG cc_start: 0.9194 (mmm-85) cc_final: 0.8802 (mmm-85) REVERT: B 680 LYS cc_start: 0.8928 (mttt) cc_final: 0.8592 (mtmt) REVERT: C 17 PHE cc_start: 0.8476 (p90) cc_final: 0.7989 (p90) REVERT: C 21 PHE cc_start: 0.8973 (m-10) cc_final: 0.8025 (m-80) REVERT: C 97 GLU cc_start: 0.7625 (tp30) cc_final: 0.7303 (tp30) REVERT: C 204 TYR cc_start: 0.9204 (t80) cc_final: 0.8943 (t80) REVERT: D 45 LYS cc_start: 0.8568 (pttt) cc_final: 0.8131 (pttt) REVERT: D 46 TYR cc_start: 0.8586 (m-80) cc_final: 0.8094 (m-80) REVERT: D 59 LEU cc_start: 0.9065 (mt) cc_final: 0.8836 (mt) REVERT: D 96 MET cc_start: 0.8679 (tpt) cc_final: 0.8380 (tpp) REVERT: D 105 TYR cc_start: 0.9160 (m-10) cc_final: 0.8418 (m-10) REVERT: D 130 TYR cc_start: 0.7118 (m-80) cc_final: 0.6773 (m-80) REVERT: D 169 TYR cc_start: 0.9029 (m-80) cc_final: 0.8562 (m-80) REVERT: D 172 PHE cc_start: 0.8928 (m-80) cc_final: 0.8635 (m-80) REVERT: D 197 ASP cc_start: 0.9126 (m-30) cc_final: 0.8801 (m-30) REVERT: D 204 TYR cc_start: 0.9653 (t80) cc_final: 0.9252 (t80) outliers start: 4 outliers final: 0 residues processed: 672 average time/residue: 0.1300 time to fit residues: 130.7135 Evaluate side-chains 598 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 598 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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: 0.9990 chunk 157 optimal weight: 10.0000 chunk 168 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 185 optimal weight: 20.0000 chunk 191 optimal weight: 10.0000 chunk 159 optimal weight: 30.0000 chunk 182 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** 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 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN C 25 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.132406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.092478 restraints weight = 41349.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.096042 restraints weight = 23309.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.098439 restraints weight = 14999.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.100099 restraints weight = 10734.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.101280 restraints weight = 8209.672| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.6234 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= 0.259 Angle : 0.656 10.259 22134 Z= 0.346 Chirality : 0.044 0.213 2360 Planarity : 0.004 0.039 2818 Dihedral : 8.971 138.661 2290 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.23 % Allowed : 2.56 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.18), residues: 1932 helix: 0.90 (0.15), residues: 1153 sheet: -0.32 (0.40), residues: 144 loop : 0.15 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 350 TYR 0.028 0.002 TYR B 574 PHE 0.023 0.002 PHE D 166 TRP 0.011 0.002 TRP B 623 HIS 0.023 0.002 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.26 (16386) covalent geometry : angle 0.65616 / 0.35 (22134) hydrogen bonds : bond 0.04169 / 2.61 ( 871) hydrogen bonds : angle 5.01683 / 3.53 ( 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 653 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 649 time to evaluate : 0.547 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: A 65 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8367 (mp0) REVERT: A 118 TYR cc_start: 0.9044 (t80) cc_final: 0.8803 (t80) REVERT: A 119 GLU cc_start: 0.8958 (mp0) cc_final: 0.8530 (mp0) REVERT: A 136 LYS cc_start: 0.9542 (tttp) cc_final: 0.9308 (tttp) REVERT: A 139 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8818 (mt-10) REVERT: A 158 ASN cc_start: 0.9355 (m-40) cc_final: 0.9098 (m-40) REVERT: A 161 ARG cc_start: 0.8612 (ttm-80) cc_final: 0.8058 (ttm-80) REVERT: A 172 LEU cc_start: 0.9575 (mp) cc_final: 0.9135 (mp) REVERT: A 173 LEU cc_start: 0.9632 (mt) cc_final: 0.9227 (mt) REVERT: A 181 ASP cc_start: 0.9031 (m-30) cc_final: 0.8555 (m-30) REVERT: A 223 VAL cc_start: 0.9610 (m) cc_final: 0.9350 (p) REVERT: A 236 TYR cc_start: 0.9077 (t80) cc_final: 0.8869 (t80) REVERT: A 335 GLU cc_start: 0.8199 (mp0) cc_final: 0.7595 (mp0) REVERT: A 357 TYR cc_start: 0.8947 (m-80) cc_final: 0.7961 (m-80) REVERT: A 366 LYS cc_start: 0.9484 (mtmt) cc_final: 0.9090 (mtmm) REVERT: A 383 SER cc_start: 0.9276 (p) cc_final: 0.8816 (p) REVERT: A 396 ASP cc_start: 0.8823 (m-30) cc_final: 0.8436 (m-30) REVERT: A 406 ASP cc_start: 0.8151 (m-30) cc_final: 0.7538 (m-30) REVERT: A 407 ILE cc_start: 0.9288 (mt) cc_final: 0.9044 (mt) REVERT: A 421 GLU cc_start: 0.8835 (pp20) cc_final: 0.8561 (pp20) REVERT: A 446 ARG cc_start: 0.8028 (mmt90) cc_final: 0.7595 (tpp80) REVERT: A 458 MET cc_start: 0.9032 (mmp) cc_final: 0.8635 (mmp) REVERT: A 491 PHE cc_start: 0.9655 (t80) cc_final: 0.9415 (t80) REVERT: A 493 MET cc_start: 0.8790 (tmm) cc_final: 0.8258 (tmm) REVERT: A 515 ASP cc_start: 0.9090 (m-30) cc_final: 0.8820 (m-30) REVERT: A 550 MET cc_start: 0.7329 (mtm) cc_final: 0.7050 (mtp) REVERT: A 583 SER cc_start: 0.9453 (m) cc_final: 0.9149 (p) REVERT: A 595 MET cc_start: 0.9190 (mmp) cc_final: 0.8927 (mmt) REVERT: A 615 MET cc_start: 0.9237 (mmp) cc_final: 0.8753 (mmp) REVERT: A 632 MET cc_start: 0.8331 (mtm) cc_final: 0.7932 (mtp) REVERT: A 639 ASP cc_start: 0.9166 (m-30) cc_final: 0.8936 (m-30) REVERT: A 645 GLN cc_start: 0.8845 (tp40) cc_final: 0.8348 (tp-100) REVERT: A 672 LEU cc_start: 0.9326 (mt) cc_final: 0.9092 (mt) REVERT: B 52 LYS cc_start: 0.9408 (tptp) cc_final: 0.9136 (tppt) REVERT: B 75 GLU cc_start: 0.9270 (mp0) cc_final: 0.9056 (pm20) REVERT: B 87 LYS cc_start: 0.9351 (tptp) cc_final: 0.8948 (tptp) REVERT: B 89 PHE cc_start: 0.9273 (t80) cc_final: 0.9021 (t80) REVERT: B 119 GLU cc_start: 0.9338 (mp0) cc_final: 0.8898 (mp0) REVERT: B 147 GLN cc_start: 0.9114 (mt0) cc_final: 0.8535 (mm-40) REVERT: B 211 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8725 (mm-30) REVERT: B 223 VAL cc_start: 0.9342 (m) cc_final: 0.8815 (m) REVERT: B 227 MET cc_start: 0.9067 (mpp) cc_final: 0.8814 (mpp) REVERT: B 235 ARG cc_start: 0.9131 (ptp-110) cc_final: 0.8662 (ptp90) REVERT: B 250 TYR cc_start: 0.9186 (m-80) cc_final: 0.8697 (m-80) REVERT: B 252 ASN cc_start: 0.9087 (t0) cc_final: 0.8874 (t0) REVERT: B 257 ASP cc_start: 0.9025 (m-30) cc_final: 0.8520 (m-30) REVERT: B 274 ARG cc_start: 0.8967 (tpp80) cc_final: 0.8680 (tpp80) REVERT: B 286 ASP cc_start: 0.8791 (m-30) cc_final: 0.8237 (m-30) REVERT: B 291 LEU cc_start: 0.9628 (mt) cc_final: 0.9268 (mt) REVERT: B 322 MET cc_start: 0.8738 (mmm) cc_final: 0.7819 (mmm) REVERT: B 333 LYS cc_start: 0.9526 (tptm) cc_final: 0.9218 (ttmm) REVERT: B 355 TYR cc_start: 0.8995 (m-80) cc_final: 0.8546 (m-80) REVERT: B 362 ASP cc_start: 0.8771 (m-30) cc_final: 0.8153 (m-30) REVERT: B 386 LEU cc_start: 0.9404 (mt) cc_final: 0.8803 (mt) REVERT: B 393 SER cc_start: 0.9486 (m) cc_final: 0.9224 (t) REVERT: B 410 ASN cc_start: 0.8954 (m110) cc_final: 0.8729 (m110) REVERT: B 415 ASN cc_start: 0.9661 (t0) cc_final: 0.9438 (t0) REVERT: B 416 ILE cc_start: 0.9692 (mt) cc_final: 0.9489 (mt) REVERT: B 441 GLU cc_start: 0.9028 (pt0) cc_final: 0.8773 (pt0) REVERT: B 459 LYS cc_start: 0.9237 (mttp) cc_final: 0.8440 (mtpt) REVERT: B 515 ASP cc_start: 0.9226 (m-30) cc_final: 0.8898 (m-30) REVERT: B 522 TYR cc_start: 0.9021 (m-10) cc_final: 0.8732 (m-10) REVERT: B 548 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8660 (mt-10) REVERT: B 571 TYR cc_start: 0.9243 (t80) cc_final: 0.8969 (t80) REVERT: B 599 GLU cc_start: 0.8544 (pt0) cc_final: 0.8061 (pt0) REVERT: B 610 LYS cc_start: 0.9356 (ptmt) cc_final: 0.9050 (ptmm) REVERT: B 628 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8418 (mm-30) REVERT: B 632 MET cc_start: 0.8587 (mpp) cc_final: 0.8238 (mpp) REVERT: B 636 LYS cc_start: 0.9557 (mmtm) cc_final: 