Starting phenix.real_space_refine on Thu Aug 6 15:18:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byy_45048/08_2026/9byy_45048_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byy_45048/08_2026/9byy_45048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9byy_45048/08_2026/9byy_45048_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byy_45048/08_2026/9byy_45048_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9byy_45048/08_2026/9byy_45048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byy_45048/08_2026/9byy_45048.map" } resolution = 4.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 3.45, per 1000 atoms: 0.22 Number of scatterers: 16038 At special positions: 0 Unit cell: (97.632, 124.074, 132.21, 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: 1.25 Conformation dependent library (CDL) restraints added in 613.4 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: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.516A 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: 3.568A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.954A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.665A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.695A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.851A 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: 4.016A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.073A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.677A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.878A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.645A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.729A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.027A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.068A 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: 3.881A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.567A 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: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.360A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.427A 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: 8.393A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.715A 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: 6.477A 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: 6.382A 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: 6.063A 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: 7.907A 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: 8.344A 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: 2.79 Time building geometry restraints manager: 1.62 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: 4819 1.34 - 1.46: 3057 1.46 - 1.58: 8329 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: 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 4.82e+01 bond pdb=" O3B TTP A 803 " pdb=" PG TTP A 803 " ideal model delta sigma weight residual 1.748 1.610 0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.600 -0.060 1.25e-02 6.40e+03 2.29e+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 1.18e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.14e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21528 2.09 - 4.18: 525 4.18 - 6.27: 64 6.27 - 8.36: 8 8.36 - 10.45: 9 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.63 -6.09 1.36e+00 5.41e-01 2.01e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.14 -4.43 1.15e+00 7.56e-01 1.48e+01 angle pdb=" N SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.20 -3.92 1.09e+00 8.42e-01 1.29e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.81 -4.31 1.23e+00 6.61e-01 1.23e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.68 -3.97 1.15e+00 7.56e-01 1.19e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.05: 9088 25.05 - 50.10: 657 50.10 - 75.16: 125 75.16 - 100.21: 26 100.21 - 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 -98.24 125.26 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 -95.59 122.61 1 2.00e+01 2.50e-03 3.69e+01 dihedral pdb=" C VAL C 125 " pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual -122.00 -134.34 12.34 0 2.50e+00 1.60e-01 2.44e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2139 0.093 - 0.186: 189 0.186 - 0.279: 27 0.279 - 0.372: 3 0.372 - 0.465: 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 5.42e+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 4.67e+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 2.16 0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.68e+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 1.11e-02 2.14e+00 pdb=" CG PHE D 92 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " 0.010 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 9.71e-03 1.88e+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 " -0.001 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: 129 2.51 - 3.11: 11557 3.11 - 3.70: 27052 3.70 - 4.30: 41529 4.30 - 4.90: 65421 Nonbonded interactions: 145688 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 1.961 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 1.991 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.012 3.040 ... (remaining 145683 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.940 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.139 16386 Z= 0.334 Angle : 0.787 10.449 22134 Z= 0.471 Chirality : 0.058 0.465 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.680 125.261 6202 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.34 % Allowed : 15.33 % Favored : 83.33 % 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: 0.59 (0.14), residues: 1151 sheet: 0.46 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 196 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.009 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 0.78748 / 0.47 (22134) hydrogen bonds : bond 0.15421 / 9.51 ( 871) hydrogen bonds : angle 6.51807 / 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 883 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 860 time to evaluate : 0.604 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 41 ILE cc_start: 0.8904 (mm) cc_final: 0.8689 (mm) REVERT: A 109 ASN cc_start: 0.8043 (m-40) cc_final: 0.7604 (p0) REVERT: A 116 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6837 (mt-10) REVERT: A 118 TYR cc_start: 0.8114 (t80) cc_final: 0.7889 (t80) REVERT: A 147 GLN cc_start: 0.8293 (mt0) cc_final: 0.7243 (mt0) REVERT: A 149 TYR cc_start: 0.8380 (t80) cc_final: 0.8010 (t80) REVERT: A 155 THR cc_start: 0.9239 (m) cc_final: 0.8920 (m) REVERT: A 162 LYS cc_start: 0.7625 (ttpt) cc_final: 0.7293 (ttmm) REVERT: A 190 MET cc_start: 0.8182 (mtt) cc_final: 0.7777 (mtt) REVERT: A 192 LEU cc_start: 0.9213 (mt) cc_final: 0.8681 (mt) REVERT: A 204 SER cc_start: 0.9231 (m) cc_final: 0.8698 (t) REVERT: A 227 MET cc_start: 0.8479 (mtp) cc_final: 0.8231 (mtp) REVERT: A 345 LYS cc_start: 0.8579 (tttt) cc_final: 0.8187 (tttt) REVERT: A 373 ILE cc_start: 0.8878 (mt) cc_final: 0.8625 (mt) REVERT: A 377 LYS cc_start: 0.8860 (mttt) cc_final: 0.8375 (mttp) REVERT: A 436 LEU cc_start: 0.8997 (mt) cc_final: 0.8616 (mm) REVERT: A 500 ILE cc_start: 0.9355 (mt) cc_final: 0.9153 (mt) REVERT: A 588 GLN cc_start: 0.7615 (mm-40) cc_final: 0.7289 (mm-40) REVERT: A 598 MET cc_start: 0.7525 (mtm) cc_final: 0.6965 (mtm) REVERT: A 606 TYR cc_start: 0.6927 (m-80) cc_final: 0.6616 (m-10) REVERT: A 610 LYS cc_start: 0.7099 (ttmm) cc_final: 0.6876 (ttmm) REVERT: A 634 MET cc_start: 0.8405 (mmp) cc_final: 0.8098 (mmm) REVERT: B 12 LEU cc_start: 0.8929 (mt) cc_final: 0.8462 (mt) REVERT: B 51 LEU cc_start: 0.8151 (tp) cc_final: 0.7910 (tp) REVERT: B 99 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8632 (mmtt) REVERT: B 147 GLN cc_start: 0.8068 (mt0) cc_final: 0.7384 (mt0) REVERT: B 161 ARG cc_start: 0.7152 (mtt180) cc_final: 0.6931 (mtt180) REVERT: B 181 ASP cc_start: 0.8428 (m-30) cc_final: 0.8063 (m-30) REVERT: B 211 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7301 (mm-30) REVERT: B 264 THR cc_start: 0.8338 (p) cc_final: 0.8067 (p) REVERT: B 286 ASP cc_start: 0.6259 (OUTLIER) cc_final: 0.5864 (m-30) REVERT: B 288 PHE cc_start: 0.7852 (t80) cc_final: 0.7546 (t80) REVERT: B 319 MET cc_start: 0.8079 (tpp) cc_final: 0.7482 (tpp) REVERT: B 394 TYR cc_start: 0.8003 (m-80) cc_final: 0.7679 (m-80) REVERT: B 425 ILE cc_start: 0.9175 (mt) cc_final: 0.8898 (mt) REVERT: B 436 LEU cc_start: 0.9111 (mt) cc_final: 0.8900 (mt) REVERT: B 460 SER cc_start: 0.8467 (t) cc_final: 0.8144 (p) REVERT: B 570 MET cc_start: 0.7289 (mtm) cc_final: 0.6929 (mtm) REVERT: B 584 ILE cc_start: 0.8989 (tp) cc_final: 0.8771 (tp) REVERT: B 585 SER cc_start: 0.9094 (p) cc_final: 0.8611 (t) REVERT: B 588 GLN cc_start: 0.7635 (mm-40) cc_final: 0.6500 (mm-40) REVERT: B 589 SER cc_start: 0.7889 (m) cc_final: 0.7527 (m) REVERT: B 640 MET cc_start: 0.7717 (tpp) cc_final: 0.7082 (tpp) REVERT: B 644 ILE cc_start: 0.8889 (mt) cc_final: 0.8582 (mt) outliers start: 23 outliers final: 7 residues processed: 874 average time/residue: 0.1426 time to fit residues: 179.2437 Evaluate side-chains 587 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 579 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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: 0.0370 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 overall best weight: 2.