Starting phenix.real_space_refine on Thu Aug 6 15:13:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz3_45052/08_2026/9bz3_45052_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz3_45052/08_2026/9bz3_45052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bz3_45052/08_2026/9bz3_45052_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz3_45052/08_2026/9bz3_45052_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bz3_45052/08_2026/9bz3_45052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz3_45052/08_2026/9bz3_45052.map" } resolution = 4.01 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: 3.62, per 1000 atoms: 0.23 Number of scatterers: 16038 At special positions: 0 Unit cell: (96.615, 129.159, 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: 1.38 Conformation dependent library (CDL) restraints added in 687.3 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: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.986A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.568A 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: 3.694A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.851A 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: 3.628A 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: 4.118A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.074A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.579A 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: 3.676A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.645A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.729A 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: 4.936A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.669A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.876A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.359A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.479A 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: 6.453A 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: 6.192A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.478A pdb=" N LEU A 656 " --> pdb=" O ARG A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.185A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.660A 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: 7.229A 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: 7.905A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.806A 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: 2.84 Time building geometry restraints manager: 1.86 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: 4851 1.34 - 1.46: 3061 1.46 - 1.58: 8293 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 4.81e+01 bond pdb=" O3B TTP A 803 " pdb=" PG TTP A 803 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.061 1.25e-02 6.40e+03 2.39e+01 bond pdb=" O3A TTP A 803 " pdb=" PB TTP A 803 " ideal model delta sigma weight residual 1.675 1.605 0.070 2.00e-02 2.50e+03 1.22e+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 1.15e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21531 2.09 - 4.18: 522 4.18 - 6.27: 63 6.27 - 8.36: 9 8.36 - 10.45: 9 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.63 -6.09 1.36e+00 5.41e-01 2.00e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.17 -4.46 1.15e+00 7.56e-01 1.50e+01 angle pdb=" N SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.25 -3.97 1.09e+00 8.42e-01 1.33e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.85 -4.35 1.23e+00 6.61e-01 1.25e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.71 -4.00 1.15e+00 7.56e-01 1.21e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.06: 9088 25.06 - 50.12: 656 50.12 - 75.17: 126 75.17 - 100.23: 26 100.23 - 125.29: 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 -98.27 125.29 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 -95.61 122.63 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 -134.27 12.27 0 2.50e+00 1.60e-01 2.41e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2144 0.094 - 0.187: 183 0.187 - 0.281: 29 0.281 - 0.375: 2 0.375 - 0.469: 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 5.49e+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 4.56e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.35 2.00e-01 2.50e+01 2.98e+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 4.13e-02 2.73e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " 0.017 2.00e-02 2.50e+03 1.12e-02 2.18e+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 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 179 " -0.017 2.00e-02 2.50e+03 9.83e-03 1.93e+00 pdb=" CG TYR D 179 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR D 179 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR D 179 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR D 179 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 179 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR D 179 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 179 " -0.005 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 129 2.51 - 3.11: 11559 3.11 - 3.70: 27043 3.70 - 4.30: 41517 4.30 - 4.90: 65377 Nonbonded interactions: 145625 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.012 3.040 ... (remaining 145620 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.940 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.139 16386 Z= 0.334 Angle : 0.788 10.455 22134 Z= 0.472 Chirality : 0.058 0.469 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.680 125.289 6202 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.34 % Allowed : 15.27 % Favored : 83.39 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.18), residues: 1932 helix: 0.58 (0.14), residues: 1151 sheet: 0.46 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 196 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.33 (16386) covalent geometry : angle 0.78792 / 0.47 (22134) hydrogen bonds : bond 0.15421 / 9.51 ( 871) hydrogen bonds : angle 6.51731 / 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 822 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 799 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8448 (t0) cc_final: 0.8229 (t70) REVERT: A 68 PHE cc_start: 0.8635 (p90) cc_final: 0.8319 (p90) REVERT: A 106 LEU cc_start: 0.9003 (tp) cc_final: 0.8700 (tp) REVERT: A 120 ASP cc_start: 0.7014 (m-30) cc_final: 0.6684 (m-30) REVERT: A 122 ILE cc_start: 0.9216 (mt) cc_final: 0.8933 (mt) REVERT: A 134 THR cc_start: 0.7929 (t) cc_final: 0.7579 (t) REVERT: A 186 ILE cc_start: 0.9310 (mt) cc_final: 0.9047 (mt) REVERT: A 200 SER cc_start: 0.9120 (t) cc_final: 0.8887 (p) REVERT: A 202 ASN cc_start: 0.9124 (t0) cc_final: 0.8612 (t0) REVERT: A 204 SER cc_start: 0.8970 (m) cc_final: 0.8634 (p) REVERT: A 227 MET cc_start: 0.8293 (mtp) cc_final: 