0.9236 (mmmm) REVERT: B 640 MET cc_start: 0.9213 (tpp) cc_final: 0.8806 (tpp) REVERT: B 650 GLN cc_start: 0.8371 (mt0) cc_final: 0.7935 (mm-40) REVERT: B 664 THR cc_start: 0.9322 (p) cc_final: 0.9112 (p) REVERT: B 668 ASN cc_start: 0.9392 (m-40) cc_final: 0.9109 (m110) REVERT: C 17 PHE cc_start: 0.8579 (p90) cc_final: 0.7769 (p90) REVERT: C 21 PHE cc_start: 0.8916 (m-10) cc_final: 0.7924 (m-80) REVERT: C 204 TYR cc_start: 0.9439 (t80) cc_final: 0.8929 (t80) REVERT: D 45 LYS cc_start: 0.8658 (pttt) cc_final: 0.8258 (pttt) REVERT: D 46 TYR cc_start: 0.8552 (m-80) cc_final: 0.7987 (m-80) REVERT: D 105 TYR cc_start: 0.9273 (m-10) cc_final: 0.8485 (m-10) REVERT: D 169 TYR cc_start: 0.9322 (m-80) cc_final: 0.8807 (m-80) REVERT: D 172 PHE cc_start: 0.9097 (m-80) cc_final: 0.8769 (m-80) REVERT: D 204 TYR cc_start: 0.9648 (t80) cc_final: 0.9409 (t80) outliers start: 4 outliers final: 0 residues processed: 651 average time/residue: 0.1236 time to fit residues: 121.1820 Evaluate side-chains 586 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 586 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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: 6.9990 chunk 46 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 126 optimal weight: 0.2980 chunk 129 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS ** 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 447 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN C 25 ASN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.136325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.096746 restraints weight = 40773.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.100302 restraints weight = 22443.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.102765 restraints weight = 14165.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.104373 restraints weight = 9996.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.105678 restraints weight = 7620.052| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 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 = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.6611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16386 Z= 0.203 Angle : 0.607 9.884 22134 Z= 0.321 Chirality : 0.043 0.211 2360 Planarity : 0.003 0.042 2818 Dihedral : 8.774 141.830 2290 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % 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 are not related in a simple way. whole: 0.77 (0.19), residues: 1932 helix: 0.95 (0.15), residues: 1148 sheet: -0.47 (0.39), residues: 144 loop : 0.15 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 256 TYR 0.045 0.002 TYR A 683 PHE 0.022 0.002 PHE A 171 TRP 0.008 0.002 TRP B 623 HIS 0.017 0.002 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 (16386) covalent geometry : angle 0.60673 / 0.32 (22134) hydrogen bonds : bond 0.03896 / 2.45 ( 871) hydrogen bonds : angle 4.95128 / 3.51 ( 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 670 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 670 time to evaluate : 0.690 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 28 LYS cc_start: 0.9567 (mmtt) cc_final: 0.9343 (mmmt) REVERT: A 29 ASP cc_start: 0.9127 (t70) cc_final: 0.8799 (t70) REVERT: A 31 GLU cc_start: 0.9074 (mp0) cc_final: 0.8747 (mp0) REVERT: A 106 LEU cc_start: 0.9531 (tp) cc_final: 0.9214 (tp) REVERT: A 118 TYR cc_start: 0.8902 (t80) cc_final: 0.8517 (t80) REVERT: A 119 GLU cc_start: 0.8942 (mp0) cc_final: 0.8551 (mp0) REVERT: A 136 LYS cc_start: 0.9559 (tttp) cc_final: 0.9281 (tttp) REVERT: A 139 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8749 (mt-10) REVERT: A 158 ASN cc_start: 0.9357 (m-40) cc_final: 0.9088 (m-40) REVERT: A 172 LEU cc_start: 0.9527 (mp) cc_final: 0.9076 (mp) REVERT: A 173 LEU cc_start: 0.9655 (mt) cc_final: 0.9167 (mt) REVERT: A 181 ASP cc_start: 0.8962 (m-30) cc_final: 0.8509 (m-30) REVERT: A 221 LYS cc_start: 0.8766 (mmtp) cc_final: 0.8465 (mttp) REVERT: A 223 VAL cc_start: 0.9578 (m) cc_final: 0.9096 (p) REVERT: A 227 MET cc_start: 0.9372 (mtp) cc_final: 0.9083 (mtp) REVERT: A 257 ASP cc_start: 0.9162 (m-30) cc_final: 0.8791 (m-30) REVERT: A 290 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8525 (tm-30) REVERT: A 291 LEU cc_start: 0.9521 (mt) cc_final: 0.9288 (mt) REVERT: A 335 GLU cc_start: 0.8098 (mp0) cc_final: 0.7719 (mp0) REVERT: A 355 TYR cc_start: 0.8866 (m-10) cc_final: 0.8663 (m-10) REVERT: A 366 LYS cc_start: 0.9541 (mtmt) cc_final: 0.9250 (mtmm) REVERT: A 396 ASP cc_start: 0.8818 (m-30) cc_final: 0.8398 (m-30) REVERT: A 406 ASP cc_start: 0.8241 (m-30) cc_final: 0.7580 (m-30) REVERT: A 407 ILE cc_start: 0.9327 (mt) cc_final: 0.9120 (mt) REVERT: A 413 SER cc_start: 0.8961 (t) cc_final: 0.8608 (t) REVERT: A 421 GLU cc_start: 0.8861 (pp20) cc_final: 0.8554 (pp20) REVERT: A 458 MET cc_start: 0.9037 (mmp) cc_final: 0.8579 (mmp) REVERT: A 489 ASN cc_start: 0.8562 (t0) cc_final: 0.8352 (t0) REVERT: A 493 MET cc_start: 0.8808 (tmm) cc_final: 0.8295 (tmm) REVERT: A 515 ASP cc_start: 0.9094 (m-30) cc_final: 0.8823 (m-30) REVERT: A 583 SER cc_start: 0.9419 (m) cc_final: 0.8989 (t) REVERT: A 595 MET cc_start: 0.9193 (mmp) cc_final: 0.8910 (mmm) REVERT: A 615 MET cc_start: 0.9307 (mmp) cc_final: 0.8768 (mmp) REVERT: A 645 GLN cc_start: 0.8755 (tp40) cc_final: 0.8414 (tp-100) REVERT: A 672 LEU cc_start: 0.9364 (mt) cc_final: 0.9114 (mt) REVERT: B 52 LYS cc_start: 0.9424 (tptp) cc_final: 0.9137 (tppt) REVERT: B 75 GLU cc_start: 0.9268 (mp0) cc_final: 0.8997 (pm20) REVERT: B 87 LYS cc_start: 0.9350 (tptp) cc_final: 0.8973 (tptp) REVERT: B 89 PHE cc_start: 0.9267 (t80) cc_final: 0.9011 (t80) REVERT: B 95 MET cc_start: 0.9239 (tpp) cc_final: 0.8783 (tpp) REVERT: B 119 GLU cc_start: 0.9284 (mp0) cc_final: 0.8832 (mp0) REVERT: B 127 LEU cc_start: 0.9551 (mm) cc_final: 0.9186 (mm) REVERT: B 147 GLN cc_start: 0.9098 (mt0) cc_final: 0.8516 (mm-40) REVERT: B 184 ARG cc_start: 0.9440 (tpp80) cc_final: 0.9185 (tpp80) REVERT: B 188 ILE cc_start: 0.9597 (mp) cc_final: 0.9335 (mp) REVERT: B 211 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8710 (mm-30) REVERT: B 223 VAL cc_start: 0.9348 (m) cc_final: 0.8767 (m) REVERT: B 227 MET cc_start: 0.9057 (mpp) cc_final: 0.8740 (mpp) REVERT: B 250 TYR cc_start: 0.9147 (m-80) cc_final: 0.8687 (m-80) REVERT: B 252 ASN cc_start: 0.9063 (t0) cc_final: 0.8744 (t0) REVERT: B 257 ASP cc_start: 0.9049 (m-30) cc_final: 0.8431 (m-30) REVERT: B 274 ARG cc_start: 0.8917 (tpp80) cc_final: 0.8678 (tpp80) REVERT: B 286 ASP cc_start: 0.8554 (m-30) cc_final: 0.8282 (m-30) REVERT: B 288 PHE cc_start: 0.9239 (t80) cc_final: 0.9019 (t80) REVERT: B 291 LEU cc_start: 0.9509 (mt) cc_final: 0.9297 (mt) REVERT: B 321 GLU cc_start: 0.8474 (pp20) cc_final: 0.8201 (pp20) REVERT: B 322 MET cc_start: 0.8701 (mmm) cc_final: 0.8031 (mmm) REVERT: B 333 LYS cc_start: 0.9570 (tptm) cc_final: 0.9269 (ttmm) REVERT: B 341 LYS cc_start: 0.9573 (mmtt) cc_final: 0.9260 (mmmm) REVERT: B 344 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8748 (mp0) REVERT: B 355 TYR cc_start: 0.9025 (m-80) cc_final: 0.8578 (m-80) REVERT: B 362 ASP cc_start: 0.8773 (m-30) cc_final: 0.8222 (m-30) REVERT: B 392 SER cc_start: 0.9105 (m) cc_final: 0.8117 (p) REVERT: B 394 TYR cc_start: 0.8699 (m-80) cc_final: 0.8482 (m-80) REVERT: B 407 ILE cc_start: 0.9013 (mt) cc_final: 0.8693 (mt) REVERT: B 410 ASN cc_start: 0.8875 (m110) cc_final: 0.8548 (m110) REVERT: B 415 ASN cc_start: 0.9627 (t0) cc_final: 0.9285 (t0) REVERT: B 416 ILE cc_start: 0.9690 (mt) cc_final: 0.9487 (mt) REVERT: B 459 LYS cc_start: 0.9157 (mttp) cc_final: 0.8388 (mtpt) REVERT: B 515 ASP cc_start: 0.9205 (m-30) cc_final: 0.8866 (m-30) REVERT: B 574 TYR cc_start: 0.8474 (m-80) cc_final: 0.8238 (m-10) REVERT: B 