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN A 259 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 HIS B 313 HIS B 387 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN B 676 HIS ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN C 84 HIS C 210 GLN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN D 71 ASN D 80 HIS D 127 GLN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.136013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.099618 restraints weight = 36823.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.103109 restraints weight = 18816.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.105506 restraints weight = 11475.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.107004 restraints weight = 7835.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.108085 restraints weight = 5959.693| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16386 Z= 0.214 Angle : 0.659 11.903 22134 Z= 0.351 Chirality : 0.044 0.334 2360 Planarity : 0.004 0.046 2818 Dihedral : 9.428 130.815 2290 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.23 % Allowed : 2.86 % Favored : 96.91 % 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: 1.30 (0.19), residues: 1932 helix: 1.27 (0.15), residues: 1127 sheet: 0.28 (0.44), residues: 134 loop : 0.50 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 350 TYR 0.023 0.002 TYR C 247 PHE 0.030 0.002 PHE D 320 TRP 0.012 0.002 TRP B 9 HIS 0.009 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (16386) covalent geometry : angle 0.65885 / 0.35 (22134) hydrogen bonds : bond 0.04726 / 2.98 ( 871) hydrogen bonds : angle 5.06408 / 3.61 ( 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 696 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 692 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASN cc_start: 0.9032 (t0) cc_final: 0.8790 (t0) REVERT: A 147 GLN cc_start: 0.8744 (mt0) cc_final: 0.8184 (mt0) REVERT: A 163 ARG cc_start: 0.8301 (mmm160) cc_final: 0.8012 (mtp180) REVERT: A 164 ARG cc_start: 0.7245 (ptt90) cc_final: 0.7038 (ptt-90) REVERT: A 266 LYS cc_start: 0.8596 (mtmm) cc_final: 0.8151 (mtmm) REVERT: A 276 LYS cc_start: 0.9203 (pttp) cc_final: 0.8955 (ptpp) REVERT: A 444 ASP cc_start: 0.8255 (t0) cc_final: 0.7336 (t0) REVERT: A 446 ARG cc_start: 0.7764 (mmm160) cc_final: 0.6931 (mmt180) REVERT: A 458 MET cc_start: 0.9196 (mmm) cc_final: 0.8433 (mmm) REVERT: A 493 MET cc_start: 0.8992 (tmm) cc_final: 0.8681 (tmm) REVERT: A 588 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8213 (mm-40) REVERT: A 640 MET cc_start: 0.9139 (ttm) cc_final: 0.8567 (ttm) REVERT: A 683 TYR cc_start: 0.8438 (t80) cc_final: 0.8166 (t80) REVERT: B 8 LYS cc_start: 0.8785 (tptp) cc_final: 0.8140 (tppt) REVERT: B 12 LEU cc_start: 0.9504 (mt) cc_final: 0.9109 (mt) REVERT: B 95 MET cc_start: 0.8767 (tpp) cc_final: 0.8565 (mmm) REVERT: B 96 SER cc_start: 0.9512 (m) cc_final: 0.9259 (p) REVERT: B 147 GLN cc_start: 0.8864 (mt0) cc_final: 0.8210 (mt0) REVERT: B 200 SER cc_start: 0.8947 (t) cc_final: 0.8671 (t) REVERT: B 253 ILE cc_start: 0.9531 (tt) cc_final: 0.9291 (tt) REVERT: B 263 ASP cc_start: 0.9016 (m-30) cc_final: 0.8726 (m-30) REVERT: B 276 LYS cc_start: 0.9192 (pttt) cc_final: 0.8838 (pttm) REVERT: B 288 PHE cc_start: 0.9261 (t80) cc_final: 0.8900 (t80) REVERT: B 290 GLU cc_start: 0.8295 (tm-30) cc_final: 0.8072 (tm-30) REVERT: B 291 LEU cc_start: 0.9472 (mt) cc_final: 0.8924 (mt) REVERT: B 312 GLN cc_start: 0.8778 (mt0) cc_final: 0.8248 (mt0) REVERT: B 348 MET cc_start: 0.8008 (tpt) cc_final: 0.7319 (tpp) REVERT: B 386 LEU cc_start: 0.9196 (mt) cc_final: 0.8992 (mt) REVERT: B 393 SER cc_start: 0.9454 (m) cc_final: 0.8987 (p) REVERT: B 394 TYR cc_start: 0.8851 (m-80) cc_final: 0.8178 (m-80) REVERT: B 413 SER cc_start: 0.7955 (p) cc_final: 0.6646 (t) REVERT: B 417 LEU cc_start: 0.9485 (tt) cc_final: 0.9283 (tt) REVERT: B 425 ILE cc_start: 0.9615 (mt) cc_final: 0.9358 (mt) REVERT: B 467 ASN cc_start: 0.9128 (t0) cc_final: 0.8813 (t0) REVERT: B 493 MET cc_start: 0.9455 (tmm) cc_final: 0.9229 (tmm) REVERT: B 526 GLU cc_start: 0.8069 (tp30) cc_final: 0.7698 (tp30) REVERT: B 550 MET cc_start: 0.7862 (mtp) cc_final: 0.7087 (ttm) REVERT: B 588 GLN cc_start: 0.9138 (mm-40) cc_final: 0.8337 (mm-40) REVERT: B 602 GLU cc_start: 0.8010 (pt0) cc_final: 0.7770 (pt0) REVERT: B 640 MET cc_start: 0.9073 (tpp) cc_final: 0.8539 (tpp) REVERT: C 53 ASP cc_start: 0.8234 (t0) cc_final: 0.8025 (t0) REVERT: C 154 PHE cc_start: 0.8255 (t80) cc_final: 0.8003 (t80) REVERT: C 212 ILE cc_start: 0.8537 (mm) cc_final: 0.8068 (mm) REVERT: C 247 TYR cc_start: 0.7871 (m-10) cc_final: 0.7465 (m-80) REVERT: D 95 MET cc_start: 0.9256 (tmm) cc_final: 0.9047 (tmm) REVERT: D 96 MET cc_start: 0.7934 (mmm) cc_final: 0.7623 (tpt) REVERT: D 100 VAL cc_start: 0.7967 (t) cc_final: 0.7548 (t) REVERT: D 149 ASP cc_start: 0.8528 (m-30) cc_final: 0.8299 (m-30) REVERT: D 178 PHE cc_start: 0.8345 (m-80) cc_final: 0.8128 (m-80) REVERT: D 189 GLU cc_start: 0.7373 (tm-30) cc_final: 0.6640 (pt0) REVERT: D 224 LEU cc_start: 0.8562 (mt) cc_final: 0.8331 (mt) REVERT: D 235 LEU cc_start: 0.9051 (mt) cc_final: 0.8650 (pp) REVERT: D 259 PHE cc_start: 0.7673 (t80) cc_final: 0.7282 (t80) REVERT: D 318 ASP cc_start: 0.8410 (m-30) cc_final: 0.7901 (m-30) outliers start: 4 outliers final: 1 residues processed: 693 average time/residue: 0.1132 time to fit residues: 117.8705 Evaluate side-chains 541 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 540 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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: 7.9990 chunk 131 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 159 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 158 optimal weight: 10.0000 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS A 645 GLN B 11 GLN B 44 ASN B 61 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN D 23 ASN D 28 GLN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.132510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.096201 restraints weight = 37848.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.099558 restraints weight = 19394.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.101656 restraints weight = 11914.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.103434 restraints weight = 8501.