0.7903 (mtp) REVERT: A 322 MET cc_start: 0.8217 (mmp) cc_final: 0.7951 (mmp) REVERT: A 362 ASP cc_start: 0.6331 (m-30) cc_final: 0.6105 (m-30) REVERT: A 367 VAL cc_start: 0.9095 (m) cc_final: 0.8712 (p) REVERT: A 417 LEU cc_start: 0.8510 (tt) cc_final: 0.7871 (tt) REVERT: A 425 ILE cc_start: 0.8978 (mt) cc_final: 0.8494 (mt) REVERT: A 436 LEU cc_start: 0.9194 (mt) cc_final: 0.8976 (mm) REVERT: A 447 ASN cc_start: 0.7972 (m-40) cc_final: 0.7770 (m-40) REVERT: A 458 MET cc_start: 0.8831 (mmm) cc_final: 0.8310 (mtm) REVERT: A 576 LEU cc_start: 0.8899 (mt) cc_final: 0.8672 (mt) REVERT: A 606 TYR cc_start: 0.6769 (m-80) cc_final: 0.6552 (m-80) REVERT: A 618 LEU cc_start: 0.9218 (tp) cc_final: 0.8984 (tp) REVERT: A 630 TYR cc_start: 0.7538 (m-80) cc_final: 0.6524 (m-80) REVERT: A 634 MET cc_start: 0.8587 (mmp) cc_final: 0.8325 (mmm) REVERT: A 640 MET cc_start: 0.7738 (tpp) cc_final: 0.7285 (tpp) REVERT: A 670 ILE cc_start: 0.9244 (mt) cc_final: 0.9024 (mt) REVERT: B 51 LEU cc_start: 0.8434 (tp) cc_final: 0.8202 (tp) REVERT: B 116 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7303 (mt-10) REVERT: B 156 PHE cc_start: 0.8455 (t80) cc_final: 0.8208 (t80) REVERT: B 167 LEU cc_start: 0.8207 (mt) cc_final: 0.7970 (mt) REVERT: B 190 MET cc_start: 0.8381 (mtm) cc_final: 0.8127 (mtm) REVERT: B 322 MET cc_start: 0.8152 (mmm) cc_final: 0.7789 (tpp) REVERT: B 362 ASP cc_start: 0.6823 (m-30) cc_final: 0.6117 (m-30) REVERT: B 373 ILE cc_start: 0.8899 (mt) cc_final: 0.8612 (mt) REVERT: B 466 MET cc_start: 0.8431 (ptp) cc_final: 0.8107 (ptm) REVERT: B 467 ASN cc_start: 0.8888 (t0) cc_final: 0.8478 (t0) REVERT: B 471 TYR cc_start: 0.8362 (t80) cc_final: 0.8153 (t80) REVERT: B 500 ILE cc_start: 0.9270 (mt) cc_final: 0.9049 (mt) REVERT: B 522 TYR cc_start: 0.8492 (m-80) cc_final: 0.8094 (m-10) REVERT: B 550 MET cc_start: 0.8179 (mtm) cc_final: 0.7348 (mtp) REVERT: B 570 MET cc_start: 0.7240 (mtm) cc_final: 0.6754 (mtm) REVERT: B 576 LEU cc_start: 0.9117 (mt) cc_final: 0.8820 (mt) REVERT: B 590 SER cc_start: 0.8861 (p) cc_final: 0.8207 (t) REVERT: B 591 THR cc_start: 0.9291 (p) cc_final: 0.8600 (m) REVERT: B 597 ILE cc_start: 0.9135 (pt) cc_final: 0.8769 (pt) REVERT: C 31 LEU cc_start: 0.5709 (mt) cc_final: 0.5442 (mt) REVERT: C 155 LYS cc_start: 0.7170 (mttt) cc_final: 0.6918 (mttm) REVERT: D 130 TYR cc_start: 0.1601 (m-80) cc_final: 0.0661 (m-10) REVERT: D 136 GLN cc_start: 0.1071 (mm-40) cc_final: 0.0602 (tm-30) REVERT: D 137 MET cc_start: -0.0170 (mtp) cc_final: -0.0759 (mtp) REVERT: D 256 VAL cc_start: 0.5301 (t) cc_final: 0.4484 (t) outliers start: 23 outliers final: 6 residues processed: 810 average time/residue: 0.1263 time to fit residues: 150.4348 Evaluate side-chains 549 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 543 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN A 242 GLN A 320 ASN A 370 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 410 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN B 668 ASN C 85 GLN D 71 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.162830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.109659 restraints weight = 33630.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.113340 restraints weight = 16342.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115655 restraints weight = 9804.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.117193 restraints weight = 6770.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.118252 restraints weight = 5141.387| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16386 Z= 0.219 Angle : 0.609 6.961 22134 Z= 0.329 Chirality : 0.043 0.235 2360 Planarity : 0.004 0.036 2818 Dihedral : 9.363 131.950 2290 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.12 % Allowed : 3.50 % Favored : 96.39 % 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: 1.41 (0.19), residues: 1932 helix: 1.42 (0.15), residues: 1128 sheet: -0.08 (0.41), residues: 146 loop : 0.54 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 453 TYR 0.021 0.002 TYR A 522 PHE 0.031 0.002 PHE C 227 TRP 0.016 0.002 TRP A 623 HIS 0.009 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.22 (16386) covalent geometry : angle 0.60851 / 0.33 (22134) hydrogen bonds : bond 0.04609 / 2.88 ( 871) hydrogen bonds : angle 5.04003 / 3.57 ( 2571) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 622 time to evaluate : 0.416 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: A 122 ILE cc_start: 0.9330 (mt) cc_final: 0.9063 (mt) REVERT: A 150 GLN cc_start: 0.9072 (tm-30) cc_final: 0.8792 (tm-30) REVERT: A 188 ILE cc_start: 0.9603 (mt) cc_final: 0.9362 (mm) REVERT: A 202 ASN cc_start: 0.9278 (t0) cc_final: 0.9041 (t0) REVERT: A 204 SER cc_start: 0.9160 (m) cc_final: 0.8611 (t) REVERT: A 214 LYS cc_start: 0.7879 (tppt) cc_final: 0.7671 (tppt) REVERT: A 232 ASN cc_start: 0.8490 (m-40) cc_final: 0.8242 (m110) REVERT: A 286 ASP cc_start: 0.8037 (m-30) cc_final: 0.7658 (m-30) REVERT: A 308 LYS cc_start: 0.9595 (mtmt) cc_final: 0.9360 (mtmm) REVERT: A 362 ASP cc_start: 0.7285 (m-30) cc_final: 0.7055 (m-30) REVERT: A 367 VAL cc_start: 0.9707 (m) cc_final: 0.9491 (p) REVERT: A 447 ASN cc_start: 0.8400 (m-40) cc_final: 0.7276 (m-40) REVERT: A 458 MET cc_start: 0.9329 (mmm) cc_final: 0.8499 (mmm) REVERT: A 485 ARG cc_start: 0.8341 (mtm-85) cc_final: 0.7413 (mtm-85) REVERT: A 494 MET cc_start: 0.8720 (mtp) cc_final: 0.8374 (mtp) REVERT: A 576 LEU cc_start: 0.9015 (mt) cc_final: 0.8778 (mt) REVERT: A 583 SER cc_start: 0.9134 (m) cc_final: 0.8720 (t) REVERT: A 586 TYR cc_start: 0.8476 (m-80) cc_final: 0.8168 (m-10) REVERT: A 590 SER cc_start: 0.9256 (t) cc_final: 0.8905 (m) REVERT: A 602 GLU cc_start: 0.7211 (pt0) cc_final: 0.6504 (pt0) REVERT: A 606 TYR cc_start: 0.7973 (m-80) cc_final: 0.7695 (m-10) REVERT: A 630 TYR cc_start: 0.8619 (m-80) cc_final: 0.8410 (m-80) REVERT: A 640 MET cc_start: 0.9061 (tpp) cc_final: 0.8652 (tpp) REVERT: A 662 MET cc_start: 0.8394 (pmm) cc_final: 0.8160 (pmm) REVERT: A 667 LEU cc_start: 0.9064 (tt) cc_final: 0.8364 (tt) REVERT: A 668 ASN cc_start: 0.8938 (m110) cc_final: 0.8535 (m110) REVERT: B 51 LEU cc_start: 0.9054 (tp) cc_final: 0.8823 (tp) REVERT: B 108 THR cc_start: 0.8982 (OUTLIER) cc_final: 0.8698 (p) REVERT: B 147 GLN cc_start: 0.8793 (mt0) cc_final: 0.8511 (mt0) REVERT: B 156 PHE cc_start: 0.9196 (t80) cc_final: 0.8950 (t80) REVERT: B 190 MET cc_start: 0.9291 (mtm) cc_final: 0.9007 (mtm) REVERT: B 253 ILE cc_start: 0.9455 (tt) cc_final: 0.9227 (tt) REVERT: B 257 ASP cc_start: 0.8950 (m-30) cc_final: 0.8692 (m-30) REVERT: B 288 PHE cc_start: 0.9429 (t80) cc_final: 0.9183 (t80) REVERT: B 318 ASP cc_start: 0.8822 (t0) cc_final: 0.8566 (p0) REVERT: B 333 LYS cc_start: 0.8797 (tptp) cc_final: 0.8552 (tppt) REVERT: B 358 ILE cc_start: 0.9450 (mm) cc_final: 0.9230 (mm) REVERT: B 362 ASP cc_start: 0.8184 (m-30) cc_final: 0.7499 (m-30) REVERT: B 393 SER cc_start: 0.9535 (m) cc_final: 0.9249 (p) REVERT: B 471 TYR cc_start: 0.9027 (t80) cc_final: 0.8628 (t80) REVERT: B 493 MET cc_start: 0.9351 (tmm) cc_final: 0.9049 (tmm) REVERT: B 512 GLU cc_start: 0.8619 (pt0) cc_final: 0.8334 (pt0) REVERT: B 550 MET cc_start: 0.8391 (mtm) cc_final: 0.8136 (mtp) REVERT: B 561 LEU cc_start: 0.9403 (tp) cc_final: 0.9151 (tp) REVERT: B 615 MET cc_start: 0.9125 (mmp) cc_final: 0.8879 (mmm) REVERT: B 627 LYS cc_start: 0.9166 (tttt) cc_final: 0.8776 (tttp) REVERT: B 662 MET cc_start: 0.8251 (ptp) cc_final: 0.7941 (ptp) REVERT: C 74 MET cc_start: 0.7241 (mtt) cc_final: 0.6486 (mtt) REVERT: C 154 PHE cc_start: 0.8598 (t80) cc_final: 0.8212 (t80) REVERT: C 239 GLU cc_start: 0.9061 (tp30) cc_final: 0.8590 (tp30) REVERT: D 95 MET cc_start: 0.7153 (ttp) cc_final: 0.6841 (ttp) REVERT: D 242 TYR cc_start: 0.7858 (t80) cc_final: 0.7453 (t80) REVERT: D 245 ASP cc_start: 0.5028 (t0) cc_final: 0.4736 (m-30) outliers start: 2 outliers final: 0 residues processed: 623 average time/residue: 0.1199 time to fit residues: 112.1844 Evaluate side-chains 477 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 476 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 182 optimal weight: 9.9990 chunk 159 optimal weight: 20.0000 chunk 91 optimal weight: 0.2980 chunk 150 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 158 optimal weight: 10.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 HIS B 158 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 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 = 0.4000 r_free = 0.4000 target = 0.162641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.111526 restraints weight = 33456.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.115310 restraints weight = 16132.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.117491 restraints weight = 9645.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.119079 restraints weight = 6584.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.120135 restraints weight = 4952.680| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16386 Z= 0.148 Angle : 0.559 8.665 22134 Z= 0.297 Chirality : 0.041 0.191 2360 Planarity : 0.003 0.028 2818 Dihedral : 8.956 130.870 2290 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.06 % Allowed : 2.62 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.49 (0.19), residues: 1932 helix: 1.54 (0.15), residues: 1126 sheet: -0.23 (0.40), residues: 146 loop : 0.51 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 669 TYR 0.016 0.002 TYR D 46 PHE 0.035 0.002 PHE C 109 TRP 0.008 0.001 TRP A 623 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (16386) covalent geometry : angle 0.55864 / 0.30 (22134) hydrogen bonds : bond 0.04087 / 2.57 ( 871) hydrogen bonds : angle 4.80603 / 3.40 ( 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 597 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 596 time to evaluate : 0.489 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: A 120 ASP cc_start: 0.8285 (m-30) cc_final: 0.8056 (m-30) REVERT: A 128 PHE cc_start: 0.8858 (t80) cc_final: 0.8632 (t80) REVERT: A 158 ASN cc_start: 0.9058 (m110) cc_final: 0.8780 (m-40) REVERT: A 202 ASN cc_start: 0.9198 (t0) cc_final: 0.8745 (t0) REVERT: A 204 SER cc_start: 0.9209 (m) cc_final: 0.8958 (p) REVERT: A 214 LYS cc_start: 0.8077 (tppt) cc_final: 0.7855 (tppt) REVERT: A 286 ASP cc_start: 0.8159 (m-30) cc_final: 0.7534 (m-30) REVERT: A 308 LYS cc_start: 0.9559 (mtmt) cc_final: 0.9339 (mtmm) REVERT: A 362 ASP cc_start: 0.7268 (m-30) cc_final: 0.7016 (m-30) REVERT: A 417 LEU cc_start: 0.9359 (tt) cc_final: 0.8472 (tt) REVERT: A 447 ASN cc_start: 0.8201 (m-40) cc_final: 0.7268 (m-40) REVERT: A 458 MET cc_start: 0.9256 (mmm) cc_final: 0.8202 (mtm) REVERT: A 583 SER cc_start: 0.9091 (m) cc_final: 0.8849 (t) REVERT: A 586 TYR cc_start: 0.8420 (m-80) cc_final: 0.8144 (m-10) REVERT: A 590 SER cc_start: 0.8917 (t) cc_final: 0.8682 (t) REVERT: A 602 GLU cc_start: 0.6976 (pt0) cc_final: 0.6167 (pt0) REVERT: A 604 ARG cc_start: 0.8441 (tpp-160) cc_final: 0.8180 (tpp-160) REVERT: A 667 LEU cc_start: 0.9135 (tt) cc_final: 0.8545 (tt) REVERT: B 51 LEU cc_start: 0.9026 (tp) cc_final: 0.8776 (tp) REVERT: B 69 LEU cc_start: 0.9434 (mt) cc_final: 0.9218 (mt) REVERT: B 147 GLN cc_start: 0.8707 (mt0) cc_final: 0.8404 (mt0) REVERT: B 190 MET cc_start: 0.9256 (mtm) cc_final: 0.8990 (mtm) REVERT: B 266 LYS cc_start: 0.8695 (mtmm) cc_final: 0.8453 (mttm) REVERT: B 276 LYS cc_start: 0.8854 (ptmt) cc_final: 0.8469 (ptpp) REVERT: B 288 PHE cc_start: 0.9446 (t80) cc_final: 0.9175 (t80) REVERT: B 291 LEU cc_start: 0.9546 (mt) cc_final: 0.9315 (mt) REVERT: B 362 ASP cc_start: 0.8207 (m-30) cc_final: 0.7416 (m-30) REVERT: B 393 SER cc_start: 0.9486 (m) cc_final: 0.9236 (p) REVERT: B 396 ASP cc_start: 0.8139 (m-30) cc_final: 0.7906 (m-30) REVERT: B 471 TYR cc_start: 0.9046 (t80) cc_final: 0.8739 (t80) REVERT: B 493 MET cc_start: 0.9330 (tmm) cc_final: 0.9039 (tmm) REVERT: B 550 MET cc_start: 0.8392 (mtm) cc_final: 0.8072 (mtp) REVERT: B 561 LEU cc_start: 0.9444 (tp) cc_final: 0.9159 (tp) REVERT: B 615 MET cc_start: 0.9166 (mmp) cc_final: 0.8960 (mmm) REVERT: B 627 LYS cc_start: 0.9098 (tttt) cc_final: 0.8834 (tttp) REVERT: B 640 MET cc_start: 0.8950 (tpp) cc_final: 0.8306 (tpp) REVERT: B 686 ARG cc_start: 0.7458 (mmt180) cc_final: 0.7240 (mmt180) REVERT: C 74 MET cc_start: 0.7112 (mtt) cc_final: 0.6476 (mtt) REVERT: C 154 PHE cc_start: 0.8570 (t80) cc_final: 0.8216 (t80) REVERT: C 239 GLU cc_start: 0.8983 (tp30) cc_final: 0.8571 (tp30) REVERT: D 21 PHE cc_start: 0.8454 (m-10) cc_final: 0.8153 (m-10) REVERT: D 117 THR cc_start: 0.8533 (p) cc_final: 0.8286 (p) REVERT: D 173 TYR cc_start: 0.7216 (t80) cc_final: 0.6734 (t80) outliers start: 1 outliers final: 0 residues processed: 596 average time/residue: 0.1209 time to fit residues: 108.6792 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 : 0.756 ------------------------------------------------------------------------------- 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: 4.9990 chunk 157 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 185 optimal weight: 6.9990 chunk 191 optimal weight: 20.0000 chunk 159 optimal weight: 6.9990 chunk 182 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN A 370 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN B 11 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.152188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.102530 restraints weight = 34439.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.105797 restraints weight = 17091.