599 GLU cc_start: 0.8556 (pt0) cc_final: 0.8166 (pt0) REVERT: B 610 LYS cc_start: 0.9341 (ptmt) cc_final: 0.9087 (ptmm) REVERT: B 628 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8536 (mm-30) REVERT: B 632 MET cc_start: 0.8412 (mpp) cc_final: 0.8127 (mpp) REVERT: B 636 LYS cc_start: 0.9566 (mmtm) cc_final: 0.9332 (mmmm) REVERT: B 640 MET cc_start: 0.9147 (tpp) cc_final: 0.8753 (tpp) REVERT: B 664 THR cc_start: 0.9347 (p) cc_final: 0.9144 (p) REVERT: B 668 ASN cc_start: 0.9356 (m-40) cc_final: 0.9065 (m-40) REVERT: B 677 ARG cc_start: 0.9293 (mmm-85) cc_final: 0.8829 (mmm-85) REVERT: C 17 PHE cc_start: 0.8639 (p90) cc_final: 0.8019 (p90) REVERT: C 21 PHE cc_start: 0.8908 (m-10) cc_final: 0.7996 (m-80) REVERT: C 74 MET cc_start: 0.8384 (mmp) cc_final: 0.8172 (mmp) REVERT: C 204 TYR cc_start: 0.9388 (t80) cc_final: 0.9012 (t80) REVERT: D 27 LYS cc_start: 0.8988 (pttp) cc_final: 0.8723 (pttp) REVERT: D 45 LYS cc_start: 0.8655 (pttt) cc_final: 0.8223 (pttt) REVERT: D 46 TYR cc_start: 0.8558 (m-80) cc_final: 0.7980 (m-80) REVERT: D 169 TYR cc_start: 0.9325 (m-80) cc_final: 0.8841 (m-80) REVERT: D 172 PHE cc_start: 0.9140 (m-80) cc_final: 0.8783 (m-80) REVERT: D 259 PHE cc_start: 0.8349 (t80) cc_final: 0.8134 (t80) outliers start: 0 outliers final: 0 residues processed: 670 average time/residue: 0.1283 time to fit residues: 129.2671 Evaluate side-chains 581 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 581 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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: 2.9990 chunk 183 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN A 147 GLN ** 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 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN B 501 GLN B 645 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN C 25 ASN C 84 HIS C 181 GLN ** 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 = 0.3735 r_free = 0.3735 target = 0.135710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.096656 restraints weight = 40860.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.100327 restraints weight = 22175.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.102740 restraints weight = 13912.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.104445 restraints weight = 9835.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.105536 restraints weight = 7461.776| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.6861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16386 Z= 0.210 Angle : 0.633 10.578 22134 Z= 0.333 Chirality : 0.044 0.259 2360 Planarity : 0.004 0.042 2818 Dihedral : 8.710 142.197 2290 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.19), residues: 1932 helix: 0.85 (0.15), residues: 1161 sheet: -0.60 (0.38), residues: 144 loop : 0.11 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 164 TYR 0.025 0.002 TYR D 130 PHE 0.026 0.002 PHE D 154 TRP 0.009 0.002 TRP C 30 HIS 0.015 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 (16386) covalent geometry : angle 0.63308 / 0.33 (22134) hydrogen bonds : bond 0.03907 / 2.46 ( 871) hydrogen bonds : angle 5.02582 / 3.55 ( 2571) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 656 time to evaluate : 0.687 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 28 LYS cc_start: 0.9562 (mmtt) cc_final: 0.9336 (mmmt) REVERT: A 29 ASP cc_start: 0.9165 (t70) cc_final: 0.8740 (t70) REVERT: A 31 GLU cc_start: 0.9057 (mp0) cc_final: 0.8710 (mp0) REVERT: A 60 GLU cc_start: 0.9288 (mt-10) cc_final: 0.9018 (pt0) REVERT: A 118 TYR cc_start: 0.8928 (t80) cc_final: 0.8616 (t80) REVERT: A 119 GLU cc_start: 0.8889 (mp0) cc_final: 0.8569 (mp0) REVERT: A 136 LYS cc_start: 0.9585 (tttp) cc_final: 0.9301 (tttp) REVERT: A 139 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8734 (mt-10) REVERT: A 158 ASN cc_start: 0.9356 (m-40) cc_final: 0.9094 (m-40) REVERT: A 172 LEU cc_start: 0.9522 (mp) cc_final: 0.9151 (mp) REVERT: A 205 LYS cc_start: 0.8434 (mttm) cc_final: 0.8205 (mmtp) REVERT: A 223 VAL cc_start: 0.9559 (m) cc_final: 0.9109 (p) REVERT: A 227 MET cc_start: 0.9348 (mtp) cc_final: 0.9100 (mtp) REVERT: A 254 PHE cc_start: 0.8529 (m-80) cc_final: 0.8325 (m-10) REVERT: A 257 ASP cc_start: 0.9178 (m-30) cc_final: 0.8813 (m-30) REVERT: A 290 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8491 (tm-30) REVERT: A 291 LEU cc_start: 0.9504 (mt) cc_final: 0.9253 (mt) REVERT: A 335 GLU cc_start: 0.8179 (mp0) cc_final: 0.7701 (mp0) REVERT: A 355 TYR cc_start: 0.8832 (m-10) cc_final: 0.8599 (m-10) REVERT: A 366 LYS cc_start: 0.9529 (mtmt) cc_final: 0.9206 (mtmm) REVERT: A 396 ASP cc_start: 0.8813 (m-30) cc_final: 0.8385 (m-30) REVERT: A 421 GLU cc_start: 0.8769 (pp20) cc_final: 0.8434 (pp20) REVERT: A 446 ARG cc_start: 0.7956 (mmt-90) cc_final: 0.7468 (mmt180) REVERT: A 458 MET cc_start: 0.9055 (mmp) cc_final: 0.8596 (mmp) REVERT: A 459 LYS cc_start: 0.9019 (mttp) cc_final: 0.8594 (mtpt) REVERT: A 483 GLU cc_start: 0.9524 (mp0) cc_final: 0.9316 (mp0) REVERT: A 493 MET cc_start: 0.8770 (tmm) cc_final: 0.8254 (tmm) REVERT: A 515 ASP cc_start: 0.9091 (m-30) cc_final: 0.8781 (m-30) REVERT: A 583 SER cc_start: 0.9399 (m) cc_final: 0.8998 (t) REVERT: A 599 GLU cc_start: 0.8829 (pt0) cc_final: 0.8459 (pt0) REVERT: A 601 ILE cc_start: 0.9322 (tp) cc_final: 0.8947 (mm) REVERT: A 615 MET cc_start: 0.9330 (mmp) cc_final: 0.8859 (mmp) REVERT: A 632 MET cc_start: 0.8371 (mtm) cc_final: 0.8049 (mtp) REVERT: A 645 GLN cc_start: 0.8879 (tp40) cc_final: 0.8353 (tp-100) REVERT: A 672 LEU cc_start: 0.9385 (mt) cc_final: 0.9141 (mt) REVERT: B 20 LYS cc_start: 0.9579 (mtpt) cc_final: 0.9263 (ptpp) REVERT: B 51 LEU cc_start: 0.9360 (tp) cc_final: 0.8988 (tp) REVERT: B 52 LYS cc_start: 0.9398 (tptp) cc_final: 0.9174 (tppt) REVERT: B 55 LEU cc_start: 0.9715 (mt) cc_final: 0.9468 (mt) REVERT: B 75 GLU cc_start: 0.9250 (mp0) cc_final: 0.8980 (pm20) REVERT: B 87 LYS cc_start: 0.9360 (tptp) cc_final: 0.8981 (tptp) REVERT: B 89 PHE cc_start: 0.9276 (t80) cc_final: 0.9040 (t80) REVERT: B 95 MET cc_start: 0.9202 (tpp) cc_final: 0.8774 (tpp) REVERT: B 119 GLU cc_start: 0.9290 (mp0) cc_final: 0.8852 (mp0) REVERT: B 127 LEU cc_start: 0.9580 (mm) cc_final: 0.9209 (mm) REVERT: B 147 GLN cc_start: 0.9126 (mt0) cc_final: 0.8538 (mm-40) REVERT: B 184 ARG cc_start: 0.9397 (tpp80) cc_final: 0.8709 (tpp80) REVERT: B 188 ILE cc_start: 0.9616 (mp) cc_final: 0.9322 (mp) REVERT: B 211 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8824 (mm-30) REVERT: B 223 VAL cc_start: 0.9300 (m) cc_final: 0.8758 (m) REVERT: B 250 TYR cc_start: 0.9197 (m-80) cc_final: 0.8740 (m-80) REVERT: B 257 ASP cc_start: 0.9077 (m-30) cc_final: 0.8515 (m-30) REVERT: B 274 ARG cc_start: 0.8947 (tpp80) cc_final: 0.8684 (tpp80) REVERT: B 291 LEU cc_start: 0.9518 (mt) cc_final: 0.9305 (mt) REVERT: B 321 GLU cc_start: 0.8383 (pp20) cc_final: 0.8126 (pp20) REVERT: B 322 MET cc_start: 0.8661 (mmm) cc_final: 0.7970 (mmm) REVERT: B 355 TYR cc_start: 0.9045 (m-80) cc_final: 0.8484 (m-10) REVERT: B 392 SER cc_start: 0.8892 (m) cc_final: 0.7974 (p) REVERT: B 407 ILE cc_start: 0.9087 (mt) cc_final: 0.8803 (mt) REVERT: B 410 ASN cc_start: 0.8808 (m110) cc_final: 0.8485 (m110) REVERT: B 415 ASN cc_start: 0.9626 (t0) cc_final: 0.9248 (t0) REVERT: B 459 LYS cc_start: 0.9192 (mttp) cc_final: 0.8420 (mtmt) REVERT: B 472 LEU cc_start: 0.9647 (mm) cc_final: 0.9424 (mm) REVERT: B 515 ASP cc_start: 0.9192 (m-30) cc_final: 0.8836 (m-30) REVERT: B 610 LYS cc_start: 0.9355 (ptmt) cc_final: 0.9102 (ptmm) REVERT: B 615 MET cc_start: 0.9197 (mmp) cc_final: 0.8992 (mmp) REVERT: B 626 TYR cc_start: 0.9116 (m-80) cc_final: 0.8439 (m-80) REVERT: B 628 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8569 (mm-30) REVERT: B 632 MET cc_start: 0.8433 (mpp) cc_final: 