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.104473 restraints weight = 6351.131| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-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: 5 (11 function evaluations) r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16386 Z= 0.207 Angle : 0.618 11.043 22134 Z= 0.329 Chirality : 0.043 0.184 2360 Planarity : 0.004 0.044 2818 Dihedral : 9.149 134.577 2290 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.23 % Allowed : 2.51 % 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: 1.20 (0.19), residues: 1932 helix: 1.24 (0.15), residues: 1129 sheet: -0.07 (0.43), residues: 134 loop : 0.43 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 293 TYR 0.029 0.002 TYR C 169 PHE 0.021 0.002 PHE A 129 TRP 0.034 0.002 TRP D 124 HIS 0.006 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.21 (16386) covalent geometry : angle 0.61777 / 0.33 (22134) hydrogen bonds : bond 0.04169 / 2.64 ( 871) hydrogen bonds : angle 4.92485 / 3.52 ( 2571) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 661 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.8947 (mmtm) cc_final: 0.8611 (mmtp) REVERT: A 117 ARG cc_start: 0.8270 (mtp85) cc_final: 0.8002 (mtp85) REVERT: A 131 ASN cc_start: 0.9211 (t0) cc_final: 0.8915 (t0) REVERT: A 147 GLN cc_start: 0.8777 (mt0) cc_final: 0.8444 (mt0) REVERT: A 266 LYS cc_start: 0.8314 (mttp) cc_final: 0.8005 (mttp) REVERT: A 274 ARG cc_start: 0.8427 (ttm110) cc_final: 0.8155 (ptp-110) REVERT: A 286 ASP cc_start: 0.8637 (m-30) cc_final: 0.7999 (m-30) REVERT: A 290 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8203 (tm-30) REVERT: A 348 MET cc_start: 0.8174 (tpt) cc_final: 0.7806 (tpt) REVERT: A 352 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7701 (mt-10) REVERT: A 362 ASP cc_start: 0.7238 (m-30) cc_final: 0.6681 (m-30) REVERT: A 399 GLU cc_start: 0.8850 (tp30) cc_final: 0.8640 (tp30) REVERT: A 442 THR cc_start: 0.8980 (p) cc_final: 0.8768 (p) REVERT: A 458 MET cc_start: 0.9221 (mmm) cc_final: 0.8447 (mmm) REVERT: A 493 MET cc_start: 0.8966 (tmm) cc_final: 0.8554 (tmm) REVERT: A 494 MET cc_start: 0.8859 (mtm) cc_final: 0.8267 (ptp) REVERT: A 550 MET cc_start: 0.7645 (mtp) cc_final: 0.7215 (mtm) REVERT: A 570 MET cc_start: 0.8986 (mtp) cc_final: 0.8756 (mtp) REVERT: A 599 GLU cc_start: 0.8370 (mp0) cc_final: 0.8152 (mp0) REVERT: A 640 MET cc_start: 0.9061 (ttm) cc_final: 0.8579 (ttm) REVERT: B 8 LYS cc_start: 0.8861 (tptp) cc_final: 0.8454 (tppt) REVERT: B 12 LEU cc_start: 0.9492 (mt) cc_final: 0.9103 (mt) REVERT: B 65 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8125 (mm-30) REVERT: B 119 GLU cc_start: 0.8838 (mp0) cc_final: 0.8422 (mp0) REVERT: B 147 GLN cc_start: 0.8946 (mt0) cc_final: 0.8034 (mt0) REVERT: B 157 LEU cc_start: 0.9113 (tp) cc_final: 0.8780 (tp) REVERT: B 173 LEU cc_start: 0.9563 (mt) cc_final: 0.9305 (mt) REVERT: B 211 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7384 (mm-30) REVERT: B 238 ASP cc_start: 0.6864 (p0) cc_final: 0.6028 (p0) REVERT: B 263 ASP cc_start: 0.9026 (m-30) cc_final: 0.8747 (m-30) REVERT: B 288 PHE cc_start: 0.9372 (t80) cc_final: 0.9020 (t80) REVERT: B 290 GLU cc_start: 0.8416 (tm-30) cc_final: 0.7935 (tm-30) REVERT: B 291 LEU cc_start: 0.9456 (mt) cc_final: 0.8916 (mt) REVERT: B 348 MET cc_start: 0.8029 (tpt) cc_final: 0.7281 (tpp) REVERT: B 373 ILE cc_start: 0.9652 (mt) cc_final: 0.9390 (mt) REVERT: B 393 SER cc_start: 0.9453 (m) cc_final: 0.8446 (p) REVERT: B 394 TYR cc_start: 0.8984 (m-80) cc_final: 0.8276 (m-80) REVERT: B 425 ILE cc_start: 0.9610 (mt) cc_final: 0.9389 (mt) REVERT: B 493 MET cc_start: 0.9492 (tmm) cc_final: 0.9175 (tmm) REVERT: B 526 GLU cc_start: 0.8048 (tp30) cc_final: 0.7597 (tp30) REVERT: B 550 MET cc_start: 0.7945 (mtp) cc_final: 0.7693 (ttm) REVERT: B 588 GLN cc_start: 0.9143 (mm-40) cc_final: 0.8251 (mm-40) REVERT: B 590 SER cc_start: 0.9122 (p) cc_final: 0.8887 (p) REVERT: B 612 TYR cc_start: 0.7905 (m-80) cc_final: 0.7500 (m-80) REVERT: B 615 MET cc_start: 0.9481 (mmm) cc_final: 0.9148 (mmm) REVERT: B 640 MET cc_start: 0.9174 (tpp) cc_final: 0.8562 (tpp) REVERT: B 644 ILE cc_start: 0.9627 (mt) cc_final: 0.9412 (mt) REVERT: B 667 LEU cc_start: 0.9510 (tp) cc_final: 0.9216 (tp) REVERT: C 27 LYS cc_start: 0.8966 (mtmm) cc_final: 0.8394 (tptp) REVERT: C 53 ASP cc_start: 0.8317 (t0) cc_final: 0.8084 (t0) REVERT: C 154 PHE cc_start: 0.8389 (t80) cc_final: 0.7945 (t80) REVERT: C 157 MET cc_start: 0.9186 (ptp) cc_final: 0.8975 (ptt) REVERT: C 212 ILE cc_start: 0.8552 (mm) cc_final: 0.8097 (mm) REVERT: C 247 TYR cc_start: 0.8028 (m-80) cc_final: 0.7650 (m-80) REVERT: D 42 LEU cc_start: 0.5887 (pp) cc_final: 0.5665 (pp) REVERT: D 46 TYR cc_start: 0.8413 (m-80) cc_final: 0.8098 (m-80) REVERT: D 51 GLU cc_start: 0.6747 (pm20) cc_final: 0.6291 (pm20) REVERT: D 56 MET cc_start: 0.6370 (mpp) cc_final: 0.5927 (mpp) REVERT: D 149 ASP cc_start: 0.8496 (m-30) cc_final: 0.8251 (m-30) REVERT: D 189 GLU cc_start: 0.7457 (tm-30) cc_final: 0.6593 (pt0) REVERT: D 211 GLU cc_start: 0.9434 (tp30) cc_final: 0.9122 (mt-10) REVERT: D 259 PHE cc_start: 0.7688 (t80) cc_final: 0.7309 (t80) REVERT: D 282 ILE cc_start: 0.3380 (OUTLIER) cc_final: 0.3124 (mm) outliers start: 4 outliers final: 0 residues processed: 662 average time/residue: 0.1080 time to fit residues: 108.2413 Evaluate side-chains 551 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 550 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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: 2.9990 chunk 157 optimal weight: 20.0000 chunk 168 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 182 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN B 14 ASN B 232 ASN B 312 GLN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 668 ASN C 24 GLN C 28 GLN C 233 ASN D 23 ASN ** 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 = 0.3662 r_free = 0.3662 target = 0.126282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.091901 restraints weight = 38772.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.095115 restraints weight = 19803.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.097323 restraints weight = 11974.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.098695 restraints weight = 8230.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.099673 restraints weight = 6256.943| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (15 function evaluations) r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 16386 Z= 0.324 Angle : 0.718 12.313 22134 Z= 0.381 Chirality : 0.046 0.235 2360 Planarity : 0.004 0.054 2818 Dihedral : 9.218 135.473 2290 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.06 % Allowed : 3.67 % Favored : 96.27 % 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: 0.69 (0.19), residues: 1932 helix: 0.85 (0.15), residues: 1132 sheet: -0.32 (0.43), residues: 134 loop : 0.18 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 669 TYR 0.027 0.002 TYR A 683 PHE 0.033 0.003 PHE B 37 TRP 0.046 0.003 TRP D 124 HIS 0.007 0.002 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00697 / 0.32 (16386) covalent geometry : angle 0.71786 / 0.38 (22134) hydrogen bonds : bond 0.04384 / 2.71 ( 871) hydrogen bonds : angle 5.13073 / 3.68 ( 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 609 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 608 time to evaluate : 0.527 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 40 TYR cc_start: 0.8847 (t80) cc_final: 0.8442 (t80) REVERT: A 131 ASN cc_start: 0.9178 (t0) cc_final: 0.8835 (t0) REVERT: A 147 GLN cc_start: 0.8919 (mt0) cc_final: 0.8612 (mt0) REVERT: A 150 GLN cc_start: 0.8931 (tp40) cc_final: 0.8726 (tp-100) REVERT: A 163 ARG cc_start: 0.8370 (mmm160) cc_final: 0.8051 (mmm160) REVERT: A 186 ILE cc_start: 0.9133 (mt) cc_final: 0.8859 (mt) REVERT: A 204 SER cc_start: 0.9411 (t) cc_final: 0.9021 (t) REVERT: A 286 ASP cc_start: 0.8715 (m-30) cc_final: 0.8092 (m-30) REVERT: A 290 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8252 (tm-30) REVERT: A 348 MET cc_start: 0.8208 (tpt) cc_final: 0.7673 (tpt) REVERT: A 352 GLU cc_start: 0.8482 (mt-10) cc_final: 0.7751 (mt-10) REVERT: A 360 PHE cc_start: 0.8704 (m-80) cc_final: 0.8486 (m-80) REVERT: A 362 ASP cc_start: 0.7468 (m-30) cc_final: 0.6741 (m-30) REVERT: A 437 THR cc_start: 0.9410 (m) cc_final: 0.9130 (p) REVERT: A 479 TYR cc_start: 0.9002 (t80) cc_final: 0.8366 (t80) REVERT: A 570 MET cc_start: 0.8758 (mtp) cc_final: 0.8507 (mtp) REVERT: A 599 GLU cc_start: 0.8304 (mp0) cc_final: 0.8012 (mp0) REVERT: A 640 MET cc_start: 0.9241 (ttm) cc_final: 0.8708 (ttm) REVERT: B 12 LEU cc_start: 0.9478 (mt) cc_final: 0.9124 (mt) REVERT: B 119 GLU cc_start: 0.8950 (mp0) cc_final: 0.8520 (mp0) REVERT: B 147 GLN cc_start: 0.9037 (mt0) cc_final: 0.8749 (mt0) REVERT: B 150 GLN cc_start: 0.9147 (tp40) cc_final: 0.8897 (tp-100) REVERT: B 157 LEU cc_start: 0.9254 (tp) cc_final: 0.8736 (tp) REVERT: B 158 ASN cc_start: 0.9030 (m110) cc_final: 0.8718 (m-40) REVERT: B 211 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7720 (mm-30) REVERT: B 217 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7985 (tm-30) REVERT: B 232 ASN cc_start: 0.8033 (t0) cc_final: 0.7554 (t0) REVERT: B 253 ILE cc_start: 0.9551 (tt) cc_final: 0.9337 (tt) REVERT: B 263 ASP cc_start: 0.8972 (m-30) cc_final: 0.8726 (m-30) REVERT: B 276 LYS cc_start: 0.9196 (pttt) cc_final: 0.8842 (pttm) REVERT: B 288 PHE cc_start: 0.9419 (t80) cc_final: 0.9201 (t80) REVERT: B 290 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8079 (tm-30) REVERT: B 291 LEU cc_start: 0.9442 (mt) cc_final: 