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107850 restraints weight = 10303.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.109213 restraints weight = 7085.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110080 restraints weight = 5391.663| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (15 function evaluations) r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.5339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.091 16386 Z= 0.423 Angle : 0.776 7.985 22134 Z= 0.409 Chirality : 0.048 0.319 2360 Planarity : 0.004 0.046 2818 Dihedral : 9.313 133.199 2290 Min Nonbonded Distance : 1.648 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.12 % Allowed : 3.26 % Favored : 96.62 % 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: 0.86 (0.19), residues: 1932 helix: 0.96 (0.15), residues: 1131 sheet: -0.57 (0.41), residues: 140 loop : 0.39 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 453 TYR 0.022 0.002 TYR B 612 PHE 0.028 0.003 PHE C 109 TRP 0.026 0.003 TRP A 623 HIS 0.007 0.002 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00914 / 0.42 (16386) covalent geometry : angle 0.77566 / 0.41 (22134) hydrogen bonds : bond 0.04616 / 2.91 ( 871) hydrogen bonds : angle 5.14740 / 3.63 ( 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 507 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 505 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.8337 (mp0) cc_final: 0.7968 (mp0) REVERT: A 174 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7649 (mt-10) REVERT: A 204 SER cc_start: 0.9173 (m) cc_final: 0.8812 (t) REVERT: A 286 ASP cc_start: 0.7965 (m-30) cc_final: 0.7538 (m-30) REVERT: A 308 LYS cc_start: 0.9585 (mtmt) cc_final: 0.9363 (mtmm) REVERT: A 319 MET cc_start: 0.9211 (tpp) cc_final: 0.8817 (tpp) REVERT: A 344 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8308 (mt-10) REVERT: A 362 ASP cc_start: 0.7496 (m-30) cc_final: 0.7219 (m-30) REVERT: A 406 ASP cc_start: 0.8602 (m-30) cc_final: 0.8264 (m-30) REVERT: A 447 ASN cc_start: 0.8078 (m-40) cc_final: 0.7548 (m-40) REVERT: A 458 MET cc_start: 0.9256 (mmm) cc_final: 0.8473 (mtm) REVERT: A 494 MET cc_start: 0.8776 (mtp) cc_final: 0.8400 (mtp) REVERT: A 583 SER cc_start: 0.9183 (m) cc_final: 0.8742 (t) REVERT: A 584 ILE cc_start: 0.9058 (pt) cc_final: 0.8851 (pt) REVERT: A 604 ARG cc_start: 0.8465 (tpp-160) cc_final: 0.8059 (tpp80) REVERT: A 645 GLN cc_start: 0.9025 (tp40) cc_final: 0.8750 (tp-100) REVERT: A 667 LEU cc_start: 0.9379 (tt) cc_final: 0.8838 (tt) REVERT: B 51 LEU cc_start: 0.9233 (tp) cc_final: 0.8871 (tp) REVERT: B 102 ASN cc_start: 0.9283 (m110) cc_final: 0.8984 (m110) REVERT: B 114 ILE cc_start: 0.9619 (mt) cc_final: 0.9384 (mp) REVERT: B 120 ASP cc_start: 0.8864 (m-30) cc_final: 0.8580 (m-30) REVERT: B 147 GLN cc_start: 0.9246 (mt0) cc_final: 0.9037 (mt0) REVERT: B 150 GLN cc_start: 0.9152 (tp40) cc_final: 0.8783 (tp40) REVERT: B 214 LYS cc_start: 0.8083 (mmtm) cc_final: 0.7752 (mmtt) REVERT: B 235 ARG cc_start: 0.8649 (ttm-80) cc_final: 0.8287 (ttm110) REVERT: B 276 LYS cc_start: 0.8816 (ptmt) cc_final: 0.8434 (ptpp) REVERT: B 333 LYS cc_start: 0.9010 (tttm) cc_final: 0.8420 (tttp) REVERT: B 358 ILE cc_start: 0.9429 (mm) cc_final: 0.9184 (mm) REVERT: B 410 ASN cc_start: 0.9067 (m-40) cc_final: 0.8853 (m-40) REVERT: B 601 ILE cc_start: 0.9401 (mm) cc_final: 0.9157 (mm) REVERT: B 604 ARG cc_start: 0.8790 (tpp80) cc_final: 0.8041 (tpp80) REVERT: B 612 TYR cc_start: 0.8046 (m-10) cc_final: 0.6967 (m-10) REVERT: B 627 LYS cc_start: 0.9096 (tttt) cc_final: 0.8665 (tttp) REVERT: B 640 MET cc_start: 0.8937 (tpp) cc_final: 0.8418 (tpp) REVERT: C 74 MET cc_start: 0.7578 (mtt) cc_final: 0.6925 (mtt) REVERT: C 89 VAL cc_start: 0.6891 (t) cc_final: 0.6381 (t) REVERT: D 95 MET cc_start: 0.7634 (ttp) cc_final: 0.7348 (ttt) REVERT: D 173 TYR cc_start: 0.7059 (t80) cc_final: 0.6702 (t80) outliers start: 2 outliers final: 0 residues processed: 505 average time/residue: 0.1288 time to fit residues: 98.4343 Evaluate side-chains 404 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 404 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 32 optimal weight: 0.0570 chunk 122 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 168 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 overall best weight: 1.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN B 588 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN D 69 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.163284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.113727 restraints weight = 33525.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.117270 restraints weight = 16008.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.119475 restraints weight = 9479.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.120895 restraints weight = 6438.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.121828 restraints weight = 4819.323| |-----------------------------------------------------------------------------| 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) = 0.112 | | 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) = 0.112 | | 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: 0.7578 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16386 Z= 0.137 Angle : 0.561 7.224 22134 Z= 0.300 Chirality : 0.041 0.187 2360 Planarity : 0.003 0.039 2818 Dihedral : 8.593 129.361 2290 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % 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: 1.18 (0.19), residues: 1932 helix: 1.35 (0.15), residues: 1131 sheet: 0.05 (0.44), residues: 110 loop : 0.10 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 686 TYR 0.020 0.001 TYR A 522 PHE 0.039 0.002 PHE C 109 TRP 0.034 0.002 TRP D 124 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (16386) covalent geometry : angle 0.56107 / 0.30 (22134) hydrogen bonds : bond 0.03797 / 2.41 ( 871) hydrogen bonds : angle 4.78993 / 3.40 ( 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 562 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 562 time to evaluate : 0.621 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: A 64 TYR cc_start: 0.8670 (m-10) cc_final: 0.8381 (m-10) REVERT: A 174 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7473 (mt-10) REVERT: A 228 LYS cc_start: 0.8910 (mmmt) cc_final: 0.8642 (mmtt) REVERT: A 257 ASP cc_start: 0.8953 (m-30) cc_final: 0.8683 (m-30) REVERT: A 286 ASP cc_start: 0.8116 (m-30) cc_final: 0.7883 (m-30) REVERT: A 290 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8387 (mm-30) REVERT: A 308 LYS cc_start: 0.9548 (mtmt) cc_final: 0.9329 (mtmm) REVERT: A 319 MET cc_start: 0.9233 (tpp) cc_final: 0.8891 (tpp) REVERT: A 344 