0.8114 (mpp) REVERT: B 636 LYS cc_start: 0.9588 (mmtm) cc_final: 0.9353 (mmmm) REVERT: B 640 MET cc_start: 0.9120 (tpp) cc_final: 0.8773 (tpp) REVERT: B 664 THR cc_start: 0.9336 (p) cc_final: 0.9107 (p) REVERT: B 668 ASN cc_start: 0.9395 (m-40) cc_final: 0.9099 (m-40) REVERT: B 677 ARG cc_start: 0.9261 (mmm-85) cc_final: 0.8747 (mmm-85) REVERT: C 17 PHE cc_start: 0.8596 (p90) cc_final: 0.8064 (p90) REVERT: C 21 PHE cc_start: 0.8959 (m-10) cc_final: 0.8089 (m-80) REVERT: C 204 TYR cc_start: 0.9435 (t80) cc_final: 0.9008 (t80) REVERT: D 45 LYS cc_start: 0.8609 (pttt) cc_final: 0.8174 (pttt) REVERT: D 46 TYR cc_start: 0.8581 (m-80) cc_final: 0.7980 (m-80) REVERT: D 169 TYR cc_start: 0.9376 (m-80) cc_final: 0.8877 (m-80) REVERT: D 172 PHE cc_start: 0.9202 (m-80) cc_final: 0.8793 (m-80) REVERT: D 259 PHE cc_start: 0.8280 (t80) cc_final: 0.7964 (t80) REVERT: D 313 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8771 (mp0) outliers start: 0 outliers final: 0 residues processed: 656 average time/residue: 0.1144 time to fit residues: 113.9776 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 : 0.672 ------------------------------------------------------------------------------- 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: 0.9990 chunk 51 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 447 ASN A 646 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 HIS ** 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 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 = 0.3768 r_free = 0.3768 target = 0.138006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.098812 restraints weight = 40256.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.102506 restraints weight = 21779.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.104955 restraints weight = 13628.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.106554 restraints weight = 9532.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.107842 restraints weight = 7222.141| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 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 = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.7134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16386 Z= 0.160 Angle : 0.606 9.488 22134 Z= 0.322 Chirality : 0.043 0.199 2360 Planarity : 0.004 0.050 2818 Dihedral : 8.493 142.000 2290 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.19), residues: 1932 helix: 0.98 (0.15), residues: 1149 sheet: -0.45 (0.40), residues: 144 loop : -0.02 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 161 TYR 0.033 0.002 TYR B 574 PHE 0.019 0.002 PHE B 492 TRP 0.018 0.002 TRP C 30 HIS 0.013 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (16386) covalent geometry : angle 0.60602 / 0.32 (22134) hydrogen bonds : bond 0.03833 / 2.40 ( 871) hydrogen bonds : angle 4.95004 / 3.49 ( 2571) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 660 time to evaluate : 0.471 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 28 LYS cc_start: 0.9578 (mmtt) cc_final: 0.9320 (mmmt) REVERT: A 29 ASP cc_start: 0.9093 (t70) cc_final: 0.8796 (t70) REVERT: A 31 GLU cc_start: 0.9093 (mp0) cc_final: 0.8729 (mp0) REVERT: A 101 TYR cc_start: 0.9488 (m-80) cc_final: 0.9185 (m-10) REVERT: A 118 TYR cc_start: 0.8911 (t80) cc_final: 0.8556 (t80) REVERT: A 119 GLU cc_start: 0.8889 (mp0) cc_final: 0.8537 (mp0) REVERT: A 136 LYS cc_start: 0.9565 (tttp) cc_final: 0.9165 (tttp) REVERT: A 139 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8746 (mt-10) REVERT: A 143 LEU cc_start: 0.9226 (tp) cc_final: 0.8962 (tp) REVERT: A 148 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8513 (mt-10) REVERT: A 158 ASN cc_start: 0.9332 (m-40) cc_final: 0.9074 (m-40) REVERT: A 172 LEU cc_start: 0.9561 (mp) cc_final: 0.9253 (mp) REVERT: A 173 LEU cc_start: 0.9628 (mt) cc_final: 0.9178 (mt) REVERT: A 174 GLU cc_start: 0.8524 (mt-10) cc_final: 0.7801 (mt-10) REVERT: A 205 LYS cc_start: 0.8412 (mttm) cc_final: 0.8154 (mmtp) REVERT: A 223 VAL cc_start: 0.9549 (m) cc_final: 0.9113 (p) REVERT: A 227 MET cc_start: 0.9317 (mtp) cc_final: 0.9067 (mtp) REVERT: A 257 ASP cc_start: 0.9187 (m-30) cc_final: 0.8786 (m-30) REVERT: A 277 THR cc_start: 0.8603 (p) cc_final: 0.8145 (t) REVERT: A 286 ASP cc_start: 0.8809 (m-30) cc_final: 0.8406 (m-30) REVERT: A 290 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8471 (tm-30) REVERT: A 291 LEU cc_start: 0.9495 (mt) cc_final: 0.9236 (mt) REVERT: A 325 LYS cc_start: 0.9257 (mppt) cc_final: 0.8887 (mmtm) REVERT: A 335 GLU cc_start: 0.8253 (mp0) cc_final: 0.7649 (mp0) REVERT: A 362 ASP cc_start: 0.8437 (m-30) cc_final: 0.8062 (m-30) REVERT: A 366 LYS cc_start: 0.9520 (mtmt) cc_final: 0.9198 (mtmm) REVERT: A 396 ASP cc_start: 0.8863 (m-30) cc_final: 0.8467 (m-30) REVERT: A 405 LEU cc_start: 0.8507 (mt) cc_final: 0.8232 (mt) REVERT: A 406 ASP cc_start: 0.8101 (m-30) cc_final: 0.7599 (m-30) REVERT: A 421 GLU cc_start: 0.8696 (pp20) cc_final: 0.8400 (pp20) REVERT: A 446 ARG cc_start: 0.7939 (mmt-90) cc_final: 0.7270 (mmt180) REVERT: A 458 MET cc_start: 0.8946 (mmp) cc_final: 0.8462 (mmp) REVERT: A 493 MET cc_start: 0.8779 (tmm) cc_final: 0.8306 (tmm) REVERT: A 515 ASP cc_start: 0.9083 (m-30) cc_final: 0.8782 (m-30) REVERT: A 583 SER cc_start: 0.9345 (m) cc_final: 0.8921 (t) REVERT: A 599 GLU cc_start: 0.8893 (pt0) cc_final: 0.8428 (pt0) REVERT: A 615 MET cc_start: 0.9284 (mmp) cc_final: 0.8668 (mmm) REVERT: A 639 ASP cc_start: 0.9073 (m-30) cc_final: 0.8855 (m-30) REVERT: A 645 GLN cc_start: 0.8825 (tp40) cc_final: 0.8369 (tp-100) REVERT: A 650 GLN cc_start: 0.8599 (tt0) cc_final: 0.8180 (tt0) REVERT: B 20 LYS cc_start: 0.9602 (mtpt) cc_final: 0.9331 (mtpp) REVERT: B 51 LEU cc_start: 0.9343 (tp) cc_final: 0.8965 (tp) REVERT: B 52 LYS cc_start: 0.9408 (tptp) cc_final: 0.9169 (tppt) REVERT: B 55 LEU cc_start: 0.9719 (mt) cc_final: 0.9496 (mt) REVERT: B 75 GLU cc_start: 0.9247 (mp0) cc_final: 0.8943 (pm20) REVERT: B 87 LYS cc_start: 0.9338 (tptp) cc_final: 0.8967 (tptp) REVERT: B 95 MET cc_start: 0.9180 (tpp) cc_final: 0.8751 (tpp) REVERT: B 119 GLU cc_start: 0.9216 (mp0) cc_final: 0.8810 (mp0) REVERT: B 127 LEU cc_start: 0.9574 (mm) cc_final: 0.9206 (mm) REVERT: B 147 GLN cc_start: 0.9141 (mt0) cc_final: 0.8624 (mm-40) REVERT: B 180 ASN cc_start: 0.8831 (m-40) cc_final: 0.8476 (t0) REVERT: B 184 ARG cc_start: 0.9436 (tpp80) cc_final: 0.9209 (tpp80) REVERT: B 188 ILE cc_start: 0.9600 (mp) cc_final: 0.9385 (mp) REVERT: B 205 LYS cc_start: 0.9028 (mmtp) cc_final: 0.8639 (mmtp) REVERT: B 211 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8415 (mm-30) REVERT: B 223 VAL cc_start: 0.9272 (m) cc_final: 0.8778 (m) REVERT: B 228 LYS cc_start: 0.9316 (mmmt) cc_final: 0.9066 (mmtm) REVERT: B 250 TYR cc_start: 0.9126 (m-80) cc_final: 0.8645 (m-80) REVERT: B 252 ASN cc_start: 0.9077 (t0) cc_final: 0.8799 (t0) REVERT: B 257 ASP cc_start: 0.9079 (m-30) cc_final: 0.8519 (m-30) REVERT: B 274 ARG cc_start: 0.8937 (tpp80) cc_final: 0.8641 (tpp80) REVERT: B 286 ASP cc_start: 0.8681 (m-30) cc_final: 0.8362 (m-30) REVERT: B 291 LEU cc_start: 0.9511 (mt) cc_final: 0.9301 (mt) REVERT: B 321 GLU cc_start: 0.8323 (pp20) cc_final: 0.7932 (pp20) REVERT: B 322 MET cc_start: 0.8582 (mmm) cc_final: 0.8313 (mmm) REVERT: B 348 MET cc_start: 0.8958 (ptp) cc_final: 0.8486 (ptp) REVERT: B 355 TYR cc_start: 0.9057 (m-80) cc_final: 0.8442 (m-10) REVERT: B 361 GLN cc_start: 0.9130 (tt0) cc_final: 0.8856 (tt0) REVERT: B 392 SER cc_start: 0.8784 (m) cc_final: 0.8058 (p) REVERT: B 407 ILE cc_start: 0.8960 (mt) cc_final: 0.8664 (mt) REVERT: B 410 ASN cc_start: 0.8951 (m110) cc_final: 0.8561 (m110) REVERT: B 415 ASN cc_start: 0.9459 (t0) cc_final: 0.9180 (t0) REVERT: B 459 LYS cc_start: 0.9102 (mttp) cc_final: 0.8189 (mtpt) REVERT: B 472 LEU cc_start: 0.9572 (mm) cc_final: 0.9359 (mm) REVERT: B 515 ASP cc_start: 0.9169 (m-30) cc_final: 0.8806 (m-30) REVERT: B 522 TYR cc_start: 0.8769 (m-10) cc_final: 0.8283 (m-10) REVERT: B 527 TYR cc_start: 0.8972 (t80) cc_final: 0.8745 (t80) REVERT: B 610 LYS cc_start: 0.9385 (ptmt) cc_final: 0.9127 (ptmm) REVERT: B 626 TYR cc_start: 0.8885 (m-80) cc_final: 0.8185 (m-80) REVERT: B 628 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8770 (mp0) REVERT: B 632 MET cc_start: 0.8473 (mpp) cc_final: 0.8214 (mpp) REVERT: B 636 LYS cc_start: 0.9578 (mmtm) cc_final: 0.9347 (mmmm) REVERT: B 640 MET cc_start: 0.9169 (tpp) cc_final: 0.8782 (tpp) REVERT: B 656 LEU cc_start: 0.9535 (mt) cc_final: 0.9315 (mt) REVERT: B 664 THR cc_start: 0.9365 (p) cc_final: 0.9060 (p) REVERT: B 668 ASN cc_start: 0.9366 (m-40) cc_final: 0.9026 (m110) REVERT: B 675 HIS cc_start: 0.8943 (t-90) cc_final: 0.8527 (t-90) REVERT: B 677 ARG cc_start: 0.9230 (mmm-85) cc_final: 0.8730 (mmm-85) REVERT: C 17 PHE cc_start: 0.8633 (p90) cc_final: 0.8128 (p90) REVERT: C 21 PHE cc_start: 0.8958 (m-10) cc_final: 0.8200 (m-80) REVERT: C 204 TYR cc_start: 0.9436 (t80) cc_final: 0.9067 (t80) REVERT: D 28 GLN cc_start: 0.8138 (mp10) cc_final: 0.7906 (mp10) REVERT: D 46 TYR cc_start: 0.8633 (m-80) cc_final: 0.8167 (m-80) REVERT: D 96 MET cc_start: 0.8307 (tpt) cc_final: 0.7797 (mmm) REVERT: D 104 SER cc_start: 0.8777 (m) cc_final: 0.8577 (m) REVERT: D 105 TYR cc_start: 0.9346 (m-10) cc_final: 0.8559 (m-10) REVERT: D 169 TYR cc_start: 0.9365 (m-80) cc_final: 0.8967 (m-80) REVERT: D 172 PHE cc_start: 0.9164 (m-80) cc_final: 0.8881 (m-80) REVERT: D 177 TYR cc_start: 0.9104 (t80) cc_final: 0.8807 (t80) REVERT: D 259 PHE cc_start: 0.8246 (t80) cc_final: 0.7841 (t80) REVERT: D 311 THR cc_start: 0.9010 (p) cc_final: 0.8793 (p) outliers start: 0 outliers final: 0 residues processed: 660 average time/residue: 0.1130 time to fit residues: 112.4622 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 : 0.602 ------------------------------------------------------------------------------- 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: 5.9990 chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 0.0060 chunk 19 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 153 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 151 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.138678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.100082 restraints weight = 40679.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.103755 restraints weight = 22176.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106247 restraints weight = 13974.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.107940 restraints weight = 9755.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.109181 restraints weight = 7370.146| |-----------------------------------------------------------------------------| 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) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.7363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16386 Z= 0.167 Angle : 0.629 10.049 22134 Z= 0.330 Chirality : 0.043 0.177 2360 Planarity : 0.004 0.044 2818 Dihedral : 8.372 142.363 2290 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 1932 helix: 0.97 (0.15), residues: 1146 sheet: -0.51 (0.40), residues: 144 loop : -0.09 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 604 TYR 0.032 0.002 TYR B 574 PHE 0.042 0.002 PHE D 154 TRP 0.011 0.001 TRP D 124 HIS 0.013 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (16386) covalent geometry : angle 0.62914 / 0.33 (22134) hydrogen bonds : bond 0.03829 / 2.38 ( 871) hydrogen bonds : angle 4.95925 / 3.50 ( 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 665 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 665 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.9536 (mmtt) cc_final: 0.9148 (mmmm) REVERT: A 31 GLU cc_start: 0.9064 (mp0) cc_final: 0.8688 (mp0) REVERT: A 103 ASP cc_start: 0.8941 (m-30) cc_final: 0.8731 (m-30) REVERT: A 118 TYR cc_start: 0.8868 (t80) cc_final: 0.8640 (t80) REVERT: A 119 GLU cc_start: 0.8804 (mp0) cc_final: 0.8526 (mp0) REVERT: A 136 LYS cc_start: 0.9581 (tttp) cc_final: 0.9185 (tttp) REVERT: A 139 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8756 (mt-10) REVERT: A 148 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8558 (mt-10) REVERT: A 158 ASN cc_start: 0.9348 (m-40) cc_final: 0.9084 (m-40) REVERT: A 172 LEU cc_start: 0.9564 (mp) cc_final: 0.9248 (mp) REVERT: A 173 LEU cc_start: 0.9603 (mt) cc_final: 0.9146 (mt) REVERT: A 174 GLU cc_start: 0.8512 (mt-10) cc_final: 0.7821 (mt-10) REVERT: A 221 LYS cc_start: 0.8678 (mmtp) cc_final: 0.8459 (mttp) REVERT: A 223 VAL cc_start: 0.9562 (m) cc_final: 0.9087 (p) REVERT: A 227 MET cc_start: 0.9315 (mtp) cc_final: 0.9064 (mtp) REVERT: A 232 ASN cc_start: 0.8731 (m110) cc_final: 0.8298 (m110) REVERT: A 257 ASP cc_start: 0.9314 (m-30) cc_final: 0.8929 (m-30) REVERT: A 277 THR cc_start: 0.8602 (p) cc_final: 0.8149 (t) REVERT: A 286 ASP cc_start: 0.8656 (m-30) cc_final: 0.8301 (m-30) REVERT: A 290 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8475 (tm-30) REVERT: A 291 LEU cc_start: 0.9480 (mt) cc_final: 0.9191 (mt) REVERT: A 335 GLU cc_start: 0.8307 (mp0) cc_final: 0.8021 (mp0) REVERT: A 348 MET cc_start: 0.8397 (tpp) cc_final: 0.7567 (tpt) REVERT: A 352 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8069 (mm-30) REVERT: A 362 ASP cc_start: 0.8395 (m-30) cc_final: 0.8056 (m-30) REVERT: A 366 LYS cc_start: 0.9506 (mtmt) cc_final: 0.9176 (mtmm) REVERT: A 383 SER cc_start: 0.9113 (p) cc_final: 0.8898 (p) REVERT: A 396 ASP cc_start: 0.8860 (m-30) cc_final: 0.8436 (m-30) REVERT: A 405 LEU cc_start: 0.8503 (mt) cc_final: 0.8226 (mt) REVERT: A 406 ASP cc_start: 0.8092 (m-30) cc_final: 0.7638 (m-30) REVERT: A 413 SER cc_start: 0.9047 (t) cc_final: 0.8800 (t) REVERT: A 421 GLU cc_start: 0.8669 (pp20) cc_final: 0.8389 (pp20) REVERT: A 458 MET cc_start: 0.8883 (mmp) cc_final: 0.8394 (mmp) REVERT: A 483 GLU cc_start: 0.9523 (mp0) cc_final: 0.9323 (mp0) REVERT: A 493 MET cc_start: 0.8754 (tmm) cc_final: 0.8178 (tmm) REVERT: A 515 ASP cc_start: 0.9083 (m-30) cc_final: 0.8803 (m-30) REVERT: A 583 SER cc_start: 0.9350 (m) cc_final: 0.8929 (t) REVERT: A 599 GLU cc_start: 0.8896 (pt0) cc_final: 0.8467 (pt0) REVERT: A 601 ILE cc_start: 0.9348 (tp) cc_final: 0.8908 (mm) REVERT: A 615 MET cc_start: 0.9315 (mmp) cc_final: 0.8658 (mmm) REVERT: A 645 GLN cc_start: 0.8859 (tp40) cc_final: 0.8441 (tp-100) REVERT: B 20 LYS cc_start: 0.9623 (mtpt) cc_final: 0.9336 (mtpp) REVERT: B 51 LEU cc_start: 0.9411 (tp) cc_final: 0.9009 (tp) REVERT: B 52 LYS cc_start: 0.9409 (tptp) cc_final: 0.9155 (tppt) REVERT: B 55 LEU cc_start: 0.9716 (mt) cc_final: 0.9501 (mt) REVERT: B 75 GLU cc_start: 0.9275 (mp0) cc_final: 0.8988 (pm20) REVERT: B 87 LYS cc_start: 0.9350 (tptp) cc_final: 0.8986 (tptp) REVERT: B 89 PHE cc_start: 0.9254 (t80) cc_final: 0.8943 (t80) REVERT: B 95 MET cc_start: 0.9174 (tpp) cc_final: 0.8805 (tpp) REVERT: B 119 GLU cc_start: 0.9230 (mp0) cc_final: 0.8831 (mp0) REVERT: B 172 LEU cc_start: 0.9540 (mp) cc_final: 0.9316 (mp) REVERT: B 184 ARG cc_start: 0.9414 (tpp80) cc_final: 0.9060 (tpp80) REVERT: B 202 ASN cc_start: 0.9206 (t0) cc_final: 0.8847 (t0) REVERT: B 205 LYS cc_start: 0.8843 (mmtp) cc_final: 0.8640 (mmtm) REVERT: B 211 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8375 (mm-30) REVERT: B 217 GLU cc_start: 0.8771 (mp0) cc_final: 0.8490 (mp0) REVERT: B 218 ASN cc_start: 0.9431 (m110) cc_final: 0.8960 (t0) REVERT: B 223 VAL cc_start: 0.9321 (m) cc_final: 0.8777 (m) REVERT: B 228 LYS cc_start: 0.9297 (mmmt) cc_final: 0.8887 (mmtm) REVERT: B 232 ASN cc_start: 0.8990 (m110) cc_final: 