0.8931 (mt) REVERT: B 348 MET cc_start: 0.7974 (tpt) cc_final: 0.7182 (tpp) REVERT: B 373 ILE cc_start: 0.9708 (mt) cc_final: 0.9354 (mt) REVERT: B 394 TYR cc_start: 0.9024 (m-80) cc_final: 0.8302 (m-80) REVERT: B 425 ILE cc_start: 0.9632 (mt) cc_final: 0.9339 (mt) REVERT: B 441 GLU cc_start: 0.8626 (mp0) cc_final: 0.8314 (mp0) REVERT: B 467 ASN cc_start: 0.9360 (t0) cc_final: 0.8554 (t0) REVERT: B 493 MET cc_start: 0.9447 (tmm) cc_final: 0.9131 (tmm) REVERT: B 526 GLU cc_start: 0.8039 (tp30) cc_final: 0.7571 (tp30) REVERT: B 584 ILE cc_start: 0.9441 (tp) cc_final: 0.9226 (tp) REVERT: B 590 SER cc_start: 0.9214 (p) cc_final: 0.8509 (t) REVERT: B 615 MET cc_start: 0.9478 (mmm) cc_final: 0.9212 (mmm) REVERT: B 640 MET cc_start: 0.9161 (tpp) cc_final: 0.8706 (tpp) REVERT: B 667 LEU cc_start: 0.9519 (tp) cc_final: 0.9194 (tp) REVERT: B 671 ASP cc_start: 0.8578 (m-30) cc_final: 0.8361 (m-30) REVERT: C 27 LYS cc_start: 0.8980 (mtmm) cc_final: 0.8568 (tptp) REVERT: C 53 ASP cc_start: 0.8345 (t0) cc_final: 0.7954 (t0) REVERT: C 93 MET cc_start: 0.9519 (mtm) cc_final: 0.9316 (mtm) REVERT: C 154 PHE cc_start: 0.8457 (t80) cc_final: 0.7986 (t80) REVERT: C 157 MET cc_start: 0.9126 (ptp) cc_final: 0.8919 (ptt) REVERT: C 243 THR cc_start: 0.7283 (p) cc_final: 0.6539 (p) REVERT: C 247 TYR cc_start: 0.8122 (m-80) cc_final: 0.7825 (m-80) REVERT: D 24 GLN cc_start: 0.8038 (mp10) cc_final: 0.7578 (tp-100) REVERT: D 46 TYR cc_start: 0.8606 (m-80) cc_final: 0.8241 (m-80) REVERT: D 56 MET cc_start: 0.5804 (mpp) cc_final: 0.5362 (mpp) REVERT: D 95 MET cc_start: 0.9330 (tmm) cc_final: 0.9089 (tmm) REVERT: D 96 MET cc_start: 0.8655 (tpt) cc_final: 0.7988 (mmm) REVERT: D 149 ASP cc_start: 0.8554 (m-30) cc_final: 0.8265 (m-30) REVERT: D 154 PHE cc_start: 0.8562 (t80) cc_final: 0.7733 (t80) REVERT: D 179 TYR cc_start: 0.8400 (t80) cc_final: 0.8112 (t80) REVERT: D 185 MET cc_start: 0.7876 (mmm) cc_final: 0.6172 (pmm) REVERT: D 211 GLU cc_start: 0.9452 (tp30) cc_final: 0.9197 (pt0) REVERT: D 233 ASN cc_start: 0.8666 (m110) cc_final: 0.8424 (m110) REVERT: D 259 PHE cc_start: 0.7549 (t80) cc_final: 0.7154 (t80) REVERT: D 282 ILE cc_start: 0.3719 (tt) cc_final: 0.3506 (tt) outliers start: 1 outliers final: 0 residues processed: 608 average time/residue: 0.1173 time to fit residues: 108.5119 Evaluate side-chains 474 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 474 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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: 0.9980 chunk 46 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 126 optimal weight: 8.9990 chunk 129 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 157 optimal weight: 20.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 365 ASN A 645 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 232 ASN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.130869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.095429 restraints weight = 37438.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.098884 restraints weight = 19047.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.101160 restraints weight = 11473.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.102605 restraints weight = 7896.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.103612 restraints weight = 5985.685| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.6127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16386 Z= 0.142 Angle : 0.599 9.191 22134 Z= 0.319 Chirality : 0.042 0.155 2360 Planarity : 0.003 0.043 2818 Dihedral : 8.747 133.990 2290 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.12 % Allowed : 1.92 % Favored : 97.96 % 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: 0.93 (0.19), residues: 1932 helix: 1.08 (0.15), residues: 1133 sheet: 0.26 (0.49), residues: 104 loop : 0.08 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 164 TYR 0.032 0.002 TYR C 174 PHE 0.028 0.002 PHE A 129 TRP 0.040 0.001 TRP D 124 HIS 0.008 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (16386) covalent geometry : angle 0.59914 / 0.32 (22134) hydrogen bonds : bond 0.03935 / 2.48 ( 871) hydrogen bonds : angle 4.91769 / 3.55 ( 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 634 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 632 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.9637 (mm) cc_final: 0.9240 (mm) REVERT: A 40 TYR cc_start: 0.8851 (t80) cc_final: 0.8610 (t80) REVERT: A 117 ARG cc_start: 0.8249 (mtp85) cc_final: 0.7927 (mtp85) REVERT: A 131 ASN cc_start: 0.9255 (t0) cc_final: 0.8861 (t0) REVERT: A 147 GLN cc_start: 0.8745 (mt0) cc_final: 0.8235 (mt0) REVERT: A 150 GLN cc_start: 0.8750 (tp40) cc_final: 0.8024 (tm-30) REVERT: A 164 ARG cc_start: 0.8122 (ptt90) cc_final: 0.7757 (ptt180) REVERT: A 204 SER cc_start: 0.9188 (t) cc_final: 0.8863 (t) REVERT: A 263 ASP cc_start: 0.8348 (m-30) cc_final: 0.8050 (m-30) REVERT: A 266 LYS cc_start: 0.8786 (mmmm) cc_final: 0.8545 (mmmm) REVERT: A 286 ASP cc_start: 0.8774 (m-30) cc_final: 0.8158 (m-30) REVERT: A 290 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8078 (tm-30) REVERT: A 315 ASP cc_start: 0.8960 (p0) cc_final: 0.8745 (p0) REVERT: A 348 MET cc_start: 0.8111 (tpt) cc_final: 0.7705 (tpt) REVERT: A 352 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7338 (mt-10) REVERT: A 362 ASP cc_start: 0.7232 (m-30) cc_final: 0.6601 (m-30) REVERT: A 493 MET cc_start: 0.8985 (tmm) cc_final: 0.8728 (tmm) REVERT: A 501 GLN cc_start: 0.9310 (tt0) cc_final: 0.9101 (tt0) REVERT: A 570 MET cc_start: 0.9040 (mtp) cc_final: 0.8612 (mtp) REVERT: A 588 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8262 (mm-40) REVERT: A 599 GLU cc_start: 0.8326 (mp0) cc_final: 0.8027 (mp0) REVERT: A 634 MET cc_start: 0.8826 (mmm) cc_final: 0.8599 (mmt) REVERT: A 640 MET cc_start: 0.9129 (ttm) cc_final: 0.8686 (ttm) REVERT: B 8 LYS cc_start: 0.9003 (tptp) cc_final: 0.8724 (tppt) REVERT: B 12 LEU cc_start: 0.9474 (mt) cc_final: 0.9205 (mt) REVERT: B 71 LEU cc_start: 0.9492 (mm) cc_final: 0.9289 (mm) REVERT: B 119 GLU cc_start: 0.8877 (mp0) cc_final: 0.8505 (mp0) REVERT: B 147 GLN cc_start: 0.8874 (mt0) cc_final: 0.8177 (mt0) REVERT: B 157 LEU cc_start: 0.9070 (tp) cc_final: 0.8707 (tp) REVERT: B 158 ASN cc_start: 0.8997 (m110) cc_final: 0.8690 (m-40) REVERT: B 211 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7426 (mm-30) REVERT: B 217 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7878 (tm-30) REVERT: B 238 ASP cc_start: 0.6991 (p0) cc_final: 0.6227 (p0) REVERT: B 253 ILE cc_start: 0.9543 (tt) cc_final: 0.9298 (tt) REVERT: B 259 ASN cc_start: 0.9142 (m-40) cc_final: 0.8741 (m-40) REVERT: B 263 ASP cc_start: 0.8973 (m-30) cc_final: 0.8669 (m-30) REVERT: B 288 PHE cc_start: 0.9340 (t80) cc_final: 0.8999 (t80) REVERT: B 290 GLU cc_start: 0.8475 (tm-30) cc_final: 0.7985 (tm-30) REVERT: B 291 LEU cc_start: 0.9410 (mt) cc_final: 0.8889 (mt) REVERT: B 322 MET cc_start: 0.8816 (tpp) cc_final: 0.8357 (mmm) REVERT: B 348 MET cc_start: 0.7917 (tpt) cc_final: 0.7192 (tpp) REVERT: B 373 ILE cc_start: 0.9678 (mt) cc_final: 0.8822 (mt) REVERT: B 394 TYR cc_start: 0.9069 (m-80) cc_final: 0.8363 (m-80) REVERT: B 425 ILE cc_start: 0.9605 (mt) cc_final: 0.9387 (mt) REVERT: B 467 ASN cc_start: 0.9256 (t0) cc_final: 0.8397 (t0) REVERT: B 493 MET cc_start: 0.9452 (tmm) cc_final: 0.9095 (tmm) REVERT: B 526 GLU cc_start: 0.7905 (tp30) cc_final: 0.7419 (tp30) REVERT: B 588 GLN cc_start: 0.9179 (mm-40) cc_final: 0.8548 (mm-40) REVERT: B 590 SER cc_start: 0.9105 (p) cc_final: 0.8287 (t) REVERT: B 615 MET cc_start: 0.9458 (mmm) cc_final: 0.9151 (mmm) REVERT: B 635 PHE cc_start: 0.8921 (m-80) cc_final: 0.8575 (m-80) REVERT: B 667 LEU cc_start: 0.9462 (tp) cc_final: 0.9171 (tp) REVERT: C 21 PHE cc_start: 0.9261 (m-80) cc_final: 0.8928 (m-10) REVERT: C 27 LYS cc_start: 0.9021 (mtmm) cc_final: 0.8624 (tptp) REVERT: C 154 PHE cc_start: 0.8436 (t80) cc_final: 0.7926 (t80) REVERT: C 176 LEU cc_start: 0.9203 (mt) cc_final: 0.8621 (mt) REVERT: C 197 ASP cc_start: 0.8921 (m-30) cc_final: 0.8077 (t0) REVERT: C 247 TYR cc_start: 0.8045 (m-80) cc_final: 0.7828 (m-80) REVERT: D 24 GLN cc_start: 0.8060 (mp10) cc_final: 0.7703 (tp-100) REVERT: D 42 LEU cc_start: 0.5987 (pp) cc_final: 0.5633 (pp) REVERT: D 46 TYR cc_start: 0.8598 (m-80) cc_final: 0.8215 (m-80) REVERT: D 95 MET cc_start: 0.9219 (tmm) cc_final: 0.8889 (tmm) REVERT: D 96 MET cc_start: 0.8471 (mmm) cc_final: 0.7594 (mmm) REVERT: D 149 ASP cc_start: 0.8538 (m-30) cc_final: 0.8259 (m-30) REVERT: D 154 PHE cc_start: 0.8329 (t80) cc_final: 0.8079 (t80) REVERT: D 185 MET cc_start: 0.7935 (mmm) cc_final: 0.6681 (pmm) REVERT: D 189 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7344 (pt0) REVERT: D 192 ASN cc_start: 0.8450 (t0) cc_final: 0.7929 (m-40) REVERT: D 205 VAL cc_start: 0.9545 (t) cc_final: 0.9203 (t) REVERT: D 233 ASN cc_start: 0.8682 (m110) cc_final: 0.8395 (m110) REVERT: D 241 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7260 (tm-30) REVERT: D 259 PHE cc_start: 0.7550 (t80) cc_final: 0.7138 (t80) outliers start: 2 outliers final: 1 residues processed: 632 average time/residue: 0.1092 time to fit residues: 104.7612 Evaluate side-chains 519 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 518 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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: 4.9990 chunk 183 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 172 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN B 218 ASN B 232 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 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 = 0.3681 r_free = 0.3681 target = 0.128912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.093632 restraints weight = 38521.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.096886 restraints weight = 19413.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.099148 restraints weight = 11688.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.100661 restraints weight = 8011.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.101600 restraints weight = 6007.142| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.6438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16386 Z= 0.252 Angle : 0.683 12.067 22134 Z= 0.362 Chirality : 0.045 0.236 2360 Planarity : 0.004 0.043 2818 Dihedral : 8.821 137.641 2290 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.17 % Allowed : 2.16 % Favored : 97.67 % 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: 0.88 (0.15), residues: 1133 sheet: -0.77 (0.42), residues: 142 loop : 0.20 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 686 TYR 0.032 0.002 TYR C 179 PHE 0.039 0.002 PHE A 129 TRP 0.047 0.002 TRP D 124 HIS 0.008 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.25 (16386) covalent geometry : angle 0.68300 / 0.36 (22134) hydrogen bonds : bond 0.04167 / 2.61 ( 871) hydrogen bonds : angle 5.13214 / 3.70 ( 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 589 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 586 time to evaluate : 0.446 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: A 40 TYR cc_start: 0.8883 (t80) cc_final: 0.8507 (t80) REVERT: A 117 ARG cc_start: 0.8260 (mtp85) cc_final: 0.7896 (mtp85) REVERT: A 131 ASN cc_start: 0.9240 (t0) cc_final: 0.8914 (t0) REVERT: A 147 GLN cc_start: 0.8893 (mt0) cc_final: 0.8548 (mt0) REVERT: A 150 GLN cc_start: 0.8848 (tp40) cc_final: 0.7976 (tm-30) REVERT: A 163 ARG cc_start: 0.8363 (mmm160) cc_final: 0.7950 (mtp180) REVERT: A 164 ARG cc_start: 0.8189 (ptt90) cc_final: 0.7901 (ptt-90) REVERT: A 204 SER cc_start: 0.9293 (t) cc_final: 0.8975 (t) REVERT: A 263 ASP cc_start: 0.8285 (m-30) cc_final: 0.7979 (m-30) REVERT: A 286 ASP cc_start: 0.8796 (m-30) cc_final: 0.8199 (m-30) REVERT: A 290 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8158 (tm-30) REVERT: A 348 MET cc_start: 0.8102 (tpt) cc_final: 0.7664 (tpt) REVERT: A 352 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7707 (mt-10) REVERT: A 362 ASP cc_start: 0.7295 (m-30) cc_final: 0.6597 (m-30) REVERT: A 437 THR cc_start: 0.9373 (m) cc_final: 0.9068 (p) REVERT: A 447 ASN cc_start: 0.8800 (m-40) cc_final: 0.8595 (m-40) REVERT: A 493 MET cc_start: 0.8975 (tmm) cc_final: 0.8641 (tmm) REVERT: A 501 GLN cc_start: 0.9289 (tt0) cc_final: 0.9065 (tt0) REVERT: A 570 MET cc_start: 0.8780 (mtp) cc_final: 0.8555 (mtp) REVERT: A 599 GLU cc_start: 0.8335 (mp0) cc_final: 0.7968 (mp0) REVERT: A 634 MET cc_start: 0.8795 (mmm) cc_final: 0.8568 (mmt) REVERT: A 640 MET cc_start: 0.9191 (ttm) cc_final: 0.8809 (ttm) REVERT: B 119 GLU cc_start: 0.8956 (mp0) cc_final: 0.8524 (mp0) REVERT: B 147 GLN cc_start: 0.9012 (mt0) cc_final: 0.8255 (mt0) REVERT: B 157 LEU cc_start: 0.9157 (tp) cc_final: 0.8753 (tp) REVERT: B 158 ASN cc_start: 0.9038 (m110) cc_final: 0.8714 (m-40) REVERT: B 211 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7466 (mm-30) REVERT: B 217 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7950 (tm-30) REVERT: B 218 ASN cc_start: 0.9220 (OUTLIER) cc_final: 0.8999 (t0) REVERT: B 232 ASN cc_start: 0.7967 (t160) cc_final: 0.7705 (t0) REVERT: B 253 ILE cc_start: 0.9590 (tt) cc_final: 0.9370 (tt) REVERT: B 259 ASN cc_start: 0.9133 (m-40) cc_final: 0.8636 (m-40) REVERT: B 263 ASP cc_start: 0.8986 (m-30) cc_final: 0.8659 (m-30) REVERT: B 288 PHE cc_start: 0.9464 (t80) cc_final: 0.9193 (t80) REVERT: B 290 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8237 (tm-30) REVERT: B 322 MET cc_start: 0.8863 (tpp) cc_final: 0.8293 (mpp) REVERT: B 348 MET cc_start: 0.7947 (tpt) cc_final: 0.7188 (tpp) REVERT: B 373 ILE cc_start: 0.9629 (mt) cc_final: 0.9226 (mt) REVERT: B 393 SER cc_start: 0.9339 (m) cc_final: 0.8792 (p) REVERT: B 394 TYR cc_start: 0.9096 (m-80) cc_final: 0.8292 (m-80) REVERT: B 425 ILE cc_start: 0.9632 (mt) cc_final: 0.9429 (mt) REVERT: B 441 GLU cc_start: 0.8703 (mp0) cc_final: 0.8490 (mp0) REVERT: B 493 MET cc_start: 0.9457 (tmm) cc_final: 0.9071 (tmm) REVERT: B 526 GLU cc_start: 0.8039 (tp30) cc_final: 0.7568 (tp30) REVERT: B 588 GLN cc_start: 0.9198 (mm-40) cc_final: 0.8558 (mm-40) REVERT: B 595 MET cc_start: 0.8903 (mmm) cc_final: 0.8265 (mmm) REVERT: B 615 MET cc_start: 0.9436 (mmm) cc_final: 0.9135 (mmm) REVERT: B 634 MET cc_start: 0.9055 (mmm) cc_final: 0.8850 (mmt) REVERT: B 635 PHE cc_start: 0.8981 (m-80) cc_final: 0.8714 (m-80) REVERT: B 667 LEU cc_start: 0.9442 (tp) cc_final: 0.9080 (tt) REVERT: C 21 PHE cc_start: 0.9212 (m-80) cc_final: 0.8920 (m-80) REVERT: C 27 LYS cc_start: 0.9021 (mtmm) cc_final: 0.8714 (tptp) REVERT: C 197 ASP cc_start: 0.8695 (m-30) cc_final: 0.8453 (t0) REVERT: C 243 THR cc_start: 0.7229 (p) cc_final: 0.6724 (t) REVERT: D 42 LEU cc_start: 0.6032 (pp) cc_final: 0.5668 (pp) REVERT: D 46 TYR cc_start: 0.8781 (m-80) cc_final: 0.8405 (m-80) REVERT: D 56 MET cc_start: 0.5903 (mpp) cc_final: 0.5665 (mpp) REVERT: D 95 MET cc_start: 0.9244 (tmm) cc_final: 0.8809 (tmm) REVERT: D 96 MET cc_start: 0.8642 (mmm) cc_final: 0.7564 (mmm) REVERT: D 138 ILE cc_start: 0.8998 (mm) cc_final: 0.8776 (mm) REVERT: D 142 TYR cc_start: 0.8567 (m-80) cc_final: 0.8365 (m-80) REVERT: D 149 ASP cc_start: 0.8540 (m-30) cc_final: 0.8240 (m-30) REVERT: D 185 MET cc_start: 0.8133 (mmm) cc_final: 0.6597 (pmm) REVERT: D 224 LEU cc_start: 0.8909 (mt) cc_final: 0.8645 (mt) REVERT: D 233 ASN cc_start: 0.8696 (m110) cc_final: 0.8456 (m110) REVERT: D 241 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7441 (tm-30) REVERT: D 259 PHE cc_start: 0.7606 (t80) cc_final: 0.7200 (t80) outliers start: 3 outliers final: 1 residues processed: 586 average time/residue: 0.1106 time to fit residues: 98.6160 Evaluate side-chains 494 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 492 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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: 3.9990 chunk 51 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 186 optimal weight: 10.0000 chunk 140 optimal weight: 40.0000 chunk 115 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 156 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN D 23 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** 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 = 0.3704 r_free = 0.3704 target = 0.129414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.094711 restraints weight = 37764.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.098017 restraints weight = 19053.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.100228 restraints weight = 11461.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.101717 restraints weight = 7829.