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8171 (mt-10) REVERT: A 362 ASP cc_start: 0.7340 (m-30) cc_final: 0.7115 (m-30) REVERT: A 383 SER cc_start: 0.8974 (p) cc_final: 0.8699 (t) REVERT: A 458 MET cc_start: 0.9162 (mmm) cc_final: 0.8360 (mtm) REVERT: A 604 ARG cc_start: 0.8338 (tpp-160) cc_final: 0.8121 (tpp80) REVERT: A 640 MET cc_start: 0.9034 (tpp) cc_final: 0.8574 (tpp) REVERT: A 645 GLN cc_start: 0.8731 (tp40) cc_final: 0.8500 (tp-100) REVERT: A 667 LEU cc_start: 0.9189 (tt) cc_final: 0.8579 (tt) REVERT: B 102 ASN cc_start: 0.9316 (m110) cc_final: 0.8960 (m110) REVERT: B 191 GLN cc_start: 0.8843 (mm-40) cc_final: 0.8233 (mm-40) REVERT: B 214 LYS cc_start: 0.8084 (mmtm) cc_final: 0.7833 (mmtm) REVERT: B 218 ASN cc_start: 0.8814 (t0) cc_final: 0.8521 (t0) REVERT: B 235 ARG cc_start: 0.8566 (ttm-80) cc_final: 0.8205 (ttm110) REVERT: B 253 ILE cc_start: 0.9364 (tt) cc_final: 0.9164 (tt) REVERT: B 276 LYS cc_start: 0.8661 (ptmt) cc_final: 0.8326 (ptpp) REVERT: B 286 ASP cc_start: 0.8446 (m-30) cc_final: 0.8152 (m-30) REVERT: B 288 PHE cc_start: 0.9473 (t80) cc_final: 0.9165 (t80) REVERT: B 322 MET cc_start: 0.8843 (mmt) cc_final: 0.8095 (mpp) REVERT: B 333 LYS cc_start: 0.9103 (tttm) cc_final: 0.8656 (tttp) REVERT: B 348 MET cc_start: 0.7937 (tpp) cc_final: 0.7350 (tpp) REVERT: B 359 MET cc_start: 0.9052 (ttp) cc_final: 0.8798 (tmm) REVERT: B 467 ASN cc_start: 0.9303 (t0) cc_final: 0.8809 (t0) REVERT: B 604 ARG cc_start: 0.8725 (tpp80) cc_final: 0.8168 (tpp80) REVERT: B 615 MET cc_start: 0.9059 (mmp) cc_final: 0.8831 (mmm) REVERT: B 640 MET cc_start: 0.8933 (tpp) cc_final: 0.8406 (tpp) REVERT: C 74 MET cc_start: 0.7416 (mtt) cc_final: 0.7179 (mtt) REVERT: C 208 LEU cc_start: 0.9348 (mt) cc_final: 0.9115 (mt) REVERT: D 95 MET cc_start: 0.7346 (ttp) cc_final: 0.7105 (ttt) REVERT: D 173 TYR cc_start: 0.7030 (t80) cc_final: 0.6734 (t80) outliers start: 0 outliers final: 0 residues processed: 562 average time/residue: 0.1241 time to fit residues: 106.4043 Evaluate side-chains 428 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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: 20.0000 chunk 72 optimal weight: 3.9990 chunk 172 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 4 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN D 69 GLN ** D 91 ASN ** 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 = 0.3959 r_free = 0.3959 target = 0.159313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.110030 restraints weight = 33444.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113402 restraints weight = 16216.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.115557 restraints weight = 9633.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.116907 restraints weight = 6545.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.117978 restraints weight = 4979.384| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3315 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16386 Z= 0.158 Angle : 0.578 7.682 22134 Z= 0.310 Chirality : 0.042 0.159 2360 Planarity : 0.003 0.041 2818 Dihedral : 8.401 132.579 2290 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.06 % Allowed : 1.63 % Favored : 98.31 % 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: 1.16 (0.19), residues: 1932 helix: 1.35 (0.15), residues: 1130 sheet: -0.04 (0.45), residues: 110 loop : 0.08 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 686 TYR 0.021 0.002 TYR B 118 PHE 0.042 0.002 PHE C 109 TRP 0.041 0.002 TRP D 124 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (16386) covalent geometry : angle 0.57815 / 0.31 (22134) hydrogen bonds : bond 0.03801 / 2.39 ( 871) hydrogen bonds : angle 4.82068 / 3.41 ( 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 524 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 523 time to evaluate : 0.615 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: A 65 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8085 (mp0) REVERT: A 150 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8579 (tm-30) REVERT: A 179 LEU cc_start: 0.9354 (tp) cc_final: 0.9118 (tp) REVERT: A 188 ILE cc_start: 0.9449 (mm) cc_final: 0.9167 (mm) REVERT: A 286 ASP cc_start: 0.8159 (m-30) cc_final: 0.7886 (m-30) REVERT: A 308 LYS cc_start: 0.9550 (mtmt) cc_final: 0.9321 (mtmm) REVERT: A 319 MET cc_start: 0.9255 (tpp) cc_final: 0.8776 (tpp) REVERT: A 344 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8105 (mt-10) REVERT: A 362 ASP cc_start: 0.7413 (m-30) cc_final: 0.7140 (m-30) REVERT: A 447 ASN cc_start: 0.8107 (m-40) cc_final: 0.7851 (m-40) REVERT: A 458 MET cc_start: 0.9171 (mmm) cc_final: 0.8457 (mtm) REVERT: A 584 ILE cc_start: 0.8992 (pt) cc_final: 0.8765 (pt) REVERT: A 604 ARG cc_start: 0.8358 (tpp-160) cc_final: 0.8122 (tpp80) REVERT: A 667 LEU cc_start: 0.9241 (tt) cc_final: 0.8639 (tt) REVERT: B 102 ASN cc_start: 0.9285 (m110) cc_final: 0.8935 (m110) REVERT: B 120 ASP cc_start: 0.8711 (m-30) cc_final: 0.8433 (m-30) REVERT: B 172 LEU cc_start: 0.9108 (mp) cc_final: 0.8820 (mp) REVERT: B 191 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8675 (mm-40) REVERT: B 214 LYS cc_start: 0.8008 (mmtm) cc_final: 0.7761 (mmtt) REVERT: B 218 ASN cc_start: 0.8894 (t0) cc_final: 0.8583 (t0) REVERT: B 253 ILE cc_start: 0.9393 (tt) cc_final: 0.9175 (tt) REVERT: B 276 LYS cc_start: 0.8611 (ptmt) cc_final: 0.8244 (ptpp) REVERT: B 286 ASP cc_start: 0.8395 (m-30) cc_final: 0.8106 (m-30) REVERT: B 288 PHE cc_start: 0.9460 (t80) cc_final: 0.9137 (t80) REVERT: B 322 MET cc_start: 0.8978 (mmt) cc_final: 0.8195 (mpp) REVERT: B 333 LYS cc_start: 0.9055 (tttm) cc_final: 0.8627 (tttp) REVERT: B 348 MET cc_start: 0.8129 (tpp) cc_final: 0.7757 (tpp) REVERT: B 379 SER cc_start: 0.8845 (t) cc_final: 0.8639 (t) REVERT: B 427 LYS cc_start: 0.9334 (pttt) cc_final: 0.9131 (pttt) REVERT: B 447 ASN cc_start: 0.8569 (m-40) cc_final: 0.8339 (m-40) REVERT: B 467 ASN cc_start: 0.9281 (t0) cc_final: 0.8741 (t0) REVERT: B 604 ARG cc_start: 0.8741 (tpp80) cc_final: 0.7954 (tpp80) REVERT: B 615 MET cc_start: 0.9084 (mmp) cc_final: 0.8795 (mmm) REVERT: B 640 MET cc_start: 0.8935 (tpp) cc_final: 0.8205 (tpp) REVERT: C 74 MET cc_start: 0.7387 (mtt) cc_final: 0.6961 (mtt) REVERT: C 89 VAL cc_start: 0.5081 (m) cc_final: 0.4418 (m) REVERT: D 95 MET cc_start: 0.7318 (ttp) cc_final: 0.7096 (ttt) REVERT: D 108 ILE cc_start: 0.8211 (tp) cc_final: 0.7964 (pt) outliers start: 1 outliers final: 0 residues processed: 524 average time/residue: 0.1258 time to fit residues: 100.8903 Evaluate side-chains 426 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 426 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 105 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 186 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 156 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.160699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.111323 restraints weight = 33354.