0.8784 (m110) REVERT: B 250 TYR cc_start: 0.9156 (m-80) cc_final: 0.8754 (m-80) REVERT: B 252 ASN cc_start: 0.9071 (t0) cc_final: 0.8794 (t0) REVERT: B 257 ASP cc_start: 0.9100 (m-30) cc_final: 0.8546 (m-30) REVERT: B 274 ARG cc_start: 0.8990 (tpp80) cc_final: 0.8710 (tpp80) REVERT: B 286 ASP cc_start: 0.8780 (m-30) cc_final: 0.8383 (m-30) REVERT: B 291 LEU cc_start: 0.9527 (mt) cc_final: 0.9320 (mt) REVERT: B 321 GLU cc_start: 0.8272 (pp20) cc_final: 0.7876 (pp20) REVERT: B 322 MET cc_start: 0.8539 (mmm) cc_final: 0.8272 (mmm) REVERT: B 344 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8922 (mm-30) REVERT: B 355 TYR cc_start: 0.9065 (m-80) cc_final: 0.8427 (m-10) REVERT: B 361 GLN cc_start: 0.9084 (tt0) cc_final: 0.8778 (tt0) REVERT: B 375 LYS cc_start: 0.9052 (mmmm) cc_final: 0.8604 (mmmm) REVERT: B 391 VAL cc_start: 0.8869 (t) cc_final: 0.8565 (p) REVERT: B 392 SER cc_start: 0.8843 (m) cc_final: 0.7677 (p) REVERT: B 410 ASN cc_start: 0.8960 (m110) cc_final: 0.8620 (m110) REVERT: B 459 LYS cc_start: 0.9120 (mttp) cc_final: 0.8212 (mtpt) REVERT: B 472 LEU cc_start: 0.9572 (mm) cc_final: 0.9331 (mm) REVERT: B 493 MET cc_start: 0.9395 (tmm) cc_final: 0.8918 (tmm) REVERT: B 494 MET cc_start: 0.9363 (mmt) cc_final: 0.9022 (mmt) REVERT: B 515 ASP cc_start: 0.8973 (m-30) cc_final: 0.8674 (m-30) REVERT: B 516 GLN cc_start: 0.9339 (mt0) cc_final: 0.9098 (tp40) REVERT: B 522 TYR cc_start: 0.8789 (m-10) cc_final: 0.8443 (m-10) REVERT: B 527 TYR cc_start: 0.8960 (t80) cc_final: 0.8736 (t80) REVERT: B 585 SER cc_start: 0.8974 (p) cc_final: 0.8300 (t) REVERT: B 597 ILE cc_start: 0.9620 (pt) cc_final: 0.9400 (pt) REVERT: B 610 LYS cc_start: 0.9388 (ptmt) cc_final: 0.9181 (ptmm) REVERT: B 626 TYR cc_start: 0.8895 (m-80) cc_final: 0.8285 (m-80) REVERT: B 628 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8717 (mt-10) REVERT: B 632 MET cc_start: 0.8218 (mpp) cc_final: 0.7932 (mpp) REVERT: B 636 LYS cc_start: 0.9586 (mmtm) cc_final: 0.9351 (mmmm) REVERT: B 640 MET cc_start: 0.9161 (tpp) cc_final: 0.8779 (tpp) REVERT: B 656 LEU cc_start: 0.9492 (mt) cc_final: 0.9250 (mt) REVERT: B 664 THR cc_start: 0.9392 (p) cc_final: 0.9170 (p) REVERT: B 668 ASN cc_start: 0.9286 (m-40) cc_final: 0.9039 (m-40) REVERT: B 675 HIS cc_start: 0.8911 (t-90) cc_final: 0.8461 (t-90) REVERT: B 677 ARG cc_start: 0.9236 (mmm-85) cc_final: 0.8736 (mmm-85) REVERT: C 17 PHE cc_start: 0.8685 (p90) cc_final: 0.8229 (p90) REVERT: C 21 PHE cc_start: 0.8899 (m-10) cc_final: 0.8104 (m-80) REVERT: C 149 ASP cc_start: 0.8791 (m-30) cc_final: 0.8580 (m-30) REVERT: C 204 TYR cc_start: 0.9361 (t80) cc_final: 0.9108 (t80) REVERT: C 281 ASP cc_start: 0.8831 (t0) cc_final: 0.8207 (p0) REVERT: D 27 LYS cc_start: 0.9207 (pttp) cc_final: 0.8999 (pttm) REVERT: D 46 TYR cc_start: 0.8775 (m-80) cc_final: 0.8031 (m-80) REVERT: D 96 MET cc_start: 0.8338 (tpt) cc_final: 0.7865 (mmm) REVERT: D 105 TYR cc_start: 0.9378 (m-10) cc_final: 0.8616 (m-10) REVERT: D 169 TYR cc_start: 0.9392 (m-80) cc_final: 0.9005 (m-80) REVERT: D 172 PHE cc_start: 0.9199 (m-80) cc_final: 0.8904 (m-80) REVERT: D 186 GLN cc_start: 0.9142 (mp10) cc_final: 0.8923 (mp10) REVERT: D 190 ILE cc_start: 0.8970 (mt) cc_final: 0.8681 (tp) REVERT: D 259 PHE cc_start: 0.8203 (t80) cc_final: 0.7814 (t80) REVERT: D 269 MET cc_start: 0.9263 (mtm) cc_final: 0.9046 (mtm) outliers start: 0 outliers final: 0 residues processed: 665 average time/residue: 0.1227 time to fit residues: 123.6179 Evaluate side-chains 572 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 572 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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: 9.9990 chunk 133 optimal weight: 7.9990 chunk 149 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN A 191 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3822 r_free = 0.3822 target = 0.142163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.102453 restraints weight = 40656.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.106211 restraints weight = 22483.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108787 restraints weight = 14274.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.110539 restraints weight = 10032.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.111839 restraints weight = 7586.776| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.7518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16386 Z= 0.133 Angle : 0.618 9.694 22134 Z= 0.327 Chirality : 0.043 0.182 2360 Planarity : 0.004 0.060 2818 Dihedral : 8.128 142.665 2290 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.19), residues: 1932 helix: 1.00 (0.15), residues: 1149 sheet: -0.47 (0.40), residues: 144 loop : -0.09 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 604 TYR 0.028 0.001 TYR D 262 PHE 0.020 0.002 PHE B 261 TRP 0.011 0.001 TRP D 124 HIS 0.012 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (16386) covalent geometry : angle 0.61832 / 0.33 (22134) hydrogen bonds : bond 0.03827 / 2.36 ( 871) hydrogen bonds : angle 4.91863 / 3.48 ( 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 652 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 652 time to evaluate : 0.642 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: A 28 LYS cc_start: 0.9534 (mmtt) cc_final: 0.9125 (mmmm) REVERT: A 31 GLU cc_start: 0.9065 (mp0) cc_final: 0.8650 (mp0) REVERT: A 101 TYR cc_start: 0.9413 (m-80) cc_final: 0.9156 (m-10) REVERT: A 119 GLU cc_start: 0.8790 (mp0) cc_final: 0.8454 (mp0) REVERT: A 136 LYS cc_start: 0.9568 (tttp) cc_final: 0.9155 (tttp) REVERT: A 139 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8799 (mt-10) REVERT: A 148 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8523 (mt-10) REVERT: A 172 LEU cc_start: 0.9559 (mp) cc_final: 0.9238 (mp) REVERT: A 174 GLU cc_start: 0.8557 (mt-10) cc_final: 0.7809 (mt-10) REVERT: A 181 ASP cc_start: 0.9204 (m-30) cc_final: 0.8970 (m-30) REVERT: A 221 LYS cc_start: 0.8707 (mmtp) cc_final: 0.8487 (mttp) REVERT: A 223 VAL cc_start: 0.9522 (m) cc_final: 0.9101 (p) REVERT: A 227 MET cc_start: 0.9307 (mtp) cc_final: 0.9022 (mtp) REVERT: A 257 ASP cc_start: 0.9258 (m-30) cc_final: 0.8900 (m-30) REVERT: A 277 THR cc_start: 0.8602 (p) cc_final: 0.8188 (t) REVERT: A 286 ASP cc_start: 0.8610 (m-30) cc_final: 0.8293 (m-30) REVERT: A 290 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8471 (tm-30) REVERT: A 291 LEU cc_start: 0.9492 (mt) cc_final: 0.9224 (mt) REVERT: A 322 MET cc_start: 0.8980 (mmp) cc_final: 0.8692 (mmm) REVERT: A 335 GLU cc_start: 0.8298 (mp0) cc_final: 0.7998 (mp0) REVERT: A 345 LYS cc_start: 0.9384 (mmmt) cc_final: 0.9105 (tttt) REVERT: A 362 ASP cc_start: 0.8307 (m-30) cc_final: 0.8000 (m-30) REVERT: A 366 LYS cc_start: 0.9506 (mtmt) cc_final: 0.9199 (mtmm) REVERT: A 396 ASP cc_start: 0.8696 (m-30) cc_final: 0.8269 (m-30) REVERT: A 405 LEU cc_start: 0.8476 (mt) cc_final: 0.8217 (mt) REVERT: A 418 ASN cc_start: 0.9257 (m-40) cc_final: 0.8821 (m-40) REVERT: A 421 GLU cc_start: 0.8741 (pp20) cc_final: 0.8306 (pp20) REVERT: A 447 ASN cc_start: 0.8709 (t0) cc_final: 0.7963 (t0) REVERT: A 458 MET cc_start: 0.8815 (mmp) cc_final: 0.8463 (mmm) REVERT: A 491 PHE cc_start: 0.9701 (t80) cc_final: 0.9479 (t80) REVERT: A 493 MET cc_start: 0.8517 (tmm) cc_final: 0.8076 (tmm) REVERT: A 515 ASP cc_start: 0.9067 (m-30) cc_final: 0.8833 (m-30) REVERT: A 583 SER cc_start: 0.9340 (m) cc_final: 0.8876 (t) REVERT: A 599 GLU cc_start: 0.8929 (pt0) cc_final: 0.8569 (pt0) REVERT: A 601 ILE cc_start: 0.9352 (tp) cc_final: 0.8938 (mm) REVERT: A 615 MET cc_start: 0.9258 (mmp) cc_final: 0.9042 (mmp) REVERT: A 645 GLN cc_start: 0.8871 (tp40) cc_final: 0.8560 (tp-100) REVERT: A 650 GLN cc_start: 0.8503 (tt0) cc_final: 0.8065 (tt0) REVERT: A 672 LEU