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.102577 restraints weight = 5879.250| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 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 = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.6606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16386 Z= 0.189 Angle : 0.632 12.775 22134 Z= 0.337 Chirality : 0.043 0.153 2360 Planarity : 0.004 0.043 2818 Dihedral : 8.618 136.968 2290 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 1932 helix: 0.90 (0.15), residues: 1128 sheet: -0.75 (0.42), residues: 142 loop : 0.15 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 686 TYR 0.033 0.002 TYR A 101 PHE 0.029 0.002 PHE A 129 TRP 0.051 0.002 TRP D 124 HIS 0.007 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (16386) covalent geometry : angle 0.63169 / 0.34 (22134) hydrogen bonds : bond 0.04009 / 2.50 ( 871) hydrogen bonds : angle 5.07207 / 3.66 ( 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 600 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 600 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.9083 (mp0) cc_final: 0.8677 (mp0) REVERT: A 40 TYR cc_start: 0.8938 (t80) cc_final: 0.8494 (t80) REVERT: A 117 ARG cc_start: 0.8174 (mtp85) cc_final: 0.7862 (mtp85) REVERT: A 131 ASN cc_start: 0.9201 (t0) cc_final: 0.8881 (t0) REVERT: A 147 GLN cc_start: 0.8833 (mt0) cc_final: 0.8465 (mt0) REVERT: A 150 GLN cc_start: 0.8832 (tp40) cc_final: 0.8018 (tm-30) REVERT: A 163 ARG cc_start: 0.8351 (mmm160) cc_final: 0.7967 (mtp180) REVERT: A 204 SER cc_start: 0.9350 (t) cc_final: 0.8899 (t) REVERT: A 263 ASP cc_start: 0.8308 (m-30) cc_final: 0.8047 (m-30) REVERT: A 278 LEU cc_start: 0.9168 (tp) cc_final: 0.8880 (tp) REVERT: A 286 ASP cc_start: 0.8654 (m-30) cc_final: 0.8240 (m-30) REVERT: A 290 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8057 (tm-30) REVERT: A 348 MET cc_start: 0.8128 (tpt) cc_final: 0.7749 (tpt) REVERT: A 352 GLU cc_start: 0.8414 (mt-10) cc_final: 0.7793 (mt-10) REVERT: A 360 PHE cc_start: 0.8700 (m-80) cc_final: 0.8220 (m-80) REVERT: A 362 ASP cc_start: 0.7215 (m-30) cc_final: 0.6554 (m-30) REVERT: A 493 MET cc_start: 0.8992 (tmm) cc_final: 0.8652 (tmm) REVERT: A 494 MET cc_start: 0.8737 (mtm) cc_final: 0.7869 (ptp) REVERT: A 501 GLN cc_start: 0.9320 (tt0) cc_final: 0.9105 (tt0) REVERT: A 634 MET cc_start: 0.8813 (mmm) cc_final: 0.8573 (mmt) REVERT: A 640 MET cc_start: 0.9152 (ttm) cc_final: 0.8732 (ttm) REVERT: B 71 LEU cc_start: 0.9525 (mm) cc_final: 0.9160 (mp) REVERT: B 119 GLU cc_start: 0.8913 (mp0) cc_final: 0.8522 (mp0) REVERT: B 147 GLN cc_start: 0.9095 (mt0) cc_final: 0.8341 (mt0) REVERT: B 157 LEU cc_start: 0.9107 (tp) cc_final: 0.8731 (tp) REVERT: B 158 ASN cc_start: 0.9025 (m110) cc_final: 0.8657 (m-40) REVERT: B 211 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7372 (mm-30) REVERT: B 217 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7882 (tm-30) REVERT: B 232 ASN cc_start: 0.7899 (t160) cc_final: 0.7629 (t0) REVERT: B 253 ILE cc_start: 0.9586 (tt) cc_final: 0.9308 (tt) REVERT: B 259 ASN cc_start: 0.9111 (m-40) cc_final: 0.8651 (m-40) REVERT: B 263 ASP cc_start: 0.8962 (m-30) cc_final: 0.8602 (m-30) REVERT: B 288 PHE cc_start: 0.9409 (t80) cc_final: 0.9096 (t80) REVERT: B 290 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8197 (tm-30) REVERT: B 348 MET cc_start: 0.8002 (tpt) cc_final: 0.7246 (tpp) REVERT: B 373 ILE cc_start: 0.9616 (mt) cc_final: 0.9400 (mt) REVERT: B 393 SER cc_start: 0.9410 (m) cc_final: 0.8959 (m) REVERT: B 394 TYR cc_start: 0.9142 (m-80) cc_final: 0.8473 (m-80) REVERT: B 425 ILE cc_start: 0.9577 (mt) cc_final: 0.9272 (mt) REVERT: B 493 MET cc_start: 0.9433 (tmm) cc_final: 0.9027 (tmm) REVERT: B 506 ILE cc_start: 0.9555 (mt) cc_final: 0.9186 (mt) REVERT: B 526 GLU cc_start: 0.8044 (tp30) cc_final: 0.7559 (tp30) REVERT: B 588 GLN cc_start: 0.9218 (mm-40) cc_final: 0.8572 (mm-40) REVERT: B 615 MET cc_start: 0.9462 (mmm) cc_final: 0.9116 (mmm) REVERT: B 667 LEU cc_start: 0.9462 (tp) cc_final: 0.9103 (tp) REVERT: B 671 ASP cc_start: 0.8621 (m-30) cc_final: 0.8403 (m-30) REVERT: C 21 PHE cc_start: 0.9211 (m-80) cc_final: 0.8901 (m-10) REVERT: C 27 LYS cc_start: 0.9016 (mtmm) cc_final: 0.8655 (tptp) REVERT: C 55 TYR cc_start: 0.7801 (t80) cc_final: 0.6651 (t80) REVERT: C 154 PHE cc_start: 0.8443 (t80) cc_final: 0.8046 (t80) REVERT: C 196 ARG cc_start: 0.8349 (ttp80) cc_final: 0.8122 (ttp80) REVERT: C 197 ASP cc_start: 0.8961 (m-30) cc_final: 0.8414 (t0) REVERT: C 200 ILE cc_start: 0.8457 (tp) cc_final: 0.8173 (tp) REVERT: D 50 ASN cc_start: 0.7863 (p0) cc_final: 0.7303 (t0) REVERT: D 95 MET cc_start: 0.9195 (tmm) cc_final: 0.8726 (tmm) REVERT: D 96 MET cc_start: 0.8609 (mmm) cc_final: 0.7405 (mmm) REVERT: D 149 ASP cc_start: 0.8576 (m-30) cc_final: 0.8326 (m-30) REVERT: D 179 TYR cc_start: 0.8190 (t80) cc_final: 0.7851 (t80) REVERT: D 185 MET cc_start: 0.8193 (mmm) cc_final: 0.7776 (mmm) REVERT: D 192 ASN cc_start: 0.8774 (t0) cc_final: 0.8263 (m-40) REVERT: D 195 LEU cc_start: 0.8919 (tt) cc_final: 0.8162 (tt) REVERT: D 205 VAL cc_start: 0.9442 (t) cc_final: 0.9211 (t) REVERT: D 214 ASN cc_start: 0.9303 (m-40) cc_final: 0.9097 (m-40) REVERT: D 224 LEU cc_start: 0.8888 (mt) cc_final: 0.8623 (mt) REVERT: D 233 ASN cc_start: 0.8680 (m110) cc_final: 0.8414 (m110) REVERT: D 259 PHE cc_start: 0.7614 (t80) cc_final: 0.7161 (t80) outliers start: 0 outliers final: 0 residues processed: 600 average time/residue: 0.1234 time to fit residues: 111.5979 Evaluate side-chains 489 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 489 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: 4.9990 chunk 99 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 158 optimal weight: 20.0000 chunk 97 optimal weight: 0.7980 chunk 151 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** 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 = 0.3733 r_free = 0.3733 target = 0.131220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.096555 restraints weight = 37873.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.099815 restraints weight = 18987.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.102112 restraints weight = 11751.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.103681 restraints weight = 7942.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.104639 restraints weight = 5890.077| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.6819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16386 Z= 0.151 Angle : 0.631 11.153 22134 Z= 0.336 Chirality : 0.043 0.219 2360 Planarity : 0.004 0.041 2818 Dihedral : 8.488 137.453 2290 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: 0.61 (0.19), residues: 1932 helix: 0.88 (0.15), residues: 1130 sheet: -0.83 (0.41), residues: 138 loop : 0.07 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 686 TYR 0.029 0.002 TYR C 179 PHE 0.036 0.002 PHE A 129 TRP 0.051 0.002 TRP D 124 HIS 0.007 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (16386) covalent geometry : angle 0.63078 / 0.34 (22134) hydrogen bonds : bond 0.03952 / 2.48 ( 871) hydrogen bonds : angle 5.08493 / 3.66 ( 2571) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 613 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.9020 (mp0) cc_final: 0.8612 (mp0) REVERT: A 40 TYR cc_start: 0.8828 (t80) cc_final: 0.8367 (t80) REVERT: A 117 ARG cc_start: 0.7989 (mtp85) cc_final: 0.7709 (mtp85) REVERT: A 131 ASN cc_start: 0.9181 (t0) cc_final: 0.8832 (p0) REVERT: A 147 GLN cc_start: 0.8752 (mt0) cc_final: 0.8444 (mt0) REVERT: A 150 GLN cc_start: 0.8763 (tp40) cc_final: 0.8083 (tm-30) REVERT: A 204 SER cc_start: 0.9481 (t) cc_final: 0.8990 (t) REVERT: A 263 ASP cc_start: 0.8356 (m-30) cc_final: 0.8132 (m-30) REVERT: A 278 LEU cc_start: 0.9179 (tp) cc_final: 0.8857 (tp) REVERT: A 286 ASP cc_start: 0.8764 (m-30) cc_final: 0.8347 (m-30) REVERT: A 290 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8043 (tm-30) REVERT: A 348 MET cc_start: 0.8180 (tpt) cc_final: 0.7748 (tpt) REVERT: A 352 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7939 (mt-10) REVERT: A 360 PHE cc_start: 0.8681 (m-80) cc_final: 0.8215 (m-80) REVERT: A 362 ASP cc_start: 0.7040 (m-30) cc_final: 0.6469 (m-30) REVERT: A 396 ASP cc_start: 0.8112 (p0) cc_final: 0.5938 (p0) REVERT: A 493 MET cc_start: 0.8956 (tmm) cc_final: 0.8600 (tmm) REVERT: A 501 GLN cc_start: 0.9319 (tt0) cc_final: 0.9105 (tt0) REVERT: A 529 ASP cc_start: 0.8384 (m-30) cc_final: 0.8155 (m-30) REVERT: A 640 MET cc_start: 0.9044 (ttm) cc_final: 0.8669 (ttm) REVERT: B 12 LEU cc_start: 0.9533 (mt) cc_final: 0.9325 (mt) REVERT: B 20 LYS cc_start: 