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.114888 restraints weight = 16214.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.117108 restraints weight = 9476.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.118529 restraints weight = 6445.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.119266 restraints weight = 4825.697| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.5828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16386 Z= 0.148 Angle : 0.568 8.040 22134 Z= 0.304 Chirality : 0.042 0.158 2360 Planarity : 0.003 0.042 2818 Dihedral : 8.184 132.947 2290 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.17 (0.19), residues: 1932 helix: 1.41 (0.15), residues: 1115 sheet: 0.03 (0.45), residues: 110 loop : 0.01 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 686 TYR 0.030 0.002 TYR A 571 PHE 0.044 0.002 PHE C 109 TRP 0.043 0.002 TRP D 124 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (16386) covalent geometry : angle 0.56835 / 0.30 (22134) hydrogen bonds : bond 0.03702 / 2.34 ( 871) hydrogen bonds : angle 4.78912 / 3.40 ( 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 515 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 0.617 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: A 65 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8094 (mp0) REVERT: A 150 GLN cc_start: 0.9005 (tm-30) cc_final: 0.8484 (tm-30) REVERT: A 158 ASN cc_start: 0.8964 (m110) cc_final: 0.8760 (m-40) REVERT: A 179 LEU cc_start: 0.9320 (tp) cc_final: 0.9061 (tp) REVERT: A 188 ILE cc_start: 0.9451 (mm) cc_final: 0.9107 (mm) REVERT: A 231 ASP cc_start: 0.8549 (t0) cc_final: 0.8335 (t0) REVERT: A 286 ASP cc_start: 0.8217 (m-30) cc_final: 0.7882 (m-30) REVERT: A 301 PHE cc_start: 0.9108 (m-80) cc_final: 0.8906 (m-10) REVERT: A 308 LYS cc_start: 0.9552 (mtmt) cc_final: 0.9323 (mtmm) REVERT: A 319 MET cc_start: 0.9281 (tpp) cc_final: 0.8835 (tpp) REVERT: A 344 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8105 (mt-10) REVERT: A 362 ASP cc_start: 0.7303 (m-30) cc_final: 0.7069 (m-30) REVERT: A 383 SER cc_start: 0.8968 (t) cc_final: 0.8763 (p) REVERT: A 458 MET cc_start: 0.9182 (mmm) cc_final: 0.8541 (mtm) REVERT: A 584 ILE cc_start: 0.9005 (pt) cc_final: 0.8732 (pt) REVERT: A 667 LEU cc_start: 0.9295 (tt) cc_final: 0.8646 (tt) REVERT: A 686 ARG cc_start: 0.8363 (mtp-110) cc_final: 0.7689 (mtp-110) REVERT: B 102 ASN cc_start: 0.9296 (m110) cc_final: 0.8927 (m110) REVERT: B 120 ASP cc_start: 0.8708 (m-30) cc_final: 0.8448 (m-30) REVERT: B 191 GLN cc_start: 0.8936 (mm-40) cc_final: 0.8663 (mm-40) REVERT: B 235 ARG cc_start: 0.8575 (ttm-80) cc_final: 0.8273 (mtm110) REVERT: B 253 ILE cc_start: 0.9395 (tt) cc_final: 0.9115 (tt) REVERT: B 258 ILE cc_start: 0.9497 (tp) cc_final: 0.9291 (tp) REVERT: B 276 LYS cc_start: 0.8581 (ptmt) cc_final: 0.8291 (ptpp) REVERT: B 288 PHE cc_start: 0.9453 (t80) cc_final: 0.9191 (t80) REVERT: B 333 LYS cc_start: 0.9092 (tttm) cc_final: 0.8718 (tttp) REVERT: B 348 MET cc_start: 0.8152 (tpp) cc_final: 0.7798 (tpp) REVERT: B 362 ASP cc_start: 0.7951 (m-30) cc_final: 0.7005 (m-30) REVERT: B 392 SER cc_start: 0.9226 (m) cc_final: 0.8804 (m) REVERT: B 414 LEU cc_start: 0.9344 (mt) cc_final: 0.9113 (mt) REVERT: B 447 ASN cc_start: 0.8570 (m-40) cc_final: 0.8369 (m-40) REVERT: B 467 ASN cc_start: 0.9240 (t0) cc_final: 0.8677 (t0) REVERT: B 586 TYR cc_start: 0.8551 (m-10) cc_final: 0.8187 (m-10) REVERT: B 604 ARG cc_start: 0.8747 (tpp80) cc_final: 0.7998 (tpp80) REVERT: B 615 MET cc_start: 0.9090 (mmp) cc_final: 0.8821 (mmm) REVERT: B 640 MET cc_start: 0.8960 (tpp) cc_final: 0.8214 (tpp) REVERT: B 652 ILE cc_start: 0.8922 (mt) cc_final: 0.8702 (mt) REVERT: C 74 MET cc_start: 0.7491 (mtt) cc_final: 0.7291 (mtp) REVERT: C 89 VAL cc_start: 0.5006 (m) cc_final: 0.4364 (m) REVERT: D 95 MET cc_start: 0.7318 (ttp) cc_final: 0.7102 (ttt) REVERT: D 108 ILE cc_start: 0.8248 (tp) cc_final: 0.7978 (pt) outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 0.1171 time to fit residues: 92.3977 Evaluate side-chains 415 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 153 optimal weight: 30.0000 chunk 11 optimal weight: 5.9990 chunk 158 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 151 optimal weight: 30.0000 chunk 81 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 390 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN A 645 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 HIS D 238 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.153747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.105059 restraints weight = 34332.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.108449 restraints weight = 16888.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.110532 restraints weight = 9937.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.111795 restraints weight = 6812.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112789 restraints weight = 5227.827| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.6072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 16386 Z= 0.326 Angle : 0.698 8.762 22134 Z= 0.372 Chirality : 0.047 0.305 2360 Planarity : 0.004 0.046 2818 Dihedral : 8.495 134.645 2290 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % 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: 0.87 (0.19), residues: 1932 helix: 1.16 (0.15), residues: 1106 sheet: -0.47 (0.41), residues: 138 loop : 0.02 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 256 TYR 0.028 0.002 TYR B 118 PHE 0.042 0.003 PHE C 109 TRP 0.049 0.003 TRP D 124 HIS 0.006 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00708 / 0.33 (16386) covalent geometry : angle 0.69836 / 0.37 (22134) hydrogen bonds : bond 0.04226 / 2.66 ( 871) hydrogen bonds : angle 5.01773 / 3.56 ( 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 470 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 470 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8115 (mp0) REVERT: A 204 SER cc_start: 0.9240 (m) cc_final: 0.8824 (t) REVERT: A 286 ASP cc_start: 0.8205 (m-30) cc_final: 0.7893 (m-30) REVERT: A 341 LYS cc_start: 0.8708 (pttp) cc_final: 0.8471 (pttp) REVERT: A 344 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8098 (mt-10) REVERT: A 362 ASP cc_start: 0.7568 (m-30) cc_final: 0.7136 (m-30) REVERT: A 447 ASN cc_start: 0.8189 (m110) cc_final: 0.7746 (m-40) REVERT: A 458 MET cc_start: 0.9211 (mmm) cc_final: 0.8474 (mtm) REVERT: A 493 MET cc_start: 0.8844 (tmm) cc_final: 0.8236 (tmm) REVERT: A 557 ASP cc_start: 0.8732 (m-30) cc_final: 0.8522 (m-30) REVERT: A 