cc_start: 0.9356 (mt) cc_final: 0.9124 (mt) REVERT: B 20 LYS cc_start: 0.9598 (mtpt) cc_final: 0.9293 (mtpp) REVERT: B 51 LEU cc_start: 0.9383 (tp) cc_final: 0.8983 (tp) REVERT: B 52 LYS cc_start: 0.9392 (tptp) cc_final: 0.9106 (tppt) REVERT: B 55 LEU cc_start: 0.9726 (mt) cc_final: 0.9516 (mt) REVERT: B 75 GLU cc_start: 0.9249 (mp0) cc_final: 0.8956 (pm20) REVERT: B 87 LYS cc_start: 0.9298 (tptp) cc_final: 0.8976 (tptp) REVERT: B 89 PHE cc_start: 0.9241 (t80) cc_final: 0.8952 (t80) REVERT: B 95 MET cc_start: 0.9137 (tpp) cc_final: 0.8787 (tpp) REVERT: B 119 GLU cc_start: 0.9197 (mp0) cc_final: 0.8807 (mp0) REVERT: B 147 GLN cc_start: 0.8838 (mt0) cc_final: 0.8612 (mm-40) REVERT: B 172 LEU cc_start: 0.9539 (mp) cc_final: 0.9305 (mp) REVERT: B 184 ARG cc_start: 0.9402 (tpp80) cc_final: 0.9066 (tpp80) REVERT: B 202 ASN cc_start: 0.9196 (t0) cc_final: 0.8473 (t0) REVERT: B 204 SER cc_start: 0.9406 (m) cc_final: 0.8921 (t) REVERT: B 205 LYS cc_start: 0.8811 (mmtp) cc_final: 0.8592 (mmtm) REVERT: B 211 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8524 (mm-30) REVERT: B 218 ASN cc_start: 0.9442 (m110) cc_final: 0.9176 (m-40) REVERT: B 223 VAL cc_start: 0.9330 (m) cc_final: 0.8841 (m) REVERT: B 228 LYS cc_start: 0.9242 (mmmt) cc_final: 0.8881 (tppt) REVERT: B 232 ASN cc_start: 0.9021 (m110) cc_final: 0.8767 (m110) REVERT: B 250 TYR cc_start: 0.9105 (m-80) cc_final: 0.8626 (m-80) REVERT: B 252 ASN cc_start: 0.9050 (t0) cc_final: 0.8644 (t0) REVERT: B 257 ASP cc_start: 0.9095 (m-30) cc_final: 0.8853 (m-30) REVERT: B 274 ARG cc_start: 0.8937 (tpp80) cc_final: 0.8734 (tpp80) REVERT: B 286 ASP cc_start: 0.8615 (m-30) cc_final: 0.8081 (m-30) REVERT: B 321 GLU cc_start: 0.8188 (pp20) cc_final: 0.7944 (pp20) REVERT: B 322 MET cc_start: 0.8474 (mmm) cc_final: 0.7814 (mmm) REVERT: B 355 TYR cc_start: 0.9124 (m-80) cc_final: 0.8456 (m-10) REVERT: B 361 GLN cc_start: 0.9023 (tt0) cc_final: 0.8727 (tt0) REVERT: B 370 ASN cc_start: 0.9392 (m110) cc_final: 0.9144 (m110) REVERT: B 375 LYS cc_start: 0.9087 (mmmm) cc_final: 0.8656 (mmmm) REVERT: B 391 VAL cc_start: 0.8929 (t) cc_final: 0.8608 (p) REVERT: B 392 SER cc_start: 0.8658 (m) cc_final: 0.8352 (p) REVERT: B 410 ASN cc_start: 0.8914 (m110) cc_final: 0.8620 (m110) REVERT: B 420 MET cc_start: 0.9165 (mmm) cc_final: 0.8818 (mmm) REVERT: B 459 LYS cc_start: 0.9069 (mttp) cc_final: 0.8224 (mtmt) REVERT: B 460 SER cc_start: 0.9483 (p) cc_final: 0.9278 (p) REVERT: B 472 LEU cc_start: 0.9504 (mm) cc_final: 0.9210 (mm) REVERT: B 505 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8606 (mt-10) REVERT: B 515 ASP cc_start: 0.8982 (m-30) cc_final: 0.8682 (m-30) REVERT: B 522 TYR cc_start: 0.8773 (m-10) cc_final: 0.8455 (m-10) REVERT: B 585 SER cc_start: 0.8959 (p) cc_final: 0.8319 (t) REVERT: B 597 ILE cc_start: 0.9545 (pt) cc_final: 0.9291 (pt) REVERT: B 626 TYR cc_start: 0.8610 (m-80) cc_final: 0.7947 (m-80) REVERT: B 628 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8762 (mt-10) REVERT: B 632 MET cc_start: 0.8264 (mpp) cc_final: 0.8039 (mpp) REVERT: B 636 LYS cc_start: 0.9570 (mmtm) cc_final: 0.9325 (mmmm) REVERT: B 640 MET cc_start: 0.9112 (tpp) cc_final: 0.8727 (tpp) REVERT: B 656 LEU cc_start: 0.9488 (mt) cc_final: 0.9247 (mt) REVERT: B 664 THR cc_start: 0.9426 (p) cc_final: 0.9174 (p) REVERT: B 668 ASN cc_start: 0.9270 (m-40) cc_final: 0.9005 (m110) REVERT: B 677 ARG cc_start: 0.9190 (mmm-85) cc_final: 0.8708 (mmm-85) REVERT: C 17 PHE cc_start: 0.8669 (p90) cc_final: 0.8355 (p90) REVERT: C 21 PHE cc_start: 0.8926 (m-10) cc_final: 0.8233 (m-80) REVERT: C 315 LEU cc_start: 0.8866 (tp) cc_final: 0.8643 (tp) REVERT: D 27 LYS cc_start: 0.9243 (pttp) cc_final: 0.9015 (pttm) REVERT: D 45 LYS cc_start: 0.8711 (pttt) cc_final: 0.8478 (ptpp) REVERT: D 46 TYR cc_start: 0.8732 (m-80) cc_final: 0.8201 (m-80) REVERT: D 96 MET cc_start: 0.8253 (tpt) cc_final: 0.7776 (mmm) REVERT: D 104 SER cc_start: 0.8711 (m) cc_final: 0.8450 (m) REVERT: D 105 TYR cc_start: 0.9355 (m-10) cc_final: 0.8643 (m-10) REVERT: D 154 PHE cc_start: 0.7925 (m-10) cc_final: 0.7057 (m-80) REVERT: D 169 TYR cc_start: 0.9390 (m-80) cc_final: 0.9069 (m-80) REVERT: D 172 PHE cc_start: 0.9101 (m-80) cc_final: 0.8864 (m-80) REVERT: D 173 TYR cc_start: 0.7872 (t80) cc_final: 0.7304 (t80) REVERT: D 259 PHE cc_start: 0.8268 (t80) cc_final: 0.7922 (t80) REVERT: D 269 MET cc_start: 0.9190 (mtm) cc_final: 0.8964 (mtm) outliers start: 0 outliers final: 0 residues processed: 652 average time/residue: 0.1242 time to fit residues: 123.0650 Evaluate side-chains 573 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 573 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 189 optimal weight: 7.9990 chunk 181 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 132 optimal weight: 0.0570 chunk 50 optimal weight: 0.9980 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.141892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.101653 restraints weight = 40410.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.105474 restraints weight = 22205.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.108031 restraints weight = 14055.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.109753 restraints weight = 9959.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.111076 restraints weight = 7604.375| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.7737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 16386 Z= 0.144 Angle : 0.648 10.501 22134 Z= 0.343 Chirality : 0.044 0.345 2360 Planarity : 0.004 0.042 2818 Dihedral : 8.042 143.172 2290 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.19), residues: 1932 helix: 0.91 (0.15), residues: 1148 sheet: -0.54 (0.40), residues: 144 loop : -0.11 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 604 TYR 0.031 0.002 TYR D 262 PHE 0.022 0.002 PHE B 128 TRP 0.027 0.002 TRP D 30 HIS 0.011 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (16386) covalent geometry : angle 0.64799 / 0.34 (22134) hydrogen bonds : bond 0.03928 / 2.44 ( 871) hydrogen bonds : angle 5.01377 / 3.54 ( 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 : 0.628 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: A 28 LYS cc_start: 0.9506 (mmtt) cc_final: 0.9090 (mmmm) REVERT: A 31 GLU cc_start: 0.9025 (mp0) cc_final: 0.8619 (mp0) REVERT: A 101 TYR cc_start: 0.9414 (m-80) cc_final: 0.9096 (m-10) REVERT: A 119 GLU cc_start: 0.8724 (mp0) cc_final: 0.8418 (mp0) REVERT: A 136 LYS cc_start: 0.9571 (tttp) cc_final: 0.9159 (tttp) REVERT: A 139 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8798 (mt-10) REVERT: A 147 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8445 (mm-40) REVERT: A 148 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8560 (mt-10) REVERT: A 172 LEU cc_start: 0.9578 (mp) cc_final: 0.9293 (mp) REVERT: A 174 GLU cc_start: 0.8536 (mt-10) cc_final: 0.7799 (mt-10) REVERT: A 223 VAL cc_start: 0.9512 (m) cc_final: 0.9091 (p) REVERT: A 227 MET cc_start: 0.9313 (mtp) cc_final: 0.9008 (mtp) REVERT: A 232 ASN cc_start: 0.8701 (m110) cc_final: 0.8281 (m110) REVERT: A 257 ASP cc_start: 0.9261 (m-30) cc_final: 0.8943 (m-30) REVERT: A 277 THR cc_start: 0.8654 (p) cc_final: 0.8247 (t) REVERT: A 286 ASP cc_start: 0.8602 (m-30) cc_final: 0.8337 (m-30) REVERT: A 290 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8529 (tm-30) REVERT: A 291 LEU cc_start: 0.9470 (mt) cc_final: 0.9137 (mt) REVERT: A 322 MET cc_start: 0.9040 (mmp) cc_final: 0.8758 (mmm) REVERT: A 335 GLU cc_start: 0.8327 (mp0) cc_final: 0.8027 (mp0) REVERT: A 345 LYS cc_start: 0.9461 (mmmt) cc_final: 0.9115 (tttt) REVERT: A 362 ASP cc_start: 0.8330 (m-30) cc_final: 0.8023 (m-30) REVERT: A 366 LYS cc_start: 0.9500 (mtmt) cc_final: 0.9175 (mtmm) REVERT: A 396 ASP cc_start: 0.8759 (m-30) cc_final: 0.8321 (m-30) REVERT: A 405 LEU cc_start: 0.8472 (mt) cc_final: 0.8183 (mt) REVERT: A 413 SER cc_start: 0.9096 (t) cc_final: 0.8733 (t) REVERT: A 418 ASN cc_start: 0.9189 (m-40) cc_final: 0.8745 (m-40) REVERT: A 421 GLU cc_start: 0.8720 (pp20) cc_final: 0.8259 (pp20) REVERT: A 458 MET cc_start: 0.8799 (mmp) cc_final: 0.8444 (mmm) REVERT: A 483 GLU cc_start: 0.9477 (mp0) cc_final: 0.9218 (mp0) REVERT: A 493 MET cc_start: 0.8591 (tmm) cc_final: 0.8084 (tmm) REVERT: A 497 PHE cc_start: 0.8923 (t80) cc_final: 0.8666 (t80) REVERT: A 515 ASP cc_start: 0.9076 (m-30) cc_final: 0.8845 (m-30) REVERT: A 583 SER cc_start: 0.9332 (m) cc_final: 0.8875 (t) REVERT: A 599 GLU cc_start: 0.8994 (pt0) cc_final: 0.8620 (pt0) REVERT: A 601 ILE cc_start: 0.9325 (tp) cc_final: 0.8940 (mm) REVERT: A 615 MET cc_start: 0.9219 (mmp) cc_final: 0.8985 (mmp) REVERT: A 645 GLN cc_start: 0.8858 (tp40) cc_final: 0.8560 (tp40) REVERT: A 650 GLN cc_start: 0.8451 (tt0) cc_final: 0.7980 (tt0) REVERT: A 672 LEU cc_start: 0.9321 (mt) cc_final: 0.9107 (mt) REVERT: B 20 LYS cc_start: 0.9595 (mtpt) cc_final: 0.9272 (mtpp) REVERT: B 51 LEU cc_start: 0.9346 (tp) cc_final: 0.8929 (tp) REVERT: B 52 LYS cc_start: 0.9427 (tptp) cc_final: 0.9069 (tppt) REVERT: B 55 LEU cc_start: 0.9733 (mt) cc_final: 0.9502 (mt) REVERT: B 56 ASP cc_start: 0.9264 (m-30) cc_final: 0.8361 (m-30) REVERT: B 75 GLU cc_start: 0.9240 (mp0) cc_final: 0.8940 (pm20) REVERT: B 87 LYS cc_start: 0.9303 (tptp) cc_final: 0.9011 (tptp) REVERT: B 89 PHE cc_start: 0.9228 (t80) cc_final: 0.8967 (t80) REVERT: B 95 MET cc_start: 0.9141 (tpp) cc_final: 0.8797 (tpp) REVERT: B 119 GLU cc_start: 0.9195 (mp0) cc_final: 0.8804 (mp0) REVERT: B 127 LEU cc_start: 0.9559 (mm) cc_final: 0.9227 (mm) REVERT: B 184 ARG cc_start: 0.9411 (tpp80) cc_final: 0.9099 (tpp80) REVERT: B 202 ASN cc_start: 0.9109 (t0) cc_final: 0.8668 (t0) REVERT: B 204 SER cc_start: 0.9411 (m) cc_final: 0.8947 (t) REVERT: B 205 LYS cc_start: 0.8836 (mmtp) cc_final: 0.8600 (mmtm) REVERT: B 211 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8564 (mm-30) REVERT: B 218 ASN cc_start: 0.9436 (m110) cc_final: 0.9171 (m-40) REVERT: B 221 LYS cc_start: 0.8895 (mmtp) cc_final: 0.8593 (mmmm) REVERT: B 223 VAL cc_start: 0.9331 (m) cc_final: 0.8857 (m) REVERT: B 228 LYS cc_start: 0.9215 (mmmt) cc_final: 0.8849 (tppt) REVERT: B 250 TYR cc_start: 0.9097 (m-80) cc_final: 0.8686 (m-80) REVERT: B 252 ASN cc_start: 0.9119 (t0) cc_final: 0.8833 (t0) REVERT: B 263 ASP cc_start: 0.8978 (m-30) cc_final: 0.8771 (m-30) REVERT: B 274 ARG cc_start: 0.8970 (tpp80) cc_final: 0.8761 (tpp80) REVERT: B 283 VAL cc_start: 0.9564 (t) cc_final: 0.9292 (t) REVERT: B 286 ASP cc_start: 0.8606 (m-30) cc_final: 0.8071 (m-30) REVERT: B 348 MET cc_start: 0.8877 (ptp) cc_final: 0.8461 (ptp) REVERT: B 355 TYR cc_start: 0.9140 (m-80) cc_final: 0.8477 (m-10) REVERT: B 361 GLN cc_start: 0.8991 (tt0) cc_final: 0.8735 (tt0) REVERT: B 370 ASN cc_start: 0.9405 (m110) cc_final: 0.9086 (m110) REVERT: B 375 LYS cc_start: 0.9064 (mmmm) cc_final: 0.8625 (mmmm) REVERT: B 391 VAL cc_start: 0.8924 (t) cc_final: 0.8562 (p) REVERT: B 392 SER cc_start: 0.8752 (m) cc_final: 0.7483 (p) REVERT: B 410 ASN cc_start: 0.8900 (m110) cc_final: 0.8574 (m110) REVERT: B 416 ILE cc_start: 0.9381 (mp) cc_final: 0.9148 (mp) REVERT: B 420 MET cc_start: 0.9276 (mmm) cc_final: 0.8987 (mmm) REVERT: B 426 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8286 (tm-30) REVERT: B 427 LYS cc_start: 0.9444 (ptmt) cc_final: 0.9140 (ptpp) REVERT: B 459 LYS cc_start: 0.9083 (mttp) cc_final: 0.8250 (mtmt) REVERT: B 460 SER cc_start: 0.9454 (p) cc_final: 0.9236 (p) REVERT: B 472 LEU cc_start: 0.9487 (mm) cc_final: 0.9215 (mm) REVERT: B 505 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8455 (mt-10) REVERT: B 515 ASP cc_start: 0.9026 (m-30) cc_final: 0.8715 (m-30) REVERT: B 522 TYR cc_start: 0.8703 (m-10) cc_final: 0.8378 (m-10) REVERT: B 585 SER cc_start: 0.8974 (p) cc_final: 0.8309 (t) REVERT: B 598 MET cc_start: 0.8709 (mtp) cc_final: 0.8102 (mtp) REVERT: B 610 LYS cc_start: 0.9395 (ptmt) cc_final: 0.9158 (ptmm) REVERT: B 626 TYR cc_start: 0.8612 (m-80) cc_final: 0.7969 (m-80) REVERT: B 628 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8729 (mt-10) REVERT: B 636 LYS cc_start: 0.9574 (mmtm) cc_final: 0.9332 (mmmm) REVERT: B 640 MET cc_start: 0.9093 (tpp) cc_final: 0.8754 (tpp) REVERT: B 656 LEU cc_start: 0.9370 (mt) cc_final: 0.9053 (mt) REVERT: B 667 LEU cc_start: 0.9470 (tp) cc_final: 0.9243 (tp) REVERT: B 668 ASN cc_start: 0.9291 (m-40) cc_final: 0.9042 (m110) REVERT: B 677 ARG cc_start: 0.9181 (mmm-85) cc_final: 0.8976 (mmm-85) REVERT: C 21 PHE cc_start: 0.8921 (m-10) cc_final: 0.8410 (m-80) REVERT: C 87 LYS cc_start: 0.8725 (mtmm) cc_final: 0.8436 (mttt) REVERT: C 154 PHE cc_start: 0.8151 (t80) cc_final: 0.7777 (t80) REVERT: C 207 LEU cc_start: 0.7995 (pp) cc_final: 0.7718 (pp) REVERT: C 315 LEU cc_start: 0.8915 (tp) cc_final: 0.8664 (tp) REVERT: D 27 LYS cc_start: 0.9222 (pttp) cc_final: 0.8962 (pttm) REVERT: D 45 LYS cc_start: 0.8736 (pttt) cc_final: 0.8493 (ptpp) REVERT: D 46 TYR cc_start: 0.8694 (m-80) cc_final: 0.8138 (m-80) REVERT: D 96 MET cc_start: 0.8348 (tpt) cc_final: 0.7928 (mmm) REVERT: D 105 TYR cc_start: 0.9348 (m-10) cc_final: 0.8642 (m-10) REVERT: D 123 GLU cc_start: 0.8679 (mp0) cc_final: 0.8330 (pm20) REVERT: D 128 ASN cc_start: 0.3055 (t0) cc_final: 0.2136 (m-40) REVERT: D 169 TYR cc_start: 0.9400 (m-80) cc_final: 0.9150 (m-80) REVERT: D 172 PHE cc_start: 0.9158 (m-80) cc_final: 0.8944 (m-80) REVERT: D 173 TYR cc_start: 0.7888 (t80) cc_final: 0.7003 (t80) REVERT: D 259 PHE cc_start: 0.8258 (t80) cc_final: 0.7883 (t80) REVERT: D 269 MET cc_start: 0.9183 (mtm) cc_final: 0.8983 (mtm) outliers start: 0 outliers final: 0 residues processed: 643 average time/residue: 0.1247 time to fit residues: 122.7462 Evaluate side-chains 576 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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: 7.9990 chunk 1 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 0.0970 chunk 148 optimal weight: 7.9990 chunk 125 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 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** B 568 HIS ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3842 r_free = 0.3842 target = 0.144199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.104616 restraints weight = 40324.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.108353 restraints weight = 22290.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.110943 restraints weight = 14211.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.112595 restraints weight = 9992.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.113998 restraints weight = 7665.256| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.7907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16386 Z= 0.139 Angle : 0.655 12.286 22134 Z= 0.346 Chirality : 0.044 0.363 2360 Planarity : 0.004 0.042 2818 Dihedral : 7.933 143.612 2290 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % 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 are not related in a simple way. whole: 0.57 (0.19), residues: 1932 helix: 0.88 (0.15), residues: 1149 sheet: -0.48 (0.40), residues: 144 loop : -0.13 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 604 TYR 0.030 0.001 TYR D 262 PHE 0.021 0.002 PHE D 178 TRP 0.039 0.002 TRP D 124 HIS 0.011 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (16386) covalent geometry : angle 0.65505 / 0.35 (22134) hydrogen bonds : bond 0.03968 / 2.46 ( 871) hydrogen bonds : angle 5.01820 / 3.57 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3430.30 seconds wall clock time: 60 minutes 4.68 seconds (3604.68 seconds total)