0.9274 (pptt) cc_final: 0.9015 (ptmm) REVERT: B 71 LEU cc_start: 0.9555 (mm) cc_final: 0.9301 (mp) REVERT: B 119 GLU cc_start: 0.8853 (mp0) cc_final: 0.8468 (mp0) REVERT: B 140 TYR cc_start: 0.9184 (m-10) cc_final: 0.8911 (m-10) REVERT: B 147 GLN cc_start: 0.9004 (mt0) cc_final: 0.8000 (mt0) REVERT: B 157 LEU cc_start: 0.9110 (tp) cc_final: 0.8727 (tp) REVERT: B 217 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7755 (tm-30) REVERT: B 253 ILE cc_start: 0.9589 (tt) cc_final: 0.9306 (tt) REVERT: B 259 ASN cc_start: 0.9074 (m-40) cc_final: 0.8549 (m-40) REVERT: B 263 ASP cc_start: 0.8978 (m-30) cc_final: 0.8520 (m-30) REVERT: B 288 PHE cc_start: 0.9407 (t80) cc_final: 0.9060 (t80) REVERT: B 290 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8113 (tm-30) REVERT: B 348 MET cc_start: 0.7992 (tpt) cc_final: 0.7271 (tpp) REVERT: B 357 TYR cc_start: 0.8874 (m-10) cc_final: 0.8617 (m-10) REVERT: B 381 LEU cc_start: 0.8732 (tp) cc_final: 0.8440 (tp) REVERT: B 393 SER cc_start: 0.9414 (m) cc_final: 0.9048 (m) REVERT: B 394 TYR cc_start: 0.9112 (m-80) cc_final: 0.8284 (m-80) REVERT: B 425 ILE cc_start: 0.9536 (mt) cc_final: 0.9275 (mt) REVERT: B 467 ASN cc_start: 0.8883 (t0) cc_final: 0.8511 (t0) REVERT: B 493 MET cc_start: 0.9431 (tmm) cc_final: 0.9013 (tmm) REVERT: B 506 ILE cc_start: 0.9350 (mt) cc_final: 0.9074 (mt) REVERT: B 526 GLU cc_start: 0.7880 (tp30) cc_final: 0.7317 (tp30) REVERT: B 588 GLN cc_start: 0.9202 (mm-40) cc_final: 0.8386 (mm-40) REVERT: B 590 SER cc_start: 0.8980 (p) cc_final: 0.8765 (p) REVERT: B 595 MET cc_start: 0.8749 (mmm) cc_final: 0.8171 (mmm) REVERT: B 667 LEU cc_start: 0.9458 (tp) cc_final: 0.9104 (tp) REVERT: C 21 PHE cc_start: 0.9182 (m-80) cc_final: 0.8898 (m-10) REVERT: C 27 LYS cc_start: 0.9015 (mtmm) cc_final: 0.8631 (tptp) REVERT: C 197 ASP cc_start: 0.8986 (m-30) cc_final: 0.8525 (t0) REVERT: C 200 ILE cc_start: 0.8457 (tp) cc_final: 0.8078 (tp) REVERT: D 50 ASN cc_start: 0.8081 (p0) cc_final: 0.7593 (t0) REVERT: D 56 MET cc_start: 0.5800 (mpp) cc_final: 0.5596 (mpp) REVERT: D 87 LYS cc_start: 0.7663 (mmtt) cc_final: 0.7387 (mmtt) REVERT: D 95 MET cc_start: 0.9166 (tmm) cc_final: 0.8719 (tmm) REVERT: D 96 MET cc_start: 0.8463 (mmm) cc_final: 0.7207 (mmm) REVERT: D 149 ASP cc_start: 0.8495 (m-30) cc_final: 0.8267 (m-30) REVERT: D 179 TYR cc_start: 0.8141 (t80) cc_final: 0.7806 (t80) REVERT: D 185 MET cc_start: 0.8198 (mmm) cc_final: 0.7788 (mmm) REVERT: D 192 ASN cc_start: 0.8739 (t0) cc_final: 0.8247 (m-40) REVERT: D 205 VAL cc_start: 0.9467 (t) cc_final: 0.9257 (t) REVERT: D 214 ASN cc_start: 0.9237 (m-40) cc_final: 0.9024 (m-40) REVERT: D 233 ASN cc_start: 0.8545 (m110) cc_final: 0.8243 (m110) REVERT: D 259 PHE cc_start: 0.7684 (t80) cc_final: 0.7249 (t80) outliers start: 0 outliers final: 0 residues processed: 613 average time/residue: 0.1233 time to fit residues: 114.8138 Evaluate side-chains 508 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 508 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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: 0.9980 chunk 133 optimal weight: 8.9990 chunk 149 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 180 ASN B 218 ASN B 232 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN C 28 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.133431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.098697 restraints weight = 38185.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.102088 restraints weight = 19156.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.104324 restraints weight = 11552.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.105816 restraints weight = 7945.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.106766 restraints weight = 5987.404| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.6949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16386 Z= 0.168 Angle : 0.667 13.321 22134 Z= 0.351 Chirality : 0.043 0.254 2360 Planarity : 0.004 0.048 2818 Dihedral : 8.512 138.447 2290 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.06 % Allowed : 0.58 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.19), residues: 1932 helix: 0.81 (0.15), residues: 1132 sheet: -0.79 (0.42), residues: 142 loop : 0.04 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 686 TYR 0.041 0.002 TYR C 179 PHE 0.039 0.002 PHE A 129 TRP 0.054 0.002 TRP D 124 HIS 0.005 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (16386) covalent geometry : angle 0.66669 / 0.35 (22134) hydrogen bonds : bond 0.03981 / 2.52 ( 871) hydrogen bonds : angle 5.10599 / 3.68 ( 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 605 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 604 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.9033 (mp0) cc_final: 0.8596 (mp0) REVERT: A 40 TYR cc_start: 0.8868 (t80) cc_final: 0.8453 (t80) REVERT: A 131 ASN cc_start: 0.9149 (t0) cc_final: 0.8851 (p0) REVERT: A 147 GLN cc_start: 0.8775 (mt0) cc_final: 0.7867 (mt0) REVERT: A 150 GLN cc_start: 0.8807 (tp40) cc_final: 0.8119 (tm-30) REVERT: A 204 SER cc_start: 0.9481 (t) cc_final: 0.8912 (t) REVERT: A 214 LYS cc_start: 0.8591 (mmpt) cc_final: 0.8389 (mmtt) REVERT: A 263 ASP cc_start: 0.8360 (m-30) cc_final: 0.7920 (m-30) REVERT: A 266 LYS cc_start: 0.8793 (mmmm) cc_final: 0.8586 (mmtm) REVERT: A 278 LEU cc_start: 0.9168 (tp) cc_final: 0.8880 (tp) REVERT: A 286 ASP cc_start: 0.8774 (m-30) cc_final: 0.8347 (m-30) REVERT: A 290 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8082 (tm-30) REVERT: A 348 MET cc_start: 0.8111 (tpt) cc_final: 0.7906 (tpt) REVERT: A 360 PHE cc_start: 0.8679 (m-80) cc_final: 0.8237 (m-80) REVERT: A 362 ASP cc_start: 0.7047 (m-30) cc_final: 0.6432 (m-30) REVERT: A 398 ASP cc_start: 0.8035 (p0) cc_final: 0.7631 (p0) REVERT: A 493 MET cc_start: 0.9013 (tmm) cc_final: 0.8657 (tmm) REVERT: A 494 MET cc_start: 0.8597 (mtm) cc_final: 0.7864 (ptp) REVERT: A 501 GLN cc_start: 0.9305 (tt0) cc_final: 0.9093 (tt0) REVERT: A 588 GLN cc_start: 0.8723 (mm-40) cc_final: 0.7995 (mm-40) REVERT: A 640 MET cc_start: 0.9126 (ttm) cc_final: 0.8758 (ttm) REVERT: B 8 LYS cc_start: 0.9021 (tptp) cc_final: 0.8667 (tppt) REVERT: B 12 LEU cc_start: 0.9515 (mt) cc_final: 0.9315 (mt) REVERT: B 119 GLU cc_start: 0.8842 (mp0) cc_final: 0.8507 (mp0) REVERT: B 140 TYR cc_start: 0.9242 (m-10) cc_final: 0.8941 (m-10) REVERT: B 147 GLN cc_start: 0.8951 (mt0) cc_final: 0.7948 (mt0) REVERT: B 157 LEU cc_start: 0.9138 (tp) cc_final: 0.8855 (tp) REVERT: B 217 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7680 (tm-30) REVERT: B 218 ASN cc_start: 0.9124 (OUTLIER) cc_final: 0.8874 (t0) REVERT: B 253 ILE cc_start: 0.9593 (tt) cc_final: 0.9302 (tt) REVERT: B 259 ASN cc_start: 0.9131 (m-40) cc_final: 0.8768 (m-40) REVERT: B 263 ASP cc_start: 0.8809 (m-30) cc_final: 0.8573 (m-30) REVERT: B 288 PHE cc_start: 0.9410 (t80) cc_final: 0.9132 (t80) REVERT: B 290 GLU cc_start: 0.8402 (tm-30) cc_final: 0.7928 (tm-30) REVERT: B 291 LEU cc_start: 0.9397 (mt) cc_final: 0.8886 (mt) REVERT: B 348 MET cc_start: 0.7857 (tpt) cc_final: 0.7316 (tpp) REVERT: B 393 SER cc_start: 0.9431 (m) cc_final: 0.9030 (m) REVERT: B 394 TYR cc_start: 0.9091 (m-80) cc_final: 0.8397 (m-80) REVERT: B 425 ILE cc_start: 0.9622 (mt) cc_final: 0.9399 (mt) REVERT: B 437 THR cc_start: 0.9358 (m) cc_final: 0.9035 (m) REVERT: B 441 GLU cc_start: 0.8640 (mp0) cc_final: 0.8439 (mp0) REVERT: B 493 MET cc_start: 0.9422 (tmm) cc_final: 0.9026 (tmm) REVERT: B 526 GLU cc_start: 0.7903 (tp30) cc_final: 0.7350 (tp30) REVERT: B 588 GLN cc_start: 0.9210 (mm-40) cc_final: 0.8382 (mm-40) REVERT: B 595 MET cc_start: 0.8811 (mmm) cc_final: 0.8149 (mmm) REVERT: B 667 LEU cc_start: 0.9476 (tp) cc_final: 0.9104 (tp) REVERT: C 21 PHE cc_start: 0.9219 (m-80) cc_final: 0.8876 (m-80) REVERT: C 27 LYS cc_start: 0.9004 (mtmm) cc_final: 0.8631 (tptp) REVERT: C 154 PHE cc_start: 0.8441 (t80) cc_final: 0.8047 (t80) REVERT: C 200 ILE cc_start: 0.8606 (tp) cc_final: 0.8291 (tp) REVERT: D 50 ASN cc_start: 0.8068 (p0) cc_final: 0.7577 (t0) REVERT: D 56 MET cc_start: 0.5915 (mpp) cc_final: 0.5618 (mpp) REVERT: D 95 MET cc_start: 0.9137 (tmm) cc_final: 0.8834 (tmm) REVERT: D 96 MET cc_start: 0.8311 (mmm) cc_final: 0.7174 (mpp) REVERT: D 149 ASP cc_start: 0.8471 (m-30) cc_final: 0.8257 (m-30) REVERT: D 192 ASN cc_start: 0.8749 (t0) cc_final: 0.8280 (m-40) REVERT: D 205 VAL cc_start: 0.9443 (t) cc_final: 0.9133 (t) REVERT: D 214 ASN cc_start: 0.9228 (m-40) cc_final: 0.9017 (m-40) REVERT: D 224 LEU cc_start: 0.8978 (mt) cc_final: 0.8766 (mt) REVERT: D 233 ASN cc_start: 0.8626 (m110) cc_final: 0.8316 (m110) REVERT: D 259 PHE cc_start: 0.7706 (t80) cc_final: 0.7226 (t80) outliers start: 1 outliers final: 0 residues processed: 604 average time/residue: 0.1231 time to fit residues: 112.8756 Evaluate side-chains 503 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 502 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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: 5.9990 chunk 62 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 189 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN C 69 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 GLN D 23 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.132453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.097957 restraints weight = 38304.