584 ILE cc_start: 0.8982 (pt) cc_final: 0.8750 (pt) REVERT: A 667 LEU cc_start: 0.9383 (tt) cc_final: 0.8769 (tt) REVERT: B 17 MET cc_start: 0.8498 (mpp) cc_final: 0.8290 (mpp) REVERT: B 102 ASN cc_start: 0.9234 (m110) cc_final: 0.8896 (m110) REVERT: B 120 ASP cc_start: 0.8882 (m-30) cc_final: 0.8607 (m-30) REVERT: B 164 ARG cc_start: 0.7813 (ptt90) cc_final: 0.7443 (ptt180) REVERT: B 190 MET cc_start: 0.9237 (mtm) cc_final: 0.8887 (mtm) REVERT: B 218 ASN cc_start: 0.8781 (t0) cc_final: 0.8529 (t0) REVERT: B 253 ILE cc_start: 0.9391 (tt) cc_final: 0.9172 (tt) REVERT: B 256 ARG cc_start: 0.9030 (tmt-80) cc_final: 0.8697 (tpt90) REVERT: B 258 ILE cc_start: 0.9557 (tp) cc_final: 0.9341 (tp) REVERT: B 262 LEU cc_start: 0.9570 (mm) cc_final: 0.9323 (mm) REVERT: B 276 LYS cc_start: 0.8784 (ptmt) cc_final: 0.8452 (ptpp) REVERT: B 333 LYS cc_start: 0.9116 (tttm) cc_final: 0.8616 (tttp) REVERT: B 348 MET cc_start: 0.8082 (tpp) cc_final: 0.7842 (tpp) REVERT: B 362 ASP cc_start: 0.8142 (m-30) cc_final: 0.7225 (m-30) REVERT: B 392 SER cc_start: 0.9258 (m) cc_final: 0.9039 (m) REVERT: B 427 LYS cc_start: 0.9424 (pttt) cc_final: 0.9204 (pttt) REVERT: B 467 ASN cc_start: 0.9370 (t0) cc_final: 0.8921 (t0) REVERT: B 576 LEU cc_start: 0.9250 (mt) cc_final: 0.9011 (mt) REVERT: B 604 ARG cc_start: 0.8714 (tpp80) cc_final: 0.7761 (tpp80) REVERT: B 612 TYR cc_start: 0.7875 (m-10) cc_final: 0.7660 (m-10) REVERT: B 615 MET cc_start: 0.9138 (mmp) cc_final: 0.8896 (mmm) REVERT: B 640 MET cc_start: 0.8870 (tpp) cc_final: 0.8216 (tpp) REVERT: C 89 VAL cc_start: 0.5891 (m) cc_final: 0.5429 (m) REVERT: C 116 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7637 (pm20) REVERT: C 157 MET cc_start: 0.8610 (mtm) cc_final: 0.8156 (ptp) REVERT: D 95 MET cc_start: 0.8024 (ttp) cc_final: 0.7733 (ttt) outliers start: 0 outliers final: 0 residues processed: 470 average time/residue: 0.1257 time to fit residues: 90.6682 Evaluate side-chains 400 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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: 2.9990 chunk 133 optimal weight: 0.7980 chunk 149 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN A 447 ASN A 645 GLN B 150 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN D 69 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.160417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.112080 restraints weight = 33510.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.115531 restraints weight = 16251.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.117729 restraints weight = 9629.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.119064 restraints weight = 6514.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.120128 restraints weight = 4928.665| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.6148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16386 Z= 0.138 Angle : 0.603 8.755 22134 Z= 0.320 Chirality : 0.042 0.249 2360 Planarity : 0.003 0.042 2818 Dihedral : 7.967 131.416 2290 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.19), residues: 1932 helix: 1.42 (0.15), residues: 1110 sheet: 0.26 (0.46), residues: 96 loop : -0.01 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 235 TYR 0.019 0.001 TYR C 242 PHE 0.049 0.002 PHE C 109 TRP 0.050 0.002 TRP D 124 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (16386) covalent geometry : angle 0.60255 / 0.32 (22134) hydrogen bonds : bond 0.03818 / 2.42 ( 871) hydrogen bonds : angle 4.86437 / 3.43 ( 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 527 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 527 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8027 (mp0) REVERT: A 150 GLN cc_start: 0.8932 (tm-30) cc_final: 0.8321 (tm-30) REVERT: A 228 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8562 (mmtt) REVERT: A 286 ASP cc_start: 0.8222 (m-30) cc_final: 0.7980 (m-30) REVERT: A 446 ARG cc_start: 0.7782 (mmm160) cc_final: 0.7550 (mmm160) REVERT: A 447 ASN cc_start: 0.8204 (m-40) cc_final: 0.7451 (m-40) REVERT: A 458 MET cc_start: 0.9212 (mmm) cc_final: 0.8492 (mtm) REVERT: A 557 ASP cc_start: 0.8723 (m-30) cc_final: 0.8523 (m-30) REVERT: A 584 ILE cc_start: 0.8936 (pt) cc_final: 0.8665 (pt) REVERT: A 604 ARG cc_start: 0.7652 (ptp-110) cc_final: 0.6744 (mtm-85) REVERT: A 606 TYR cc_start: 0.7490 (m-10) cc_final: 0.7008 (m-10) REVERT: A 667 LEU cc_start: 0.9245 (tt) cc_final: 0.8573 (tt) REVERT: A 686 ARG cc_start: 0.8400 (mtp-110) cc_final: 0.7959 (mtp-110) REVERT: B 102 ASN cc_start: 0.9264 (m110) cc_final: 0.8960 (m110) REVERT: B 120 ASP cc_start: 0.8710 (m-30) cc_final: 0.8436 (m-30) REVERT: B 147 GLN cc_start: 0.9213 (mt0) cc_final: 0.8944 (mt0) REVERT: B 164 ARG cc_start: 0.7767 (ptt90) cc_final: 0.7350 (ptt-90) REVERT: B 172 LEU cc_start: 0.9148 (mp) cc_final: 0.8944 (mp) REVERT: B 191 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8308 (mm-40) REVERT: B 214 LYS cc_start: 0.7981 (mmtt) cc_final: 0.7721 (mmtt) REVERT: B 235 ARG cc_start: 0.8496 (ttm110) cc_final: 0.8108 (mtm110) REVERT: B 253 ILE cc_start: 0.9412 (tt) cc_final: 0.9176 (tt) REVERT: B 256 ARG cc_start: 0.8971 (tmt-80) cc_final: 0.8746 (tpt90) REVERT: B 267 ILE cc_start: 0.9456 (pt) cc_final: 0.9252 (pt) REVERT: B 274 ARG cc_start: 0.8102 (ttm-80) cc_final: 0.7520 (ttm-80) REVERT: B 276 LYS cc_start: 0.8923 (ptmt) cc_final: 0.8561 (ptpp) REVERT: B 288 PHE cc_start: 0.9478 (t80) cc_final: 0.9217 (t80) REVERT: B 333 LYS cc_start: 0.9154 (tttm) cc_final: 0.8782 (tttp) REVERT: B 348 MET cc_start: 0.7948 (tpp) cc_final: 0.7650 (tpp) REVERT: B 392 SER cc_start: 0.9170 (m) cc_final: 0.8775 (m) REVERT: B 458 MET cc_start: 0.8903 (mmm) cc_final: 0.8026 (mmm) REVERT: B 467 ASN cc_start: 0.9193 (t0) cc_final: 0.8587 (t0) REVERT: B 588 GLN cc_start: 0.9377 (mm-40) cc_final: 0.8863 (mm-40) REVERT: B 604 ARG cc_start: 0.8638 (tpp80) cc_final: 0.7831 (tpp80) REVERT: B 615 MET cc_start: 0.9004 (mmp) cc_final: 0.8734 (mmm) REVERT: B 627 LYS cc_start: 0.9218 (ttpp) cc_final: 0.8864 (tttp) REVERT: B 640 MET cc_start: 0.8893 (tpp) cc_final: 0.8221 (tpp) REVERT: B 644 ILE cc_start: 0.9418 (mt) cc_final: 0.8927 (mp) REVERT: B 652 ILE cc_start: 0.8859 (mt) cc_final: 0.8637 (mt) REVERT: B 687 THR cc_start: 0.9053 (p) cc_final: 0.8827 (p) REVERT: C 89 VAL cc_start: 0.5687 (m) cc_final: 0.5329 (m) REVERT: C 134 LYS cc_start: 0.7956 (mtmm) cc_final: 0.7625 (mmpt) REVERT: C 154 PHE cc_start: 0.8552 (t80) cc_final: 0.7420 (t80) REVERT: C 157 MET cc_start: 0.8439 (mtm) cc_final: 0.7932 (ptp) REVERT: C 224 LEU cc_start: 0.9107 (mt) cc_final: 0.8771 (mt) REVERT: D 95 MET cc_start: 0.7638 (ttp) cc_final: 0.7423 (ttt) REVERT: D 173 TYR cc_start: 0.5903 (t80) cc_final: 0.5451 (t80) outliers start: 0 outliers final: 0 residues processed: 527 average time/residue: 0.1225 time to fit residues: 98.0185 Evaluate side-chains 434 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 434 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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: 6.9990 chunk 62 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 0.0470 chunk 189 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN A 646 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.159475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.111454 restraints weight = 33844.