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.101321 restraints weight = 19229.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.103539 restraints weight = 11619.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.105107 restraints weight = 7935.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.105996 restraints weight = 5948.233| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.7096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16386 Z= 0.197 Angle : 0.692 16.888 22134 Z= 0.364 Chirality : 0.044 0.261 2360 Planarity : 0.004 0.053 2818 Dihedral : 8.582 139.232 2290 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.06 % Allowed : 0.47 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.19), residues: 1932 helix: 0.75 (0.15), residues: 1133 sheet: -0.97 (0.40), residues: 142 loop : 0.02 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 686 TYR 0.036 0.002 TYR D 142 PHE 0.030 0.002 PHE D 109 TRP 0.059 0.002 TRP D 124 HIS 0.009 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (16386) covalent geometry : angle 0.69202 / 0.36 (22134) hydrogen bonds : bond 0.03994 / 2.52 ( 871) hydrogen bonds : angle 5.16369 / 3.72 ( 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 581 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 580 time to evaluate : 0.531 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 15 GLU cc_start: 0.9022 (mp0) cc_final: 0.8677 (mp0) REVERT: A 40 TYR cc_start: 0.8905 (t80) cc_final: 0.8409 (t80) REVERT: A 131 ASN cc_start: 0.9204 (t0) cc_final: 0.8945 (p0) REVERT: A 147 GLN cc_start: 0.8794 (mt0) cc_final: 0.8035 (mt0) REVERT: A 150 GLN cc_start: 0.8982 (tp40) cc_final: 0.8201 (tm-30) REVERT: A 204 SER cc_start: 0.9377 (t) cc_final: 0.8889 (t) REVERT: A 214 LYS cc_start: 0.8539 (mmpt) cc_final: 0.8329 (mmtt) REVERT: A 263 ASP cc_start: 0.8373 (m-30) cc_final: 0.7935 (m-30) REVERT: A 278 LEU cc_start: 0.9184 (tp) cc_final: 0.8887 (tp) REVERT: A 286 ASP cc_start: 0.8761 (m-30) cc_final: 0.8328 (m-30) REVERT: A 290 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8100 (tm-30) REVERT: A 360 PHE cc_start: 0.8710 (m-80) cc_final: 0.8253 (m-80) REVERT: A 362 ASP cc_start: 0.7125 (m-30) cc_final: 0.6501 (m-30) REVERT: A 396 ASP cc_start: 0.7792 (p0) cc_final: 0.6528 (p0) REVERT: A 493 MET cc_start: 0.8989 (tmm) cc_final: 0.8625 (tmm) REVERT: A 494 MET cc_start: 0.8609 (mtm) cc_final: 0.7865 (ptp) REVERT: A 501 GLN cc_start: 0.9316 (tt0) cc_final: 0.9104 (tt0) REVERT: A 584 ILE cc_start: 0.9147 (pt) cc_final: 0.8749 (pt) REVERT: A 588 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8106 (mm-40) REVERT: A 597 ILE cc_start: 0.9127 (pt) cc_final: 0.8907 (pt) REVERT: A 640 MET cc_start: 0.9095 (ttm) cc_final: 0.8727 (ttm) REVERT: B 119 GLU cc_start: 0.8917 (mp0) cc_final: 0.8535 (mp0) REVERT: B 140 TYR cc_start: 0.9244 (m-10) cc_final: 0.8980 (m-10) REVERT: B 147 GLN cc_start: 0.9012 (mt0) cc_final: 0.8128 (mt0) REVERT: B 157 LEU cc_start: 0.9178 (tp) cc_final: 0.8924 (tp) REVERT: B 211 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7024 (mt-10) REVERT: B 217 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7642 (tm-30) REVERT: B 218 ASN cc_start: 0.9178 (t0) cc_final: 0.8929 (t0) REVERT: B 253 ILE cc_start: 0.9611 (tt) cc_final: 0.9309 (tt) REVERT: B 259 ASN cc_start: 0.9119 (m-40) cc_final: 0.8650 (m-40) REVERT: B 263 ASP cc_start: 0.8821 (m-30) cc_final: 0.8468 (m-30) REVERT: B 288 PHE cc_start: 0.9438 (t80) cc_final: 0.9154 (t80) REVERT: B 290 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8149 (tm-30) REVERT: B 348 MET cc_start: 0.7692 (tpt) cc_final: 0.7197 (tpp) REVERT: B 373 ILE cc_start: 0.9591 (mt) cc_final: 0.9227 (mt) REVERT: B 393 SER cc_start: 0.9380 (m) cc_final: 0.8917 (m) REVERT: B 394 TYR cc_start: 0.9079 (m-80) cc_final: 0.8470 (m-80) REVERT: B 425 ILE cc_start: 0.9634 (mt) cc_final: 0.9311 (mt) REVERT: B 437 THR cc_start: 0.9343 (m) cc_final: 0.8983 (m) REVERT: B 441 GLU cc_start: 0.8647 (mp0) cc_final: 0.8400 (mp0) REVERT: B 463 LEU cc_start: 0.9610 (tp) cc_final: 0.9406 (tp) REVERT: B 467 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8604 (t0) REVERT: B 493 MET cc_start: 0.9434 (tmm) cc_final: 0.9233 (tmm) REVERT: B 526 GLU cc_start: 0.7918 (tp30) cc_final: 0.7365 (tp30) REVERT: B 588 GLN cc_start: 0.9218 (mm-40) cc_final: 0.8591 (mm-40) REVERT: B 595 MET cc_start: 0.8820 (mmm) cc_final: 0.8060 (mmm) REVERT: B 601 ILE cc_start: 0.9026 (mm) cc_final: 0.8798 (mm) REVERT: B 615 MET cc_start: 0.9496 (mmp) cc_final: 0.9169 (mmm) REVERT: B 667 LEU cc_start: 0.9472 (tp) cc_final: 0.9089 (tp) REVERT: C 21 PHE cc_start: 0.9339 (m-80) cc_final: 0.8878 (m-80) REVERT: C 24 GLN cc_start: 0.8935 (pt0) cc_final: 0.8586 (pt0) REVERT: C 27 LYS cc_start: 0.9024 (mtmm) cc_final: 0.8683 (tptp) REVERT: C 137 MET cc_start: 0.5353 (mpp) cc_final: 0.4825 (mpp) REVERT: C 185 MET cc_start: 0.3385 (mpp) cc_final: 0.3106 (mpp) REVERT: C 200 ILE cc_start: 0.8767 (tp) cc_final: 0.8327 (tp) REVERT: D 50 ASN cc_start: 0.8084 (p0) cc_final: 0.7512 (t0) REVERT: D 56 MET cc_start: 0.5949 (mpp) cc_final: 0.5640 (mpp) REVERT: D 74 MET cc_start: 0.6095 (tmm) cc_final: 0.5281 (tmm) REVERT: D 95 MET cc_start: 0.9079 (tmm) cc_final: 0.8614 (tmm) REVERT: D 96 MET cc_start: 0.8457 (mmm) cc_final: 0.7131 (mmm) REVERT: D 149 ASP cc_start: 0.8472 (m-30) cc_final: 0.8260 (m-30) REVERT: D 185 MET cc_start: 0.7863 (mmp) cc_final: 0.6683 (pmm) REVERT: D 192 ASN cc_start: 0.8811 (t0) cc_final: 0.8338 (m-40) REVERT: D 233 ASN cc_start: 0.8647 (m110) cc_final: 0.8373 (m110) REVERT: D 259 PHE cc_start: 0.7711 (t80) cc_final: 0.7235 (t80) outliers start: 1 outliers final: 0 residues processed: 580 average time/residue: 0.1223 time to fit residues: 108.0238 Evaluate side-chains 499 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 498 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 125 optimal weight: 0.1980 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 ASN A 474 GLN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN D 214 ASN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.137279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.102527 restraints weight = 37345.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105832 restraints weight = 18730.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.108242 restraints weight = 11663.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.109850 restraints weight = 7847.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.110794 restraints weight = 5824.034| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.7295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16386 Z= 0.134 Angle : 0.666 15.522 22134 Z= 0.346 Chirality : 0.044 0.322 2360 Planarity : 0.004 0.058 2818 Dihedral : 8.405 137.344 2290 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.06 % Allowed : 0.52 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.19), residues: 1932 helix: 0.77 (0.15), residues: 1129 sheet: -0.54 (0.44), residues: 122 loop : -0.17 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 235 TYR 0.030 0.001 TYR D 142 PHE 0.028 0.002 PHE D 109 TRP 0.059 0.002 TRP D 124 HIS 0.006 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (16386) covalent geometry : angle 0.66596 / 0.35 (22134) hydrogen bonds : bond 0.03950 / 2.48 ( 871) hydrogen bonds : angle 5.08985 / 3.66 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3103.26 seconds wall clock time: 54 minutes 41.30 seconds (3281.30 seconds total)