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.114898 restraints weight = 16362.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.117098 restraints weight = 9728.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.118527 restraints weight = 6602.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.119412 restraints weight = 4947.631| |-----------------------------------------------------------------------------| 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) = 0.112 | | 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) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (19 function evaluations) r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.6282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 16386 Z= 0.163 Angle : 0.605 8.824 22134 Z= 0.321 Chirality : 0.043 0.167 2360 Planarity : 0.003 0.040 2818 Dihedral : 7.861 133.593 2290 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.39 (0.15), residues: 1124 sheet: 0.27 (0.46), residues: 96 loop : 0.04 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 235 TYR 0.022 0.002 TYR C 242 PHE 0.048 0.002 PHE C 109 TRP 0.051 0.002 TRP D 124 HIS 0.005 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (16386) covalent geometry : angle 0.60493 / 0.32 (22134) hydrogen bonds : bond 0.03816 / 2.41 ( 871) hydrogen bonds : angle 4.90394 / 3.47 ( 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 486 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 486 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: A 65 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7951 (mp0) REVERT: A 139 GLU cc_start: 0.8205 (mp0) cc_final: 0.7899 (mp0) REVERT: A 150 GLN cc_start: 0.8954 (tm-30) cc_final: 0.8710 (tm-30) REVERT: A 179 LEU cc_start: 0.9351 (tp) cc_final: 0.9125 (tp) REVERT: A 344 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8331 (mt-10) REVERT: A 447 ASN cc_start: 0.8280 (m-40) cc_final: 0.7966 (m-40) REVERT: A 458 MET cc_start: 0.9219 (mmm) cc_final: 0.8504 (mtm) REVERT: A 477 ILE cc_start: 0.9600 (mt) cc_final: 0.9364 (mp) REVERT: A 584 ILE cc_start: 0.8931 (pt) cc_final: 0.8654 (pt) REVERT: A 604 ARG cc_start: 0.7644 (ptp-110) cc_final: 0.7380 (mtm-85) REVERT: A 630 TYR cc_start: 0.8463 (m-80) cc_final: 0.8049 (m-80) REVERT: A 645 GLN cc_start: 0.8652 (tp40) cc_final: 0.8390 (tp-100) REVERT: A 667 LEU cc_start: 0.9279 (tt) cc_final: 0.8621 (tt) REVERT: A 686 ARG cc_start: 0.8361 (mtp-110) cc_final: 0.7890 (mtp-110) REVERT: B 102 ASN cc_start: 0.9213 (m110) cc_final: 0.8858 (m110) REVERT: B 120 ASP cc_start: 0.8665 (m-30) cc_final: 0.8377 (m-30) REVERT: B 150 GLN cc_start: 0.8722 (tp40) cc_final: 0.8516 (tp40) REVERT: B 191 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8663 (mm-40) REVERT: B 213 ILE cc_start: 0.8629 (mp) cc_final: 0.8414 (mt) REVERT: B 235 ARG cc_start: 0.8513 (ttm110) cc_final: 0.8046 (mtm110) REVERT: B 253 ILE cc_start: 0.9398 (tt) cc_final: 0.9146 (tt) REVERT: B 256 ARG cc_start: 0.9015 (tmt-80) cc_final: 0.8776 (tpt90) REVERT: B 274 ARG cc_start: 0.8195 (ttm-80) cc_final: 0.7702 (tpp80) REVERT: B 276 LYS cc_start: 0.8924 (ptmt) cc_final: 0.8550 (ptpp) REVERT: B 286 ASP cc_start: 0.8269 (m-30) cc_final: 0.8012 (m-30) REVERT: B 288 PHE cc_start: 0.9489 (t80) cc_final: 0.9192 (t80) REVERT: B 333 LYS cc_start: 0.9117 (tttm) cc_final: 0.8893 (tttp) REVERT: B 348 MET cc_start: 0.8155 (tpp) cc_final: 0.7852 (tpp) REVERT: B 447 ASN cc_start: 0.8533 (m-40) cc_final: 0.8220 (m-40) REVERT: B 458 MET cc_start: 0.8975 (mmm) cc_final: 0.8089 (mmm) REVERT: B 467 ASN cc_start: 0.9202 (t0) cc_final: 0.8654 (t0) REVERT: B 604 ARG cc_start: 0.8625 (tpp80) cc_final: 0.7835 (tpp80) REVERT: B 615 MET cc_start: 0.9023 (mmp) cc_final: 0.8742 (mmm) REVERT: B 640 MET cc_start: 0.8905 (tpp) cc_final: 0.8290 (tpp) REVERT: B 652 ILE cc_start: 0.9012 (mt) cc_final: 0.8778 (mt) REVERT: C 89 VAL cc_start: 0.5323 (m) cc_final: 0.4986 (m) REVERT: C 134 LYS cc_start: 0.7871 (mtmm) cc_final: 0.7566 (mmpt) REVERT: C 154 PHE cc_start: 0.8593 (t80) cc_final: 0.7493 (t80) REVERT: C 157 MET cc_start: 0.8563 (mtm) cc_final: 0.8122 (ptp) REVERT: C 224 LEU cc_start: 0.9138 (mt) cc_final: 0.8777 (mt) REVERT: D 56 MET cc_start: -0.0944 (mmm) cc_final: -0.1205 (mmm) REVERT: D 95 MET cc_start: 0.7747 (ttp) cc_final: 0.7514 (ttt) outliers start: 0 outliers final: 0 residues processed: 486 average time/residue: 0.1205 time to fit residues: 88.8353 Evaluate side-chains 421 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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: 0.0370 chunk 1 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 148 optimal weight: 9.9990 chunk 125 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 29 optimal weight: 0.8980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 HIS D 85 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.163864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.116263 restraints weight = 33366.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.119794 restraints weight = 16163.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.122081 restraints weight = 9546.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.123509 restraints weight = 6463.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.124428 restraints weight = 4815.835| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.6469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16386 Z= 0.123 Angle : 0.597 9.692 22134 Z= 0.314 Chirality : 0.042 0.168 2360 Planarity : 0.003 0.039 2818 Dihedral : 7.543 132.260 2290 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: 1.27 (0.19), residues: 1932 helix: 1.45 (0.15), residues: 1126 sheet: 0.34 (0.46), residues: 96 loop : 0.07 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 235 TYR 0.020 0.001 TYR C 242 PHE 0.049 0.002 PHE C 109 TRP 0.047 0.002 TRP D 124 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (16386) covalent geometry : angle 0.59725 / 0.31 (22134) hydrogen bonds : bond 0.03693 / 2.35 ( 871) hydrogen bonds : angle 4.81473 / 3.42 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3373.54 seconds wall clock time: 59 minutes 12.09 seconds (3552.09 seconds total)